bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive replication origin activation alters chromatin dynamics and stability in cancer cells
Authors: Pérez-Venteo Alejandro , Unzueta Fernando , Feu Sonia , Llinàs-Arias Pere , Mauvezin Caroline , Agell Neus
Published: December 2024

Genome duplication, critical for cell survival and identity, requires precise origin activation to ensure accurate DNA replication and chromatin structure maintenance. In colorectal cancer cells, prolonged replication stress does not hinder cell proliferation, although the mechanisms driving cancer cell adaptability remain largely unclear. Here, we demonstrate that upon recovery, cancer cells are able to activate new replication origins in distinct domains, causing persistent changes in chromatin accessibility, nuclear morphology, and replication timing, ultimately promoting chromatin instability. Chromatin accessibility, particularly in promoter regions, increased following replication stress in a subset of cells, correlating with altered gene expression and nuclear expansion. Additionally, some genes with enhanced promoter accessibility displayed sustained expression changes, further suggesting a transcriptional shift linked to stress adaptation. Our findings reveal that colorectal cancer cells recover from severe replication stress through new origin activation, a mechanism that not only maintains cell proliferation under stress but may also accelerate tumour heterogeneity. This research underscores replication origin activation as a potential therapeutic target in combating cancer cell resilience.

GRAPHICAL ABSTRACT

MAIN HIGHLIGHTS

Colorectal cancer cells under severe replication stress activate new replication origins upon recovery.

The firing of new origins in distinct replication domains results in long-lasting changes in chromatin accessibility, especially in promoter regions, and is associated with alterations in nuclear morphology and replication timing.

Increased chromatin accessibility in certain promoter regions correlates with prolonged gene expression changes.

The capacity of CRC cells to recover from severe replication stress fosters chromatin instability and tumour heterogeneity.
Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis, Dyspersa pallida, and Trioza urticae (Hemiptera: Psylloidea)
Authors: Heaven Thomas , Mathers Thomas C , Mugford Sam T , Jordan Anna , Lethmayer Christa , Nissinen Anne I , Hogetveit Lars-Arne , Highet Fiona , Soria-Carrasco Victor , Sumner-Kalkun Jason , Goldberg Jay K , Hogenhout Saskia Adriane
Published: December 2024

Psyllids are major vectors of plant diseases, including Candidatus Liberibacter solanacearum (CLso), the bacterial agent associated with 'zebra chip' disease in potatoes and 'carrot yellows' disease in carrot. Despite their agricultural significance, there is limited knowledge on the genome structure and genetic diversity of psyllids. In this study, we provide chromosome-level genome assemblies for three psyllid species known to transmit CLso: Dyspersa apicalis (carrot psyllid), Dyspersa pallida, and Trioza urticae (nettle psyllid). As D. apicalis is recognised as the primary vector of CLso by carrot growers in Northern Europe, we also resequenced populations of this species from Finland, Norway, and Austria. Genome assemblies were constructed using PacBio HiFi and Hi-C sequencing data, yielding genome sizes of: 594.01 Mbp for D. apicalis; 587.80 Mbp for D. pallida; and 655.58 Mbp for T. urticae. Over 90% of sequences anchored into 13 pseudo-chromosomes per species. The assemblies for D. apicalis and D. pallida exhibited high completeness, capturing over 92% of conserved Hemiptera single-copy orthologues, as assessed by Benchmarking Universal Single-Copy Orthologues (BUSCO) analysis. Furthermore, we identified sequences of the primary psyllid symbiont, Candidatus Carsonella ruddii, in all three species. Comparative genomic analyses demonstrated synteny with other psyllid species. Notably, we observed significant expansions in gene families, particularly those linked to potential insecticide detoxification, within the Dyspersa lineage. Resequencing efforts also revealed the existence of multiple subpopulations of D. apicalis across Europe. These high-quality genome resources will support future research on genome evolution, insect-plant-pest interactions, and strategies for disease management.
Bluetongue virus serotype 12 in the Netherlands in 2024 - A BTV serotype reported in Europe for the first time
Authors: van den Brom René , Santman-Berends Inge , van der Heijden Mark G. , Harders Frank , Engelsma Marc , van Gennip Rene G.P. , Maris-Veldhuis Mieke A. , Feddema Arno-Jan , Peterson Karianne , Golender Natalia , Spierenburg Marcel , van Rijn Piet A. , Holwerda Melle
Published: December 2024

Bluetongue (BT) is a viral midge borne disease primarily affecting ruminants such as sheep, cattle, and goats. In 2023, the Netherlands reported the first case of bluetongue virus serotype 3 (BTV-3), after being BTV free for eleven years. Since May 2024, vaccination with inactivated BT vaccines for serotype 3 was applied in the Netherlands. Nonetheless, in late June/July 2024, BTV-3 re-emerged and spread over large parts of Europe. In October 2024, BTV-12 was identified by follow-up diagnostics after a BTV-3 vaccinated sheep with signs of BT was tested positive for BTV but negative for serotype 3. This marks a significant event, as BTV-12 had never been reported in Europe. Screening of farms in close proximity to the sheep farm and retrospective analysis of previously BTV PCR positive tested clinical suspicions, resulted in nine BTV-12 affected farms in total. The emergence of BTV-12 in the Netherlands raises important questions about the route of introduction of BT in the Netherlands and mechanisms of viral spread of this specific serotype. Possible adaptation of new BTV serotypes to the European climatic and husbandry conditions prompts reconsideration of surveillance, prevention, and control strategies in relation to changing ecological conditions and vector dynamics. The initial findings, respective studies as well as the initial attempts to trace the origin of BTV-12 are described.
Identification of candidate biomarkers and signaling pathways associated with Alzheimer’s disease using bioinformatics analysis of next generation sequencing data
Authors: Vastrad Basavaraj , Vastrad Chanabasayya
Published: December 2024

