bluuebunny/crossref_metadata_2025 huggingface dataset:
Single cell transcriptional analysis of human adenoids identifies molecular features of airway microfold cells
Authors: Alvarez-Arguedas Samuel , Mazhar Khadijah , Wangzhou Andi , Sankaranarayanan Ishwarya , Gaona Gabriela , Lafin John T. , Mitchell Ron B. , Price Theodore J. , Shiloh Michael U.
Published: October 2024

The nasal, oropharyngeal, and bronchial mucosa are primary contact points for airborne pathogens likeMycobacterium tuberculosis(Mtb), SARS-CoV-2, and influenza virus. While mucosal surfaces can function as both entry points and barriers to infection, mucosa-associated lymphoid tissues (MALT) facilitate early immune responses to mucosal antigens. MALT contains a variety of specialized epithelial cells, including a rare cell type called a microfold cell (M cell) that functions to transport apical antigens to basolateral antigen-presenting cells, a crucial step in the initiation of mucosal immunity. M cells have been extensively characterized in the gastrointestinal (GI) tract in murine and human models. However, the precise development and functions of human airway M cells is unknown. Here, using single-nucleus RNA sequencing (snRNA-seq), we generated an atlas of cells from the human adenoid and identified 16 unique cell types representing basal, club, hillock, and hematopoietic lineages, defined their developmental trajectories, and determined cell-cell relationships. Using trajectory analysis, we found that human airway M cells develop from progenitor club cells and express a gene signature distinct from intestinal M cells. Surprisingly, we also identified a heretofore unknown epithelial cell type demonstrating a robust interferon-stimulated gene signature. Our analysis of human adenoid cells enhances our understanding of mucosal immune responses and the role of M cells in airway immunity. This work also provides a resource for understanding early interactions of pathogens with airway mucosa and a platform for development of mucosal vaccines.
Transcriptomic profiling identifies breed-specific immune signatures of Tuberculosis susceptibility in cattle
Authors: Kumar Rishi , Gandham Sripratyusha , Maity Hemant Kumar , Sarkar Uttam , Dey Bappaditya
Published: October 2024

Tuberculosis (TB) remains a major chronic infectious disease in cattle, particularly challenging in India which hosts the world’s largest and most diverse cattle population farmed in close proximity to its human settlements. This study investigates the hypothesis that genetic and immune variations drive differential TB susceptibility in cattle breeds. Using comprehensive transcriptomic analyses, we examined immune responses in peripheral blood mononuclear cells (PBMCs) from Sahiwal and Sahiwal-Holstein Friesian (SHF) crossbred cattle. Responses to both the virulentMycobacterium tuberculosisand the vaccine strainM. bovisBCG were compared. Notably, Sahiwal cattle exhibited a robust early immune response characterized by upregulation of interferon signaling, enhanced cytotoxic activity by CD8+ T and NK cells, and pronounced T cell recruitment and activation pathways compared to SHF crossbreds. PBMCs of this breed also demonstrated superior control ofM. tuberculosisreplicationin vitro. A distinctive immune signature comprising 8 genes, includingCXCL10, ISG15, CTLA4, SELL, TLR3, MYD88, IRF1, and EOMESwas significantly upregulated in Sahiwal cattle PBMCs, potentially driving their reduced TB susceptibility. These findings underscore the importance of breed-specific immune profiling in devising effective TB control strategies, and could lead to targeted interventions that leverage genetic and immunological insights to mitigate TB in regions with high cattle diversity.
Mathematical modeling of the frozen zone dynamics: towards using thermal imagers in cryotherapy
Authors: Ivakhnenko O. V. , Todrin O. F. , Globa V.Yu. , Chyzh M.O. , Kovalov G.O. , Shevchenko S.N.
Published: October 2024

Using thermal imaging for cryoablation and cryotherapy is a convenient technique but it does not allow for visualization of what is inside. We model thermal field distribution which can help relate surface thermal field images to in-depth temperature field dynamics that show freezing and thawing processes dynamics. We consider the spatio-temporal distribution of temperature using examples of hydrogel and living tissue subjected to a cryoprobe. Freezing in the hydrogel is compared with the measurements using visual morphometry. Such studies can be useful for comparingin-vitroandin-vivothermal field dynamics and for estimating the correct timing for cryoapplication.
Spatial and temporal occurrences of prairie moose across an urban to rural gradient in Saskatoon, Canada
Authors: Harris Kaitlyn E. , Brook Ryan K
Published: October 2024

The geographic range of North American moose (Alces alces) has expanded over recent decades as the population has recolonized historical habitats and dispersed into new areas, including a notable increase in moose sightings near developed, urban areas. The City of Saskatoon, Saskatchewan is situated on what would traditionally be considered atypical moose habitat, being in the semi-arid, open prairies and surrounded by high-intensity agriculture. However, this area has seen a persistent increase in the frequency of moose occurrences at the urban-rural interface over the last 30 years. We characterized spatial and temporal patterns in moose occurrences over the course of three years (2020-2023) using 29 trail cameras distributed along an urban to rural gradient within the city boundary of Saskatoon. We employed a generalized linear modelling method to assess the potential significance behind where and when moose were occurring along the gradient. Moose occurrence was negatively associated with urban sites containing higher proportions of development (>50% impervious surface cover). While we expected high occurrences during the rut, we found that moose occurrence was low through the fall months. This may be due to the high levels of human disturbance characteristic of the urban-rural interface acting as a deterrent for moose during the breeding season. Future research is warranted to better understand the underlying cause for this result. Moose also occurred most at night, coinciding with the period of lowest visibility and raising concerns for human safety. We provide suggestions and recommendations for future urban moose research and management.
Correlating Disordered Activation Domain Ensembles with Gene Expression Levels
Authors: Flores Eduardo , Camacho Aleah R. , Cuevas-Zepeda Estefania , McCoy Mary B. , Yu Feng , Staller Max V. , Sukenik Shahar
Published: October 2024

