bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of microplastics on Daphnia-associated microbiomes in situ and in vitro
Authors: Krzynowek Anna , Van de Moortel Broos , Pichler Nikola , Vanoverberghe Isabel , Lapere Johanna , Jenisch Liliana M. , Deloof Daphné , Thielemans Wim , Muylaert Koenraad , Dusselier Michiel , Springael Dirk , Faust Karoline , Decaestecker Ellen
Published: July 2024

Microplastics (MP) pollution in aquatic environments is a growing global concern. MP, defined as plastic fragments smaller than 5mm, accumulate in freshwater reservoirs, especially those located in urban areas, impacting the resident biota. This study investigated the effects of MP on the performance and microbiome of Daphnia, a keystone organism in freshwater ecosystems, through both in situ sampling of freshwater ponds and a controlled 23-day in vitro exposure experiment. Using 16S rRNA gene sequencing and whole-genome shotgun sequencing, the microbiome community composition and functional capacity was analysed and correlated with MP pollution levels. Urban ponds showed higher MP concentrations in both water and sediment than natural ponds with significant differences in MP composition. Bacterioplankton communities were more diverse and richer than the Daphnia-associated microbiomes. Overall, the in situ study showed that the composition of the Daphnia-associated community co-varied with high MP levels but also with temperature and redox potential. Moreover, the functional analysis showed increased relative abundances of PET degradation enzymes and antibiotic resistance genes (ARGs) in microbiomes from high-MP ponds. In the in vitro experiment, the bacterioplankton inoculum source significantly influenced Daphnia survival and microbiome composition. Daphnia exposed to high MP concentrations inoculated with bacterioplankton pre-exposed to MP exhibited significantly higher survival rates, suggesting potential adaptive benefits from MP-associated microbiomes. Network analysis identified specific taxa associated with MP within the Daphnia microbiome. Our study suggests adaptive responses of freshwater host-associated microbiomes to MP pollution including biodegradation with potential benefits for the host.
Protocol for open-source Automated Universal high-content multiplex fluorescence for RNAin situAnalysis (AURA)
Authors: Descarpentrie Jean , Bernard Florian , Souleyreau Wilfried , Brisson Lucie , Mathivet Thomas , Pateras Ioannis S. , Martin Océane C. B. , Lopez Chiloexhes Maria , Frisan Teresa
Published: July 2024

In situ hybridization visualizes RNA in cells, but image analysis is complex. We present a protocol based on open-source software for automated high-content multiplex fluorescencein situtranscriptomics analysis. Steps include nuclei segmentation with a Fiji macro and quantification of up to 14 mRNA probes per image. We describe procedures for storing raw data, quality control images and the use of a Python app to summarize all the results in one spreadsheet detailing the number of single or co-positive cells.
Fast 3D imaging in the auditory cortex of awake mice reveals that astrocytes control neurovascular coupling responses locally at arteriole-capillary junctions
Authors: Lind Barbara Lykke , Volterra Andrea
Published: July 2024

During neuronal activity, cerebral blood flow increases to ensure adequate glucose and oxygen supply, a crucial mechanism known as the neurovascular coupling response. Blood is drawn from the brain’s surface through penetrating arterioles (PA) and locally redistributed via branching capillaries in the cerebral cortex. All blood vessels, regardless of cortical layer or size, are covered by astrocytic end-feet, suggesting a potential regulatory role. Though the regulatory machinery is known to be present in astrocyte end-feet, its role in this blood recruitment is still controversial. A likely explanation for the controversy is that studies so far have been done without considering the structural basis for blood flow regulation and the heterogeneity in blood vessel dilation patterns. We performed our experiments in awake mice, using a 3D+t two-photon imaging approach by which we could image regions at the branching point between PA and capillary bed at high speed. This led us to detect rapid, localized astrocytic Ca2+ signals in the end-feet surrounding the sphincter connecting the two vascular compartments. Mice often moved during experiments, and we noticed that in these cases, most of the natural vessel dilations in our imaged region were multicompartmental, extending from the PA to the 1storder capillary across the pre-capillary sphincter or vice versa. In contrast, when the mouse was at rest, dilations were more spatially restricted, with at least half of them remaining confined to one of the two compartments. The local Ca2+ rises in the end-feet encircling the pre-capillary sphincters preceded dilations spread and were notably correlated with multicompartment dilations. These Ca2+ signals were attenuated in IP3R2KO mice, lacking a major source of astrocyte Ca2+ rises, and the number of dilations crossing the sphincter was significantly reduced or slowed down compared to wild-type mice. When we induced dilations by auditory stimulation, we found that they had patterns and dependency on local astrocyte Ca2+ activity analogous to those of naturally occurring dilations. In conclusion, we discovered that pre-capillary sphincters play a pivotal role in the bidirectional dilation spread between vascular compartments and that local astrocyte Ca2+ signaling controls this function. This mechanism, described here for the first time, allows astrocytes to control the dilation transition across the sphincters and contribute to laminar blood flow regulation during neurovascular coupling responses.
PV+ optogenetic stimulations at specific frequencies in specific brain regions can restore navigational flexibility in an acute MK801 mouse model of schizophrenia
Authors: Patrono Enrico , Černotová Daniela , Svoboda Jan , Stuchlík Aleš
Published: July 2024

