bluuebunny/crossref_metadata_2025 huggingface dataset:
A laboratory framework for ongoing optimisation of amplification based genomic surveillance programs
Authors: Lam Connie , Johnson-Mackinnon Jessica , Basile Kerri , Fong Winkie , Suster Carl J.E. , Gall Mailie , Agius Jessica , Chandra Shona , Draper Jenny , Martinez Elena , Drew Alexander , Wang Qinning , Chen Sharon C , Kok Jen , Dwyer Dominic E , Sintchenko Vitali , Rockett Rebecca J.
Published: July 2023

Constantly evolving viral populations affect the specificity of primers and quality of genomic surveillance. This study presents a framework for continuous optimisation of sequencing efficiency for public health surveillance based on the ongoing evolution of the COVID-19 pandemic. SARS-CoV-2 genomic clustering capacity based on three amplification based whole genome sequencing schemes was assessed using decreasing thresholds of genome coverage and measured against epidemiologically linked cases. Overall genome coverage depth and individual amplicon depth were used to calculate an amplification efficiency metric. Significant loss of genome coverage over time was documented which was recovered by optimisation of primer pooling or implementation of new primer sets. A minimum of 95% genome coverage was required to cluster 94% of epidemiologically defined SARS-CoV-2 transmission events. Clustering resolution fell to 70% when only 85% of genome coverage was achieved. The framework presented in this study can provide public health genomic surveillance programs a systematic process to ensure an agile and effective laboratory response during rapidly evolving viral outbreaks.
Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system
Authors: Taminishi Shunta , Li Songling , Higuchi Yusuke , Kirita Yuhei , Motooka Daisuke , Ozaki Yuki , Arimori Takao , Ikemura Nariko , Itoh Yumi , Matoba Satoaki , Okamoto Toru , Takagi Junichi , Standley Daron M , Hoshino Atsushi
Published: July 2023

In order to investigate SARS-CoV-2 mutations and their impact on immune evasion and infectivity, we developed a Deep Mutational Scanning (DMS) platform utilizing an inverted infection assay to measure spike expression, ACE2 affinity, and viral infectivity in human cells. Surprisingly, our analysis reveals that spike protein expression, rather than ACE2 affinity, is the primary factor affecting viral infectivity and correlated with SARS-CoV-2 evolution. Notably, within the N-terminal domain (NTD), spike expression and infectivity-enhancing mutations are concentrated in flexible loops. We also observed that Omicron variants BA.1 and BA.2 exhibit immune evasion through receptor binding domain (RBD) mutations, although these mutations reduce structural stability. Interestingly, the NTD has evolved to increase stability, compensating for the RBD instability and resulting in heightened overall infectivity. Our findings, available in SpikeScanDB, emphasize the importance of spike expression levels and compensatory mutations in both the NTD and RBD domains for shaping Omicron variant infectivity.
Assessing generalizability of a dengue classifier across multiple datasets
Authors: Lu Bingqian , Li Yanni , Evans Ciaran
Published: July 2023

Early diagnosis of dengue fever is important for individual treatment and monitoring disease prevalence in the population. To assist diagnosis, previous studies have proposed classification models to detect dengue from symptoms and clinical measurements. However, there has been little exploration of whether existing models can be used to make predictions for new populations. We trained logistic regression models on five publicly available dengue datasets from previous studies, using three explanatory variables identified as important in prior work: age, white blood cell count, and platelet count. These five datasets were collected at different times in different locations, with a variety of disease rates and patient ages. A model was trained on each dataset, and predictive performance and model calibration was evaluated on both the original (training) dataset, and the other (test) datasets from different studies. We further compared performance with larger models and other classification methods. In-sample area under the receiver operating characteristic curve (AUC) values for the logistic regression models ranged from 0.74 to 0.89, while out-of-sample AUCs ranged from 0.55 to 0.89. Matching age ranges in training/test datasets increased AUC values and balanced the sensitivity and specificity. Adjusting the predicted probabilities to account for differences in dengue prevalence improved calibration in 20/28 training-test pairs. Results were similar when other explanatory variables were included and when other classification methods (decision trees and support vector machines) were used. The in-sample performance of the logistic regression model was consistent with previous dengue classifiers, suggesting the chosen model is a good choice in a variety of settings and has decent overall performance. However, adjustments are required to make predictions on new datasets. Practitioners can use existing dengue classifiers in new settings but should be careful with different patient ages and disease rates.
Is biomedical research self-correcting? Modeling insights on the persistence of spurious science
Authors: Grimes David Robert
Published: July 2023

