bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells
Authors: Cepika Alma-Martina , Amaya Laura , Waichler Colin , Narula Mansi , Mantilla Michelle M. , Thomas Benjamin C. , Chen Pauline P. , Freeborn Robert Arthur , Pavel-Dinu Mara , Nideffer Jason , Porteus Matthew , Bacchetta Rosa , Müller Fabian , Greenleaf William J. , Chang Howard Y. , Roncarolo Maria Grazia
Published: March 2024

Human adaptive immunity is orchestrated by effector and regulatory T (Treg) cells. Natural Tregs arise in the thymus where they are shaped to recognize self-antigens, while type 1 Tregs or Tr1 cells are induced from conventional peripheral CD4+T cells in response to peripheral antigens, such as alloantigens and allergens. Tr1 cells have been developed as a potential therapy for inducing antigen-specific tolerance, because they can be rapidly differentiatedin vitroin response to a target antigen. However, the epigenetic landscape and the identity of transcription factors (TFs) that regulate differentiation, phenotype, and functions of human antigen-specific Tr1 cells is largely unknown, hindering Tr1 research and broader clinical development. Here, we reveal the unique epigenetic signature of antigen-specific Tr1 cells, and TFs that regulate their differentiation, phenotype and function. We showed thatin vitroinduced antigen-specific Tr1 cells are distinct both clonally and transcriptionally from natural Tregs and other conventional CD4+T cells on a single-cell level. An integrative analysis of Tr1 cell epigenome and transcriptome identified a TF signature unique to antigen-specific Tr1 cells, and predicted that IRF4, BATF, and MAF act as their transcriptional regulators. Using functional genomics, we showed that each of these TFs play a non-redundant role in regulating Tr1 cell differentiation, suppressive function, and expression of co-inhibitory and cytotoxic proteins. By using the Tr1-specific TF signature as a molecular fingerprint, we tracked Tr1 cells in peripheral blood of recipients of allogeneic hematopoietic stem cell transplantation treated with adoptive Tr1 cell therapy. Furthermore, the same signature identified Tr1 cells in resident CD4+T cells in solid tumors. Altogether, these results reveal the epigenetic signature and the key transcriptional regulators of human Tr1 cells. These data will guide mechanistic studies of human Tr1 cell biology and the development and optimization of adoptive Tr1 cell therapies.
A cryopreservation strategy for myoblast storage in paper-based scaffolds for inter-laboratory studies of skeletal muscle health
Authors: Rjaibi Saifedine T. , Jacques Erik , Ni Jiaru , Xu Bin , Kouthouridis Sonya , Sitolle Julie , Lad Heta , Gulati Nitya , Li Nancy T. , Ahn Henry , Ginsberg Howard J. , Zhang Boyang , Grand Fabien Le , Gilbert Penney M. , McGuigan Alison P.
Published: March 2024

Three-dimensional tissue-engineered models are poised to facilitate understanding of skeletal muscle pathophysiology and identify novel therapeutic agents to improve muscle health. Adopting these culture models within the broader biology community is a challenge as many models involve complex methodologies and significant investments of time and resources to optimize manufacturing protocols. To alleviate this barrier, we developed a protocol with commercially available reagents to cryopreserve myoblasts in a 96-well compatible format that allows tissues to be transferred to users without expertise in 2D or 3D skeletal muscle cell culture. We validate that myoblasts encapsulated in a hydrogel and cryopreserved in paper-based scaffolds maintain cell viability, differentiation, and function via acetylcholine-induced transient calcium responses. Furthermore, we demonstrate successful shipping of myoblasts cryopreserved in paper-based scaffolds to intra-provincial and international collaborators who successfully thawed, cultured, and used the 3D muscle tissues. Finally, we confirm the application of our method to study muscle endogenous repair by seeding freshly isolated skeletal muscle stem cells to cryopreserved then differentiated and injured tissues, demonstrating expected responses to a known stimulator of muscle stem cell self-renewal, p38α/β MAPKi. Altogether, our 3D myoblast cryopreservation protocol offers broadened access of a complex skeletal muscle tissue model to the research community.
Road density simplifies regional food webs
Authors: Mestre Frederico , Bastazini Vinicius A. G. , Ascensao Fernando
Published: March 2024

Roads stands as major threats to biodiversity, affecting the functioning of ecosystems and their provision of ecosystem services. Understanding how road-related impacts affect the dynamics of ecological interactions is essential to help manage human impacts on biodiversity, but such studies remain largely unexplored. We investigated the intricate relationship between roads, species vulnerability to road density, and the ensuing effects on food webs across Europe. Utilizing species-specific road density thresholds and trophic interaction data, we constructed regional food webs to assess the potential loss of trophic interactions due to roadkill. Our analysis, encompassing 551 species across three trophic levels, revealed spatially varied impacts, with areas surrounding major cities facing drastic losses of trophic interaction exceeding 90%. Notably, 191 species may be affected by trophic interaction losses (loss of prey or predator). Apex predators exhibited lower direct impacts from road density, while basal-level species seem to be more exposed to direct road-related effects, potentially triggering a cascade of interaction disruptions. Our findings emphasize the need for informed road infrastructure development and targeted conservation strategies to mitigate the negative impacts of roads and traffic, thereby preserving the integrity of ecological networks. This research offers valuable insights for policymakers and conservation practitioners globally by identifying critical areas where road-induced cascade effects may be most pronounced and highlighting trophic groups of species that may be at higher risk.
A simple regulatory network coordinates a bacterial stress response in space and time
Authors: Choudhary Divya , Foster Kevin R. , Uphoff Stephan
Published: March 2024