Impairments of decision-making and behavioral flexibility in schizophrenia (SCZ) are currently the most investigated features. One convincing hypothesis explaining this cognitive impairment is the excitatory/inhibitory (E/I) ratio imbalance in brain regions such as the medial prefrontal cortex (mPFC) and the ventral hippocampus (vHPC). An increased GLUergic excitatory activity and a decreased GABAergic inhibitory activity induces an mPFC-vHPC γ/θ band desynchronization in many tasks testing behavioral flexibility. However, these tasks were carried out using “perceptual” decision-making/flexibility but not navigational decision-making/flexibility. Our study addressed the role of frequency-specific optogenetic stimulations of GABAergic parvalbumin-positive (PV+) interneurons in mPFC (50Hz, γ-like) and vHPC (10Hz, θ-like) in an acute-MK801 mouse model of navigational inflexibility. We used the active place avoidance task on a rotating arena. Results showed that frequency-specific optogenetic stimulations of mPFC or vHPC acted differently in restoring navigational flexibility, advancing our knowledge of the pivotal role of PV+ activity in SCZ-like navigational decision-making/flexibility.
Navigating the Maze of Mass Spectra: A Machine-Learning Guide to Identifying Diagnostic Ions in O-Glycan Analysis
Authors: Urban James , Joeres Roman , Thomès Luc , Thomsson Kristina A. , Bojar Daniel
Published: July 2024

Structural details of oligosaccharides, or glycans, often carry biological relevance, which is why they are typically elucidated using tandem mass spectrometry. Common approaches to distinguish isomers rely on diagnostic glycan fragments for annotating topologies or linkages. Diagnostic fragments are often only known informally among practitioners or stem from individual studies, with unclear validity or generalizability, causing annotation heterogeneity and hampering new analysts. Drawing on a curated set of 237,000O-glycomics spectra, we here present a rule-based machine learning workflow to uncover quantifiably valid and generalizable diagnostic fragments. This results in fragmentation rules to robustly distinguish commonO-glycan isomers. We envision this resource to improve glycan annotation accuracy and concomitantly make annotations more transparent and homogeneous across analysts.
Non-autonomous insulin signaling delays mitotic progression inC. elegansgermline stem and progenitor cells
Authors: Cheng Eric , Lu Ran , Gerhold Abigail R.
Published: July 2024

Stem and progenitor cell mitosis is essential for tissue development and homeostasis. How these cells ensure proper chromosome segregation, and thereby maintain mitotic fidelity, in the complex physiological environment of a living animal is poorly understood. Here we usein situlive-cell imaging ofC. elegansgermline stem and progenitor cells (GSPCs) to ask how the signaling environment influences stem and progenitor cell mitosisin vivo. Through a candidate screen we identify a new role for the insulin/IGF receptor (IGFR),daf-2,during GSPC mitosis. Mitosis is delayed indaf-2/IGFR mutants, and these delays require canonical, DAF-2/IGFR to DAF-16/FoxO insulin signaling, here acting cell non-autonomously from the soma. Interestingly, mitotic delays indaf-2/IGFR mutants depend on the spindle assembly checkpoint but are not accompanied by a loss of mitotic fidelity. Correspondingly, we show that caloric restriction, which delays GSPC mitosis and compromises mitotic fidelity, does not act via the canonical insulin signaling pathway, and instead requires AMP-activated kinase (AMPK). Together this work demonstrates that GSPC mitosis is influenced by at least two genetically separable signaling pathways and highlights the importance of signaling networks for proper stem and progenitor cell mitosisin vivo.

Author Summary

Stem and progenitor cells drive tissue development and sustain adult tissue turnover by producing new daughter cells via cell division, the success of which depends on proper chromosome segregation during mitosis. Stem and progenitor cells perform mitosis in the complex environment of a living animal, yet relatively little is known about how events during mitosis are influenced by thisin vivocontext. In particular, whether signaling pathways that coordinate other aspects of stem and progenitor cell behavior with animal physiology also play a role during mitosis is poorly understood. Here we took advantage of the germline stem and progenitor cells of the model nematodeC. elegansto address this question. Through live-cell imaging of germline stem and progenitor cell mitosis, we uncover a new role for the insulin signaling pathway. We find that reducing insulin signaling delays germline stem and progenitor cell mitosis, but, surprisingly, these delays are not accompanied by a loss of mitotic fidelity. In addition, we find that reducing insulin signaling in somatic tissues is sufficient to delay germline stem and progenitor mitosis, indicating that the pathway acts non-autonomously. Finally, while insulin signaling is known to link cell division with nutritional status in many species, we found that it did not mediate the effects of caloric restriction on germline stem and progenitor cell mitosis. Instead, caloric restriction acts via the conserved energy-sensing regulator AMPK. These results uncover new regulators of germline stem and progenitor cell mitosis and emphasize the importance of signaling pathways for proper stem and progenitor cell mitosisin vivo.
Characterization of Multicellular Niches Supporting Hematopoietic Stem Cells Within Distinct Zones
Authors: Dong Ruochen , Li Hua , He Xi C , Wang Chen , Perera Anoja , Malloy Seth , Russell Jonathon , Li Wenting , Petentler Kaitlyn , Mao Xinjian , Yang Zhe , Epp Michael , Hall Kate , Scott Allison , McKinney Mary C. , Huang Shengping , Smith Sarah E , Hembree Mark , Wang Yongfu , Yu Zulin , Haug Jeffery S. , Unruh Jay , Slaughter Brian , Kang Xunlei , Li Linheng
Published: July 2024