The reality that volumes of published research are not reproducible has been increasingly recognised in recent years, notably in biomedical science. In many fields, spurious results are common, reducing trustworthiness of reported results. While this increases research waste, a common response is that science is ultimately self-correcting, and trustworthy science will eventually triumph. While this is likely true from a philosophy of science perspective, it does not yield information on how much effort is required to nullify suspect findings, nor factors that shape how quickly science may be correcting in the publish-or-perish environment scientists operate. There is also a paucity of information on how perverse incentives of the publishing ecosystem, which reward novel positive findings over null results, shaping the ability of published science to self-correct. Precisely what factors shape self-correction of science remain obscure, limiting our ability to mitigate harms. This modelling study illuminates these questions, introducing a simple model to capture dynamics of the publication ecosystem, exploring factors influencing research waste, trustworthiness, corrective effort, and time to correction. Results from this work indicate that research waste and corrective effort are highly dependent on field-specific false positive rates and the time delay before corrective results to spurious findings are propagated. The model also suggests conditions under which biomedical science is self-correcting, and those under which publication of correctives alone cannot stem the propagation of untrustworthy results. Finally, this work models a variety of potential mitigation strategies, including researcher and publication driven interventions.

Significance statement

In biomedical science, there is increasing recognition that many results fail to replicate, impeding both scientific advances and trust in science. While science is self-correcting over long time-scales, there has been little work done on the factors that shape time to correction, the scale of corrective efforts, and the research waste generated in these endeavours. Similarly, there has been little work done on quantifying factors that might reduce negative impacts of spurious science. This work takes a modeling approach to illuminate these questions, uncovering new strategies for mitigating the impact of untrustworthy research.
PhageScanner, a flexible machine learning pipeline for automated bacteriophage genomic and metagenomic feature annotation
Authors: Albin Dreycey , Alistar Mirela
Published: July 2023

Even though bacteriophages are the most plentiful organisms on Earth, many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. Most proteins in bacteriophages are structural, known as Phage Virion Proteins (PVPs), but a considerable number remain unclassified. Complicating matters further, conventional lab-based methods for PVP identification are time-consuming and tedious. To expedite the process of identifying PVPs, machine-learning models are increasingly being employed. While existing tools have developed models for predicting PVPs from protein sequences as input, none of these efforts have built software allowing for genomic and metagenomic as input. In addition, there isn’t a framework available for easily curating data and creating new types of models. In response, we introduce PhageScanner, an open-source platform that streamlines data collection, model training and testing, and includes a prediction pipeline for annotating genomic and metagenomic data. PhageScanner also features a graphical user interface (GUI) for visualizing annotations on genomic and metagenomic data. We also introduce a BLAST-based classifier that outperforms ML-based models (achieving an F1 score of 94% for multiclass PVP detection and 97% for binary PVP detection) and an efficient Long Short-Term Memory (LSTM) classifier. We showcase the capabilities of PhageScanner by predicting PVPs in six previously uncharacterized bacteriophage genomes. In addition, showing the utility of the framework, we create a new model that predicts phage-encoded toxins within bacteriophage genomes.
Exploring Gene Expression Patterns and Evolutionary Responses in Host-Parasite inteactions: Insights from theSchistocephalus solidus– Threespine stickleback System
Authors: Wohlleben Anika M. , Tabima Javier F. , Meyer Néva P. , Steinel Natalie C.
Published: July 2023

Helminth parasites pose a significant threat to host survival and reproductive success, imposing strong selection pressure on hosts to evolve countermessures (e.g., immune responses and behavioral changes). To gain insights into the underlying mechanisms of host-parasite co-evolution, we examined differences in gene expression in immune tissues of two Alaskan stickleback (Gasterosteus aculeatus) populations with varying susceptibility to infection by the cestodeSchistocephalus solidus. Our analyses revealed distinct patterns of immune gene expression at the population-level in response to infection. Infected fish from the high infection population displayed signs of immune manipulation by the parasite, whereas this phenomenon was absent in fish from the low infection population. Notably, we found significant differences in immune gene expression between the populations, with uninfected Rocky Lake fish showing up-regulation of innate immune genes associated with inflammation compared to uninfected Walby Lake fish. These findings highlight the divergent evolutionary paths taken by different stickleback populations in their response to the same parasite.
Dimension reduction of microbiome data linkedBifidobacteriumto allergic rhinitis
Authors: Komaki Shohei , Sahoyama Yukari , Hachiya Tsuyoshi , Koseki Keita , Ogata Yusuke , Hamazato Fumiaki , Shiozawa Manabu , Nakagawa Tohru , Suda Wataru , Hattori Masahira , Kawakami Eiryo
Published: July 2023