Alzheimer’s disease (AD) is the most common cause of dementia, and one of the most common health problems all over the world. However, the specific molecular mechanisms of AD have not been fully investigated. The current investigation aimed to elucidate potential key candidate genes and signaling pathways in AD. Next generation sequencing (NGS) dataset GSE203206 was downloaded from the Gene Expression Omnibus (GEO) database, which included data from 39 AD samples and 8 normal control samples. Differentially expressed genes (DEGs) were identified using t-tests in the limma R bioconductor package. These DEGs were subsequently investigated by Gene ontology (GO) and pathway enrichment analysis, and a protein-protein interaction (PPI) network and modules were constructed and analyzed. The miRNA-hub gene regulatory network and TF-hub gene regulatory network analysis were performed to identify key miRNAs and TFs. The receiver operating characteristic (ROC) curve analysis was performed to estimate the clinical diagnostic value of the hub genes. A total of 958 DEGs, including 479 up regulated genes and 479 down regulated genes, were screened between AD and normal control samples. GO and pathway enrichment analysis results revealed that the up regulated genes were mainly enriched in response to stimulus, cytoplasm, small molecule binding and signal transduction, whereas down regulated genes were mainly enriched in multicellular organism development, cell junction, ion binding and cardiac conduction. The PPI network contained 4886 nodes and 10342 edges. HSP90AA1, FN1, KIT, YAP1, LSM2, SKP1, EIF5A2, TAF9, DDX39B and CDK7 were identified as the top hub genes. The regulatory network analysis revealed that microRNA (miRNA) hsa-mir-545-3p and hsa-miR-548f-5p, and transcription factor (TF) PLAG1 and MEF2A might be involved in the development of AD. These findings provide new insights into the pathogenesis of AD. The hub genes, miRNAs and TFs have the potential to be used as diagnostic and therapeutic markers.
Phase-specific premotor inhibition modulates leech rhythmic motor output
Authors: Radice Martina , Sanchez Merlinsky Agustin , Yulita Federico , Szczupak Lidia
Published: December 2024

Understanding how motoneuron activity is finely tuned remains an open question. Leeches are a highly suitable organism for studying motor control due to their well-characterized behaviors and relatively simple nervous system. On solid surfaces leeches display crawling, a rhythmic motor pattern that can be elicited in the isolated nerve cord or even in ganglia isolated from it. This study aimed to learn how this motor output is shaped by concurrent premotor signals. Specifically, we analyzed how electrophysiological manipulation of a premotor nonspiking (NS) neuron, that forms a recurrent inhibitory circuit (homologous to vertebrate Renshaw cells), shapes the leech crawling motor pattern. The study included a quantitative analysis of motor units active throughout the fictive crawling cycle that shows that the rhythmic motor output in isolated ganglia mirrors the phase relationships observed in vivo. Taken together, the study reveals that the premotor NS neurons, under the control of the segmental pattern generator, modulated the degree of excitation of motoneurons during crawling in a phase-specific manner.
Lactococcus lactissubsp.cremorisC60 creates a type I regulatory T cell-dominant anti-inflammatory intestinal environment through functional modification of dendritic cells
Authors: Saito Suguru , Kakizaki Nanae , Okuno Alato , Maekawa Toshio , Tsuji Noriko M.
Published: December 2024

Lactic acid bacteria (LAB)-mediated probiotics have the capability to modulate intestinal immunity, creating an anti-inflammatory environment. Among the immune-modulatory effects, interleukin (IL)-10-producing CD4+T cells are often discussed for their anti-inflammatory roles. While regulatory T cells (Tregs) are a well-known subset, type I regulatory T (Tr1) cells, which also produce abundant IL-10, receive less attention in LAB-induced anti-inflammatory effects. Here, we report thatLactococcus lactissubsp.cremorisC60, a probiotic LAB strain, increases IL-10-producing Tr1 cells in the intestinal environment, contributing to resistance against inflammatory conditions such as dextran sodium sulfate (DSS)-induced colitis. Intragastric administration of heat-killed (HK)-C60 significantly increased IL-10+CD4+T cells in intestinal tissues compared to control treatment. These populations predominantly consisted of Forkhead box protein P3 (Foxp3)-negative cells, indicating that Tr1 cells were primarily expanded by HK-C60 stimulation. Further analysis revealed that IL-10+Tr1 cells could be classified into two major subpopulations: IL-10 single-positive (SP) and IFN-γ/IL-10 double-positive (DP) cells. Anin vitroco-culture system using CD4+T cells and bone marrow-derived dendritic cells (BMDCs) demonstrated that HK-C60 stimulation modified dendritic cell function, promoting Tr1 cell differentiation. Moreover, pro-inflammatory IFN-γ+CD4+T (Th1) cells differentiated into IL-10+Tr1 cells in the presence of HK-C60-stimulated BMDCs, with the effect being particularly pronounced in DP Tr1 cells. HK-C60-administration attenuated inflammation and reduced pro-inflammatory leukocyte infiltration in the colon of DSS-induced colitis mice, accompanied by the expansion of DP Tr1 cells. The suppressive effect of intestinal CD4+T cells in HK-C60-treated mice was IL-10-dependent, as demonstrated by anin vitroIL-10 neutralizing assay. Thus, C60-based probiotics promote the creation of an anti-inflammatory intestinal environment by increasing IL-10+Tr1 cells rather than Tregs.
Voluntary action sharpens sensory prediction and facilitates neural processing of contingent sensory stimuli
Authors: Ody Edward , Kircher Tilo , Straube Benjamin , He Yifei
Published: December 2024

