bluuebunny/crossref_metadata_2025 huggingface dataset:
“Investigating mcr Genes in CRAB Isolates during a NICU outbreak and Advancements in Colistin Sensitivity Testing"
Authors: Raza Mubashir , Khan Saadullah Jan , Masood. Muhammad Faisal , Jafri Laila , Rani Rehana , Ali Roomana , Sadiq Sara , Aakhtar Nosheen , Jamil Bushra
Published: October 2024

Purpose : Colistin-resistant Acinetobacter baumannii (CRAB) poses a growing challenge in neonatal intensive care units (NICUs) due to the emergence of plasmid-mediated Mobile Colistin Resistance (mcr) genes that can rapidly spread among neonates. This pioneering study conducted a comprehensive analysis of mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes in A. baumannii strains isolated from a Pakistani NICU. Notably, this investigation marks the first of its kind in this setting.
In addition to genotypic analyses, the study incorporated phenotypic assays to identify the most effective method for detecting colistin resistance in these A. baumannii strains. The research also encompassed the examination of A. baumannii blood isolates exhibiting low to mid-level colistin resistance during an outbreak in a tertiary care hospital.
Methods: In the genotypic investigation, DNA was extracted from strains of colistin-resistant A. baumannii, collected from the NICU of the local hospital of Islamabad, Pakistan. The specific set of primers for each mcr gene was used to detect their presence. Various phenotypic methods such as; disc diffusion, broth macro dilution, Minimum Inhibition Concentration (MIC), disc elusion and colistin agar methods were performed using predetermined calculations for phenotypic studies.
Results: The study confirms the distribution of the mcr-1 gene among the eight strains, which contributes 66 % of the total number, whereas mcr-2, 3, 4 and 5 genes were not detected in all strains. Based on phenotypic analysis, A. baumannii had shown resistance against colistin at < 2µg/mL. In contrast, MIC varies from strain to strain.
Conclusions: The horizontal transfer of the mcr-1 gene is responsible for developing resistance against colistin among A. baumannii in neonates. All phenotypic methods adopted in this study generated the same results, so the method selection depends upon individual comfort. However, we propose that the colistin agar method offers multiple advantages over other methods as it is more economical, easy to perform, multiple samples can be assessed simultaneously and fewer calculations are involved for colistin resistance determination and finding out clinical breakpoints.
RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation
Authors: Ganguli Sourav , Gupta Divya , Ramaswamy Rajashree , Kadumuri Rajashekar Varma , Krishnan Aswathy G , Tandel Dixit , David Deena T , Bunk Soumya , Chavali Sreenivas , Harshan Krishnan , Chavali Pavithra L
Published: October 2024

Musashi RNA binding proteins are important post-transcriptional regulators of stem cell homeostasis and are known to be involved in viral infections. However, their role in SARS-CoV-2 infection remains largely unknown. Using computational studies, in vivo RNA immunoprecipitation and biochemical assays, here, we establish that Musashi 1 (Msi1) interacts with viral genomic RNA through direct binding to the SARS-CoV-2 3'UTR. Importantly, binding of Msi1 to the viral 3'UTR results in translational repression mediated by inhibition of Poly (A) binding protein (PABP). Conversely, Msi1 knockout promotes robust viral replication and increased viral protein expression. Using 2D cell cultures, stem cells and 3D organoids, we show that depletion of Msi1 in intestinal cells augments infection. This finding explains why the human intestine serves as a reservoir for the SARS-CoV-2 virus, wherein differentiated enterocytes, which have negligible levels of Msi1, are highly affected. Contrarily, stem cells which are enriched for Msi1 expression, are known to be less permissive to SARS-CoV-2 infection despite expressing the entry receptors. Our findings show how translation repression of SARS-CoV-2 by stem cell RNA binding proteins such as Msi1 could help evasion of infection.
Change in Social Participation of Adults with Spinal Cord Injury During the First Two Waves of the COVID-19 Pandemic in Canada
Authors: Fortin-Bédard Noémie , Nindorera Félix , Leblond Jean , Rahn Caroline , Best Krista L. , Borisoff Jaimie , Sweet Shane N. , Arbour-Nicitopoulos Kelly P. , Routhier François
Published: October 2024

Introduction

The change in environmental and social context measures during the COVID-19 pandemic affected daily activities of people with spinal cord injury (SCI), their interactions within the community, and consequently their social participation during the first wave of the pandemic. However, there is little information about the changes in social participation as the pandemic evolved in Canada. Objective: To describe the change in social participation of adults with SCI after the first two years of the COVID-19 pandemic in Canada.

Methods

A follow-up from a previous study exploring the social participation of adults with SCI living during the first wave was conducted eight months later (second wave). Social participation was measured using the Assessment of Life Habits (LIFE-H 4.0) and Measure of Quality of the Environment (MQE) among 18 adults with SCI.

Results

Participants reported increases between both waves of COVID-19 in life habits categories, including mobility, personal care and health, nutrition, and recreation. New environmental factors were identified as facilitators, including the increased availability of businesses in the community.