Bacteria employ diverse gene regulatory networks to protect themselves from stressful environments. While transcriptomics and proteomics show that the expression of different genes can shift strongly in response to stress, the underlying logic of large regulatory networks is difficult to understand from bulk measurements performed at discrete time points. As a result, it remains challenging to predict how these regulatory networks function at a system level. Here we use time-resolved single-cell imaging to explore the functioning of a key bacterial stress response: TheEscherichia coliresponse to oxidative stress. Our work reveals a striking diversity in the expression dynamics of genes in the regulatory network, with differences in the timing, magnitude, and direction of expression changes. Nevertheless, we find that these patterns have a simple underlying logic. Firstly, all genes exhibit a transient increase in their protein levels simply due to the slowing down of cell growth under stress. Controlling for this effect reveals three classes of gene regulation driven by the transcription factor OxyR. Downregulated genes drop in expression level, while upregulated genes either show pulsatile expression that decays rapidly or gradual induction, dependent upon transcription factor binding dynamics. These classes appear to serve distinct functional roles in cell populations. Pulsatile genes are stress-sensitive and activate rapidly and transiently in a few cells, which provides an initial protection for cell groups. Gradually upregulated genes are less sensitive and induce more evenly generating a lasting protection that involves a larger number of cells. Our study shows how bacterial populations use simple regulatory principles to coordinate a stress response in space and time.
Identification of Neural Crest and Neural Crest-Derived Cancer Cell Invasion and Migration Genes Using High-throughput Screening and Deep Attention Networks
Authors: Kasemeier-Kulesa JC , Martina Perez S , Baker RE , Kulesa PM
Published: March 2024

Background

Cell migration and invasion are well-coordinated processes in development and disease but remain poorly understood. We previously showed that highly migratory neural crest (NC) cells share a 45-gene panel with other cell invasion phenomena, including cancer. To identify critical genes of the 45-gene panel, we performed a high-throughput siRNA screen and used statistical and deep learning methods to compare NC- versus non-NC-derived human cell lines.

Results

We find 14 out of 45 genes significantly reduces c8161 melanoma cell migration; only 4 are shared with HT1080 fibrosarcoma cells (BMP4, ITGB1, KCNE3, RASGRP1). Deep learning attention network analysis identified distinct cell-cell interaction patterns and significant alterations after BMP4 or RASGRP1 knockdown in c8161 cells. Addition of recombinant proteins to the culture media identified 5 out of the 10 known secreted molecules stimulate c8161 cell migration, including BMP4. BMP4 siRNA knockdown inhibited c8161 cell invasionin vivoandin vitro; however, its addition to the culture media rescued c8161 cell invasion.

Conclusion

A high-throughput screen and deep learning rapidly distilled a 45-gene panel to a small subset of genes that appear critical to melanoma cell invasion and warrant deeperin vivofunctional analysis for their role in driving the neural crest.
The human reward system encodes the subjective value of ideas during creative thinking
Authors: Moreno-Rodriguez Sarah , Béranger Benoît , Volle Emmanuelle , Lopez-Persem Alizée
Published: March 2024

Creative thinking is composed of a generation phase, where individuals form candidate ideas, and an evaluation phase, where individuals monitor the quality of their ideas, in terms of both their originality and adequacy, to select the best one. Here, we conceptualize creative evaluation as a specific type of decision-making, where participants attribute subjective values to ideas to guide their choice. Yet, while subjective values and preferences have been the focus of many studies in classical decision-making, their involvement in creative decision-making remains largely unexplored. Combining creative generation tasks and rating tasks, the present study demonstrates that individuals assign subjective values to ideas and that these values depend on a relative balance of the ideas’ originality and adequacy, which is determined by individual preferences and predicts their creative abilities. Using functional Magnetic Resonance Imaging, we found that the human reward system encodes the subjective value of ideas, and that the Default Mode and the Executive Control Networks, rather than being split into idea generation and evaluation, respectively reflect the originality and adequacy of ideas. Interestingly, the relative functional connectivity of the Default Mode and Executive Control Networks with the human reward system correlates with the relative balance of adequacy and originality in individuals’ preferences. These results bridge a gap in the current literature by providing new evidence regarding the neural bases for originality and adequacy monitoring and add valuation to the incomplete behavioral and neural accounts of creativity, offering perspectives on the influence of individual preferences on creative abilities.
Loss of Bbs8 leads to cystic kidney disease in mice and affects tubulin acetylation through HDAC2
Authors: Kieckhöfer Emilia , Matthiessen Peter A. , Ebert Lena K. , Klausen Christina , Wachten Dagmar , Benzing Thomas , May-Simera Helen , Schermer Bernhard
Published: March 2024