Transcription factor proteins bind to specific DNA promoter sequences and initiate gene transcription. In eukaryotes, most transcription factors contain intrinsically disordered activation domains (ADs) that regulate their transcriptional activity. Like other disordered protein regions, ADs do not have a fixed three-dimensional structure and instead exist in an ensemble of conformations. Disordered ensembles contain sequence-encoded structural preferences which are often linked to their function. We hypothesize this link exists between the structural preferences of disordered AD ensembles and their ability to induce gene expression. To test this, we used FRET microscopy to measure the ensemble dimensions of two activation domains, HIF-1α and CITED2, in live cells, and correlate this structural information with transcriptional activity. We find that point mutations that expanded the HIF-1α ensemble increased transcriptional activity, while those that compacted it reduced activity. Conversely, CITED2 showed no correlation between ensemble dimensions and activity. Our results reveal a sequence-dependent relationship between AD ensemble dimensions and their transcriptional activity.

WHY IT MATTERS

Transcription factors have activation domains (ADs) that bind to coactivator complexes to initiate gene transcription. Despite their key role, a comprehensive understanding of what drives their transcriptional activity has remained elusive. Efforts to understand AD activity have largely focused on their amino acid composition. In recent years, it is increasingly realized that the structural ensembles of disordered proteins contain biases that dictate their structural properties. For ADs, ensemble structures remain poorly explored, especially in relation to their activity. Here we report a mutational study of two ADs, HIF-1α and CITED2, that examines how ensemble dimensions correlate with activity. Our findings suggest that ensemble dimensions may drive activity in some ADs, and that AD ensemble dimensions can be modulated not only through mutations, but also through changes in the cellular environment.
Complete genome sequences of nine isolates from microplastics in the Bow River, Calgary, Canada
Authors: Goff Kira L , Suresh Sneha , Stadfeld Jonas M , Bhatnagar Srijak
Published: October 2024

We present the complete genome sequences of nine bacterial strains isolated from microplastics from water or sediments of the Bow River in Calgary, Alberta. These isolates provide insight into the freshwater microplastic microbiome and their plastic biodegradation potential.
Impact of winter enclosures on energy expenditure and movement activity of european reed deer
Authors: Silovský Václav , Pilská Anna , Faltusová Monika , Ježek Miloš
Published: October 2024

The management of red deer enclosures, combined with supplementary feeding, can reduce the energy expenditure of confined animals. These enclosed individuals minimize their spatio-temporal movement and energy usage during their time inside the winter enclosure compared to those living in free range during the same period. The datasets used in this study were based on biologging technology. All measured animals (n=11) were equipped with GPS collars and Daily Dairy sensors to record Vectorial Dynamic Body Acceleration (VeDBA). The study revealed differences in the daily summary and daily mean of VeDBA parameters between enclosed and free-living animals in the study area. Energy expenditure was similar for both groups only at the moment of winter enclosure release. After the enclosure was opened, the released individuals increased their movement and energy expenditure. The use of winter enclosures for red deer management can reduce animal movement and minimize potential damage to young forest stands and seedlings. The opening of the winter enclosure must be synchronized with the availability of natural food resources in the locality. The management of winter enclosures should be carried out with a system of supplementary feeding inside.
Multiscale heterogeneity of functional connectivity in autism
Authors: Ilioska Iva , Oldehinkel Marianne , Llera Alberto , Rovný Maroš , Mei Ting , Kia Seyed Mostafa , Floris Dorothea L. , Tillmann Julian , Holt Rosemary J. , Loth Eva , Charman Tony , Murphy Declan G. M. , Ecker Christine , Banaschewski Tobias , Mennes Maarten , Beckmann Christian F. , Marquand Andre , Buitelaar Jan K. , Fornito Alex
Published: October 2024

Atypical functional connectivity (FC) in autism is a common finding, but the results of individual studies are often inconsistent and sometimes contradictory. Classical reliance on case-control comparisons of group means that ignore the inter-individual heterogeneity in autism may be a key drive of this inconsistency. Here, we used normative modelling to examine FC heterogeneity at the level of pair-wise inter-regional connections, specific brain regions, and broader functional networks in 1,824 participants (796 autistic) aged 5-58 years recruited across 32 different sites. Connection-level heterogeneity was high in both groups, with no single connection deviating in more than 4% of participants. However, deviant connections tended to converge on common regions and networks in autistic individuals more than in controls. Autistic individuals showed significantly greater overlap for positive deviations (i.e., atypically increased FC) in transmodal systems and negative deviations (atypically decreased FC) in sensory-motor areas. FC deviation patterns across coarser levels correlated with social functioning symptoms and intellectual ability. This work suggests that clinical variability in autism may be associated with extreme heterogeneity in the specific functional connections, whereas commonalities may be driven by convergence of atypical FC increases in transmodal systems and atypical decreases in sensorimotor networks, pointing to an imbalance in the functional organization of the brain’s sensorimotor-association axis.
Improved Sensitivity For Detection Of Clinical Deterioration When Diagnostic Pathology And Patient Trends Are Included In Machine Learning Models
Authors: Greenberg Jonathan D. , Huberts Leo C.E. , Ritchie Angus , Ooi Sze-Yuan , Flynn Gordon M. , Hart Graeme K. , Gallego Blanca
Published: October 2024

Objectives

This study aimed to develop and validate a machine learning model to predict deterioration using Australian hospital data, paying particular attention to the role of predictors not included in current scoring systems.