Conclusion

These findings suggest that people with SCI increased fulfillment and satisfaction of certain life habits. Reduced environmental barriers and increased facilitators improved social participation as the pandemic evolved.
Motor network reorganization associated with rTMS-induced writing improvement in writer’s cramp dystonia
Authors: Bukhari-Parlakturk Noreen , Mulcahey Patrick J. , Lutz Michael W. , Ghazi Rabia , Huang Ziping , Dannhauer Moritz , Termsarasab Pichet , Scott Burton , Simsek Zeynep B. , Groves Skylar , Lipp Mikaela , Fei Michael , Tran Tiffany K. , Wood Eleanor , Beynel Lysianne , Petty Chris , Voyvodic James T. , Appelbaum Lawrence G. , Al-Khalidi Hussein R. , Davis Simon W. , Michael Andrew M. , Peterchev Angel V. , Calakos Nicole
Published: October 2024

Background

Writer’s cramp (WC) dystonia is an involuntary movement disorder with distributed abnormalities in the brain’s motor network. Prior studies established the potential for repetitive transcranial magnetic stimulation (rTMS) to either premotor cortex (PMC) or primary somatosensory cortex (PSC) to modify symptoms. However, clinical effects have been modest with limited understanding of the neural mechanisms hindering therapeutic advancement of this promising approach.

Objective

This study aimed to understand the motor network effects of rTMS in WC that correspond with behavioral efficacy. We hypothesized that behavioral efficacy is associated with modulation of cortical and subcortical regions of the motor network.

Methods

In a double-blind, cross-over design, twelve WC participants underwent rTMS in one of three conditions (Sham-TMS, 10 Hz PSC-rTMS, 10 Hz PMC-rTMS) while engaged in a writing task to activate dystonic movements and measure writing fluency. Brain connectivity was evaluated using task-based fMRI after each TMS session.

Results

10 Hz rTMS to PSC, but not PMC, significantly improved writing dysfluency. PSC-TMS also significantly weakened cortico-basal ganglia, cortico-cerebellum, and intra-cerebellum functional connectivity (FC), and strengthened striatal FC relative to Sham. Changes in PSC and SPC BOLD activity were associated with reduced dysfluent writing behavior.

Conclusions

10 Hz rTMS to PSC improved writing dysfluency by redistributing motor network connectivity and strengthening somatosensory-parietal connectivity. A key signature for effective stimulation at PSC and improvement in writing dysfluency may be strengthening of intra-cortical connectivity between primary somatosensory and superior parietal cortices. These findings offer mechanistic hypotheses to advance the therapeutic application of TMS for dystonia.

Highlights

10 Hz repetitive TMS to somatosensory cortex reduces writing dysfluency in dystonia

Increased somatosensory cortex activity correlates with reduced writing dysfluency

In dystonia + sham-TMS, writing dysfluency correlates with cerebellar connectivity.

10 Hz rTMS to somatosensory cortex induces reorganization of the motor network
Development, Testing, and Calibration of LINCS: A New Microsimulation Model of Maternal and Fetal Cytomegalovirus Infection
Authors: Wu Aaron S. , Coskun Elif , Prabhu Malavika , Santos Emily M. , Kakkar Fatima , Flanagan Clare F. , Dugdale Caitlin M. , Pesch Megan , Giardina John C. , Ciaranello Andrea L.
Published: October 2024

Background

Congenital cytomegalovirus (cCMV) is a leading cause of birth defects and the most common cause of non-genetic sensorineural hearing loss in children. There is a lack of decision modeling frameworks that can project cytomegalovirus (CMV)-related patient outcomes and inform health policy. We created, tested, and calibrated a model of CMV acquisition and transmission in pregnancy using linked mother-infant dyads.

Methods

We developed theLinkingINfants and Mothers inCytomegalovirusSimulation (LINCS) dyad-level Monte-Carlo microsimulation model of CMV infection among pregnant people and fetuses throughout pregnancy. We parameterized the model with data from the existing literature, implemented rigorous code testing procedures, and calibrated a key set of parameters to match model output to external data on cCMV prevalence and symptom risk.

Results

A fully parameterized model for CMV among pregnant people and fetuses was developed, and the model code was confirmed to perform as specified. The calibration procedure identified parameter sets that generated model output closely matching the target values from the available data on cCMV prevalence and symptom risk.

Conclusions

The LINCS model’s ability to simulate the natural history of CMV infection during pregnancy was described and demonstrated, and the model was tested and calibrated to ensure proper functioning. Base case parameters were derived for CMV infection natural history to be used in future decision analyses of CMV testing and treatment strategies.
Rapid, Non-Invasive Breath Analysis for Enhancing Detection of Silicosis Using Mass Spectrometry and Interpretable Machine Learning
Authors: Baker Merryn J , Gordon Jeff , Thiruvarudchelvan Aruvi , Yates Deborah , Donald William A
Published: October 2024