Bardet-Biedl Syndrome (BBS) is a genetic disorder marked by considerable genetic and phenotypic diversity. BBS often presents as a combination of retinitis pigmentosa, obesity, polydactyly, and cystic kidney disease and is considered a model ciliopathy. The syndrome is caused by pathogenic variants in BBS genes, some of which encode components of a ciliary multi-protein complex, known as the BBSome, as well as a chaperonin-like complex, which is required for BBSome assembly. In this study, we describe the occurrence of kidney cysts in a BBS mouse model. Specifically, loss of BBS8 led to the development of cystic kidney disease by the end of the first year of life. In addition to transcriptional changes of key genes involved in regulated cell death and inflammation, proteomic approaches revealed increased expression and altered phosphorylation of histone deacetylase HDAC2 in knockout kidneys. Consistently, loss ofBbs8resulted in a reduction of acetylated alpha-tubulin in primary cilia. This leads to diminished stability and altered dynamics of primary cilia, potentially contributing to the formation of cystic kidneys and other BBS manifestations previously described inBbs8deficient mice.
Integrating spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Authors: Millard Nghia , Chen Jonathan H. , Palshikar Mukta G. , Pelka Karin , Spurrell Maxwell , Price Colles , He Jiang , Hacohen Nir , Raychaudhuri Soumya , Korsunsky Ilya
Published: March 2024

Spatial transcriptomics allows for the analysis of a cell’s gene expression in the context of its physical location. With spatial transcriptomics data, investigators often want to find genes of interest whose spatial patterns are biologically relevant in multiple samples. However, due to confounding factors in spatial data that produce noise across samples, datasets, and technologies, it is challenging to visualize genes and their spatial patterns across samples. We present Crescendo, an integration algorithm that performs correction directly on gene expression counts to reduce variation from technical confounders. We first apply Crescendo to a 3-sample spatial transcriptomics mouse brain dataset to show how Crescendo enables accurate visualization of gene expression across these spatial transcriptomic samples. We then demonstrate Crescendo’s scalability by integrating a 16-sample immuno-oncology dataset of 7 million cells. Finally, we show that Crescendo can perform cross-technology integration by merging a colorectal cancer (CRC) scRNA-seq dataset with two CRC spatial transcriptomics samples. By transferring information between technologies, Crescendo can impute poorly expressed genes to improve detection of gene-gene colocalization, such as ligand-receptor interactions.
Bridging geometric morphometrics to medical anatomy: An example from an experimental study of the human smile
Authors: Bookstein Fred L. , Kent John T. , Khambay Balvinder , Mardia Kanti V.
Published: March 2024

The method of Cartesian transformations introduced by D’Arcy Thompson a century ago in his celebrated bookOn Growth and Formprecipitated an important development in 20th-century biometrics: a fusion of the geometrical and biological approaches to morphology. Some decades later this fusion, in turn, spun off another multidisciplinary focus,statistical shape analysis,that bridges between biostatistics and biomedical imaging. Our article is intended to seed a complementary focus: a bridge between biostatistics and medical anatomy, a field that has to this day remained mainly verbal rather than quantitative. Specifically, we are proposing a novel methodology for arriving at anatomical interpretations of statistical findings about large-scale contrasts of organismal morphology or its dynamics by combining two toolkits hitherto separate in their notation and their disciplinary housing: morphometrics and psychometrics. A contemporary morphometric analysis deals with patterns of shape coordinate covariation in terms of their geometric adjacency; psychometric factor analysis, the same patterns of covariation in terms of simplicity of interpretation. By combining these tools we account for the dynamics of a facial expression in terms of the actions of the underlying muscles, thereby realizing Thompson’s original metaphor, the “origins of form in force,” for systems that “vary in a more or less uniform manner.”

This paper reviews the history of Thompson’s metaphor and then the current literature quantifying smiles, in order to set the stage for the combination of scaling analysis and factor analysis that we are putting forward. We demonstrate the new approach by reanalyzing a data set of ten landmarks around the vermilion borders of the human lip contrasting the dynamics of two socially stereotyped physiological cycles, the open-lip smile and the closed-lip smile, over a sample of 14 normal faces. Our analysis centers on just two dimensions of statistical shape space, those of largest geometrical scale, which can be identified with the action of two different muscles, orbicularis oris and zygomaticus major. The two smiles differ radically in their achieved deformations. Furthermore, while the closed-lip smiles arrived at their final forms along similar shape trajectories, the open-lip smiles did not. Our closing discussion explores some aspects of morphodynamics that are illuminated by the example here.
Spatially conserved pathoprotein profiling in the human suprachiasmatic nucleus in progressive Alzheimer disease stages
Authors: Son Gowoon , Mladinov Mihovil , Pereira Felipe Luiz , Li Song Hua , Tu Chia-Ling , Judge Grace , Yang Yumi , Suemoto Claudia Kimie , Paraízo Leite Renata Elaine , Paes Vitor , Pasqualucci Carlos A. , Jacob-Filho Wilson , Spina Salvatore , Seeley William W. , Chang Wenhan , Neylan Thomas , Grinberg Lea T.
Published: March 2024