Design

Retrospective cohort study using electronic health records from a large metropolitan health service.

Setting

General hospital wards, excluding the Emergency Department, Intensive Care Unit, or Palliative Care.

Participants

Inpatients over the age of 18.

Main Outcome Measures

The primary outcomes of deterioration were mortality and ICU transfer within 24 hours of a newly available observation. A Gradient Boosted Tree model was estimated using patient demographics, vital signs, pathology results, and linear trends. Resulting feature importance was investigated using Shapley values. The model performance was validated against existing scoring systems, including Between the Flags (BTF) and the Modified / National Early Warning Score (MEWS/NEWS).

Results

A Gradient Boosted Tree was developed from 121,608 patients and tested in 20,605 patients. The model, named aWARE, demonstrated higher discriminative ability (AUROCmortality=0.93, AUROCICU transfer=0.84), and calibration when compared to baseline scores. Overall, the 10 most influential features unique between both outcomes were age, oxygen saturation to inspired oxygen ratio, respiratory rate, white cell count, venous lactate, heart rate to systolic blood pressure ratio, albumin, oxygen saturation, urea and heart rate. Of these, only 3 are included in BTF.

Conclusion

The machine learning model proposed in this study identified more deteriorating patients and produced less false positive alerts than Between the Flags. Feature importance highlighted the deficit between strong predictors of deterioration and the parameters used in current scoring systems.
PERSONALIZED GLYCEMIC RESPONSES TO FOOD AMONG INDIVIDUALS WITH TYPE 2 DIABETES IN INDIA: DEVELOPMENT OF A MACHINE LEARNING PREDICTION MODEL
Authors: Choudhry Niteesh K. , Priyadarshini Shweta , Swamy Jaganath , Mehta Mridul
Published: October 2024

Objective

Emerging global evidence demonstrates marked inter-individual differences in post-prandial glucose response (PPGR) although no such data exists in India and prior studies have primarily evaluated PPGR variation in individuals without diabetes. This study sought to develop a machine learning model to predict individual PPGR responses to facilitate the prescription of personalized diets for individuals with type 2 diabetes.

Research Design and Methods

Adults with type 2 diabetes and a hemoglobin A1c (HbA1c) ≥7 were enrolled from 14 sites around India. Subjects wore a continuous glucose monitor and logged meals. PPGR was calculated for each meal, based on the incremental area under the curve, and a machine learning predictor of PPGR was developed using stochastic gradient boosting regression. Model calibration and discrimination was assessed using a Pearson product moment correlation and area under a receiver operating curve (AUC), respectively, and its performance was compared to models based only on meal carbohydrate and calorie content.

Results

The study included data from 488 patients (mean age 52.5 years, 36% female, mean duration of diabetes 6.4 years, mean hemoglobin A1c 8.16%). Mean PPGR to common foods varied substantially (e.g. PPGR for “aloo paratha with curd” ranged from 10 to 170 mg/dl*h). PPGR values predicted by the machine learning model were highly correlated with observed PPGR (r=0.69) and model calibration was substantially stronger than for a model based only on calorie (r=0.57) or carbohydrate (r=0.39) content. The machine learning model also demonstrated very strong discriminative ability (AUC 0.80).

Conclusions

A machine learning model built with nutritional content, health habits, biometric information and common laboratory data produced highly accurate individualized predictions of PPGRs that substantially outperformed predictions based upon calorie and carbohydrate content. These results could be used to facilitate the delivery of personalized medical nutritional therapy as is widely recommended by type 2 diabetes practice guideline in India and globally.
Evaluation of Self-Directed Learning Activities at King Abdulaziz University: A Qualitative Study of Faculty Perceptions
Authors: Balkheyour Ammar , Tombs Michal
Published: October 2024

Purpose

Doctors are expected to be lifelong learners and engage in continuous professional development throughout their careers. Learning to be a self-directed learner as early as possible is therefore likely to lay the foundation for future learning and development. For this reason, Self-Directed Learning (SDL) has recently been incorporated into the internal medicine curriculum at the Faculty of Medicine in Rabigh at King Abdulaziz University, Saudi Arabia. The purpose of this study was to evaluate faculty perceptions of the effectiveness of these SDL activities.

Methods

The evaluation framework for this study was underpinned by Stufflebeam’s Context, Input, Process and Product (CIPP) evaluation model. Seven faculty members took part in semi-structured interviews that explored their understandings of SDL objectives (Context), their perceptions of the methods and resources used (Input), the implementation of SDL activities (Process) and whether they meet their intended educational goals (Product). Interviews were transcribed and analysed using the thematic analysis method.