Occupational lung diseases, such as silicosis, are a significant global health concern, especially with increasing exposure to engineered stone dust. Early detection of silicosis is helpful for preventing disease progression, but existing diagnostic methods, including X-rays, CT scans, and spirometry, often detect the disease only at late stages. This study investigates a rapid, non-invasive diagnostic approach using atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) to analyse volatile organic compounds (VOCs) in exhaled breath from 31 silicosis patients and 60 healthy controls. Six different interpretable machine learning (ML) models with Shapley additive explanations (SHAP) were applied to classify these samples and determine VOC features that contribute the most significantly to model accuracy. The extreme gradient boosting (XGB) classifier demonstrated the best performance, achieving an area under the receiver-operator characteristic curve of 0.933 with the top ten SHAP features. Them/z442 feature, potentially corresponding to leukotriene-E3, emerged as a significant predictor for silicosis. The VOC sampling and measurement process takes less than five minutes per sample, highlighting its potential suitability for large-scale population screening. Moreover, the ML models are interpretable through SHAP, providing insights into the features contributing to the model’s predictions. This study suggests that APCI-MS breath analysis could enable early and non-invasive diagnosis of silicosis, helping to improve disease outcomes.
Hydroxyzine in Acute Hypertension: A Cohort Study
Authors: Nożewski Jakub , Remiszewski Piotr , Filipek Kinga , Pisklak Agata , Abramczyk Aleksandra , Pyzel Stanisław , Śliż Daniel
Published: October 2024

Captopril, an ACE inhibitor, is widely used for acute hypertensive episodes, while hydroxyzine, an antihistamine with sedative and anxiolytic effects, is also employed in Poland despite limited research on its efficacy for this purpose. To our knowledge, no prior studies have specifically investigated the direct impact of hydroxyzine on hypertension, despite its common use in Polish medical practice.

A retrospective cohort analysis of 2144 patients who required emergency intervention for hypertension or had high blood pressure during other interventions. Effectiveness was based on blood pressure improvement post-intervention.

84.28% of interventions were performed by basic emergency teams, and 15.72% by specialist teams. Captopril and hydroxyzine were the most commonly used medications. Blood pressure improved in 36.61% of patients, with no improvement in 41.47%. Hydroxyzine was more frequently administered by paramedic teams, while captopril was favoured by specialist teams. There were no statistically significant differences in captopril use across age groups, with approximately 80% receiving it. Hydroxyzine use did not vary significantly by age, though its overall use was low. Hydroxyzine showed a non-significant trend towards greater blood pressure reduction compared to captopril.

Captopril is the primary treatment for acute hypertension in emergency settings, but hydroxyzine may have potential benefits, especially in patients with anxiety-related hypertension. However, due to the lack of significant evidence and current guidelines advising against hydroxyzine in elderly patients, further research is needed to establish protocols and optimize hypertension treatment strategies. Additionally, incorporating anxiolytics into guidelines and an official statement on their use would aid clinical practice.
Introducing Haptic Feedback in Real-Time fMRI Neurofeedback: A Novel Approach to Modulate Primary Motor Cortex Activity
Authors: Fleury Mathis , Cloerec Pauline , Duche Quentin , Lioi Giulia , Lécuyer Anatole
Published: October 2024

As fMRI-Neurofeedback (fMRI-NF) is still in its early stages, many questions remain regarding the optimal methodology, particularly in relation to feedback modalities. One of the core components of neurofeedback is the feedback itself, which the participant relies on to regulate, learn, and refine their mental strategies. However, most fMRI-NF protocols to date have primarily used visual feedback, which may not be ideal in all cases. Certain individuals or populations might benefit from alternative or additional feedback modalities, such as haptic feedback —a novel approach in this field— along with auditory, virtual reality/immersive environments, or a combination of these. In this study, we assess the performance of neurofeedback elicited by a motor imagery (MI) task using visuo-haptic feedback and compare it to unisensory visual and haptic feedback. Our results suggest that combining visual and haptic feedback in neurofeedback may be more engaging than conventional visual feedback alone, particularly in neurorehabilitation, by more effectively activating the primary motor cortex—a region considered a key target for promoting motor recovery.
The solute carrier superfamily interactome
Authors: Frommelt Fabian , Ladurner Rene , Goldmann Ulrich , Wolf Gernot , Ingles-Prieto Alvaro , Lineiro-Retes Eva , Gelová Zuzana , Hopp Ann-Katrin , Christodoulaki Eirini , Teoh Shao Thing , Leippe Philipp , Rebsamen Manuele , Lindinger Sabrina , Serrano Iciar , Onstein Svenja , Klimek Christoph , Barbosa Barbara , Pantielieieva Anastasiia , Dvorak Vojtech , Hannich J. Thomas , Schoenbett Julian , Sansig Gilles , Mocking Tamara A.M. , Ooms Jasper F. , IJzerman Adriaan P. , Heitman Laura H. , Sykacek Peter , Reinhardt Juergen , Müller André C , Wiedmer Tabea , Superti-Furga Giulio
Published: October 2024

Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of diverse substrates including nutrients, ions and drugs. There are about 450 different SLCs, residing in a variety of subcellular membranes. Loss-of-function of an unusually high proportion of SLC transporters is genetically associated with a plethora of human diseases, making SLCs a rapidly emerging but challenging drug target class. Knowledge of their protein environment may elucidate the molecular basis for their functional integration with metabolic and cellular pathways and help conceive pharmacological interventions based on modulating proteostatic regulation. We aimed at obtaining a global survey of the SLC protein interaction landscape and mapped the protein-protein interactions of 396 SLCs by interaction proteomics. We employed a functional assessment based on RNA interference of interactors in combination with measurement of protein stability and localization. As an example, we detail the role of a SLC16A6 phospho-degron, and the contributions of PDZ-domain proteins LIN7C and MPP1 to the trafficking of SLC43A2. Overall, our work offers a resource for SLC-protein interactions for the scientific community.
Enhanced prediction of protein functional identity through the integration of sequence and structural features
Authors: Fujita Suguru , Terada Tohru
Published: October 2024