Individuals with Alzheimer’s Disease (AD) experience circadian rhythm disorder. The circadian rhythm is synchronized by a master clock, the suprachiasmatic nucleus (SCN), which is a tiny hypothalamic nucleus. Little is known about the molecular and pathological changes that occur in the SCN during AD progression. We examined postmortem brains of 12 controls without AD neuropathological changes (Braak stage 0) and 36 subjects at progressive Braak stages (I, II, and VI). To investigate potential AD-specific changes, we measured the neuronal counts of arginine vasopressin (AVP) and vasoactive intestinal peptide (VIP) positive neurons, along with the Braak stages in the SCN. We investigated in adjacent hypothalamic nuclei which are also composed of AVP+ neurons but show more resilience to AD: paraventricular nucleus (PVN) and supraoptic nucleus (SON). To understand the dysregulated proteins associated to AD progression, we performed in-situ proteomics, investigating 57 proteins, including commonly dysregulated in AD, using GeoMx Digital Spatial Profiling (DSP) in the three nuclei (total of 703 area of interests). Neurofibrillary tangles (NFTs) and tau fibrils were found selectively in SCN. We failed to detect NFTs in SON, only a mild dysregulation of p-tau at Braak VI in PVN and SON. Amyloid plaque was absent in the SCN and SON. Additionally, the SCN showed increased glial proteins already at Braak stage I, whereas the level of these proteins sustained in the other nuclei. The SCN is exclusively vulnerable to AD-tau pathology and show immune dysregulation even at Braak I but is protected against amyloid plaque. This finding revealed selectively in amnestic AD, showing more resilience in AD variant. This tau-related molecular dysregulation in the SCN contributes to circadian rhythm disturbances in AD, a phenomenon observed before the onset of cognitive disorder.
Nucleobindin-1(Nucb1)disruption affects feeding, metabolism, and glucose homeostasis in mice in an age-, sex-, diet- and light cycle-dependent manner
Authors: Nasri Atefeh , Vélez Emilio J , Rajeswari Jithine Jayakumar , Hatef Azadeh , Unniappan Suraj
Published: March 2024

Background

Nesfatin-1 (NESF-1), encoded in the calcium and DNA binding protein (Nucleobindin 2, NUCB2) is an orphan ligand with metabolic effects. Recently, our lab provided evidence for a NESF-1-like peptide (NLP) in a NUCB2-related precursor, NUCB1, in zebrafish and rodents. This research aims to determine whether endogenous NUCB1 is critical for energy homeostasis.

Methods and Main Findings

Global genetic disruption ofNucb1(Nucb1knockout/KO mice) led to increased food intake in chow-fed male and female mice across different points of light and dark phases. A similar increase in water intake was seen in femaleNucb1KO mice but not in males. White adipose tissue weight was significantly increased in male and femaleNucb1KO mice. Dark phase total activity was increased in maleNucb1KO mice, while it was decreased in femaleNucb1KO mice compared to wildtype littermates. Energy derived from carbohydrates was raised during the dark phase; while energy derived from fat was significantly decreased in both male and femaleNucb1KO mice. MaleNucb1KO mice were lighter in the early stages, but these differences disappeared as they aged. Meanwhile, no differences in bodyweight were observed in femaleNucb1KO mice. MaleNucb1KO mice handled glucose better during an oral glucose tolerance test, while the opposite effect was found in an intraperitoneal (IP) glucose tolerance test. The above results from chow-fed mice were largely true in 10% and 60% fat diet-fed mice. A significant two-way interaction between mice group and time was observed on weekly food intake of male and femaleNucb1KO mice fed control fat diet, but not in 60% fat-fed group. Handling of blood glucose during IPGTT was better in maleNucb1KO mice fed both diets, while such an effect was not observed in female KO mice. A significant two-way interaction of mice group and time on food and water intake value in 24 h was observed for maleNucb1KO mice fed 10% fat diet. The total physical activity during the dark phase and energy expenditure during the light phase showed a sex-specific pattern in male and femaleNucb1KO mice fed 10% fat diet. Energy expenditure showed a sex-specific pattern inNucb1KO mice during the dark phase. Moreover, adiposity increased in maleNucb1KO mice fed a high fat diet.

Conclusions

Our results indicate that the disruption ofNucb1leads to metabolic changesin vivo. The phenotype appears to depend on sex, age, diet, and the light-dark cycle. In conclusion, these outcomes furnish important evidence supporting critical roles for endogenous NUCB1 in energy homeostasis.
Smad4 Loss in the Mouse Intestinal Epithelium Alleviates the Pathological Fibrotic Response to Injury in the Colon
Authors: Hashemi Zahra , Hui Thompson , Wu Alex , Matouba Dahlia , Zukowski Steven , Nejati Shima , Lim Crystal , Bruzzese Julianna , Seabold Kyle , Mills Connor , Lin Cindy , Wrath Kylee , Wang Haoyu , Wang Hongjun , Verzi Michael P. , Perekatt Ansu
Published: March 2024

Mucosal healing is associated with better clinical outcomes in patients with inflammatory bowel diseases (IBDs). Unresolved injury and inflammation, on the other hand, increases pathological fibrosis and the predisposition to cancer. Loss of Smad4, a tumor suppressor, is known to increase colitis-associated cancer in mouse models of chronic IBD. Since common biological processes are involved in both injury repair and tumor growth, we sought to investigate the effect of Smad4 loss on the response to epithelial injury. To this end, Smad4 was knocked out specifically in the intestinal epithelium and transcriptomic and morphological changes compared between wild type mice and Smad4 knock out mice after DSS-induced injury. We find that Smad4 loss alleviates pathological fibrosis and enhances mucosal repair. The transcriptomic changes specific to epithelium indicate molecular changes that affect epithelial extracellular matrix (ECM) and promote enhanced mucosal repair. These findings suggest that the biological processes that promote wound healing alleviate the pathological fibrotic response to DSS. Therefore, these mucosal repair processes could be exploited to develop therapies that promote normal wound healing and prevent fibrosis.