Results

Four themes emerged from data and were mapped against the elements of CIPP model: these themes are as follows: faculty perception of SDL (context), content and resources (input), facilitation and scheduling (process) and student engagement and assessment (product).

Conclusions

The faculty had different opinions about the objectives and content of SDL sessions; however, they agreed that these are aligned with internal medicine objectives and clinical content. Faculty perceived SDL activities as a reading task for students to complete prior to group discussion. The data revealed the necessity for faculty training to conduct such sessions. Challenges in the learning environment were reported, including issues in the library access and scheduling of the academic activities. Participants reported poor engagement from students to be a particular challenge and have made suggestions on how this could be addressed. In addition, they emphasized the need for assessment for these sessions.
Early Diagnosis of Vascular Ehlers-Danlos Syndrome Through AI-Powered Facial Analysis: Results from the Montalcino Aortic Consortium
Authors: Murdock David R. , Suresh Adarsh , Martinez Ernesto Calderon , Marin Isabella , Marin Frances , Braverman Alan C. , Yetman Angela T. , Morris Shaine A. , Milewicz Dianna M.
Published: October 2024

Purpose

Vascular Ehlers-Danlos syndrome (vEDS), caused byCOL3A1pathogenic variants, is a rare heritable aortic and arterial disorder associated with early mortality, mainly due to spontaneous vascular dissections and ruptures. Improved methods for diagnosing vEDS are needed so that guideline-based management can be initiated to prevent deadly complications and differentiate vEDS from overlapping conditions like hypermobile EDS (hEDS).

Methods

We implemented an AI facial recognition model based on the PhenoScore framework using a support vector machine (SVM) trained on facial images of thirty individuals, aged 6-65 years, with vEDS from the Montalcino Aortic Consortium (MAC), control images from the Chicago Face Database (CFD), and publicly available images of individuals with hEDS. Cross- validation was used to train the SVM, and statistical measures to evaluate the model performance were calculated. Local Interpretable Model-agnostic Explanations (LIME) was used to generate facial heatmaps highlighting the features driving the model’s predictions.

Results

The AI classifier showed excellent performance with as few as thirteen vEDS training images and distinguished vEDS from both controls and individuals with hEDS with high accuracy, achieving an area under the receiver operating characteristic curve (AUC) ≥ 0.97. LIME highlighted facial regions already established to characterize the facial features of vEDS patients (e.g., prominent eyes).

Conclusion

Our results demonstrate the potential of AI-based facial analysis for diagnosing vEDS. This method democratizes the early diagnosis of vEDS by reducing dependence on genetic testing, enabling optimal management and improved outcomes, particularly in resource-limited areas.
Controlling interfacial protein adsorption, desorption and aggregation in biomolecular condensates
Authors: Visser Brent , van Haren Merlijn , Lipiński Wojciech , van Leijenhorst-Groener Kirsten , Claessens Mireille , Queiros Marcos , Ramos Carlos , Spruijt Evan
Published: October 2024

The aggregation of amyloidogenic proteins is linked to age-related diseases. The presence of interfaces can affect their aggregation mechanism, often speeding up aggregation. α-Synuclein (αSyn) can adsorb to biomolecular condensates, leading to heterogenous nucleation and faster aggregation. Understanding the mechanism underlying localization of amyloidogenic proteins at condensate interfaces is crucial for developing strategies to prevent or reverse their binding. We show that αSyn localization to the surface of peptide-based heterotypic condensates is an adsorption process governed by the protein's condensate-amphiphilic nature. Adsorption occurs in multiple layers and levels off at micromolar concentrations. Based on these findings, we design three strategies to modulate αSyn accumulation: (i) addition of biomolecules that decrease the condensate ζ-potential, such as NTPs and RNA, (ii) competitive adsorption of proteins targeting the condensate interface, such as G3BP1, DDX4-YFP, EGFP-NPM1, Hsp70, Hsc70, and (iii) preferential adsorption of αSyn to membranes. Removing αSyn from the condensate interface slows aggregation, highlighting potential cellular control over protein adsorption and implications for therapeutic strategies.
PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+sensor proteins
Authors: Horne Christopher R. , Dite Toby A. , Young Samuel N. , Mather Lucy J. , Dagley Laura F. , Johnson Jared L. , Yaron-Barir Tomer M. , Huntsman Emily M. , Daly Leonard A. , Byrne Dominic P. , Cadell Antonia L. , Ng Boaz H. , Yousef Jumana , Multari Dylan H. , Shen Lianju , McAloon Luke M. , Manning Gerard , Febbraio Mark A. , Means Anthony R. , Cantley Lewis C. , Tanzer Maria C. , Croucher David R. , Eyers Claire E. , Eyers Patrick A. , Scott John W. , Murphy James M.
Published: October 2024