Although over 300 million protein sequences are registered in a reference sequence database, only 0.2% have experimentally determined functions. This suggests that many valuable proteins, potentially catalyzing novel enzymatic reactions, remain undiscovered among the vast number of function-unknown proteins. In this study, we developed a method to predict whether two proteins catalyze the same enzymatic reaction by analyzing sequence and structural similarities, utilizing structural models predicted by AlphaFold2. We performed pocket detection and domain decomposition for each structural model. The similarity between protein pairs was assessed using features such as full-length sequence similarity, domain structural similarity, and pocket similarity. We developed several models using conventional machine learning algorithms and found that the LightGBM-based model outperformed the models. Our method also surpassed existing approaches, including those based solely on full-length sequence similarity and state-of-the-art deep learning models. Feature importance analysis revealed that domain sequence identity, calculated through structural alignment, had the greatest influence on the prediction. Therefore, our findings demonstrate that integrating sequence and structural information improves the accuracy of protein function prediction.
SAMURAI: Shallow Analysis of copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline
Authors: Potente Sara , Boscarino Diego , Paladin Dino , Marchini Sergio , Beltrame Luca , Romualdi Chiara
Published: October 2024

Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.

SAMURAI is built using established community standards, ensuring portability, scalability, and reproducibility. The pipeline features a modular design with independent blocks for data pre-processing, copy number analysis, and customized reporting. Users can select workflows tailored for either solid or liquid biopsy analysis (e.g., circulating tumor DNA), with specific tools integrated for each sample type. The final report generated by SAMURAI provides detailed results to facilitate data interpretation and potential downstream analyses.To demonstrate its robustness, SAMURAI was validated using simulated and real-world data sets. The pipeline achieved high concordance with ground truth data and maintained consistent performance across various scenarios.

By promoting standardization and offering a versatile workflow, SAMURAI empowers researchers in diverse environments to reliably analyze CNAs from sWGS data. This, in turn, holds promise for advancements in precision medicine.
RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
Authors: Hemm Luisa , Rabsch Dominik , Ropp Halie R. , Reimann Viktoria , Gerth Philip , Bartel Jürgen , Brenes-Álvarez Manuel , Maaß Sandra , Becher Dörte , Hess Wolfgang R. , Backofen Rolf
Published: October 2024

The computational analysis of large proteomics datasets, such as those from gradient profiling or spatially resolved proteomics, is often as crucial as the experimental design. We present RAPDOR, a tool for intuitive analyzing and visualizing such datasets, based on the Jensen-Shannon distance and subsequent analysis of similarities between replicates, applied to three datasets. First, we examined the in-gradient distribution profiles of protein complexes with or without RNase treatment (GradR) to identify the set of RNA-binding proteins (RBPs) in the cyanobacteriumSynechocystissp. PCC 6803. RBPs play pivotal regulatory and structural roles; although numerous RBPs have been identified, the complete set is unknown for any species. RAPDOR identified 80 potential RBPs, including ribosomal proteins, likely RNA-modifying enzymes, and several proteins not previously associated with RNA binding. High-ranking putative RBPs, such as the universal stress protein Sll1388, or the translation inhibitor LrtA/RaiA, were predicted by RAPDOR but not the TriPepSVM algorithm, indicating uncharacterized RBP domains. These data are available online athttps://synecho-rapdor.biologie.uni-freiburg.de, providing a comprehensive resource for RNase-sensitive protein complexes in cyanobacteria. We then show by reanalyzing existing datasets, that RAPDOR is effective in examining the intracellular redistribution of proteins under stress conditions. RAPDOR is a generic, non-parametric tool for the intuitive and versatile analysis of highly complex data sets such as the study of protein distributions using fractionation protocols.
Deciphering shared molecular dysregulation across Parkinson’s Disease variants using a multi-modal network-based data integration and analysis
Authors: Zagare Alise , Balaur Irina , Rougny Adrien , Saraiva Claudia , Gobin Matthieu , Monzel Anna S. , Ghosh Soumyabrata , Satagopam Venkata P. , Schwamborn Jens C.
Published: October 2024

Parkinson’s disease (PD) is a progressive neurodegenerative disorder with no effective treatment. Advances in neuroscience and systems biomedicine now enable the use of complex patient-specificin vitrodisease models and cutting-edge computational tools for data integration, enhancing our understanding of complex PD mechanisms. To explore common biomedical features across monogenic PD forms, we developed a knowledge graph (KG) by integrating previously published high-content imaging and RNA sequencing data of PD patient-specific midbrain organoids harbouring LRRK2-G2019S, SNCA triplication, GBA-N370S or MIRO1-R272Q mutations with publicly available biological data. Furthermore, we generated a single-cell RNA sequencing dataset of midbrain organoids derived fromidiopathic PD patients (IPD) to stratify IPD patients towards genetic forms of PD. Despite high PD heterogeneity, we found that common transcriptomic dysregulation in monogenic PD forms is reflected in IPD glial cells. In addition, dysregulation in ROBO signalling might be involved in shared pathophysiology between monogenic PD and IPD cases.
CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells
Authors: Meng Xiaoyu , Zhu Yezhang , Liu Kuai , Wang Yuxi , Liu Xiaoqian , Liu Chenxin , Zeng Yan , Wang Shuai , Gao Xianzhi , Shen Xin , Chen Jing , Tao Sijue , Xu Qianying , Dong Linjia , Shen Li , Wang Lie
Published: October 2024