Self- and externally generated sensations differ in sensory responses and motor preparation. However, mechanistic evidence linking the two is scarce. Here, participants made active (self-initiated) or passive (finger moved by electromagnet) movements that triggered a bimodal auditory/visual stimulus. These were followed, in a block-wise manner, by a unimodal auditory/visual comparison stimulus, and participants judged which stimulus was brighter or louder. Motor preparation ERPs encoded task modality and movement, while sensory ERPs showed reduced task differences for active, demonstrating sensory suppression. Next, we decoded task modality within active and passive. During motor preparation, the active condition showed higher accuracy, reflecting enhanced predictive processes. In the sensory perception period, accuracy was higher in the passive condition, mirroring previous reports of reduced sensory responses to self-generated stimuli. Temporal generalisation showed pattern similarities in the alpha band amplitude between the motor preparation and the stimulus perception windows. This suggests that alpha oscillations may encode sensory predictions generated during motor preparation. Our findings provide mechanistic evidence of action-effect prediction during voluntary actions.
Simulations provide a mechanistic interpretation of Bateman gradients
Authors: Sanghvi Krish , Henshaw Jonathan M. , Kacelnik Alex , Janicke Tim , Sepil Irem
Published: December 2024

The Bateman gradient (BG or 𝛽𝑠𝑠) is a fundamental metric of sexual selection, and is often interpreted as the fitness advantage individuals can gain by increasing their number of mates. However, researchers commonly misconceive the relationship between mating success (MS) and reproductive success (RS) as always being causal, leading to a misinterpretation of the BG. The BG is phenomenological and therefore uninformative about the mechanisms leading to correlations between MS and RS. Here, we simulate sequential matings in males from biological systems with varying levels of anisogamy and sperm competition, to better understand the underlying processes that modulate male BGs. We show that the BG does not solely reflect the causal influence of MS on RS as is typically interpreted, but is also a consequence of covariances between male MS and male ejaculate traits, female fecundity, or female post-mating decisions. For example, we show that the BG is substantially shallower when the ejaculate size of males negatively co-varies with their MS, such as in species with alternative male reproductive tactics. Such covariances can lead to a misinterpretation of the measured BG, because here, it does not merely represent the strength of selection on intra-sexual competition for mates. We suggest how such covariances can be visually assessed, and accounted for using partial Bateman gradients, to better interpret the influence of MS on RS, thus the strength of pre-copulatory sexual selection. Among other simplifications, our simulations have a male-only focus, but they provide insights into the mechanisms driving inter- and intra-specific variation in the BG, clarify its meaning, and improve our understand of sexual selection.
Mechanism of small heat shock protein client sequestration and induced polydispersity
Authors: Miller Adam P. , Reichow Steve L.
Published: December 2024

Small heat shock proteins (sHSPs) act as first responders during cellular stress by recognizing and sequestering destabilized proteins (clients), preventing their aggregation and facilitating downstream refolding or degradation1–3. This chaperone function is critically important to proteostasis, conserved across all kingdoms of life, and associated with various protein misfolding diseases in humans4,5. Mechanistic insights into how sHSPs sequester destabilized clients have been limited due to the extreme molecular plasticity and client-induced polydispersity of sHSP/client complexes6–8. Here, we present high-resolution cryo-EM structures of the sHSP fromMethanocaldococcus jannaschii(mjHSP16.5) in both the apo-state and in an ensemble of client-bound states. The ensemble not only reveals key molecular mechanisms by which sHSPs respond to and sequester client proteins, but also provides insights into the cooperative nature of chaperone-client interactions. Engagement with destabilized client induces a polarization of stability across themjHSP16.5 scaffold, proposed to facilitate higher-order assembly and enhance client sequestration capacity. Some higher-order sHSP oligomers appear to form through simple insertion of dimeric subunits into new geometrical features, while other higher-order states suggest multiple sHSP/client assembly pathways. Together, these results provide long-sought insights into the chaperone function of sHSPs and highlight the relationship between polydispersity and client sequestration under stress conditions.
Isolation and Characterization of Antibodies Against VCAM-1 Reveals Putative Role for Ig-like Domains 2 and 3 in Cell-to-Cell Interaction
Authors: Perera Binura , Wu Yuao , Pickett Jessica R. , Panagides Nadya , Barretto Francisca M. , Fercher Christian , Sester David P. , Jones Martina L. , Ta Hang T. , Zacchi Lucía F.
Published: December 2024