Protein Serine Kinase H1 (PSKH1) was recently identified as a crucial factor in kidney development and is overexpressed in prostate, lung and kidney cancers. However, little is known about PSKH1 regulatory mechanisms, leading to its classification as a “dark” kinase. Here, we used biochemistry and mass spectrometry to define PSKH1’s consensus substrate motif, protein interactors, and how interactors, including Ca2+sensor proteins, promote or suppress activity. Intriguingly, despite the absence of a canonical Calmodulin binding motif, Ca2+-Calmodulin activated PSKH1 while, in contrast, the ER-resident Ca2+sensor of the CREC family, Reticulocalbin-3, suppressed PSKH1 catalytic activity. In addition to antagonistic regulation of the PSKH1 kinase domain by Ca2+sensing proteins, we identified UNC119B as a protein interactor that activates PSKH1 via direct engagement of the kinase domain. Our findings identify complementary allosteric mechanisms by which regulatory proteins tune PSKH1’s catalytic activity, and raise the possibility that different Ca2+sensors may act more broadly to tune kinase activities by detecting and decoding extremes of intracellular Ca2+concentrations.
Modeling Glioma Intratumoral Heterogeneity with Primary Human Neural Stem and Progenitor Cells
Authors: Gao Daniel , Liu Daniel Dan , Eastman Anna E. , Womack Nicole L. , Ohene-Gambill Benjamin F. , Baez Michelle , Weissman Irving L.
Published: October 2024

Glioblastoma multiforme (GBM) is a deadly form of glioma notable for its significant intratumoral heterogeneity, which is believed to drive therapy resistance. GBM has been observed to mimic a neural stem cell hierarchy reminiscent of normal brain development. However, it is still unclear how cell-of-origin shapes intratumoral heterogeneity. Here, we develop a model of glioma initiation using neural stem and progenitor cells (NSPCs) purified from fetal human brain tissue. We previously described a method to prospectively isolate and culture tripotent neural stem cells (NSCs), bipotent glial progenitor cells (GPCs), and unipotent oligodendrocyte precursor cells (OPCs). We transduced these isogenic lines with dominant-negative TP53R175Hand NF1 knockdown, a commonly-used genetic model of GBM in mice. These reprogrammed lines robustly engrafted when transplanted into the brains of immunodeficient mice, and showed significant expansion over time. Engrafted cells were reextracted from the mouse brain for single cell RNA sequencing (scRNA-seq), in order to quantify how the cell-of-origin modulates the cellular subtypes found in the resulting tumor. This result revealed the strong influence the cell-of-origin plays in glioma heterogeneity. Our platform is highly adaptable and allows for modular and systematic interrogation of how cell-of-origin shape the tumor landscape.
Multifunctional Systems in Synthetic Biology: Single-Stranded DNA Signaling for Precise Control of Gene Activation
Authors: Ng Brian , Ding Yuying , Cornall Matthew , Kumar Ravinash Krishna , Qing Yujia , Bayley Hagan
Published: October 2024

Controllable gene circuits that respond to defined inputs are essential tools in synthetic biology. By leveraging regulatory mechanisms at either transcriptional or translational levels, synthetic responsive systems have been engineered to recognize diverse signals, such as small molecules (e.g., tetracycline) or physical stimuli (e.g., light). However, these approaches have limitations: small-molecule signals often require high concentrations to be effective, and sophisticated engineering is needed to generate responsive effectors. Here, we establish a simple, versatile gene activation system in which short single-stranded DNAs trigger RNA or protein production by complementing defective single-stranded promoters upstream of target genes. We demonstrate selective gene activation with orthogonal promoters, and logic-gate operations with signal pairs. The signaling system operates in compartmentalized nanoliter droplets scaffolded by bilayers. Signal delivery is controlled by selectively disrupting bilayers or applying transmembrane potential to move signals through protein pores, thereby activating genes within the receiver compartments. This work expands the toolset for engineering multifunctional, responsive materials to meet biotechnological and medical needs, enabling gene activation in response to specific cues.
Medicinal chemistry of benzo[d]isoxazole-4,7-dione analogues identifies the ribosomal small subunit as a target for specific mycobacterial translational fidelity
Authors: Wu Jie , Chaudhuri Swarnava , Feid Sarah Caldwell , Pan Miaomiao , Kawaji Qingwen , Liu Gang , Javid Babak
Published: October 2024

Mycobacteria have high rates of error in the translation of glutamine and asparagine codons due to a two-step indirect tRNA aminoacylation pathway involving the essential amidotransferase GatCAB. This specific mycobacterial mistranslation is both necessary and sufficient for tolerance to the antibiotic rifampicin. Furthermore, we identified the natural product kasugamycin as a small molecule that could decrease this type of translational error, and potentiate rifampicin-mediated killing of mycobacteria, but whether other small molecules can decrease this specific type of mistranslation is unknown. We screened a library of synthetic small molecules using a pathway-specific whole-cell screen in a reporter strain ofMycobacterium smegmatisfor their ability to decrease specific mycobacterial mistranslation. We synthesized 110 analogs of a parent hit compound and analyzed their bioactivity. To identify the cellular target of the compounds, we biotinylated active and inactive analogs and performed pull-down and mass-spectrometry of bound cellular proteins. We identified benzo[d]isoxazole-4,7-diones as a class of small molecules able to decrease mycobacterial mistranslation. Of the 110 analogs synthesized, we identified 10 with superior potency to the parent compound and analyzed the compounds to infer structure-activity relationships. Pull-down and mass spectrometry of bound cellular proteins identified RpS5 as a potential target of active compounds. Our study identified synthetic small molecules able to decrease mycobacterial mistranslation and confirmed that the small ribosomal subunit can be targeted to decrease mistranslation rates arising from physiologically mischarged tRNAs. Targeting mistranslation may be a potentially attractive means of targeting antibiotic-tolerant bacteria.
THRESHOLD: A Comprehensive Transcriptomic Analysis Tool for Evaluating Gene Saturation and Impact in Disease Progression
Authors: Gammell Finán , Li Jennifer , Elco Christopher , Plavicki Jessica , Uzun Alper
Published: October 2024