FOXP3-expressing regulatory T (Treg) cells play a pivotal role in maintaining immune homeostasis and tolerance, with their activation being crucial for preventing various inflammatory responses. However, the mechanisms governing the epigenetic program in Tregcells during their dynamic activation remain unclear. In this study, we demonstrate that CXXC finger protein 1 (CXXC1) interacts with the transcription factor FOXP3 and facilitates the regulation of target genes by modulating H3K4me3 deposition.Cxxc1deletion in Tregcells leads to severe inflammatory disease and spontaneous T-cell activation, with impaired immunosuppressive function. As a transcriptional regulator, CXXC1 promotes the expression of key Tregfunctional markers under steady-state conditions, which are essential for the maintenance of Tregcell homeostasis and their suppressive functions. Epigenetically, CXXC1 binds to the genomic regulatory regions of Tregprogram genes in mouse Tregcells, overlapping with FOXP3 binding sites. Given its critical role in Tregcell homeostasis, CXXC1 presents itself as a promising therapeutic target for autoimmune diseases.
Sex-specific role of epigenetic modification of a leptin upstream enhancer in the adipose tissue
Authors: Müller Luise , Oelkrug Rebecca , Mittag Jens , Hoffmann Anne , Ghosh Adhideb , Noé Falko , Wolfrum Christian , Jurado Esther Guiu , Klöting Nora , Dietrich Arne , Blüher Matthias , Kovacs Peter , Krause Kerstin , Keller Maria
Published: October 2024

Objective

Maternal hormonal status can have long-term effects on offspring metabolic health, likely regulated via epigenetic mechanisms. We elucidated the effect of maternal thyroid hormones on epigenetic regulation ofLeptin(Lep) transcription in adipose tissue (AT) and investigated the role of DNA methylation at aLepupstream enhancer (UE) in adipocyte biology.

Methods

Pregnant mice were treated with Triiodothyronine (T3). Offspring body composition and adipose tissue were analysed at 6 months (treatment:N= 8, control:N= 12). DNA methylation at theLepUE andLepmRNA levels in gonadal white adipose tissue (gWAT) and leptin serum levels were measured. TheLepUE was hypomethylated in murine preadipocytes using a dCas9-SunTag-TET1 system, followed by differentiation. In human visceral AT samples (N= 52) from the Leipzig Obesity BioBank (LOBB)LEPUE methylation andLEPmRNA levels were assessed alongside leptin serum levels and correlated with body fat percentage. Causal relationships were explored using mediation analysis.

Results

High maternal T3 levels reduced offspring body weight, total fat, and gWAT mass. Female offspring of T3-treated mothers showed lowerLepmRNA levels and higherLepUE methylation compared to controls. CRISPR/dCas9 editing reducedLepUE methylation by ∼20% in preadipocytes without alteringLepexpression or lipid accumulation after differentiation. In humans, a mediation of sex-specific difference in body fat percentage viaLepUE methylation was found.

Conclusion

Maternal thyroid hormones might affect offspring gWATLepexpression in a sex-specific manner, potentially driven by DNA methylation at theLepUE, influencing body fat percentage.
Experience in developing the human genome standard E701
Authors: Vasiliadis Iuliia , Belova Vera , Shmitko Anna , Kuznetsova Anna , Samitova Alina , Suchalko Oleg , Goltsov Andrey , Shatalov Peter , Shegai Peter , Melkova Olga , Kulyabina Tatiana , Kulyabina Elena , Rebrikov Denis , Korostin Dmitriy
Published: October 2024

The first Russian human genome standard E701 was developed through a collaborative research involving four laboratories: Pirogov Russian National Research Medical University, National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov, National Research Center Kurchatov Institute, and National Medical Research Radiological Centre. Whole-genome sequencing of short reads on various platforms (MGI Tech, Illumina) and alignment to the reference human genome GRCh38.p14 were performed for the E701 sample. Subsequently, 3842877 high confidence genomic variants were identified, which can be used as a standard for calculating statistical quality metrics while analyzing sequencing data. Furthermore, 9096 biallelic variants were identified on the autosomes and the X chromosome, with a minor allele frequency exceeding 0.4. Additionally, mitochondrial DNA sequencing was performed with the breadth of coverage over 99.9% at 1000X.
Dopamine activity encodes the changing valence of the same stimulus in conditioned taste aversion paradigms
Authors: Loh Maxine K. , Hurh Samantha , Bazzino Paula , Donka Rachel M. , Keinath Alexandra T. , Roitman Jamie D. , Roitman Mitchell F.
Published: October 2024