Previous studies of hematopoietic stem cells (HSCs) primarily focused on single cell-based niche models, yielding fruitful but conflicting findings1–5. Here we report our investigation on the fetal liver (FL) as the primary fetal hematopoietic site using spatial transcriptomics. Our study reveals two distinct niches: the portal-vessel (PV) niche and the sinusoidal niche. The PV niche, composing N-cadherin (N-cad)HiPdgfrα+mesenchymal stromal cells (MSCs), endothelial cells (ECs), and N-cadLoAlbumin+hepatoblasts, maintains quiescent and multipotential FL-HSCs. Conversely, the sinusoidal niche, comprising ECs, hepatoblasts and hepatocytes, as well as potential macrophages and megakaryocytes, supports proliferative FL-HSCs biased towards myeloid lineages. Unlike prior reports on the role of Cxcl12, with its depletion from vessel-associated stromal cells leading to 80% of HSCs’ reduction in the adult bone marrow (BM)6,7, depletion ofCxcl12viaCdh2CreERT(encoding N-cad) induces altered localization of HSCs from the PV to the sinusoidal niches, resulting in an increase of HSC number but with myeloid-bias. Similarly, we discovered that adult BM encompasses two niches within different zones, each composed of multi-cellular components: trabecular bone area (TBA, or metaphysis) supporting deep-quiescent HSCs, and central marrow (CM, or diaphysis) fostering heterogenous proliferative HSCs. This study transforms our understanding of niches by shifting from single cell-based to multicellular components within distinct zones, illuminating the intricate regulation of HSCs tailored to their different cycling states.
Label-Free Melanoma Phenotype Classification Using Artificial Intelligence-Based Morphological Profiling
Authors: Lattmann Evelyn , Jovic Andreja , Kim Julie , Pham Tiffine , Corona Christian , Lian Zhouyang , Saini Kiran , Ray Manisha , Lu Vivian , Tastanova Aizhan , Boutet Stephane C. , Levesque Mitchell P.
Published: July 2024

Melanomas are the deadliest skin cancers, in part due to cellular plasticity and heterogeneity. Intratumoral heterogeneity drives varied mutable phenotypes, specifically “melanocytic” and “mesenchymal” cell states, which result in differential functional properties and drug responses. Definitive and rigorous classification of these phenotypic states has been challenging with conventional biomarker-based methods, and high-parameter molecular methods are cell-destructive, labor-intensive, and time-consuming. To overcome these technical and practical limitations, we utilized label-free artificial intelligence-based morphological profiling to classify live melanoma cells into melanocytic and mesenchymal phenotypes based on high resolution imaging of single cells.

To predict the phenotypes of single melanoma cells based on morphology alone, we developed the AI-based ‘Melanoma Phenotype Classifier’ trained with 19 patient-derived cell lines with known melanocytic or mesenchymal transcriptional profiles. To link phenotypic state with high-dimensional morphological profiles, cells were subjected to genetic and chemical perturbations known to shift phenotypic states. The AI classifier successfully predicted phenotypic shifts which were confirmed by single-cell RNA-Seq (scRNA-Seq). These results demonstrate that correlations between melanoma cell phenotypes and morphological changes are detectable by AI. Additionally, the Melanoma Phenotype Classifier was applied to dissociated tumor biopsy samples and characterization of phenotypic heterogeneity was supported by scRNA-Seq transcriptional profiles.

This work establishes a link between cell morphology and melanoma phenotypes, laying the groundwork for the use of a label-free morphology-based method for phenotyping live melanoma cells combined with additional analyses.
The RNA binding ubiquitination ligase MEX3B regulates bFGF-dependent neuronal proliferation
Authors: Garg Kamakshi , Sharma Gourav , Samaddar Sarbani , Banerjee Sourav
Published: July 2024

Background

E3 ubiquitin ligases, integral components of the proteasomal degradation cascade, are critical for regulating the cellular proteome via canonical proteasome-mediated protein degradation; however, the non-canonical functions of these ligases in neuronal development are poorly understood. Our study focuses on a special class of E3 ubiquitin ligases known as RNA Binding Ubiquitin Ligases (RBUL) that harbour RNA-binding domains; allowing them to acquire all the properties of RNA-binding proteins (RBPs) and regulate transcriptional or post-transcriptional changes associated with the control of gene expression in cellular phenotypes. We aim to identify one such RUBL in the context of the highly dynamic yet stringently controlled process of neural proliferation and neural fate determination.

Results

MEX3B protein is a member of the MEX3 family and a part of the RBUL class of E3 ligases. It is differentially expressed in Neural Progenitor Cells (NPCs) upon differentiation. Mex3b RNA and protein were found to have temporally opposing expression patterns in presence of basic fibroblast growth factor (bFGF), a key signalling protein involved in neuronal proliferation. MEX3B is required for maintenance of the proliferative state of NPCs, whereas, its knockdown promotes transition from proliferative to differentiation state even in presence of bFGF that restricts differentiation. Furthermore, the knockdown of MEX3B protein results in the appearance of morphological hallmarks associated with early stages of neuronal differentiation including increase in neurite length and complexity. MEX3B interacts with the pro-proliferative transcription activator REST and the long non-coding RNA,HOTAIR. The study suggests the existence of a bFGF-dependent, combinatorial axis involving Mex3b, REST andHOTAIR, for the maintenance of NPC proliferative states.