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis (PCA), principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization (NMF), to a microbiome dataset from 186 subjects with symptoms of AR and 106 controls. All the dimension reduction methods supported that the enterotype clusters were overlapped in the dimension reduction plots, and that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed between the dimension reduction methods. The second composite variable calculated from PCoA was significantly associated with the intake of several nutrients, including omega-3 polyunsaturated fatty acids, and the risk of AR. The composite variable was also correlated with the relative abundance ofBifidobacterium, and thus,Bifidobacteriumwas related to the risk of AR and intake of several nutrients through dimension reduction. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.
Pax37 gene function inOikopleura dioicasupports a neuroepithelial-like origin for its house-making Fol territory
Authors: Lagman David , Leon Anthony , Cieminska Nadia , Deng Wei , Chatzigeorgiou Marios , Henriet Simon , Chourrout Daniel
Published: July 2023

Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we have shown that several homeobox transcription factors may play a role in patterning the OE. Among these are twoPax3/7duplicates that we namedPax37AandPax37B. The vertebrate homologs,PAX3andPAX7, are involved in developmental processes related to neural crest and muscles. In the ascidian tunicateCiona robusta,Pax3/7has been given a role in development of cells deriving from the neural plate border including trunk epidermal sensory neurons and tail nerve cord neurons as well as in neural tube closure. Here we have investigated the roles ofPax37AandPax37Bin the development of the OE using CRISPR-Cas9, analyzing scRNA-seq data from wild-type animals that were compared with scRNA-seq data fromC. robusta. We revealed thatPax37Bbut notPax37Ais essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Lineage analysis supports that expression ofPax37is under influence of Wnt signaling and that Fol cells have a neuroepithelial-like transcriptional signature. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features as do “glue” secreting collocytes of ascidians. Their development seems to be controlled by a GRN that also operates in some ascidian neurons.
An aiHumanoid Simulation of Gram-Negative Sepsis: A Comprehensive Multi-Organoid Platform for Advanced Disease Modeling, Drug Discovery, and Personalized Medicine
Authors: Danter Wayne R
Published: July 2023

Organoids are three-dimensional cellular structures resembling human organs, which have emerged as valuable tools for studying organ development, disease modeling, and drug discovery. Integrating multiple organoid systems allows for the examination of complex interactions between different organs. In this study, we present the development and initial validation of the aiHumanoid simulation, an advanced AI-based computational framework that integrates 18 individual organoid simulations through a common cardiovascular system. Our aim is to investigate the systemic effects of gram-negative sepsis, a life-threatening condition that affects multiple organ systems.

In this study, we evaluated the impact of gram-negative sepsis on the organoid systems that make up the aiHumanoid simulation. Our findings indicate significant alterations in cardiovascular, nervous system, respiratory, renal, hepatic, hematologic, gastrointestinal, musculoskeletal, immune, and endocrine parameters in both male and female sepsis-affected organoids. Notably, markers of inflammation, coagulation, renal dysfunction, liver damage, immune response, and endocrine regulation were significantly affected by sepsis. While some parameters showed gender-specific differences in response, such as hormonal changes, the overall impact of gram-negative sepsis was observed in both sexes.

This study demonstrates the potential of the aiHumanoid to accurately simulate the systemic effects of diseases on various organ systems. The integration of computational simulations with organoid systems offers a powerful approach for understanding disease mechanisms and evaluating potential therapies. By providing a more efficient and physiologically relevant platform for drug testing, the aiHumanoid simulation has the potential to accelerate the drug development process, reduce costs, and minimize the need for animal testing. Further research and ongoing validation will be crucial to fully exploit the capabilities of this revolutionary computational framework for advancing disease modeling and therapeutic interventions.
The impact of late Pleistocene mammal extinctions on pathogen richness in extant hosts
Authors: Prys-Jones Tomos O. , Abraham Andrew J. , Mihaljevic Joseph R. , Murray Kris A. , Doughty Christopher E.
Published: July 2023