Vascular cell adhesion molecule-1 (VCAM-1) plays an important role in inflammation, where it facilitates the recruitment of leukocytes to the inflamed area via leukocytes’ VLA-4 and endothelial cells’ VCAM-1 interaction. VCAM-1 expression is also upregulated in certain cancers. VCAM-1 has 7 Ig-like domains, with domains 1 and 4 shown to be critical for VLA-4 binding. However, the specific functions of individual VCAM-1 Ig-like domains remain poorly understood. In this study, we identified single-chain variable fragment (scFvs) antibodies targeting domains 2, 3, and 5 of VCAM-1, and investigated the ability of these antibodies to block VCAM-1-mediated cell adhesion to macrophages. We show that scFv antibodies against Ig-like domains 2 and 3 significantly interfere with the ability of macrophages to bind endothelial cells, suggesting that these domains also play a role in facilitating this interaction. These results emphasize the need to more carefully study the role of each domain on VCAM-1 function and highlight the potential of targeting these VCAM-1 domains for more tailored therapeutic interventions in inflammatory diseases and cancer.
Dementia Care Specialists Perspectives of Diagnosis and Early Psychosocial Care: A Qualitative Analysis of Focus Groups in Two Large Academic Medical Centers
Authors: Hicks Amelia J. , Brewer Julie , Ahmad Nina , Cornelius Talea , Parker Robert A. , Dams-O’Connor Kristen , Dickerson Bradford , Ritchie Christine , Vranceanu Ana-Maria , Bannon Sarah M.
Published: December 2024

Background and Objective

Alzheimer’s disease and related dementias (ADRDs) are progressive conditions that substantially impact individuals and families. Timely diagnosis and early support are critical for long-term adjustment. However, current dementia care models do not meet needs of patients and families. Dementia care specialists treating individuals with dementia offer unique insight into care needs of diverse groups of patients, families, and healthcare systems that can be used to identify opportunities to improve care.

To understand dementia care specialists’ impressions of factors impacting ADRD diagnosis and post-diagnosis support. We aimed to identify factors that impact: (1) timely and accurate diagnosis, (2) diagnostic disclosure and provision of post-diagnosis support, and (3) patient and care-partner adjustment after diagnosis.

Research Design and Methods

We recruited dementia care specialists treating persons living with dementia (n=19) from two academic medical centers. Participants completed 60-minute qualitative focus groups or individual interviews. Data were analyzed using a hybrid inductive-deductive approach to thematic analysis.

Results

We identified subthemes within three overarching a-priori determined themes. Participants highlighted the presence of delays in referrals, time constraints, specialist discomfort, and lack of training as factors impacting the timeliness and accuracy of diagnosis. They also highlighted information needed in disclosure visits, ways of coordinating care, and identifying early support needs. Finally, participants highlighted factors impacting adjustment including families’ insight and acceptance, distress, and available resources.

Discussion and Implications

Our study highlights the challenges dementia care specialist specialists face in delivering early support for individuals and families impacted by ADRDs and suggests avenues for revising existing care models.
Structural and functional connectivity of the posterior default mode network is associated with sleep disturbance rather than pain in the Twin sub-study of the MAPP Research Network
Authors: Sudhakar Tejaswi , Bogic Marija , Elliott Jonathan E. , Lim Miranda M. , Buchwald Dedra , Strachan Eric , Levendovszky Swati Rane
Published: December 2024

The neurophysiological underpinnings of chronic pain and sleep disturbances, which are commonly comorbid are not well understood. Investigation of common structural and functional brain network alterations of sleep disturbance in the setting of chronic pain may shed light on common mechanisms and improve specificity of treatment for these conditions. Our study examines the association between sleep parameters (including sleep duration, sleep difficulty, and sleep chronotype), pain phenotype, and brain structural and functional connectivity in individuals with chronic pelvic pain by leveraging data from the Twin Studies of the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network. Participants (n= 34 pairs) completed extensive clinical phenotyping and 3T MRI, including resting-state functional MRI (rs-fMRI), diffusion tensor imaging (DTI), and subjective sleep assessments. We observed significant differences in total sleep time (420 ± 58 min vs. 466 ± 61 min) and sleep difficulty (study-specific Likert scale 0-3: 1.35 ± 0.81 vs. 0.95 ± 0.68) among individuals with chronic pelvic pain compared to those without chronic pelvic pain, with sleep difficulty being associated with altered default mode network (DMN) connectivity. No associations were found with the salience network (SN), a network implicated in chronic pain. Additionally, increased total sleep time was associated with decreased posterior callosal white matter integrity. These findings underscore the complex interplay between chronic pain and sleep disturbances and have implications for distinct treatment approaches for patients with comorbid pain and sleep disorders.
Integrated DNA estimation in tissue biopsy and detection in liquid biopsy by HBV-targeted NGS assay
Authors: Liu Hsin-Ni , Lin Selena Y. , Ramirez Ricardo , Chen Shin-En , Heimer Zach , Kubas Roman , Shieh Fwu-Shan , Kim Elena S. , Liu Yuanjie , Lau Daryl T.Y. , Chang Ting-Tsung , Guo Haitao , Wang Zhili , Su Ying-Hsiu
Published: December 2024

Background & Aims

Integrated HBV DNA (iDNA) plays a critical role in HBV pathogenesis, particularly in predicting treatment response and HCC. This study aimed to use an HBV hybridization-capture next-generation sequencing (HBV-NGS) assay to detect HBV-host junction sequences (HBV-JS) in a sensitive nonbiased manner to detect and estimate the iDNA fraction in tissue biopsies and HBV genetics by liquid biopsy.