Mesolimbic dopamine encoding of non-contingent rewards and reward-predictive cues has been well established. Considerable debate remains over how mesolimbic dopamine responds to aversion and in the context of aversive conditioning. Inconsistencies may arise from the use of aversive stimuli that are transduced along different neural paths relative to reward or the conflation of responses to avoidance and aversion. Here, we made intraoral infusions of sucrose and measured how dopamine and behavioral responses varied to the changing valence of sucrose. Pairing intraoral sucrose with malaise via injection of lithium chloride (LiCl) caused the development of a conditioned taste aversion (CTA), which rendered the typically rewarding taste of sucrose aversive upon subsequent re-exposure. Following CTA formation, intraoral sucrose suppressed the activity of ventral tegmental area dopamine neurons (VTADA) and nucleus accumbens (NAc) dopamine release. This pattern of dopamine signaling after CTA is similar to intraoral infusions of innately aversive quinine and contrasts with that to sucrose when it was novel or not paired with LiCl. Dopamine responses were negatively correlated with behavioral reactivity to intraoral sucrose and predicted home cage sucrose preference. Further, dopamine responses scaled with the strength of the CTA, which was increased by repeated LiCl pairings and weakened through extinction. Thus, the findings demonstrate differential dopamine encoding of the same taste stimulus according to its valence, which is aligned to distinct behavioral responses.
Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and Ca2+
Authors: Tsai Shang-Jui , Gong Yijing , Dabbs Austin , Zahra Fiddia , Xu Junhao , Geske Aleksander , Caterina Michael J. , Gould Stephen J.
Published: October 2024

Kinase translocation reporters (KTRs) are powerful tools for single-cell measurement of time-integrated kinase activity but suffer from restricted dynamic range and limited sensitivity, particularly in neurons. To address these limitations, we developed enhanced KTRs (eKTRs) for protein kinase A (PKA) and extracellular signal-regulated kinase (ERK) that display high sensitivity, rapid response kinetics, broad dynamic range, cell type-specific tuning, and an ability to detect PKA and ERK activity in primary sensory neurons. Moreover, co-expression of optically separable eKTRs for PKA and ERK revealed the kinetics of expected and unexpected crosstalk between PKA, ERK, protein kinase C, and calcium signaling pathways, demonstrating the utility of eKTRs for live cell monitoring of diverse and interacting signaling pathways. These results open the door to improved live-cell and in vivo measurements of key signaling pathways in neurons, while at the same time demonstrating the importance of KTR size and NLS strength to KTR dynamics.
Posterior parietal cortex regulates neural timescales and stimulus-driven attentional modulation in the prefrontal cortex
Authors: Soyuhos Orhan , Moore Tirin , Chaudhuri Rishidev , Chen Xiaomo
Published: October 2024

Intrinsic neural timescales characterize the dynamics of endogenous fluctuations in neural activity. We measured the intrinsic timescales of prefrontal neurons and examined their changes during posterior parietal cortex (PPC) inactivation. Frontal eye field (FEF) neurons within the prefrontal cortex (PFC) exhibited a bimodal distribution of timescales: short-timescale neurons showed stronger transient visual responses, while long-timescale neurons exhibited stronger sustained modulation during stimulus-driven attention. PPC inactivation increased intrinsic timescales in both neuron types, with a 15-fold greater increase in short-timescale neurons. Additionally, it reduced visual and attentional modulation, particularly impairing attentional modulation in long-timescale neurons. Our results provide the first causal evidence that the intrinsic timescales of FEF neurons depend on PPC and suggest the presence of at least two network motifs with distinct timescales that contribute to neuronal dynamics and functional computations within FEF. The heterogeneity in these timescales may facilitate cognitive flexibility, allowing PFC to adapt to varying task demands.
Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording
Authors: McDiarmid Troy A. , Taylor Megan L. , Chen Wei , Chardon Florence M. , Choi Junhong , Liao Hanna , Li Xiaoyi , Kim Haedong , Lalanne Jean-Benoît , Li Tony , Nathans Jenny F. , Martin Beth K. , Knuth Jordan , Coradini Alessandro L.V. , Gray Jesse M. , Pinglay Sudarshan , Shendure Jay
Published: October 2024

As the synthetic biology and genome engineering fields mature and converge, there is a clear need for a “parts list” of components that are diversified with respect to both functional activity (to facilitate design) and primary sequence (to facilitate assembly). Here we designed libraries composed of extant, ancestral, mutagenized or miniaturized variants of Pol III promoters or guide RNA (gRNA) scaffolds and quantified their ability to mediate precise edits to the mammalian genome via multiplex prime editing. We identified thousands of parts that reproducibly drive a range of editing activities in human and mouse stem cells and cancer cell lines, including hundreds exhibiting similar or greater activity than the sequences used in conventional genome engineering constructs. We further conducted saturation mutagenesis screens of canonical Pol III promoters (U6p, 7SKp, H1p) and the prime editing guide RNA (pegRNA) scaffold, which identified tolerated variants that can be superimposed on baseline parts to further enhance sequence diversity. While characterizing thousands of orthologous promoters from hundreds of extant or ancestral genomes, we incidentally mapped the functional landscape of mammalian Pol III promoter evolution. Finally, to showcase the usefulness of these parts, we designed a “ten key” molecular recording array that lacks repetitive subsequences in order to facilitate its one-step assembly in yeast. Upon delivering this 15.8 kb tandem array of promoters and guides to mammalian cells, individual pegRNAs exhibited balanced activities as predicted by the activity of component parts, despite their relocation to a single locus. Looking forward, we anticipate that the diversified parts and variant effect maps reported here can be leveraged for the design, assembly and deployment of synthetic loci encoding arrays of gRNAs exhibiting predictable, differentiated levels of activity, which will be useful for multiplex perturbation, advanced biological recorders and complex genetic circuits.
Identification of Long Non-coding RNA Candidate Disease Genes Associated with Clinically Reported CNVs in Congenital Heart Disease
Authors: Penaloza Jacqueline S. , Moreland Blythe , Gaither Jeffrey B. , Landis Benjamin J. , Ware Stephanie M. , McBride Kim L. , White Peter ,   CCVM Consortium
Published: October 2024

Abstract

Background

Copy Number Variants (CNVs) contribute to 3-10% of isolated Congenital Heart Disease (CHD) cases, but their roles in disease pathogenesis are often unclear. Traditionally, diagnostics have focused on protein-coding genes, overlooking the pathogenic potential of non-coding regions constituting 99% of the genome. Long non-coding RNAs (lncRNAs) are increasingly recognized for their roles in development and disease.