Conclusion

MEX3B, containing RNA binding motifs, is a unique E3 ligase that is necessary for bFGF-dependent proliferation. Mex3b protein invokes its non-canonical function of an RNA binding protein to form a tripartite complex with the transcription activator REST andHOTAIRlncRNA to define the proliferative state of NPCs. The study highlights a unique feature of special E3 ligases in neuronal proliferation during brain development that was previously overlooked.
Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation
Authors: Amith Weththasinghage D. , Chen Vincent T. , Dutagaci Bercem
Published: July 2024

RNA Polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeats (2CTDs) models at different phosphorylation patterns, protein, and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intra-peptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.
Trends in Sudden Cardiac Death in Pilots: A Post COVID-19 Challenging Crisis of Global Perspectives (2011-2023) - A Systematic Review and Meta-Analysis
Authors: Borges Julian Yin Vieira
Published: July 2024

Background

Sudden cardiac death (SCD) remains a significant threat to pilots and is a leading cause of death worldwide, jeopardizing flight safety and causing devastating consequences. This review examines trends in SCD among pilots from a global perspective, analyzing evidence from 2011 to 2023, with a focus on its growing impact as a global crisis and recent findings pointing to a potential rise in incidence, particularly after 2019.

Objectives

To analyze the prevalence, risk factors, and prevention strategies for SCD in pilots, particularly post-COVID-19.

Methods

The PRISMA guidelines for systematic meta-analysis was used, a search of peer-reviewed literature for international aviation databases, and pilot associations was conducted to identify relevant data. The analysis focused on trends in SCD prevalence, risk factors, prevention strategies, and recent findings, including the potential impact of COVID-19, the role of vaccination, and important biomarkers to screen for predisposition. Eligibility criteria included studies reporting SCD incidence, risk factors, or prevention strategies in pilots. Data were extracted, and meta-analyses conducted.

Results

Recent studies suggest a potential increase in SCD incidence among pilots following the COVID-19 pandemic. Cardiovascular complications, increased stress, disruptions in healthcare, and changes in lifestyle may contribute to this potential rise. Identified risk factors include age, male gender, and cardiovascular comorbidities.

Biomarkers such as troponin, N-terminal pro-B-type natriuretic peptide (NT-proBNP), and high-sensitivity C-reactive protein (hs-CRP) have been identified as potential indicators of increased SCD risk in pilots. Preventive measures include regular cardiovascular assessments and lifestyle modifications.

Conclusion

SCD remains a significant and rising threat to pilots, posing a global crisis that requires immediate attention. Through a comprehensive approach that includes risk assessment, preventive measures, emergency response, and preventive protocols, the aviation industry can mitigate this risk and safeguard the lives of pilots and passengers.

This review also suggests standardized examination protocol for pilots includes regular cardiovascular risk assessment, biomarker screening, monitoring of COVID-19 and vaccination status, lifestyle modifications, and a standardized reporting system. The adoption of a standardized protocol by aviation regulatory bodies and airlines worldwide is crucial to address the growing threat of SCD among pilots and ensure the highest standards of aviation safety.
Diagnostic accuracy of Chest X-Ray Computer Aided Detection software and blood biomarkers for detection of prevalent and incident tuberculosis in household contacts followed up for 5 years
Authors: Macpherson Liana , Kik Sandra V. , Quartagno Matteo , Lakay Francisco , Jaftha Marche , Yende Nombuso , Galant Shireen , Aziz Saalikha , Daroowala Remy , Court Richard , Taliep Arshad , Serole Keboile , Goliath Rene T. , Davies Nashreen Omar , Jackson Amanda , Douglass Emily , Sossen Bianca , Mukasa Sandra , Thienemann Friedrich , Song Taeksun , Ruhwald Morten , Wilkinson Robert J. , Coussens Anna K. , Esmail Hanif
Published: July 2024

Background

WHO Tuberculosis (TB) screening guidelines recommend computer-aided detection (CAD) software for chest radiograph (CXR) interpretation. However, studies evaluating their diagnostic and prognostic accuracy are limited.

Methods

We conducted a prospective cohort study of household TB contacts in South Africa. Participants all underwent baseline CXR and sputum investigation (routine [single spontaneous] and enhanced [additionally 2-3 induced] sputum investigation and passive and active follow-up for incident TB. CXR were processed comparing 3 CAD softwares (CAD4TBv7.0, qXRv3.0.0, and Lunit INSIGHT CXR 3.1.4.111). We evaluated their performance to detect routine and enhanced prevalent, and incident TB, comparing the performance to blood-based biomarkers (Xpert MTB host-response, Erythrocyte Sedimentation Rate, C-Reactive Protein, QuantiFERON) in a subgroup.