Gene expression studies serve as a foundational tool in molecular biology, providing insights into developmental, physiological, and pathological processes. Variations in gene expression can indicate disease states, which are vital in understanding disease progression, subtype manifestations, and identifying therapeutic targets based on detailed expression patterns. To effectively investigate gene expression patterns, especially in large datasets, a robust and precise analysis tool is crucial. In response to this critical analytical need, we developed THRESHOLD, a novel tool that goes beyond traditional gene expression analysis by introducing the concept of gene saturation. Unlike conventional methods that focus on absolute expression levels or binary differential expression, THRESHOLD quantifies the consistency of gene expression across patients, revealing co-regulation patterns that may otherwise be overlooked. This novel metric offers a unique perspective on gene expression patterns by highlighting consistent trends across patient samples, which are critical for understanding disease mechanisms and stratifying patients based on molecular signatures. The tool offers several features, including user-defined parameters, statistical comparisons, and interactive data visualization. THRESHOLD has uncovered compelling insights into disease progression using TCGA Cancer Datasets. For instance, bladder urothelial carcinoma demonstrated increasing upregulated gene saturation in progressive cancer stages (p < 0.00001). Moreover, THRESHOLD identified heightened gene saturation in patients with earlier onset of prostate adenocarcinoma (p < 0.0001) and revealed a critical fusion transcript, SLC45A2-AMACR, implicated in prostate adenocarcinoma progression, recurrence, and metastasis. Additionally, novel biomarkers and potential candidates for drug therapies were identified through protein-protein interaction networks and functional analyses of saturation data in colon adenocarcinoma and breast invasive carcinoma. Collectively, THRESHOLD advances our understanding of patient stratification and molecular signatures by offering a more detailed view of gene expression dynamics. The THRESHOLD tool is publicly available at:https://github.com/alperuzun/THRESHOLD.
Loss of Cdc42 causes abnormal optic cup morphogenesis and microphthalmia in mouse
Authors: Hofstetter Katrina S. , Haas Paula M. , Kuntz Jonathon P. , Zheng Yi , Fuhrmann Sabine
Published: October 2024

Congenital ocular malformations originate from defective morphogenesis during early eye development and cause 25% of childhood blindness. Formation of the eye is a multi-step, dynamic process; it involves evagination of the optic vesicle, followed by distal and ventral invagination, leading to the formation of a two-layered optic cup with a transient optic fissure. These tissue folding events require extensive changes in cell shape and tissue growth mediated by cytoskeleton mechanics and intercellular adhesion. We hypothesized that the Rho GTPase Cdc42 may be an essential, convergent effector downstream of key regulatory factors required for ocular morphogenesis. CDC42 controls actin remodeling, apicobasal polarity, and junction assembly. Here we identify a novel essential function for Cdc42 during eye morphogenesis in mouse; inCdc42mutant eyes expansion of the ventral optic cup is arrested, resulting in microphthalmia and a wide coloboma. Our analyses show that Cdc42 is required for expression of the polarity effector proteins PRKCZ and PARD6, intercellular junction protein tight junction protein 1, β-catenin, actin cytoskeleton F-actin, and contractile protein phospho myosin light chain 2. Expression of RPE fate determinants OTX2 and MITF, and formation of the RPE layer are severely affected in the temporal domain of the proximal optic cup. EdU incorporation is significantly downregulated. In addition, mitotic retinal progenitor cells mis-localized deeper, basal regions, likely contributing to decreased proliferation. We propose that morphogenesis of the ventral optic cup requires Cdc42 function for coordinated optic cup expansion and establishment of subretinal space, tissue tension, and differentiation of the ventral RPE layer.
Serum PFAS and Lipid Concentrations in Ecuadorian Adolescents
Authors: Guerra Michelle , Kayser Georgia , Checkoway Harvey , Suarez-Torres Jose , Lopez Dolores , Martinez Danilo , Huset Carin A. , Peterson Lisa A. , Suarez-Lopez Jose Ricardo
Published: October 2024

There is growing evidence that per- and polyfluoroalkyl substances (PFAS) may alter serum lipid concentrations; however, this topic is understudied in adolescents and Latin American populations. We aimed to characterize these associations among adolescents in Ecuador’s main floricultural region.

This cross-sectional study included 97 adolescents ages 11-17 years from Pedro Moncayo County, Ecuador. Generalized estimating equation models were applied to estimate the associations of serum perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and perfluorononanoic acid (PFNA) concentrations with serum lipids. Models were adjusted for age, gender, height, body mass index (BMI), acetylcholinesterase (AChE) activity, and hemoglobin concentrations.

We observed statistically significant sex-specific associations of all PFAS with triglycerides. Significant inverse relationships between PFAS and triglycerides were observed in females (% lipid difference per 50% increase in: PFOS= −15.0% [95%CI: −24.72, −4.06], PFNA= −25.49% [−36.93, −12.00], and PFOA= −16.55% [−28.16, −3.07]) but not in males. No associations were observed between total cholesterol, high-density lipoprotein (HDL), or low-density lipoprotein (LDL) cholesterol and any PFAS.