Methods

In this study, we systematically analyzed candidate lncRNAs overlapping with clinically validated CNVs in 1,363 CHD patients from the Cytogenomics of Cardiovascular Malformations (CCVM) Consortium. We identified heart-expressed lncRNAs, constructed a gene regulatory network using Weighted Gene Co-expression Network Analysis (WGCNA), and identified gene modules significantly associated with heart development. Functional enrichment analyses and network visualizations were conducted to elucidate the roles of these lncRNAs in cardiac development and disease. The code is stably archived athttps://doi.org/10.5281/zenodo.13799847.

Results

We identified 18 lncRNA candidate genes within modules significantly correlated with heart tissue, highlighting their potential involvement in CHD pathogenesis. Notably, lncRNAs such aslnc-STK32C-3, lnc-TBX20-1, andCRMAdemonstrated strong associations with known CHD genes. Strikingly, while only 7.6% of known CHD genes were impacted by a CNV, 68.8% of the CNVs contained a lncRNA expressed in the heart.

Conclusions

Our findings highlight the critical yet underexplored role of lncRNAs in the genomics of CHD. By investigating CNV-associated lncRNAs, this study paves the way for deeper insights into the genetic basis of CHD by incorporating non-coding genomic regions. The research underscores the need for advanced annotation techniques and broader genetic database inclusion to fully capture the potential of lncRNAs in disease mechanisms. Overall, this work emphasizes the importance of the non-coding genome as a pivotal factor in CHD pathogenesis, potentially uncovering novel contributors to disease risk.
In vitrodiscovery of a therapeutic lead for HFMD from a library screen of rocaglates/aglains
Authors: Oo Adrian , Borge Angel , Lee Regina Ching Hua , Salim Cyrill Kafi , Wang Wenyu , Ricca Michael , Fong Deborah Yuhui , Alonso Sylvie , Brown Lauren E. , Porco John A. , Chu Justin Jang Hann
Published: October 2024

The lack of an effective antiviral treatment for enteroviruses, including the human enterovirus A71 (EV-A71), has resulted in an immense global healthcare burden associated with hand-foot-and-mouth disease (HFMD). Rocaglates and aglains belong to a family of compounds produced byAglaiagenus plants. Since the initial discovery of rocaglates in 1982, various rocaglates and aglains have been synthesized and extensively studied as anticancer and antiviral agents. Here, we report our studies towards the discovery of a novel aglain derivative as an EV-A71 inhibitor and work to decipher its antiviral effect. From an immunofluorescence-based phenotypic screen of a library of 296 rocaglate and aglain derivatives, we identified a lead aglain derivative which effectively suppressed EV-A71 replication by 2.3 log fold at a non-cytotoxic concentration. Further validation revealed inhibition of EV-A71 across multiple cell types and a pan-enterovirus inhibitory spectrum against other enteroviruses. Subsequent mechanistic investigation revealed interference with EV-A71 intracellular post-entry events including viral RNA transcription and translation. Findings from this study have established a strong foundation for development of aglain scaffolds as much needed antiviral agents for HFMD, paving the way for future medicinal chemistry optimization andin vivostudies.
Concordance between Infectious Disease Society of America Criteria for Urinary Tract Infection Testing and Treating Vs. Actual Emergency Department Practice
Authors: Harhash Tarek , Chen Yi-Ru , Dokku Sahit , Menoudakos Demetra , Argueta Keyleen , Almiggaber Musa , Richman Mark
Published: October 2024

Introduction

Symptomatic and asymptomatic urinary tract infections (UTIs) are common. The Infectious Disease Society of America (IDSA) discourages testing and treating ASB other than in pregnant women during routine obstetric visit screening and patients undergoing urologic procedures with expected mucosal bleeding. Unnecessary urinalysis (UA) and inappropriate antibiotic use persist in Emergency Departments (EDs). This study aims to evaluate UA testing and antibiotic treatment patterns for ASB in an urban ED, assessing adherence to IDSA guidelines and setting baseline rates for an educational intervention to align testing and treatment with IDSA guidelines.

Methods

We conducted a 15-month study to assess adherence to IDSA guidelines for proper UTI screenings and prescribing. We reviewed records of 50 adult patients who had a UA at the Long Island Jewish Medical Center ED to determine whether they met IDSA criteria for UA testing and appropriate antibiotic use. Patients with sepsis or other conditions requiring empiric antibiotics were excluded. We performed a univariate analysis to describe the population and factors associated with treating urinalysis findings. Statistical significance was set at p <0.05.