Findings

483 participants were followed-up for 4.6 years (median). There were 23 prevalent (7 routinely diagnosed) and 38 incident TB cases. The AUC ROC to identify prevalent TB for CAD4TB, qXR and Lunit INSIGHT CXR were 0.87 (95% CI 0.77-0.96), 0.88 (95% CI 0.79-0.97) and 0.91 (95% CI 0.83-0.99) respectively. >30% with scores above recommended CAD thresholds who were bacteriologically negative on routine baseline sputum were subsequently diagnosed by enhanced baseline sputum investigation or during follow-up. The AUC performance of baseline CAD to identify incident cases ranged between 0.60-0.65. The diagnostic performance of CAD for prevalent TB was superior to blood-based biomarkers.

Interpretation

Our findings suggest that the potential of CAD-CXR screening for TB is not maximised as a high proportion of those above current thresholds but with a negative routine confirmatory sputum have true TB disease that may benefit intervention.

Funding

UKRI-MRC

We found that the diagnostic accuracy of CAD-CXR to identify prevalent TB cases in household TB contacts was high but >30% with scores above recommended CAD thresholds who were bacteriologically negative on routine testing baseline were subsequently diagnosed suggest that the potential of CAD-CXR screening is not maximised.
Blood biomarker profiles in young-onset neurocognitive disorders: a cohort study
Authors: Bhalala Oneil G. , Beamish Jessica , Eratne Dhamidhu , Summerell Patrick , Porter Tenielle , Laws Simon M. , Kang Matthew JY , Huq Aamira J. , Chiu Wei-Hsuan , Cadwallader Claire , Walterfang Mark , Farrand Sarah , Evans Andrew H. , Kelso Wendy , Churilov Leonid , Watson Rosie , Yassi Nawaf , Velakoulis Dennis , Loi Samantha M.
Published: July 2024

INTRODUCTION

Young-onset neurocognitive symptoms result from a heterogeneous group of neurological and psychiatric disorders which present a diagnostic challenge. To identify such factors, we analysed the BeYOND (Biomarkers in Younger-Onset Neurocognitive Disorders) cohort, a study of individuals less than 65 years old presenting with neurocognitive symptoms for a diagnosis and who have undergone cognitive and biomarker analyses.

METHODS

Sixty-five participants (median age at assessment of 56 years, 45% female) were recruited during their index presentation to the Royal Melbourne Hospital Neuropsychiatry Centre, a tertiary specialist service in Melbourne, Australia, and categorised as either early-onset Alzheimer’s disease (EOAD, n=18), non-AD neurodegeneration (nAD-ND, n=23) or primary psychiatric disorders (PPD, n=24). Levels of neurofilament light chain, glial fibrillary acidic protein and phosphorylated-tau 181, apolipoprotein E genotype and late-onset AD polygenic risk scores were determined. Information-theoretic model selection identified discriminatory factors.

RESULTS

Neurofilament light chain, glial fibrillary acidic protein and phosphorylated-tau 181 levels were elevated in EOAD compared to other diagnostic categories. A multi-omic model selection identified that a combination of cognitive and blood biomarkers, but not the polygenic risk score, discriminated between EOAD and PPD (AUC≥0.975, 95% CI: 0.825-1.000). Phosphorylated-tau 181 alone significantly discriminated between EOAD and nAD-ND causes (AUC=0.950, 95% CI: 0.877-1.00).

DISCUSSION

Discriminating between EOAD, nAD-ND and PPD causes of young-onset neurocognitive symptoms is possible by combining cognitive profiles with blood biomarkers. These results support utilising blood biomarkers for the work-up of young-onset neurocognitive symptoms and highlight the need for the development of a young-onset AD-specific polygenic risk score.
Streamlined screening platforms lead to the discovery of pachysiphine synthase fromTabernanthe iboga
Authors: Kamileen Mohamed O. , Nakamura Yoko , Luck Katrin , Heinicke Sarah , Hong Benke , Colinas Maite , Lichman Benjamin R. , O’Connor Sarah E.
Published: July 2024

Plant-specialized metabolism is largely driven by the oxidative tailoring of key chemical scaffolds catalyzed by cytochrome P450 (CYP450s) enzymes. The monoterpene indole alkaloids tabersonine and pseudo-tabersonine, found in the medicinal plantTabernanthe iboga, are extensively modified by oxidative reactions. Here we developed a streamlined screening strategy to screen the activity ofT. ibogaCYP450s inNicotiana benthamiana.Using multigene constructs encoding the biosynthesis of tabersonine and pseudo-tabersonine scaffolds, we set out to uncover the CYP450s responsible for oxidative transformations of these scaffolds. Our approach identified twoT. ibogacytochrome P450 enzymes: pachysiphine synthase (PS) and 16-hydroxy-tabersonine synthase (T16H). These enzymes catalyze an epoxidation and site-specific hydroxylation of tabersonine to produce pachysiphine and 16-OH-tabersonine, respectively. We further demonstrated that these genes produced the expected products when expressed inCatharanthus roseusflowers. This work provides new insights into the biosynthetic pathways of MIAs and underscores the utility ofN. benthamianaandC. roseusas platforms for the functional characterization of plant enzymes.
Endothelial Zmiz1 modulates physiological and pathophysiological angiogenesis during retinal development
Authors: Patel Nehal R , K C Rajan , Chiang Mark Y , Meadows Stryder M
Published: July 2024