NEW AND NOTEWORTHY

We show that transcriptomic changes due to Smad4 loss in the colonic epithelium alleviates the pathological fibrotic response to DSS in an IBD mouse model of acute inflammation. Most notably, we find that collagen deposition in the epithelial ECM, as opposed to that in the lamina propria, correlates with epithelial changes that enhance wound healing. This is the first report on a mouse model providing alleviated fibrotic response in a DSS-IBD mouse modelin vivo.
Natural slab photonic crystals and where to find them among the girdle bands of diatoms
Authors: Ashworth Matt P. , Lam Daryl W. , Lopez-Garcia Martin , Manning Schonna R. , Goessling Johannes W.
Published: March 2024

Slab photonic crystals, nanomaterials characterized by periodic pores for manipulating light, have applications in advanced optical technologies. Remarkably, similar materials have been identified in the silica shell of diatoms, in particular the girdle bands. Despite the potential applications and significance for diatom biology, their prevalence remains uncertain due to limited observations across a few species. In this study of 393 SEM girdle band micrographs across major taxonomic groups, we identified slab photonic crystals using Fast Fourier Transform (FFT) analysis. A correlation analysis of these properties on a phylogenetic tree revealed their distribution across the diversity of species and taxonomic groups. Square and hexagonal lattice varieties are prevalent in earlier-diverging groups, and linked to phytoplanktonic lifestyles. More recently-diverged clades lack these structures entirely in their girdle bands. Numerical analysis indicates that square lattice types exhibit anticipated photonic properties (stopbands) in the visible spectrum, while hexagonal lattice types are primarily linked to the near to mid-infrared range. This suggests that girdle band slab photonic crystal morphologies 1) originate from quasi-periodic photonic structures, 2) are primarily found in evolutionarily older clades (Coscinodiscophyceae and Mediophyceae), 3) lost square lattice types through diversification in the Mediophyceae, and 4) are absent in more recent clades (Fragilariophyceae and Bacillariophyceae). The limited inter-species distribution of slab photonic crystals may offer experimental cues to study their biological functionality. While these data suggest that stopband functionalities are a derived frustule trait, the ultimate purpose of slab photonic crystals in nature remains a mystery.
Growing older, growing more diverse: sea turtles and epibiotic cyanobacteria
Authors: Kanjer Lucija , Filek Klara , Mucko Maja , Lupić Mateja Zekan , Frleta-Valić Maša , Gračan Romana , Bosak Sunčica
Published: March 2024

Cyanobacteria are known for forming associations with various animals, including sea turtles, yet our understanding of sea turtles associated cyanobacteria remains limited. This study aims to address this knowledge gap by investigating the diversity of cyanobacteria in biofilm samples from loggerhead sea turtle carapaces, utilizing a 16S rDNA amplicon sequencing approach. The predominant cyanobacterial order identified wasNodosilineales, with the genusRhodoplocahaving highest relative abundance. Our results suggest that cyanobacterial communities became more diverse as sea turtles age as we had found a positive correlation between community diversity and the length of a sea turtle’s carapace. Since larger and older turtles predominantly utilize neritic habitats, the shift to more diverse cyanobacterial community aligned with a shift in loggerheads habitat. Our research provided detailed insights into the cyanobacterial communities associated with loggerhead sea turtles, establishing a foundation for future studies delving into this fascinating ecological relationship and its potential implications for sea turtle conservation.
3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation
Authors: Chen Haoran , Murphy Robert F.
Published: March 2024

Background

Cell segmentation is crucial in bioimage informatics, as its accuracy directly impacts conclusions drawn from cellular analyses. While many approaches to 2D cell segmentation have been described, 3D cell segmentation has received much less attention. 3D segmentation faces significant challenges, including limited training data availability due to the difficulty of the task for human annotators, and inherent three-dimensional complexity. As a result, existing 3D cell segmentation methods often lack broad applicability across different imaging modalities.

Results

To address this, we developed a generalizable approach for using 2D cell segmentation methods to produce accurate 3D cell segmentations. We implemented this approach in 3DCellComposer, a versatile, open-source package that allows users to choose any existing 2D segmentation model appropriate for their tissue or cell type(s) without requiring any additional training. Importantly, we have enhanced our open source CellSegmentationEvaluator quality evaluation tool to support 3D images. It provides metrics that allow selection of the best approach for a given imaging source and modality, without the need for human annotations to assess performance. Using these metrics, we demonstrated that our approach produced high-quality 3D segmentations of tissue images, and that it could outperform an existing 3D segmentation method on the cell culture images with which it was trained.