PFOS, PFOA, and PFNA were inversely associated with triglycerides in adolescent females but not males. Further characterization of sex-specific associations of PFAS and blood lipids in adolescents is warranted.
Mapping the Cellular Etiology of Schizophrenia and Diverse Brain Phenotypes
Authors: Duncan Laramie E , Li Tayden , Salem Madeleine , Li Will , Mortazavi Leili , Senturk Hazal , Shargh Naghmeh , Vesuna Sam , Shen Hanyang , Yoon Jong , Wang Gordon , Ballon Jacob , Tan Longzhi , Pruett Brandon Scott , Knutson Brian , Deisseroth Karl , Giardino William J
Published: October 2024

Summary paragraph

Psychiatric disorders account for a substantial fraction of the world’s disease burden1, and yet the development of novel therapeutics has been notoriously slow2. Likely contributing factors include the complexity of the human brain and the high polygenicity of psychiatric disorders3–5, meaning that thousands of genetic factors contribute to disease risk. Fortunately, technological advances have enabled comprehensive surveys of human brain cell types using transcriptomes from single nuclei (snRNAseq)6–8. Additionally, genome-wide association studies (GWAS) have linked thousands of risk loci to psychiatric disorders9–11. Here, we combined these two landmark data resources to infer the cell types involved in the etiology of schizophrenia and comparison phenotypes. This work demonstrated: 1) cell types that are concordant with prior findings about schizophrenia, 2) novel cell type associations for schizophrenia, 3) greater molecular specificity regarding schizophrenia-associated cell types than was previously available, 4) evidence that well powered genome-wide and brain-wide datasets are required for these analyses, 5) distinct cellular profiles for five brain-related phenotypes, 6) a prototype for a cell-type based classification system for psychiatric and other brain disorders, and 7) a roadmap toward drug repurposing, novel drug development, and personalized treatment recommendations. Thus, this work formalizes a data-driven, cellular and molecular model of complex brain disorders.
TRAUMATIC MICROHEMORHAGES ARE NOT SYNONYMOUS WITH AXONAL INJURY
Authors: Mittenzwei Rhonda , Maioli Heather , Sytsma Karinn , Kirkland Amanda , Keene C. Dirk , Diaz-Arrastia Ramon , Mac Donald Christine , Maffei Chiara , Edlow Brian L. , Nolan Amber L.
Published: October 2024

Diffuse axonal injury (DAI) is caused by acceleration-deceleration forces during trauma that shear white matter tracts. Susceptibility-weighted MRI (SWI) identifies microbleeds that are considered the radiologic hallmark of DAI and are used in clinical prognostication. However, this assumption is limited by a lack of systematic radiologic-pathologic correlation studies. Here, we performedex vivoSWI on three brains from patients who died after severe TBI and assessed axonal injury around SWI microbleeds using immunohistochemistry to the amyloid beta precursor protein. Axonal injury was present in 28/44 microbleeds (64%), undermining the assumed pathophysiologic 1:1 link between traumatic vascular and axonal injury.
IRAK2 deficiency causes a new immune dysregulation disorder
Authors: Fei Yudie , Liu Lin , Ma Shuangyue , Wang Shihao , Lu Meiping , Xue Jing , Jin Ying , Wang Yusha , Sun Xiangwei , Chen Xiang , Han Xu , Zhang Changming , Guo Li , Zhang Jiahui , Zhong Hua , Wen Lihong , Yu Xiaomin , Zhou Qing , Liu Zhihong
Published: October 2024

Interleukin 1 receptor-associated kinase 2 (IRAK2) plays a critical role in immune response by participating in the formation of the Myddosome complex in Toll-like receptor (TLR) signaling pathways. Here, we identified a loss-of-function mutation (IRAK2-Δex2) in theIRAK2gene in three patients, presenting with immune dysregulation, including systemic lupus erythematosus (SLE) and autoinflammatory disease. This mutation leads to the skipping of exon 2 inIRAK2, disrupting its interaction with IRAK4 and impairing the activation of nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways via Myddosome. The patients exhibited aberrantly upregulated type I interferon (IFN) response following LPS stimulation, which was further confirmed in bone marrow-derived macrophages (BMDMs) in mice. Our study suggests that IRAK2 deficiency results in immune dysregulation due to compromised TLR signaling and activated IFN signaling primarily in monocyte-macrophage lineage.

One Sentence Summary

A new immune dysregulation disorder caused by a loss-of-function mutation in theIRAK2gene, which disrupts TLR signaling via Myddosome, results in impaired NF-κB activation and upregulated type I interferon responses.
Identification and molecular characterization of missense mutations in orphan GPCR GPR61 occurring in severe obesity
Authors: Tsang Choi Har , Rosa Alexander De , Kozielewicz Paweł
Published: October 2024