Many species of large mammals were driven to extinction during the late Pleistocene and early Holocene (approx. 10,000 – 50,000 years ago), with cascading effects on the physical structure of ecosystems and the dispersal of seeds, nutrients, and microbes. However, it remains uncertain whether the parasites associated with these extinct hosts also disappeared or persisted in surviving (extant) mammals. We hypothesize that if some parasites endured, extant mammals sharing their ranges with phylogenetically similar extinct mammals would have a greater pathogen richness than expected based on current levels of host diversity. We find that the inclusion of variables related to these extinctions account for an additional 5% of deviance when modelling per-host viral and bacterial richness, compared to models run without these variables. Partial dependence plots show a positive correlation between the number of extinct mammals lost and per-host viral and bacterial richness (p < 0.001 and p = 0.03, respectively). Additionally, decreasing phylogenetic distance between the extinct and extant species is associated with an increasing viral richness (p < 0.001). We discuss four mechanisms that may be driving these patterns and highlight future research to distinguish between them. Next, we use the models and IUCN range maps to identify geographic regions where viral and bacterial richness differs due to the inclusion of extinction variables. Notably, the richness of both pathogen types is increased in South America (viruses: +6.8%; bacteria: +3.1%) and decreased in Africa (viruses: −2.6%; bacteria: −13.6%), two continents known to have high and low levels of historical mammal extinctions, respectively. Viral richness is also elevated in North America (+8.6%), Europe (+5.1%), Oceania (+3.3%), and Asia (+2.3%). These results support the inclusion of extinction variables in future models of pathogen richness and may allow for improved targeting of future surveillance efforts.
Profiling human hypothalamic neurons reveals a candidate combination drug therapy for weight loss
Authors: Chen Hsiao-Jou Cortina , Yang Andrian , Mazzaferro Simone , Mali Iman , Cahn Olivier , Kentistou Katherine , Rowley Christine , Stewart Natasha , Seah Jun Wen Eugene , Pisupati Venkat , Kirwan Peter , Aggarwal Sanya , Toyohara Takafumi , Florido Mary H.C. , Cowan Chad A. , Quambusch Lena , Hyvönen Marko , Livesey Matthew R. , Perry John R.B. , Marioni John C. , Merkle Florian T.
Published: July 2023

Obesity substantially increases the risk of type 2 diabetes, cardiovascular disease, and other diseases, making it a leading preventable cause of death in developed countries. It has a strong genetic basis, with obesity-associated genetic variants preferentially acting in the brain. This includes the hypothalamic pro-opiomelanocortin (POMC) neurons that inhibit food intake and are stimulated by drugs that agonise glucagon-like 1 peptide receptor (GLP1R) including Semaglutide (Ozempic/Wegovy). We therefore hypothesised that drugs which selectively activate human POMC neurons would suppress appetite and promote weight loss, and that focusing on drugs already approved for use would facilitate rapid clinical translation. We therefore generated POMC neurons from human pluripotent stem cells (hPSCs) and identified enriched genes that were genetically associated with obesity and targeted by approved drugs. We found that human POMC neurons are enriched in GLP1R, reliably activated by Semaglutide, and their responses are further increased by co-administration of Ceritinib, an FDA-approved drug potently and selectively inhibiting anaplastic lymphoma kinase (ALK). Ceritinib reduced food intake and body weight in obese but not lean mice, and upregulated the expression of GLP1R in the mouse hypothalamus and hPSC-derived human hypothalamic neurons. These studies reveal a new potential therapeutic strategy for reducing food intake and body weight, and demonstrate the utility of hPSC-derived hypothalamic neurons for drug discovery.
Stem cell transcriptional profiles from mouse subspecies revealcis-regulatory evolution at translation genes
Authors: Simon Noah M. , Kim Yujin , Bautista Diana M. , Dutton James R. , Brem Rachel B.
Published: July 2023

A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells fromMus musculussubspecies as a model. Using a test of directional,cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouseM. m. castaneusrelative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique toM. m. castaneusat the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures acrossMus musculusin stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.
Development and Validation of a multi-target TaqMan qPCR method for detection ofBorrelia burgdorferisensu lato
Authors: Masséglia Sébastien , René-Martellet Magalie , Rates Maxime , Hizo-Teufel Cecilia , Fingerle Volker , Margos Gabriele , Bailly Xavier
Published: July 2023

Reliable detection of bacteria belonging to theBorrelia burgdorferisensu lato species complex in vertebrate reservoirs, tick vectors, and patients is key to answer questions regarding Lyme borreliosis epidemiology. Nevertheless, the description of characteristics of qPCRs for the detection ofB. burgdorferis. l. are often limited. This study covers the development and validation of two duplex taqman qPCR assays used to target four markers on the chromosome of genospecies ofB. burgdorferis. l..

Analytical specificity was determined with a panel of spirochete strains. qPCR characteristics were specified using water or tick DNA spiked with controlled quantities of the targeted DNA sequences ofB. afzelii,B. burgdorferisensu stricto orB. bavariensis. The effectiveness of detection results was finally evaluated using DNA extracted from ticks and biopsies from mammals whose infectious status had been determined by other detection assays.

The developed qPCR assays allow exclusive detection ofB. burgdorferis. l. with the exception of the M16 marker which also detect relapsing feverBorreliaspecies. The limit of detection is between 10 and 40 copies per qPCR reaction depending on the sample type, theB. burgdorferigenospecies and the targeted marker. Detection tests performed on various kind of samples illustrated the accuracy and robustness of our qPCR assays.