Conclusions

3DCellComposer, when paired with well-trained 2D segmentation models, provides an important alternative to acquiring human-annotated 3D images for new sample types or imaging modalities and then training 3D segmentation models using them. It is expected to be of significant value for large scale projects such as the Human BioMolecular Atlas Program.
The carrier proteome limit should be reassessed for each mass analyzer architecture
Authors: Orsburn Benjamin C.
Published: March 2024

A clever utilization of classic proteomics reagents now allows the effective amplification of peptide sequencing potential in shotgun proteomics. The application of this method has helped usher in the exciting new field of single cell proteomics. While it was easy to first think that the discovery of Budnik et al., was finally the answer for protein PCR, limitations were carefully described by the authors and others. A study by Cheung et al., systematically identified the consequences of higher concentration carrier proteomes and defined the “carrier proteome limit”. While this work has been replicated by others, every analysis published to date has used a variation of the same mass analyzer. When the same analysis is performed on alternative instruments, these limits appear to be very different and attributable to defined characteristics of each mass analyzer. Specifically, in mass analyzers with higher relative intrascan linear dynamic range, increased carrier channels appear far less detrimental to quantitative accuracy. As such, we may be limiting the power of isobaric peptide signal “amplification” by restricting ourselves to traditional mass analyzer options.
Aberrant lipid accumulation and retinal pigmental epithelium dysfunction in PRCD-deficient mice
Authors: Motipally Sree I. , Kolson Douglas R. , Guan Tongju , Kolandaivelu Saravanan
Published: March 2024

Progressive Rod-Cone Degeneration (PRCD) is an integral membrane protein found in photoreceptor outer segment (OS) disc membranes and its function remains unknown. Mutations inPrcdare implicated inRetinitis pigmentosa(RP) in humans and multiple dog breeds. PRCD-deficient models exhibit decreased levels of cholesterol in the plasma. However, potential changes in the retinal cholesterol remain unexplored. In addition, impaired phagocytosis observed in these animal models points to potential deficits in the retinal pigment epithelium (RPE). Here, using aPrcd-/-murine model we investigated the alterations in the retinal cholesterol levels and impairments in the structural and functional integrity of the RPE. Lipidomic and immunohistochemical analyses show a 5-fold increase in the levels of cholesteryl esters (C.Es) and accumulation of neutral lipids in the PRCD-deficient retina, respectively, indicating alterations in total retinal cholesterol. Longitudinal fundus and spectral domain optical coherence tomography (SD-OCT) examinations showed focal lesions and RPE hyperreflectivity. Strikingly, the RPE ofPrcd-/-mice exhibited age-related pathological features such as neutral lipid deposits, lipofuscin accumulation, Bruch’s membrane (BrM) thickening and drusenoid focal deposits, mirroring an Age-related Macular Degeneration (AMD)-like phenotype. We propose that the extensive lipofuscin accumulation likely impairs lysosomal function, leading to the defective phagocytosis observed inPrcd-/-mice. Our findings support the dysregulation of retinal cholesterol homeostasis in the absence of PRCD. Further, we demonstrate that progressive photoreceptor degeneration inPrcd-/-mice is accompanied by progressive structural and functional deficits in the RPE, which likely exacerbates vision loss over time.
Effect of prior tuberculosis on cardiovascular status in perinatally HIV-1-infected adolescents
Authors: Magodoro Itai M , Guerrero-Chalela Carlos E , Myer Landon , Jao Jennifer , Ntsekhe Mpiko , Wilkinson Katalin A , Wilkinson Robert J , Zar Heather , Ntusi Ntobeko AB
Published: March 2024

Whether, and how, co-occurring HIV-1 infection (HIV) and tuberculosis (TB) impact cardiovascular status, especially in adolescents with perinatally acquired HIV (APHIV), have not been examined. We hypothesized that APHIV with previous active TB have worse cardiac efficiency than APHIV without TB, which is mediated by increased inflammation. Arterial elastance (Ea) and ventricular end-systolic elastance (Ees) were assessed by cardiovascular magnetic resonance, and ventriculoarterial coupling (VAC) estimated as Ea/Ees ratio. Inflammation was measured by high sensitivity C-reactive protein (hsCRP). Previous TB in APHIV was associated with reduced cardiac efficiency, related to an altered ventriculoarterial coupling. However, we did not find evidence of hsCRP mediated effects in the association between prior TB and cardiac efficiency. The clinical significance of these findings requires further study, including a wider range of biomarkers of specific immune pathways.
A mechanistic modeling approach to assessing the sensitivity of outcomes of water, sanitation, and hygiene interventions to local contexts and intervention factors
Authors: Brouwer Andrew F. , Kraay Alicia N.M. , Zahid Mondal H. , Eisenberg Marisa C. , Freeman Matthew C. , Eisenberg Joseph N.S.
Published: March 2024

Background

Diarrheal disease is a leading cause of morbidity and mortality in young children. Water, sanitation, and hygiene (WASH) improvements have historically been responsible for major public health gains by reducing exposure to enteropathogens, but many individual interventions have failed to consistently reduce diarrheal disease burden. Analytical tools that can estimate the potential impacts of individual WASH improvements in specific contexts would support program managers and policymakers to set targets that would yield health gains.

Methods

To understand the impact of WASH improvements on diarrhea, we developed a disease transmission model to simulate an intervention trial with a single intervention. We accounted for contextual factors, including preexisting WASH conditions and baseline disease prevalence, as well as intervention WASH factors, including community coverage, compliance, efficacy, and the intervenable fraction of transmission. We illustrated the sensitivity of intervention effectiveness to the contextual and intervention factors in each of two scenarios in which a 50% reduction in disease was achieved through a different combination of factors (higher preexisting WASH conditions, compliance, and intervenable fraction vs higher intervention efficacy and community coverage).

Results

Achieving disease elimination depended on more than one factor, and factors that could be used to achieve disease elimination in one scenario could be ineffective in the other scenario. Community coverage interacted strongly with both the contextual and intervention factors. For example, the positive impact of increasing intervention community coverage increased non-linearly with increasing intervention compliance. Additionally, counterfactually improving the contextual preexisting WASH conditions could have a positive or negative effect on the intervention effectiveness, depending on the values of other factors.