Methods

HBV DNA from plasmid monomers, HBV-HCC cell line (SNU398, Hep3B, and PLC/PRF/5), tissue biopsies of patients with serum HBV DNA <4 log IU/ml, and matched urine and plasma of HBV patients were assessed by HBV-NGS. Junction-specific qPCR (JS-qPCR) assays were developed to quantify abundant HBV-JS.

Results

We demonstrated high coverage uniformity, reproducibility across all HBV genotypes A-D, and 0.1% sensitivity for detecting iDNA by the HBV-NGS assay. The sequence and structures of iDNA molecules from SNU398 and Hep3B are reported. An iDNA estimation model was developed using six abundant HBV-JS sequences identified from tissue biopsies by HBV-NGS assay and validated using total DNA of SNU398 and Hep3B cells. Furthermore, the utility of the HBV-NGS assay for HBV genetic analysis in liquid biopsies was explored using matched plasma-urine samples from three patients with serum HBV DNA levels ranging from high to undetectable. HBV-JS was detected in all body fluids tested, regardless of viral load.

Conclusion

These findings suggest that the iDNA fraction in tissue biopsies from patients with limited or undetectable serum HBV DNA can be estimated using a robust HBV-NGS assay, and a sensitive HBV genetics liquid biopsy can be obtained. This study highlights the potential of NGS-based methods to advance HBV management.

Impact and implications

This study applied an unbiased, sensitive, and robust HBV-captured NGS method to detect integrated HBV DNA (iDNA) in both tissue and liquid (blood and urine) biopsies and generated a model to estimate the intrahepatic iDNA quantity. The availability of this technology makes possible to not only estimate iDNA fraction in total HBV DNA in tissue biopsies, but also perform HBV genetics in a minimally invasive manner in chronic HBV patients for disease monitoring, HCC risk assessment, and for clinical research.
Exploring clinical characteristics of COVID-19 in children and adolescents using a machine-learning approach
Authors: Fiandrino Stefania , Doná Daniele , Giaquinto Carlo , Poletti Piero , Tira Micheal Davis , Di Chiara Costanza , Paolotti Daniela
Published: December 2024

Introduction

The epidemiology and clinical characteristics of COVID-19 evolved due to new SARS-CoV-2 variants of concern (VOCs). The Omicron VOC’s higher transmissibility increased pediatric COVID-19 cases and hospital admissions. Most research during the Omicron period has focused on hospitalized cases, leaving a gap in understanding the disease’s evolution in community settings. This study targets children with mild to moderate COVID-19 during pre-Omicron and Omicron periods. It aims to identify patterns in COVID-19 morbidity by clustering individuals based on symptom similarities and duration of symptoms and develop a machine-learning tool to classify new cases into risk groups.

Methods

We propose a data-driven approach to explore changes in COVID-19 characteristics analyzing data collected within a pediatric cohort at the University Hospital of Padua. First, we apply an unsupervised machine-learning algorithm to cluster individuals into different groups. Second, we classify new patient risk groups using a Random-Forest classifier model based on sociodemographic information, pre-existing medical conditions, vaccination status, and the VOC as predictive variables. Third, we explore the key features influencing the classification.

Results

The unsupervised clustering identified three severity risk profile groups. The classification model effectively distinguished these groups, with age, gender, COVID-19 vaccination, VOC, and presence of comorbidities as top predictive features. A high number and longer duration of symptoms were associated with younger age groups, males, unvaccinated individuals, Omicron infections, and those with comorbidities. These results are consistent with evidence of severe COVID-19 in infants, older children with comorbidities, and unvaccinated children.

Conclusion

Our classification model has the potential to provide clinicians with insights into the children’s risk profile of COVID-19 using readily available data. This approach can support public health efforts by clarifying disease burden and improving patient care strategies. Furthermore, it underscores the importance of integrating risk classification models to monitor and manage infectious diseases.
Monitoring sexual hormones in women going to high altitude – a pilot study
Authors: Taalaibekova Aijan , Meyer Michelle , Ulrich Stefanie , Mirzalieva Gulzada , Mademilov Maamed , Lichtblau Mona , Betschart Cornelia , Sooronbaev Talant M. , Ulrich Silvia , Bloch Konrad E. , Furian Michael
Published: December 2024

Background

The susceptibility to acute mountain sickness (AMS) in relation to sexual hormones in women remains elusive, partly because hormones could not be conveniently measured. We evaluated a novel kit for self-monitoring sexual hormones in women and recorded AMS incidence during high-altitude sojourns.

Methods

Two groups of healthy, premenopausal women, mean±SD age 23.1±2.3 y, residing <1,000m underwent baseline evaluations at 760 m before travelling to and staying for 2 days and nights (48 hours) at 3,100 m or 3,600 m, respectively. Participants self-monitored morning urine sexual hormone concentrations (estrone-1-glucuronide, E1G, pregnanediol-3-alpha-glucuronide, PdG, and luteinizing hormone, LH) daily for 30d including altitude sojourns using the simple“Proov”kit (MFB Fertility Inc). Follicular and luteal menstrual cycle phases detected by LH peak, altitude-related adverse health effects (ARAHE), AMS (Lake Louise score 2018 [LLS] ≥ 3 points including headache) and pulse oximetry (SpO2) were assessed.