Within the defined limits, this multi-target qPCR method allows a versatile detection ofB. burgdorferis. l., regardless of the genospecies and the sample material analyzed, with a sensitivity that would be compatible with most applications and a reproducibility of 100% under measurement conditions and limits of detection, thereby limiting result ambiguities.

Highlights

Four qPCR assays used in duplex were developed to detectBorrelia burgdorferisensu lato. The limits of detection and quantification were defined according to state of the art standards. The specifications allow to detectB. burgdorferisensu lato from different sampling sources.
Molecular Surface Descriptors to Predict Antibody Developability
Authors: Park Eliott , Izadi Saeed
Published: July 2023

Understanding the molecular surface properties of monoclonal antibodies (mAbs) is crucial for determining their function, affinity, and developability. Yet, robust methods to accurately represent the key structural and biophysical features of mAbs on their molecular surface are still limited. Here, we introduce MolDesk, a set of molecular surface descriptors specifically designed for predicting antibody developability characteristics. We assess the performance of these descriptors by directly benchmarking their correlations with an extensive array ofin vitroandin vivodata, including viscosity at high concentration, aggregation, hydrophobic interaction chromatography (HIC), human pharmacokinetic (PK) clearance, Heparin retention time, and polyspecificity. Additionally, we investigate the sensitivity of these surface descriptors to methodological nuances, such as the choice of interior dielectric constant for electrostatic potential calculations, residue-level hydrophobicity scales, initial antibody structure models, and the impact of conformational sampling. Based on our benchmarking analysis, we propose sixin silicodevelopability rules that leverage these molecular surface descriptors and demonstrate their superior ability to predict the clinical progression of therapeutic antibodies compared to established models like TAP.1
Taste shaped the use of botanical drugs
Authors: Leonti Marco , Baker Joanna , Staub Peter , Casu Laura , Hawkins Julie
Published: July 2023

The perception of taste and flavour (a combination of taste, smell and chemesthesis) here also referred to as chemosensation, enables animals to find high-value foods and avoid toxins. Humans have learned to use unpalatable and toxic substances as medicines, yet the importance of chemosensation in this process is poorly understood. Here we generate tasting-panel data for botanical drugs and apply phylogenetic generalised linear mixed models to test whether intensity and complexity of chemosensory qualities as well as particular tastes and flavours can predict ancient Graeco-Roman drug use. We found chemosensation to be strongly predictive of therapeutic use: botanical drugs with high therapeutic versatility have simple yet intense tastes and flavours, and 21 of 22 chemosensory qualities predicted at least one therapeutic use. In addition to the common notion of bitter tasting medicines, we also found starchy, musky, sweet, cooling, and soapy drugs associated with versatility. In ancient Greece and Rome, illness was thought to arise from imbalance in bodily fluids or humours, yet our study suggests that uses of drugs were based on observed physiological effects that are often consistent with modern understanding of chemesthesis and taste receptor pharmacology.
Dynamic corticothalamic modulation of the somatosensory thalamocortical circuit during wakefulness
Authors: Dimwamwa Elaida D. , Pala Aurélie , Chundru Vivek , Wright Nathaniel C. , Stanley Garrett B.
Published: July 2023

The feedback projections from cortical layer 6 (L6CT) to sensory thalamus have long been implicated in playing a primary role in gating sensory signaling but remain poorly understood. To causally elucidate the full range of effects of these projections, we targeted silicon probe recordings to the whisker thalamocortical circuit of awake mice selectively expressing Channelrhodopsin-2 in L6CT neurons. Through optogenetic manipulation of L6CT neurons, multi-site electrophysiological recordings, and modeling of L6CT circuitry, we establish L6CT neurons as dynamic modulators of ongoing spiking in the ventro-posterior-medial nucleus of thalamus (VPm), either suppressing or enhancing VPm spiking depending on L6CT neurons’ firing rate and synchrony. Differential effects across the cortical excitatory and inhibitory sub-populations point to an overall influence of L6CT feedback on cortical excitability that could have profound implications for regulating sensory signaling across a range of ethologically relevant conditions.
mEthAE: an Explainable AutoEncoder for methylation data
Authors: Katz Sonja , Martins dos Santos Vitor A.P. , Saccenti Edoardo , Roshchupkin Gennady V.
Published: July 2023