Obesity is a disease defined as “abnormal or excessive fat accumulation that presents a health risk, with a body mass index (BMI) over 30” (World Health Organization). Signalling mediated by hypothalamus-expressed membrane proteins from the GPCR family regulates food intake and metabolism. The orphan GPCR GPR61 was linked to regulation of metabolism and, here, we identify 34 mutations in the GPR61 gene which are present with much higher frequency in severe obesity samples from UK10K obesity screen than in the normal population. The cumulative sum of mutations was higher for the GPR61 gene compared to the highly mutated and well-established target, melanocortin 4 receptor (MC4R). The majority of the GPR61 mutations reduced cell surface expression of overexpressed HiBiT-GPR61 in HEK293A cells. Additionally, the mutations T92P, R236C and R262C reduced ligand-independent GPR61-induced cAMP production, and R236C compromised Gsprotein activation. Therefore, we suggest that GPR61 indeed represents a Gs-coupled receptor with a potential role in the regulation of metabolism. Our data warrant further studies to assess role of this orphan GPCR in metabolism in greater detail.
Blink rates in patients with schizophrenia compared to healthy controls: A meta-analysis
Authors: Nielsen Johannes Reinau Windelborg , Dietz Martin , Jefsen Oskar Hougaard
Published: October 2024

Background

Eyeblink rates vary with cognitive states and may be related to dopaminergic activity. Early reports have found elevated blink rates in patients with schizophrenia, possibly related to hyperdopaminergia, but findings appear inconsistent. We performed a systematic review and meta-analysis to evaluate the evidence regarding blink rates in patients with schizophrenia compared to healthy controls and the impact of medication.

Methods

We registered a protocol for the review on PROSPERO. We searched PubMed, SCOPUS, and Embase, performed title- and abstract-screening, full-text screening, data extraction, and risk-of-bias assessment. We calculated meta-level effect sizes, assessed effect size heterogeneity, and tested for small-study effects.

Results

We included 22 studies in the systematic review and of those, 19 in the meta-analysis. The studies included a total of 632 patients and 791 healthy controls. The risk of bias was high in all but two studies, particularly due to the lack of blinding and confounding by medication. Meta-analysis revealed an elevated blink rate in patients with schizophrenia (irrespective of medication status) compared to healthy controls (Hedges’g= 0.48; 95% CI [0.13,0.82]). Stratified meta-analyses revealed elevated blink rates in unmedicated patients with schizophrenia compared with healthy controls (Hedges’g= 0.83; 95% CI [0.34, 1.31]), but not in medicated patients compared with controls (Hedges’g= -0.09; 95% CI [-0.64, 0.46]).

Conclusion

Blink rates are elevated in unmedicated, but not medicated, patients with schizophrenia compared with healthy controls. These findings motivate further study of the link between blink rates, central dopamine, and schizophrenia.
Developing Del2Phen: a novel phenotype description tool for chromosome deletions
Authors: Rraku Eleana , Medina Tyler D. , van Ravenswaaij-Arts Conny M.A. , Slofstra Mariska K. , Swertz Morris A. , Dijkhuizen Trijnie , Johansson Lennart F. , Engwerda Aafke
Published: October 2024

Information on the health-related consequences of rare chromosome disorders is often limited, posing challenges for both patients and their families. The Chromosome 6 Project aims to bridge this knowledge gap for structural aberrations involving chromosome 6 by providing parents of affected children with information on the expected phenotypes of their child. To achieve this, detailed phenotype and genotype data is collected directly from parents worldwide and supplemented with data from literature reports, resulting thus far in a dataset of over 500 individuals. This comprehensive data pool was used to develop Del2Phen, a software tool introduced in this paper that generates aberration-specific phenotype information for chromosome disorders. Del2Phen identifies individuals with a deletion or duplication similar to that of a new patient (index) and produces a clinical description for the index based on phenotypic features observed in these genotypically similar individuals. Genotypic similarity is determined using existing knowledge on the haploinsufficiency effect of genes and established gene-phenotype relationships. The optimal genotypic similarity parameters for chromosome 6 deletions were evaluated, which lead to thorough and reliable clinical descriptions based on sufficiently large groups of individuals with highly similar deletions. Although currently applied to and optimized for chromosome 6 deletions, Del2Phen can be used on deletions involving other chromosomes and is easily adapted for use on duplications, provided sufficient data is available. Del2Phen can already be used to expedite data analysis for chromosome disorders, thus aiding healthcare professionals in providing clinical care. Lastly, this tool will also be integrated into an interactive website aimed at parents of children with a chromosome 6 aberration, providing them with essential health information in an efficient and timely manner.
CardioBrain: A Novel User-Friendly Software for Assessing Dynamic Cerebral Autoregulation and Cardiovascular Interactions
Authors: Pecanha Tiago , Bartels Rhenan , Rodrigues Gabriel Dias
Published: October 2024

Cerebral autoregulation (CA) is a critical mechanism that maintains cerebral blood flow (CBF) relatively stable despite fluctuations in arterial blood pressure (ABP), ensuring protection against ischemia and hyperperfusion. Alterations in CA are linked to adverse outcomes in various conditions, highlighting the need for precise and accessible methods to analyse CA.CardioBrainis a freely available user-friendly software developed to assess dynamic CA by performing Transfer Function Analysis (TFA) on continuously recorded ABP and CBF data. The software utilizes the Welch method for spectral density and cross-spectral analysis. Following TFA, the software calculates different dCA metrics as gain, phase, and coherence across various frequency bands (VLF, LF, HF).CardioBrainallows users to easily manipulate signal processing parameters, visualize data, and export results, making it suitable for both research and clinical settings without requiring advanced programming skills. Additionally, the software includes tools to address signal misalignments, such as a temporal shift feature, and ensures adherence to recommended standards for TFA analysis. Future development will focus on incorporating user feedback, validating the software against simulated and real-world data, and expanding its functionality for a broader range of regulatory analyses.