Conclusions

When developing interventions, it is important to account for both contextual conditions and the intervention parameters. Our mechanistic modeling approach can provide guidance for developing locally specific policy recommendations.
Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility
Authors: Garg Ankit , Jansen Silvia , Zhang Rui , Lavine Kory J. , Greenberg Michael J.
Published: March 2024

Skeletal muscle actin (ACTA1) mutations are a prevalent cause of skeletal myopathies consistent with ACTA1’s high expression in skeletal muscle. Rarede novomutations in ACTA1 associated with combined cardiac and skeletal myopathies have been reported, but ACTA1 represents only ∼20% of the total actin pool in cardiomyocytes, making its role in cardiomyopathy controversial. Here we demonstrate how a mutation in an actin isoform expressed at low levels in cardiomyocytes can cause cardiomyopathy by focusing on a unique ACTA1 mutation, R256H. We previously identified this mutation in multiple family members with dilated cardiomyopathy (DCM), who had reduced systolic function without clinical skeletal myopathy. Using a battery of multiscale biophysical tools, we show that R256H has potent functional effects on ACTA1 function at the molecular scale and in human cardiomyocytes. Importantly, we demonstrate that R256H acts in a dominant manner, where the incorporation of small amounts of mutant protein into thin filaments is sufficient to disrupt molecular contractility, and that this effect is dependent on thepresenceof troponin and tropomyosin. To understand the structural basis of this change in regulation, we resolved a structure of R256H filaments using Cryo-EM, and we see alterations in actin’s structure that have the potential to disrupt interactions with tropomyosin. Finally, we show thatACTA1R256H/+human induced pluripotent stem cell cardiomyocytes demonstrate reduced contractility and sarcomeric disorganization. Taken together, we demonstrate that R256H has multiple effects on ACTA1 function that are sufficient to cause reduced contractility and establish a likely causative relationship between ACTA1 R256H and clinical cardiomyopathy.

Significance Statement

Skeletal muscle actin mutations are well-known to cause skeletal myopathies, but their role in cardiomyopathies have been controversial as skeletal muscle actin is only expressed at modest levels in the heart. Here, we demonstrate that a skeletal muscle actin mutation potently causes multiple defects in actin function at the atomic and molecular scales, and it functions in a dominant fashion, leading to cardiomyocyte contractile defects. Our results establish how skeletal muscle actin mutations may cause cardiomyocyte dysfunction and lay the foundation for future studies of the role of skeletal muscle actin in cardiomyopathy.
Increased layer 5 Martinotti cell excitation reduces pyramidal cell population plasticity and improves motor execution
Authors: Malfatti Thawann , Velica Anna , Winne Jéssica , Ciralli Barbara , Henriksson Katharina , Nascimento George , Leao Richardson , Kullander Klas
Published: March 2024

During motor activity and motor learning, pyramidal cells in the motor cortex receive inputs from local interneurons as well as deeper structures. Layer 5 pyramidal cells in the primary motor cortex then feed commands to spinal circuits for motor execution. The genetic ablation of layer 5 Chrna2 Martinotti cells, which selectively target pyramidal tract pyramidal cells, results in disturbed fine motor functions. Using calcium imaging combined with chemogenetics, we show that activation of layer 5 Chrna2 Martinotti cells during training increases pyramidal cell tuning, temporal patterning and assembly reconfiguration while not affecting motor learning success rates. However, in mice that had already learned a reach-and-grasp (prehension) task, Chrna2 Martinotti cell activation resulted in improved prehension and increased power in low theta and high gamma bands of local field potentials in the motor cortex. This work indicates that activation of Chrna2 Martinotti cells reduces pyramidal cell assembly plasticity during learning, facilitating preservation of already acquired motor skills.
Competitive assembly resolves the stoichiometry of essential proteins in infectious HIV-1 virions
Authors: Durden Haley , Preece Benjamin , Gallegos Rodrigo , Saha Ipsita , MacArthur Brian , Petersen Abby , Peppel Wiley , Saffarian Saveez
Published: March 2024

During assembly on the plasma membrane, HIV-1 virions incorporate Gag-Pol as well as gp120/gp41 trimers. The Pol region consists of protease, reverse transcriptase and integrase precursors which are essential enzymes required for maturation, reverse transcription, and integration of the viral genome in the next host. gp120/gp41 trimers catalyze the fusion of the virion with its next host. Only a fraction of released virions are infectious. The stoichiometry of gp120/gp41 and Gag-Pol proteins in HIV virions was previously measured using cryotomography and ratiometric protein analysis, but what is the stoichiometry of these proteins in infectious virions remained to be determined. Here we developed a method based on competition between infectious HIV backbones with noninfectious mutants and measured 100 ± 10 Gag-Pol and 15 ± 3 gp120/gp41 proteins incorporated in infectious virions assembled in HEK293 cells from NL4.3 HIV-1 backbone. Our measurements are in broad agreement with cryotomography and ratiometric protein analysis and therefore stoichiometry of gp120/gp41 and Gag-Pol in infectious virions is the same as all released virions. With the development of appropriate mutants and infectivity assays, our method is applicable to other infectious viruses.