1

In the quest to unravel the mysteries of our epigenetic landscape, researchers are continually challenged by the relationships among CpG sites. Traditional approaches are often limited by the immense complexity and high dimensionality of DNA methylation data. To address this problem, deep learning algorithms, such as autoencoders, are increasingly applied to capture the complex patterns and reduce dimensionality into latent space. In this pioneering study, we introduce an innovative chromosome-wise autoencoder, termed mEthAE, specifically designed for the interpretive reduction of methylation data. mEthAE achieves an impressive 400-fold reduction in data dimensions without compromising on reconstruction accuracy or predictive power in the latent space. In attempt to go beyond mere data compression, we developed a perturbation-based method for interpretation of latent dimensions. Through our approach we identified clusters of CpG sites that exhibit strong connections across all latent dimensions, which we refer to as ‘global CpGs’. Remarkably, these global CpGs are more frequently highlighted in epigenome-wide association studies (EWAS), suggesting our method’s ability to pinpoint biologically significant CpG sites. Our findings reveal a surprising lack of correlation patterns, or even physical proximity on the chromosome among these connected CpGs. This leads us to propose an intriguing hypothesis: our autoencoder may be detecting complex, long-range, non-linear interaction patterns among CpGs. These patterns, largely uncharacterised in current epigenetic research, hold the potential to shed new light on our understanding of epigenetics. In conclusion, this study not only showcases the power of autoencoders in untangling the complexities of epigenetic data but also opens up new avenues for understanding the hidden connections within CpGs.
Network and structural analysis of quail mucins with expression pattern of MUC1 and MUC4 in the intestines of the Iraqi Common Quail (Coturnix Coturnix)
Authors: Almhanna Hazem , Mahdi AL-Mahmodi Aqeel Mohsin , Kadhim Abdulrazzaq B , Kumar Arun HS
Published: July 2023

Background

Mucins have vital pathophysiological role in gastrointestinal tract (GIT) of avian and other species. However, despite this very little is known about the types of mucins expressed in quail GIT. Hence in this study we examined the expression pattern of mucins (MUC1, and MUC4) in the GIT of the Iraqi Common Quail (Coturnix Coturnix) and performed the network and structural analysis of all reported types of mucins in various breeds of quails.

Materials and methods

This study protocol was approved by the animal ethics research committee of the College of Veterinary Medicine, University of Al-Qadisiyah, Iraq. Fresh samples of small and large intestines were used for histological and gene expression analysis of MUC1, and MUC4. Network and structural analysis of all reported types of mucins in quails was performed using the STRING Database, Chimera software and PrankWeb-Ligand Binding Site Prediction tool.

Results

The histological analysis using Alcian blue and PAS stains indicated that most mucins in the intestines of quails were of the acidic mucin type, with minimal prevalence of neutral mucins. The expression of acidic mucins was relatively higher in the duodenum, ileum, caecum, and colon, while the jejunum showed a relatively higher expression of neutral mucins. Gene expression analysis revealed higher expression levels of MUC1 and MUC4 mRNA in the jejunum and colon, with its least expression in the duodenum and ilium. Network analysis indicated predominantly mucin-mucin interactions, with MUC 1, 15, 16 and 24 showing preferential homologous networks while the MUC 2, 4, 5 and 6 showed heterologous networks. Detailed evaluation of intermolecular hydrogen bond formation highlighted the interactions between specific mucin combinations, with certain combinations showing higher affinity, such as MUC5A-MUC6, MUC5A-MUC5B, and MUC5B-MUC6. In contrast, MUC15, MUC16, and MUC24 exhibited limited interactions with other mucin types. Binding site analysis indicated that MUC5B and MUC6 had the most number of binding sites with high probability scores, while MUC2, MUC4, and MUC5A showed lower probability scores despite having more binding sites. In contrast MUC 1, 15, and 16 had very few binding sites (<3 binding sites) all with very low probability scores.

Conclusion

The findings of this study provide valuable insights into the composition, expression, network interactions, and binding sites of mucins in the quails, contributing to the understanding of mucin-related processes in gastrointestinal physiology and potential implications for gastrointestinal diseases.
Measuring RBC deformability and its heterogeneity using a fast microfluidic device
Authors: Kumari Savita , Mehendale Ninad , Roy Tanusri , Sen Shamik , Mitra Dhrubaditya , Paul Debjani
Published: July 2023

We report a high-throughput microfluidic device to determine the Young’s modulus of single red blood cells (RBCs). Our device consists of a single channel opening into a funnel, with a semi-circular obstacle placed at the mouth of the funnel. As a RBC passes the obstacle, it deflects from its original path. Using populations of artificially-stiffened RBCs, we show that the stiffer RBCs deflect more compared to the healthy RBCs. We then generate a calibration curve that maps each RBC trajectory to its Young’s modulus obtained using an atomic force microscope. Finally, we sort a mixed population of RBCs based on their deformability alone. Our device could potentially be further miniaturized to sort and obtain the elastic constants of nanoscale objects, such exosomes, whose shape change is difficult to monitor by optical microscopy.
Trophic diversity and evolution in Enantiornithes: a synthesis including new insights from Bohaiornithidae
Authors: Miller Case Vincent , Bright Jen A. , Wang Xiaoli , Zheng Xiaoting , Pittman Michael
Published: July 2023