Results

1,172 of 1,250 (93.8%) hormone measurements were successful, 78 of 1,250 (6.2%) failed due to nonadherence or technical failure. At 3,600 m, mean differences in urinary PdG concentration were 3.8 mcg/ml (95%CI, 0.6 to 7.1) between luteal and follicular cycle phases. At 3,100 m, corresponding difference was 8.5 mcg/ml (95%CI, 5.0 to 12.0). At 3,100 m, 9 of 21 (43%) women were diagnosed with AMS with SpO2of 93.0±1.6% and LLS of 0.3±1.4 in the morning after the first night. At 3,600 m, 12 of 21 (57%) women had AMS (p=0.355 versus 3,100 m) with SpO2of 86.8±1.8% (p<0.05 vs. 3,100 m) and LLS of 1.9±1.4 (p<0.05 vs. 3,100 m).

Conclusion

Self-monitoring female sexual hormones during high-altitude field studies with the employed kit is feasible and provides physiologically plausible trends of hormone levels over the menstrual cycle. Our data provide a valuable basis for designing further studies to evaluate AMS susceptibility in women.
Establishing methods to monitor H5N1 influenza virus in dairy cattle milk
Authors: Stachler Elyse , Gnirke Andreas , McMahon Kyle , Gomez Michael , Stenson Liam , Guevara-Reyes Charelisse , Knoll Hannah , Hill Toni , Hill Sellers , Messer Katelyn S. , Arizti-Sanz Jon , Albeez Fatinah , Curtis Elizabeth , Samani Pedram , Wewior Natalia , O’Connor David H. , Vuyk William , Khoury Sophia , Schnizlein Matthew K. , Rockey Nicole C. , Broemmel Zachariah , Mina Michael , Madoff Lawrence C. , Wohl Shirlee , O’Connor Lorraine , Brown Catherine M. , Ozonoff Al , Park Daniel J. , MacInnis Bronwyn L. , Sabeti Pardis C.
Published: December 2024

Highly Pathogenic Avian Influenza strain H5N1 has caused a multi-state outbreak among US dairy cattle, spreading across 15 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk from 20 states for methods development, we found that H5N1 concentrations by digital PCR strongly correlated with qPCR cycle threshold (Ct) values, with dPCR exhibiting greater sensitivity. We also found that metagenomic sequencing after hybrid selection was best for higher concentration samples while amplicon sequencing performs best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to test bulk milk samples monthly from all cattle dairy farms within Massachusetts, which remain negative to date. The methods, workflow, and recommendations described here provide a framework for others aiming to conduct H5N1 surveillance efforts.
A Decade of Radiological Examinations in the Emergency Department: A Monocentric Retrospective Observational Study
Authors: Goumballa Ndiaw , de Oliveira Fabien , Coisy Fabien , Goupil Jean , Frandon Julien , Longueville Florence , Daladouire Catherine , Grandpierre Romain Genre , Beregi Jean Paul
Published: December 2024

Purpose

To analyze the evolution of various radiological examinations requested for patients admitted to the emergency department (ED) of a University Hospital.

Materials and Methods

We analyzed data on MRI, CT scan, Ultrasound (US), and X-ray activities, along with ED patient admissions over a ten-year period from 2014 to 2023. The patient data for each modality, categorized by age and sex, were extracted from the Radiological Information System database.

Results

The number of patients undergoing radiological examinations increased from 35,532 in 2014 to 44,592 in 2023, marking a 25.9% increase, while the number of ED admissions rose from 71,776 to 103,456, a 44.1% increase. The ratio of radiological examinations to ED admissions decreased from 49.5% in 2014 to 43.1% in 2023. Over the study period, the number of patients receiving MRI and CT scans increased by 80.4% and 105.8%, respectively. The number of patients undergoing ultrasound remained relatively stable, with 2,616 in 2014 and 2,432 in 2023. In contrast, the number of X-ray patients decreased by 33.1% from 22,236 in 2014 to 14,847 in 2020 but rebounded to 20,492 in 2023. Male patients more frequently underwent CT (51.7%) and X-ray examinations (53.3%).

Conclusion

This study highlights a significant increase in radiological activity within the emergency department, especially in CT scans and MRI usage over the ten-year period while ultrasound examinations stayed flat, accompanied by a decline in the ratio of radiological examinations to ED admissions.
Crackling Cloud: an event-driven, cloud-based CRISPR-Cas9 guide RNA design tool
Authors: Bradford Jacob , Joy Divya , Winsen Mattias , Meurant Nicholas , Wilkins Mackenzie , Wilson Laurence , Bauer Denis , Perrin Dimitri
Published: December 2024