Angiogenesis is a highly coordinated process involving the control of various endothelial cell behaviors. Mechanisms for transcription factor involvement in the regulation of endothelial cell dynamics and angiogenesis have become better understood, however much remains unknown, especially the role of non-DNA binding transcriptional cofactors. Here, we show that Zmiz1, a transcription cofactor, is enriched in the endothelium and critical for embryonic vascular development, postnatal retinal angiogenesis, and pathological angiogenesis in oxygen induced retinopathy (OIR). In mice, endothelial cell-specific deletion ofZmiz1during embryogenesis led to lethality due to abnormal angiogenesis and vascular defects. Inducible endothelial cell-specific ablation ofZmiz1postnatally resulted in impaired retinal vascular outgrowth, decreased vascular density, and increased vessel regression. In addition, angiogenic sprouting in the superficial and deep layers of the retina was markedly reduced. Correspondingly, vascular sprouting in fibrin bead assays was significantly reduced in the absence of Zmiz1, while furtherin vitroandin vivoevidence also suggested deficits in EC migration. In agreement with the defective sprouting angiogenesis phenotype, gene expression analysis of isolated retinal endothelial cells revealed downregulation of tip-cell enriched genes upon inactivation ofZmiz1. Lastly, our study suggested that endothelial Zmiz1 is critical for intraretinal revascularization following hypoxia exposure in the OIR model. Taken together, these findings begin to define the previously unspecified role of endothelial Zmiz1 in physiological and pathological angiogenesis.
Leveraging Basecaller’s Move Table to Generate a Lightweight k-mer Model
Authors: Samarakoon Hiruna , Wan Yuk Kei , Parameswaran Sri , Göke Jonathan , Gamaarachchi Hasindu , Deveson Ira W.
Published: July 2024

Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in k-mer models. Particularly in cases where official models are lacking or unsuitable for specific sequencing conditions, tailored k-mer models are crucial to ensure precise signal-to-sequence alignment and interpretation. The process of transforming raw signals into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing. In this study, we leverage the basecaller’s move table to create a lightweight denovo k-mer model for RNA004 chemistry. We showcase the effectiveness of our custom k-mer model through high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models in m6A methylation detection.
Genetic susceptibility to neurodevelopmental conditions associates with neonatal DNA methylation patterns in the general population: an individual participant data meta-analysis
Authors: Schuurmans I. K. , Smajlagic D. , Baltramonaityte V. , Malmberg A. L. K. , Neumann A. , Creasey N. , Felix J. F. , Tiemeier H , Pingault J. B. , Czamara D. , Raïkkönen K. , Page C. M. , Lyle R. , Havdahl A. , Lahti J. , Walton E. , Bekkhus M. , Cecil C. A. M.
Published: July 2024

Background

Autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and schizophrenia (SCZ) are highly heritable and linked to disruptions in foetal (neuro)development. While epigenetic processes are considered an important underlying pathway between genetic susceptibility and neurodevelopmental conditions, it is unclear (i) whether genetic susceptibility to these conditions is associated with epigenetic patterns, specifically DNA methylation (DNAm), already at birth; (ii) to what extent DNAm patterns are unique or shared across conditions, and (iii) whether these neonatal DNAm patterns can be leveraged to enhance genetic prediction of (neuro)developmental outcomes.

Methods

We conducted epigenome-wide meta-analyses of genetic susceptibility to ASD, ADHD, and schizophrenia, quantified using polygenic scores (PGSs) on cord blood DNAm, using four population-based cohorts (npooled=5,802), all North European. Heterogeneity statistics were used to estimate overlap in DNAm patterns between PGSs. Subsequently, DNAm-based measures of PGSs were built in a target sample, and used as predictors to test incremental variance explained over PGS in 130 (neuro)developmental outcomes spanning birth to 14 years.

Outcomes

In probe-level analyses, SCZ-PGS associated with neonatal DNAm at 246 loci (p<9×10−8), predominantly in the major histocompatibility complex. Functional characterization of these DNAm loci confirmed strong genetic effects, significant blood-brain concordance and enrichment for immune-related pathways. 8 loci were identified for ASD-PGS (mapping toFDFT1andMFHAS1), and none for ADHD-PGS. Regional analyses indicated a large number of differentially methylated regions for all PGSs (SCZ-PGS: 157, ASD-PGS: 130, ADHD-PGS: 166). DNAm signals showed little overlap between PGSs. We found suggestive evidence that incorporating DNAm-based measures of genetic susceptibility at birth increases explained variance for several child cognitive and motor outcomes over and above PGS.

Interpretation

Genetic susceptibility for neurodevelopmental conditions, particularly schizophrenia, is detectable in cord blood DNAm at birth in a population-based sample, with largely distinct DNAm patterns between PGSs. These findings support an early-origins perspective on schizophrenia.

Funding

HorizonEurope; European Research Council

Abstract Figure
Ocular Surface Microbiome: Influences of Physiological, Environmental, and Lifestyle Factors
Authors: Rizzuto Vincenzo , Settino Marzia , Stroffolini Giacomo , Covello Giuseppe , Vanags Juris , Naccarato Marta , Montanari Roberto , Rocha de Lossada Carlos , Mazzotta Cosimo , Adornetto Carlo , Rechichi Miguel , Ricca Francesco , Greco Gianluigi , Laganovska Guna , Borroni Davide
Published: July 2024

Purpose

Purpose: The ocular surface (OS) microbiome is influenced by various factors and impacts ocular health. Understanding its composition and dynamics is crucial for developing targeted interventions for ocular diseases. This study aims to identify host variables, including physiological, environmental, and lifestyle (PEL) factors, that influence the ocular microbiome composition and establish valid associations between the ocular microbiome and health outcomes.