The “opposite birds” Enantiornithines were the dominant birds of the Mesozoic, but our understanding of their ecology is still tenuous. In particular, diets of enantiornithine species have remained speculative until recently. While this new work has been effective at determining diet within groups of enantiornithines, diet data thus far has been too sparse to comment on larger trends in the diversity and evolution of enantiornithine ecology. We introduce new data on the enantiornithine family Bohaiornithidae, famous for their large size and strong teeth and claws. In tandem with previously-published data on the earlier-diverging pengornithids and later-diverging longipterygids, we comment on the breadth of enantiornithine ecology and potential patterns in which it evolved. Body mass, jaw mechanical advantage, finite element analysis of the jaw, and traditional morphometrics of the claws and skull are compared between bohaiornithids and living birds. The sample size for living bird body mass is over ten times larger than previous studies on longipterygid and pengornithid diet, with implications in interpreting their results. We find bohaiornithids to be ecologically diverse:BohaiornisandParabohaiornisare similar to living plant-eating birds;Longusunguisresembles raptorial carnivores;Zhouornisis similar to both fruit-eating birds and generalist feeders; andShenqiornisandSulcavisplausibly ate fish, plants, or a mix of both. This ecological diversity is wider than any other enantiornithine family studied previously, which may be driven by strengthening of the jaw relative to other early birds. This strong jaw would allow bohaiornithids to eat harder foods than other birds at the time, but their jaws were weaker than most “strong-jawed” living birds. With these reconstructions of diet in Bohaiornithidae, there is quantitative support for enantiornithines inhabiting nearly every trophic level. By combining these reconstructions with past dietary predictions for Longipterygidae and Pengornithidae, we predict the ancestral enantiornithine bird to have been a generalist which ate a wide variety of foods. This would suggest that the ecological diversity of enantiornithine birds represents specialisation in taking foods their ancestors were already eating, rather than many dramatic changes in diet. However, more quantitative data from across the enantiornithine tree is needed to refine this prediction. By the Early Cretaceous, enantiornithine birds had diversified into a variety of ecological niches in a similar way to crown birds after the K-Pg extinction, adding to the body of evidence that traits unique to crown birds (e.g. a toothless beak or cranial kinesis) cannot completely explain their ecological success.
Phage inducible chromosomal minimalist island (PICMI), a family of satellites of marine virulent phages
Authors: Barcia-Cruz Rubén , Goudenège David , Moura de Sousa Jorge A. , Piel Damien , Marbouty Martial , Rocha Eduardo P.C. , Roux Frédérique Le
Published: July 2023

Phage satellites are genetic elements that hijack the phage machinery for their own dissemination. However, only few phage satellites have been characterized, and mechanisms by which they influence microbial evolution in nature are unclear. Here we identify a new family of satellites, the Phage Inducible Chromosomal Minimalist Island (PICMI), which is broadly distributed in the marine bacteriaVibrionaceae. PICMI is characterized by reduced gene content, does not encode genes for capsid remodeling and packages its DNA as a concatemer. PICMI is integrated in the bacterial host genome at the end of thefisregulator and encodes three core proteins necessary for excision and replication. PICMI is dependent on virulent phage particles to spread to other bacteria and confers host protection from other competitive phages, without interfering with its helper phage. The discovery of PICMI strongly suggests that phages, including virulent ones, play important roles for mobility of phage defense elements.
C2C12 muscle myotubes, but not kidney proximal tubule HK-2 cells, elevate erythritol synthesis in response to oxidative stress
Authors: Ortiz Semira R. , Field Martha S.
Published: July 2023

Background

As a biomarker, elevated serum erythritol predicts type 2 diabetes and cardiovascular disease onset. Erythritol was recently shown to be a product of human glucose metabolism through the pentose phosphate pathway. The regulation of erythritol synthesis from glucose has been explored in cancer cells, but not in non-transformed cells.

Objective

The kidneys and skeletal muscle have increased erythritol content in response to dietary sucrose, which suggests that they may significantly contribute to circulating erythritol levels. In the present study, we evaluated if conditions that promote erythritol synthesis in cancer cells are consistent in skeletal muscle and kidney cells.

Methods

C2C12 myotubules were used as a model for skeletal muscle and HK-2 human proximal tubule cells were used to model kidney. C2C12 cells were exposed to high-or low-glucose conditions. Both C2C12 and HK-2 cells were exposed to the free radical generator menadione, then intracellular reactive oxygen species (ROS) and erythritol were measured. Intracellular sorbitol levels were also measured because increased polyol flux is also observed after exposure to excess glucose and oxidative stress.