Gene editing has been revolutionised by the CRISPR-Cas9 technology. The versatility and ease-of-use of the technology far exceeds its predecessors, however, the selection of a high-quality guide RNA (gRNA) is critical to directing it to a target site. Selecting gRNA calls upon high-performance algorithms that evaluate nuclease activity at on-target and off-target sites. While there are a suite of programs available, many struggle to analyse the largest genomes, or their predictive accuracy is low. We have previously published a program, named Crackling that is amongst the fastest and most accurate tools available, however, it requires an end-user to have access to a traditional high-performance computing environment. Here, we present an adaptation of Crackling, named Crackling Cloud, that takes advantage of modern serverless cloud technologies that are widely available to anyone, and do not consume resources and incur costs when sitting idle, but can scale to use large volumes of resources when analyses require that. Crackling Cloud is provided as a templated solution using technologies of Amazon Web Services, and is available for free on GitHub under the terms of the BSD 3-clause licence:https://github.com/bmds-lab/Crackling-AWS
Targeted blocking of gene splicing can dysregulate intron-embedded microRNAs
Authors: Ali Md Hasan , Kwiatkowski Wojciech , Kopec Piotr , Nedunchezhian Naveen , Pecherz Sebastian , Kowalewska Natalia , Gnutti Barbara , Finazzi Dario , Anbalagan Savani
Published: December 2024

ASOs (antisense oligonucleotides) are a promising therapeutic approach for suppression, induction of gene expression or the correction of aberrant splicing. Addressing whether ASOs targeting genes embedded with intronic noncoding RNAs (ncRNAs) affect the expression and function of intronic ncRNAs is of importance to the success of ASOs in clinical trials. While studying the development of the zebrafish posterior pituitary (neurohypophysis), an important neuroendocrine interface, we observed that an ASO targeting the splice site, in contrast to the one targeting the translation site of the gene slit3, disrupts neurohypophyseal axonal morphogenesis. In addition to altered slit3 splicing, we also observed an increase in the expression of slit3 and slit3 intron-embedded primary mir218a-1 transcripts. The ASO-induced phenotype was not observed when mature mir218a-1 was blocked by an ASO or in mir218a-1-/- mutants. In addition, we also found that previously reported phenotypes due to ASOs targeting the splice site of pank2 and dnm2a were partially rescued when the mature mir103 and mir199-5p embedded in their introns, respectively, were blocked by ASOs. Our observation that ASOs targeting splice sites can affect intronic microRNA expression and function warrants further validation for other classes of ncRNAs. In addition, the idiosyncratic phenotypes when using translation and splice-blocking ASOs can be potentially used as a marker to identify the role of intronic ncRNAs.
Pseudomonas aeruginosaperforms chemotaxis to serotonin, dopamine, epinephrine, and norepinephrine
Authors: Monteagudo-Cascales Elizabet , Lozano-Montoya Andrea , Krell Tino
Published: December 2024

Bacteria use chemotaxis to move to favorable ecological niches. For many pathogenic bacteria, chemotaxis is required for full virulence, particularly for the initiation of host colonization. There do not appear to be limits to the type of compounds that attract bacteria, and we are just beginning to understand how chemotaxis adapts them to their lifestyles. Quantitative capillary assays for chemotaxis show thatP. aeruginosais strongly attracted to serotonin, dopamine, epinephrine, and norepinephrine. Chemotaxis to these compounds is greatly decreased in a mutant lacking the TlpQ chemoreceptor, and complementation of this mutant with a plasmid harboring thetlpQgene restores wild-type-like chemotaxis. Microcalorimetric titrations of the TlpQ sensor domain with these four compounds indicate that they bind directly to TlpQ. All four compounds are hormones and neurotransmitters that control a variety of processes and are also important signal molecules involved in the virulence ofP. aeruginosa. They modulate motility, biofilm formation, the production of virulence factors and serve as siderophores that chelate iron. Therefore, chemotaxis to these four compounds is likely to alterP. aeruginosavirulence. Additionally, we believe that this is the first report of bacterial chemotaxis to serotonin and dopamine. This study provides an incentive for research to define the contribution of chemotaxis to these host signaling molecules to the virulence ofP. aeruginosa.
Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron richCryptococcus neoformanstranscriptome
Authors: Negi Manendra Singh , Krishnan Vishnu Priya , Saraf Niharika , Vijayraghavan Usha
Published: December 2024

The DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodeling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeastCryptococcus neoformans. The presence of multiple introns per transcript with intronic features more similar to higher eukaryotes makes it a promising model to study spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered its genome-wide but substrate-specific roles inC. neoformanssplicing. The splicing functions of Prp16 are dependent on its helicase motif I and motif II that are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity, were investigated to discover that exonic sequences at the 5’ splice site (5’SS) and 3’ splice site (3’SS) with stronger affinity for U5 loop 1 as a common feature in these introns. Furthermore, short (60-100nts) and ultra-short introns (<60nts) prevalent in theC. neoformanstranscriptome were more sensitive to Prp16 knockdown than longer introns, indicating Prp16 is required for the efficient splicing of short and ultra-short introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable the efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into the fine-tuning spliceosomal helicase functions with variations incis-element features.
Mycobacterium tuberculosisCrgA Forms a Dimeric Structure with Its Transmembrane Domain Sandwiched between Cytoplasmic and Periplasmic β-Sheets, Enabling Multiple Interactions with Other Divisome Proteins
Authors: Shin Yiseul , Prasad Ramesh , Das Nabanita , Taylor Joshua A. , Qin Huajun , Hu Wenhao , Hu Yan-Yan , Fu Riqiang , Zhang Rongfu , Zhou Huan-Xiang , Cross Timothy A.
Published: December 2024