Methods

The 16S rRNA gene sequencing was performed on OS samples collected using eSwab. DNA was extracted, libraries prepared, and PCR products purified and analyzed. PEL confounding factors were identified, and a cross-validation strategy using various bioinformatics methods including Machine learning was used to identify features that classify microbial profiles.

Results

Nationality, sport practice, and eyeglasses usage are significant PEL confounding factors influencing the eye microbiome. Alpha-diversity analysis showed higher microbial richness in Spanish subjects compared to Italian subjects and higher biodiversity in sports practitioners. Beta-diversity analysis indicated significant differences in microbial community composition based on nationality, age, sport, and eyeglasses usage. Differential abundance analysis identified several microbial genera associated with these PEL factors. ML approach confirmed the significance of nationality in classifying microbial profiles.

Conclusion

This study underscores the importance of considering PEL factors when studying the ocular microbiome. Our findings highlight the complex interplay between environmental, lifestyle, and demographic factors in shaping the OS microbiome. Future research should further explore these interactions to develop personalized approaches for managing ocular health.

Key Points

Identify confounding factors influencing the ocular microbiome composition;

Characterize the ocular surface microbiome;

Analyse 16S rRNA gene sequencing data from ocular surface samples;

Perform Diversity Analysis (i.e.; Alpha-diversity and Beta-diversity) and Difference Abundance Analysis;
Down regulation ofEngaseinCaenorhabditis elegansmay improve its stresses adaptivity
Authors: Lu Xinrong , Tong Yongliang , Wu Mengting , Lyu Shaoxian , Fan Jiale , Zheng Junyu , Zou Lin , Shen Danfeng , Rao Lin , Hou Linlin , Chen Cuiying , Cheng Xunjia , Sun Guiqin , Shao Zhiyong , Chen Li
Published: July 2024

Endo-beta-N-acetylglucosaminidase (ENGASE) is one of the key enzymes involved in the regulation of structure and function of glycoproteins. It is conserved from prokaryotic to eukaryotic cells. Although their activitiesin vitroand applications have been well studied, the biological function of ENGASE remains to be illustrated. In this study, we analyzed the molecular and physiological function ofEngasefromCaenorhabditis eleganshomologeng-1(CeEngase). We found thatCeEngaseknockout or knockdown increased the environmental stresses adaptability, such as heat stress and osmotic stress. Preliminary glycomics analysis showed that the basement membrane proteins of extracellular matrix may be the main targets of CeENGASE. In addition, CeENGASE may selectively prefer to N2H7 glycans on glycoproteins. In conclusion, our data illustrated that the defection and/or down regulation ofCeEngasemay provide a beneficially adaptation for stresses.
Interhemispheric Connectivity of the Human Temporal Lobes
Authors: Binder Jeffrey R. , Giraldo-Chica Mónica , Mathis Jedediah , Tong Jia-Qing , Schoenrock Sidney , Arpinar Volkan , Heffernan Joseph , Muftuler L. Tugan
Published: July 2024

Much is known regarding the major white matter pathways connecting the right and left temporal lobes, which project through the posterior corpus callosum, the anterior commissure, and the dorsal hippocampal commissure. However, details about the spatial location of these tracts are unclear, including their exact course and proximity to cortical and subcortical structures, the spatial relations between corpus callosum and anterior commissure projections, and the caudal extent of transcallosal connections within the splenium. We present an atlas of these tracts derived from high angular resolution diffusion tractography maps, providing improved visualization of the spatial relationships of these tracts. The data show several new details, including branching of the transcallosal pathway into medial and lateral divisions, projections of the transcallosal pathway into the external capsule and claustrum, complex patterns of overlap and interdigitation of the transcallosal and anterior commissure tracts, distinct dorsal and ventral regions of the splenium with high tract densities, and absence of temporal lobe projections in the caudal third of the splenium. Intersection of individual tract probability maps with individual cortical surfaces were used to identify likely regions with relatively higher cortical termination densities. These data should be useful for planning surgical approaches involving the temporal lobe and for developing functional-anatomical models of processes that depend on interhemispheric temporal lobe integration, including speech perception, semantic memory, and social cognition.

Highlights

Interhemispheric connections of the human temporal lobes were visualized using high angular resolution diffusion tensor imaging tractography.

Results are displayed on serial orthogonal sections to reveal detailed spatial relationships.

Corpus callosum projections through the splenium form distinct dorsal and ventral bundles and are absent from the caudal splenium.

The transcallosal pathway consists of distinct medial and lateral divisions.

The results reveal projections to the external capsule and claustrum not previously described.

Transcallosal and anterior commissural pathways show complex patterns of overlap and interdigitation.