Results

Intracellular erythritol was significantly elevated in C2C12 cells following both high glucose and menadione treatment. In contrast, HK-2 cells did not increase erythritol synthesis in response to oxidative stress. Generation of ROS through hydrogen peroxide (H2O2) exposure elevated sorbitol levels in both C2C12 and HK-2 cells, whereas generation of radicals with menadione treatment did not affect sorbitol production in either cell type.

Conclusions

These findings highlight that the factors contributing to elevated erythritol synthesis vary between cell types. More specifically, these studies demonstrate that muscle cells increase erythritol synthesis in response to both high glucose in culture medium and oxidative stress, whereas kidney cells increase erythritol synthesis only in response to high glucose.
A modular chemigenetic calcium indicator enables in vivo functional imaging with near-infrared light
Authors: Farrants Helen , Shuai Yichun , Lemon William C. , Hernandez Christian Monroy , Yang Shang , Patel Ronak , Qiao Guanda , Frei Michelle S. , Grimm Jonathan B. , Hanson Timothy L. , Tomaska Filip , Turner Glenn C. , Stringer Carsen , Keller Philipp J. , Beyene Abraham G. , Chen Yao , Liang Yajie , Lavis Luke D. , Schreiter Eric R.
Published: July 2023

Genetically encoded fluorescent calcium indicators have revolutionized neuroscience and other biological fields by allowing cellular-resolution recording of physiology during behavior. However, we currently lack bright, genetically targetable indicators in the near infrared that can be used in animals. Here, we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains that can be genetically targeted to specific cell populations. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several dye-ligands that efficiently label the central nervous system in animals. When bound to a near-infrared dye-ligand, WHaloCaMP1a is more than twice as bright as jGCaMP8s, and shows a 7× increase in fluorescence intensity and a 2.1 ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a with near-infrared fluorescence emission to image Ca2+responses in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae, and to quantitate calcium concentration using fluorescence lifetime imaging microscopy (FLIM).
Analysis of culture and RNA isolation methods for precision-cut liver slices from cirrhotic rats
Authors: Leaker Ben D. , Wang Yongtao , Tam Joshua , Anderson R. Rox
Published: July 2023

Precision-cut liver slices (PCLS) are increasingly used as a model to investigate anti-fibrotic therapies. However, many studies use PCLS from healthy animals treated with pro-fibrotic stimuli in culture, which reflects only the early stages of fibrosis. The performance of PCLS from cirrhotic animals has not been well characterized and there is no consensus on optimal culture conditions. In this study, we report a method for the collection and culture of cirrhotic PCLS and compare the effect of common culture conditions on viability, function, and gene expression. Additionally, we compared three methods of RNA isolation and identified a protocol with high yield and purity. We observed significantly increased albumin production when cultured with insulin and dexamethasone, and when incubated on a rocking platform. Culturing with insulin and dexamethasone maintained gene expression closer to the levels in fresh slices. However, despite stable viability and function up to 4 days, we found significant changes in expression by day 2. Due to the influence of matrix stiffness on fibrosis and hepatocellular function, it is important to evaluate prospective anti-fibrotic therapies in a platform that preserves tissue biomechanics. PCLS from cirrhotic animals represent a promising tool for the development of treatments for chronic liver disease.
Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages
Authors: Heimberg Graham , Kuo Tony , DePianto Daryle , Heigl Tobias , Diamant Nathaniel , Salem Omar , Scalia Gabriele , Biancalani Tommaso , Turley Shannon , Rock Jason , Bravo Héctor Corrada , Kaminker Josh , Heiden Jason A. Vander , Regev Aviv
Published: July 2023

Single-cell RNA-seq (scRNA-seq) studies have profiled over 100 million human cells across diseases, developmental stages, and perturbations to date. A singular view of this vast and growing expression landscape could help reveal novel associations between cell states and diseases, discover cell states in unexpected tissue contexts, and relatein vivocells toin vitromodels. However, these require a common, scalable representation of cell profiles from across the body, a general measure of their similarity, and an efficient way to query these data. Here, we present SCimilarity, a metric learning framework to learn and search a unified and interpretable representation that annotates cell types and instantaneously queries for a cell state across tens of millions of profiles. We demonstrate SCimilarity on a 22.7 million cell corpus assembled across 399 published scRNA-seq studies, showing accurate integration, annotation and querying. We experimentally validated SCimilarity by querying across tissues for a macrophage subset originally identified in interstitial lung disease, and showing that cells with similar profiles are found in other fibrotic diseases, tissues, and a 3D hydrogel system, which we then repurposed to yield this cell statein vitro. SCimilarity serves as a foundational model for single cell gene expression data and enables researchers to query for similar cellular states across the entire human body, providing a powerful tool for generating novel biological insights from the growing Human Cell Atlas.