CrgA is a key transmembrane (TM) protein in the cell division process ofMycobacterium tuberculosis(Mtb), the pathogen responsible for tuberculosis. While many of theMtbdivisome proteins have been identified, their structures and interactions remain largely unknown. Previous studies of CrgA using oriented-sample solid-state NMR have defined the tilt and rotation of the TM helices, but the cytoplasmic and periplasmic domains and even the oligomeric state were uncharacterized. Here, combining oriented-sample and magic-angle spinning solid-state NMR spectra, we solved the full-length structure of CrgA. The structure features a dimer with a TM domain sandwiched between a cytoplasmic β-sheet and a periplasmic β-sheet. The β-sheets stabilize dimerization, which in turn increases CrgA’s ability to participate in multiple protein interactions. Within the membrane, CrgA binds FtsQ, CwsA, PbpA, FtsI, and MmPL3 via its TM helices; in the cytoplasm, Lys23 and Lys25 project outward from the β-sheet to interact with acidic residues of FtsQ and FtsZ. The structural determination of CrgA thus provides significant insights into its roles in recruiting other divisome proteins and stabilizing their complexes forMtbcell wall synthesis and polar growth.
Structural mechanisms of PIP2activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1
Authors: Xue Jing , Zeng Weizhong , John Scott , Attiq Nicole , Ottolia Michela , Jiang Youxing
Published: December 2024

Na+/Ca2+exchangers (NCXs) transport Ca2+across the plasma membrane in exchange for Na+and play a vital role in maintaining cellular Ca2+homeostasis. Our previous structural study of human cardiac NCX1 (HsNCX1) reveals the overall architecture of the eukaryotic exchanger and the formation of the inactivation assembly by the intracellular regulatory domain that underlies the cytosolic Na+-dependent inactivation and Ca2+activation of NCX1. Here we present the cryo-EM structures of HsNCX1 in complex with a physiological activator phosphatidylinositol 4,5-bisphosphate (PIP2), or pharmacological inhibitor SEA0400 that enhances the inactivation of the exchanger. We demonstrate that PIP2binding stimulates NCX1 activity by inducing a conformational change at the interface between the TM and cytosolic domains that destabilizes the inactivation assembly. In contrast, SEA0400 binding in the TM domain of NCX1 stabilizes the exchanger in an inward-facing conformation that facilitates the formation of the inactivation assembly, thereby promoting the Na+-dependent inactivation of NCX1. Thus, this study reveals the structural basis of PIP2activation and SEA0400 inhibition of NCX1 and provides some mechanistic understandings of cellular regulation and pharmacology of NCX family proteins.
High-order harmonic generation driven by perfect optical vortex beams: Exploring the orbital angular momentum upscaling law
Authors: Das Bikash Kumar , Granados C. , Krüger M. , Ciappina Marcelo F.
Published: December 2024

Orbital angular momentum (OAM) light beams for high-order harmonic generation (HHG) provide an additional degree of freedom to study the light-matter interaction at ultrafast timescales. A more sophisticated configuration is a perfect optical vortex (POV) beam, a light beam with a helical wave front characterized by a phase singularity at its center and an azimuthal phase variation. POV beams are characterized by a radial profile which is independent of the OAM. Here, we study the nonperturbative process of gas-phase HHG using a linearly polarized POV beam. We observe that the harmonics are emitted with similar divergence due to the perfectness of the POV-driven harmonic generation. Furthermore, the topological charge upscaling is rigorously followed. We show that a POV beam is more advantageous than that of the Laguerre-Gaussian beam for cases where a large topological charge with a small core size is required. Our research establishes a pathway for producing bright structured extreme ultraviolet coherent radiation sources—a pivotal tool with multifaceted applications across various technological domains.

Published by the American Physical Society
2024
A personal account of the history of X-ray crystallography at the University of La Plata, Argentina
Authors: Piro Oscar Enrique
Published: December 2024

Prompted by visionary political leaders and a flowering economy, the University of La Plata was founded in 1905, the third Argentinian university after the Universities of Cordoba (1613) and Buenos Aires (1821). Differing from the older universities, more prone to professional formation, the new university was oriented towards teaching and scientific research following western European academic tradition. Along with the university was created the Institute of Physics, the first of its kind in Latin America. To pursue the foundational plan, the university recruited distinguished German physicists, some of whom became the first directors. From the start, the institute became acquainted with Röntgen rays, their generation and use, initially for radiographic images and later in occasional diffraction studies. The first dedicated crystallographic X-ray diffraction laboratory was set up in the early 1970s, when it solved the first molecular structures. Soon the fascination brought about by a methodology that afforded the visualization of atoms, molecules and crystals lured the local and national physical chemistry communities. In close partnership with an equally oriented laboratory at the University of Sao Paulo, Brazil, and in collaboration with several physical chemistry laboratories from Argentina and the Latin American region, and also from Europe, we undertook studies on the crystal structures and physicochemical and spectroscopic properties of a wide range of materials, including inorganic, organic, bioinorganic, metal–organic, organic–metal, supramolecular, pharmaceutical, organic minerals and liquid crystals. The present essay is a personal account of the origin and development of structural X-ray crystallography at the University of La Plata and its impact on the scientific research of Argentina and Latin America.