Results

Sixty-four percent of patients were asymptomatic and 36% were symptomatic. None of the asymptomatic patients met IDSA criteria for UA testing. Symptomatic patients were nearly-statistically more likely than asymptomatic patients to have a positive UA (72.2% vs. 43.8%, p = 0.06), and were more-often prescribed antibiotics for a positive UA (61.5% vs. 14.3%; p = 0.0128). They were also more-often prescribed antibiotics for a negative UA (20.0% vs. 0%; p = 0.05).

Discussion

The study findings revealed significant discordance between IDSA guidelines and current ED practices, with 64% of UA tests deemed unnecessary for ASB patients. These results align with previous studies highlighting the prevalence of over-testing with UAs and over-treatment of ASB. Unnecessary testing and inappropriate antibiotic treatment lead to increased costs and risks of antibiotic resistance, adverse drug events, and Clostridium difficile infection. This study highlights the necessity for planned educational initiatives to reduce unnecessary UAs and treatment and improve adherence to evidence-based guidelines.
Brain-heart interactions are associated with mortality and acute encephalopathy in ICU patients with severe COVID-19
Authors: Hermann Bertrand , Benghanem Sarah , Pruvost-Robieux Estelle , Sharshar Tarek , Gavaret Martine , Cariou Alain , Diehl Jean-Luc , Candia-Rivera Diego
Published: October 2024

Objective

Research in critical care has revealed the significance of autonomic dysfunctions, and more recently of brain-heart interactions, as valuable biomarkers for evaluating patients’ physiological status. These biomarkers provide insights into consciousness levels, severity, and outcomes. This study aims to determine the potential of these biomarkers in predicting the mortality and neurological outcome of severe COVID-19 patients.

Methods

We examined severe COVID-19 patients who required mechanical ventilation and observed them both during sedation and after sedation cessation. Standard EEG and ECG recordings were conducted at bedside, from which 5 minutes of continuous data were analyzed. Using a synthetic data generation model, we evaluated bidirectional brain-heart interactions from EEG power and heartbeat dynamics series.

Results

Our findings indicate that brain-heart interactions, especially involving cardiac parasympathetic activity, can provide information about patients’ severity. We observed correlations with acute encephalopathy duration (coma and delirium), particularly evident in top-down markers (from brain to heart) while bottom-up signaling (from heart to brain) correlated with ICU mortality. Additionally, we noted stronger modulation of brain-heart interactions in milder patients when comparing sedation versus non-sedation conditions, compared to those in more severe states.

Conclusions

Our results imply that autonomic dysfunctions, as measured through brain-heart interactions, can track the pathophysiology of comatose states following COVID-19 infection.

Significance

These findings highlight the potential of brain-heart interactions as an integrated marker for autonomic function in critical care, offering a more accurate assessment of patient severity and outcomes compared to isolated cardiac or brain measures.

Highlights

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Brain-heart interactions provide valuable insights into patient severity and neurological outcomes in severe COVID-19 pneumonia.

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Brain-to-heart markers correlate with acute encephalopathy duration, while heart-to-brain signaling predicts ICU mortality.

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Brain-heart interactions are modulated differently based on assessment timing and the presence of acute encephalopathy.
Percentile Scores for the Revised University of Pennsylvania Smell Identification Test for 16,972 Individuals 60 years of Age and Older
Authors: Pierz Kerri A. , Aamodt Whitley , Gochanour Caroline , Kurth Ryan , Brumm Michael C. , Coffey Christopher S. , Heathers Laura E. , Totten Michelle , Doty Richard L. , Marek Kenneth , Siderowf Andrew ,   the Parkinson’s Progression Markers Initiative
Published: October 2024

Background and Objectives

The University of Pennsylvania Smell Identification Test (UPSIT) is a widely employed objective measure of smell function. A revised version of this test, termed the UPSIT-R, was developed in 2020 to update certain odorants and response options. The goal of this study was to establish normative age- and sex-specific data for the UPSIT-R in a large adult cohort and to compare the resultant percentiles to those of the original UPSIT. A second study was performed to compare the relative performance of these two tests in a small cohort of persons with and without Parkinson’s disease (PD).

Methods

UPSIT-R percentiles were derived separately by age (60-64, 65-69, 70-74, 75-59, and ≥80 years) and sex (male, female) categories in 16,972 volunteers who were predominantly white and non-Hispanic. Percentiles were derived statistically using an empirical distribution averaging procedure. A Bland-Altman plot was employed to visualize the level of agreement between percentiles for the UPSIT-R and UPSIT. For the second study, non-parametric statistics were employed to compare the results of those with and without PD.

Results

UPSIT-R performance declined with increasing age; deficits were more pronounced in men than in women. The magnitude of the difference between the original and revised test percentile scores differed by age and sex; women had up to a 3-point improvement with the UPSIT-R whereas the oldest male age had up to a 3-point decline in percentile scores. Olfactory deficits in PD were confirmed on the UPSIT-R.

Discussion

This study provides normative data clinically useful for assessing the relative degree of dysfunction in persons 60 years of age and older using the UPSIT-R. Like the traditional version of the UPSIT, this version demonstrates that smell function declines with age and is generally better in women than in men, providing a solid clinical basis for physicians to accurately determine the degree of smell dysfunction in their patients.

Trial Registration Information

ClinicalTrials.govNCT05065060