Statement of significance

There are 30 million people who have succumbed to the AIDS pandemic with 600,000 additional deaths per year. HIV has an accelerated rate of mutational accumulation with the virus mutating out of neutralizing antibodies within the same patient making development of vaccines challenging. Like most enveloped viruses, only a fraction of released virions are infectious and the question of what selects these virions has remained a mystery. The method developed in this article will allow stoichiometric measurements on infectious virions and therefore allows further studies of causes of infectivity.
Detection of Chikungunya virus in The Gambia through a newly implemented sentinel surveillance program
Authors: Jallow Amadou Woury , Dieng Idrissa , Sanneh Bakary , Barry Mamadou Aliou , Talla Cheikh , Sanneh Modou Lamin , Sagne Samba Niang , Cisse Mamadou , Mendy Alphonse , Kijera Muhammed , York Karamo , Faal Alieu , Sey Alhagie Papa , Jallow Ebrima K. , Manneh Lamin , Darboe Sheriffo M.K. , Jatta Balla , Kalisa Momodou , Sanneh Adama M.B. , Njie Modou , Nyassi Momodou T. , Bittaye Mustapha , Dia Ndongo , Sall Amadou Alpha , Faye Ousmane , Diagne Moussa Moise , Faye Oumar , Diallo Boubacar , Jagne Sheriffo , Sow Abdourahmane
Published: March 2024

We characterized 01 autochthonous chikungunya virus (CHIKV) case from (The Gambia) through a newly implemented local arboviruses surveillance program in the, highlighting the first notification of the virus in the Country. Identified virus is closely related to CHIKV West African genotype detected in Kédougou (Senegal) in 2023 and responsible of a large outbreak with up to 300 confirmed cases. This work describes the first genomic proof subregional spread of CHIKV West African genotype in West Africa.
Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models
Authors: Li Wenhui , Jiang Xianyue , Wang Wuke , Hou Liya , Cai Runze , Li Yongqian , Gu Qiuxi , Chuai Guohui , Chen Qinchang , Ma Peixiang , Tang Jin , Guo Menghao , Huang Xingxu , Zhang Jun , Liu Qi
Published: March 2024

The discovery and functional annotation of CRISPR-Cas systems laid the groundwork for the development of novel CRISPR-based gene editing tools. Traditional similarity- search-based Cas discovery strategies, which rely heavily on local sequence alignment and reference Cas homologs, may overlook a significant number of remote homologs with limited sequence similarity; and it can not be applied directly for functional recognition. With the rapid development of protein large language models (LLMs), protein foundation models are expected to help model Cas systems with limited Cas homologs without extensive task-specific training data; however, the full potential of these models for Cas discovery and functional annotation has yet to be determined. To this end, we present a novel, effective and unified AI framework, CHOOSER (CasHOmlogObserving andSElf-processing scReening), for alignment-free discovery of novel CRISPR-Cas systems with self-processing precursor CRISPR RNA (pre-crRNA) capability utilizing protein foundation models. CHOOSER successfully retrieved 11 novel homologs of Casλ, the majority of which are predicted to be able to self-process pre-crRNA, nearly doubling the current catalog. One of the candidates, EphcCasλ, was subsequently experimentally validated for its ability to self-process pre-crRNA, target DNA cleavage, and trans-cleavage and was shown to be a promising candidate for use as a CRISPR-Cas-based pathogen detection system. Overall, our study provides an unprecedented perspective and methodology for discovering novel CRISPR-Cas systems with specific functions using foundation models, underscoring the potential for transforming newly identified Cas homologs into genetic editing tools.
Distinct Patterns of SARS-CoV-2 BA.2.87.1 and JN.1 Variants in Immune Evasion, Antigenicity and Cell-Cell Fusion
Authors: Li Pei , Liu Yajie , Faraone Julia , Hsu Cheng Chih , Chamblee Michelle , Zheng Yi-Min , Carlin Claire , Bednash Joseph S. , Horowitz Jeffrey C. , Mallampalli Rama K. , Saif Linda J. , Oltz Eugene M. , Jones Daniel , Li Jianrong , Gumina Richard J. , Liu Shan-Lu
Published: March 2024

The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization resistance, infectivity, antigenicity, cell-cell fusion, and spike processing. Neutralizing antibody (nAb) titers were assessed in diverse cohorts, including individuals who received a bivalent mRNA vaccine booster, patients infected during the BA.2.86/JN.1-wave, and hamsters vaccinated with XBB.1.5-monovalent vaccine. We found that BA.2.87.1 shows much less nAb escape from WT-BA.4/5 bivalent mRNA vaccination and JN.1-wave breakthrough infection sera compared to JN.1 and XBB.1.5. Interestingly. BA.2.87.1 is more resistant to neutralization by XBB.15-monovalent-vaccinated hamster sera than BA.2.86/JN.1 and XBB.1.5, but efficiently neutralized by a class III monoclonal antibody S309, which largely fails to neutralize BA.2.86/JN.1. Importantly, BA.2.87.1 exhibits higher levels of infectivity, cell-cell fusion activity, and furin cleavage efficiency than BA.2.86/JN.1. Antigenically, we found that BA.2.87.1 is closer to the ancestral BA.2 compared to other recently emerged Omicron subvariants including BA.2.86/JN.1 and XBB.1.5. Altogether, these results highlight immune escape properties as well as biology of new variants and underscore the importance of continuous surveillance and informed decision-making in the development of effective vaccines.