Surface mapping revealed areas with relatively high density of projections to the cortical surface.
Universal chemical formula dependence of
ab initio
low-energy effective Hamiltonian in single-layer carrier-doped cuprate superconductors: Study using a hierarchical dependence extraction algorithm
Authors: Morée Jean-Baptiste , Arita Ryotaro
Published: July 2024

We explore the possibility to control the superconducting transition temperature at optimal hole doping Tcopt in cuprates by tuning the chemical formula (CF). Tcopt can be theoretically predicted from the parameters of the low-energy effective Hamiltonian with one antibonding (AB) Cu3dx2−y2/O2pσ orbital per Cu atom in the CuO2 plane, notably the nearest-neighbor hopping amplitude |t1| and the ratio u=U/|t1|, where U is the onsite effective Coulomb repulsion. However, the CF dependence of |t1| and u is a highly nontrivial question. In this paper, we propose the universal dependence of |t1| and u on the CF and structural features in hole doped cuprates with a single CuO2 layer sandwiched between block layers. To do so, we perform extensive calculations of |t1| and u and analyze the results by employing a machine-learning method called hierarchical dependence extraction (HDE). The main results are (a)

|

t

1

|

has a main-order dependence on the radii RX and RA of the apical anion X and cation A in the block layer. (|t1| increases when RX or RA decreases.) (b) u has a main-order dependence on the ionic charge ZX of X and the hole doping δ of the AB orbital. (u decreases when |ZX| increases or δ increases.) We elucidate and discuss the microscopic mechanism of items (a) and (b). We demonstrate the predictive power of the HDE by showing the consistency between items (a) and (b) and results from previous works. The present results provide a basis for optimizing superconducting properties in cuprates and possibly akin materials. Also, the HDE method offers a general platform to identify dependencies between physical quantities.

Published by the American Physical Society
2024
Entanglement suppression and low-energy scattering of heavy mesons
Authors: Hu Tao-Ran , Chen Su , Guo Feng-Kun
Published: July 2024

Recently entanglement suppression was proposed to be one possible origin of emergent symmetries. Here we test this conjecture in the context of heavy meson scatterings. The low-energy interactions of D(*)D¯(*) and D(*)D(*) are closely related to the hadronic molecular candidates X(3872) and Tcc(3875)+, respectively, and can be described by a nonrelativistic effective Lagrangian manifesting heavy-quark spin symmetry, which includes only constant contact potentials at leading order. We explore entanglement suppression in a tensor-product framework to treat both the isospin and spin degrees of freedom. Using the X(3872) and Tcc(3875)+ as inputs, we find that entanglement suppression indeed leads to an emergent symmetry, namely, a light-quark spin symmetry, and as such the D(*)D¯(*) or D(*)D(*) interaction strengths for a given total isospin do not depend on the total angular momentum of light (anti)quarks. The X(3872) and Tcc(3875)+ are predicted to have five isoscalar partners and one isoscalar partner, respectively, while the corresponding partner numbers derived solely from heavy-quark spin symmetry are three and one, respectively. The predictions need to be confronted with experimental data and lattice quantum chromodynamics results to further test the entanglement suppression conjecture.

Published by the American Physical Society
2024
Extreme heterogeneity in the microrheology of lamellar surfactant gels analyzed with neural networks
Authors: Watts Moore Owen , Lewis Conor , Ross Thomas , Waigh Thomas Andrew , Korabel Nickolay , Mendoza Cesar
Published: July 2024

The heterogeneity of the viscoelasticity of a lamellar gel network based on cetyl-trimethylammonium chloride and cetostearyl alcohol was studied using particle-tracking microrheology. A recurrent neural network (RNN) architecture was used for estimating the Hurst exponent, H, on small sections of tracks of probe spheres moving with fractional Brownian motion. Thus, dynamic segmentation of tracks via neural networks was used in microrheology and it is significantly more accurate than using mean square displacements (MSDs). An ensemble of 414 particles produces a MSD that is subdiffusive in time, t, with a power law of the form t0.74±0.02, indicating power law viscoelasticity. RNN analysis of the probability distributions of H, combined with detailed analysis of the time-averaged MSDs of individual tracks, revealed diverse diffusion processes belied by the simple scaling of the ensemble MSD, such as caging phenomena, which give rise to the complex viscoelasticity of lamellar gels.

Published by the American Physical Society
2024
Social network analysis for identifying the significant drivers of off-site construction adoption in Egypt
Authors: Shaker Rana Ahmed , Elbeltagi Emad , Motawa Ibrahim , Elmasoudi Islam , Elnabwy Mohamed T.
Published: July 2024

Purpose

Rapid urbanization and the shortcomings of traditional construction methods motivate construction professionals to explore faster and more sustainable approaches such as off-site construction (OSC). Thus, the purpose of this paper is to identify the drivers influencing OSC adoption and to explore the key drivers of its widespread adoption in Egypt.

Design/methodology/approach

A comprehensive global literature review was performed initially to develop an up-to-date list of OSC adoption drivers, which was confirmed in the Egyptian context through a pilot study. Then, social network analysis (SNA) was utilized to determine the most influential drivers as well as shortlist them to construct the final questionnaire survey. A total of 57 stakeholders in the Egyptian construction industry responded. Lastly, the relative importance index (RII) was calculated to rank the drivers, revealing the key drivers.

Findings

The results revealed that higher productivity, improving project quality control, shortening construction time, improving product quality and improving supervision and inspection are the top five drivers. On the contrary, government policies and regulations is the least significant driver.

Originality/value

This research contributes to the body of knowledge by introducing a comprehensive, up-to-date list of drivers, which helps the stakeholders gain a better understanding of the driving enablers of adopting OSC generally and helps Egyptian stakeholders make more informed decisions about its implementation specifically.