bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic regulation by TET1 in gene-environmental interactions influencing susceptibility to congenital malformations
Authors: van der Veer Bernard K. , Chen Lehua , Tsaniras Spyridon Champeris , Brangers Wannes , Chen Qiuying , Schroiff Mariana , Custers Colin , Kwak Harm H.M. , Khoueiry Rita , Cabrera Robert , Gross Steven S. , Finnell Richard H. , Lei Yunping , Koh Kian Peng
Published: February 2024

The etiology of neural tube defects (NTDs) involves complex gene-environmental interactions. Folic acid (FA) prevents NTDs, but the mechanisms remain poorly understood and at least 30% of human NTDs resist the beneficial effects of FA supplementation. Here, we identify the DNA demethylase TET1 as a nexus of folate-dependent one-carbon metabolism and genetic risk factors post-neural tube closure. We determine that cranial NTDs inTet1-/-embryos occur at two to three times higher penetrance in genetically heterogeneous than in homogeneous genetic backgrounds, suggesting a strong impact of genetic modifiers on phenotypic expression. Quantitative trait locus mapping identified a strong NTD risk locus in the 129S6 strain, which harbors missense and modifier variants at genes implicated in intracellular endocytic trafficking and developmental signaling. NTDs acrossTet1-/-strains are resistant to FA supplementation. However, both excess and depleted maternal FA diets modify the impact ofTet1loss on offspring DNA methylation primarily at neurodevelopmental loci. FA deficiency reveals susceptibility to NTD and other structural brain defects due to haploinsufficiency ofTet1. In contrast, excess FA inTet1-/-embryos drives promoter DNA hypermethylation and reduced expression of multiple membrane solute transporters, including a FA transporter, accompanied by loss of phospholipid metabolites. Overall, our study unravels interactions between modified maternal FA status,Tet1gene dosage and genetic backgrounds that impact neurotransmitter functions, cellular methylation and individual susceptibilities to congenital malformations, further implicating that epigenetic dysregulation may underlie NTDs resistant to FA supplementation.
Contracted Functional Connectivity Profiles in Autism
Authors: Weber Clara F. , Kebets Valeria , Benkarim Oualid , Lariviere Sara , Wang Yezhou , Ngo Alexander , Jiang Hongxiu , Chai Xiaoqian , Park Bo-yong , Milham Michael P. , Di Martino Adriana , Valk Sofie , Hong Seok-Jun , Bernhardt Boris C.
Published: February 2024

Objective

Autism spectrum disorder (ASD) is a pervasive neurodevelopmental condition that is associated with atypical brain network organization, with prior work suggesting differential connectivity alterations with respect to functional connection length. Here, we tested whether functional connectopathy in ASD specifically relates to disruptions in long-relative to short-range functional connectivity profiles. Our approach combined functional connectomics with geodesic distance mapping, and we studied associations to macroscale networks, microarchitectural patterns, as well as socio-demographic and clinical phenotypes.

Methods

We studied 211 males from three sites of the ABIDE-I dataset comprising 103 participants with an ASD diagnosis (mean±SD age=20.8±8.1 years) and 108 neurotypical controls (NT, 19.2±7.2 years). For each participant, we computed cortex-wide connectivity distance (CD) measures by combining geodesic distance mapping with resting-state functional connectivity profiling. We compared CD between ASD and NT participants using surface-based linear models, and studied associations with age, symptom severity, and intelligence scores. We contextualized CD alterations relative to canonical networks and explored spatial associations with functional and microstructural cortical gradients as well as cytoarchitectonic cortical types.

Results

Compared to NT, ASD participants presented with widespread reductions in CD, generally indicating shorter average connection length and thus suggesting reduced long-range connectivity but increased short-range connections. Peak reductions were localized in transmodal systems (i.e., heteromodal and paralimbic regions in the prefrontal, temporal, and parietal and temporo-parieto-occipital cortex), and effect sizes correlated with the sensory-transmodal gradient of brain function. ASD-related CD reductions appeared consistent across inter-individual differences in age and symptom severity, and we observed a positive correlation of CD to IQ scores.

Conclusions

Our study showed reductions in CD as a relatively stable imaging phenotype of ASD that preferentially impacted paralimbic and heteromodal association systems. CD reductions in ASD corroborate previous reports of ASD-related imbalance between short-range overconnectivity and long-range underconnectivity.
Super-resolution expansion microscopy in plant roots
Authors: Gallei Michelle , Truckenbrodt Sven , Kreuzinger Caroline , Inumella Syamala , Vistunou Vitali , Sommer Christoph , Tavakoli Mojtaba R. , Agudelo-Dueñas Nathalie , Vorlaufer Jakob , Jahr Wiebke , Randuch Marek , Johnson Alexander , Benková Eva , Friml Jiří , Danzl Johann G.
Published: February 2024

Super-resolution methods enable spatial resolution far better than the optical diffraction limit of about half the wavelength of light (∼200-300 nm) but have yet to attain widespread use in plants, owing in large part to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing physical distances between sample structures while preserving relative spatial arrangements, and clears the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy ofArabidopsis thalianaroot tissues (PlantEx), achieving 4-fold resolution increase over conventional microscopy, highlighting microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. By combining PlantEx with STED microscopy, we increase nanoscale resolution further and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into cellular structural context.
MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies
Authors: Martínez-Redondo Gemma I. , Vargas-Chávez Carlos , Eleftheriadi Klara , Benítez-Álvarez Lisandra , Vázquez-Valls Marçal , Fernández Rosa
Published: February 2024

Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (1) we include data from all animal phyla where public data is available, (2) we provide gene annotations extracted from the original GFF genome files using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.
The modification landscape ofP. aeruginosatRNAs
Authors: Mandler Mariana D. , Maligireddy Siddhardha S. , Guiblet Wilfried M. , Fitzsimmons Christina M. , McDonald Kayla S. , Warrell Delayna L. , Batista Pedro J.
Published: February 2024

RNA modifications have a substantial impact on tRNA function, with modifications in the anticodon loop contributing to translational fidelity and modifications in the tRNA core impacting structural stability. In bacteria, tRNA modifications are crucial for responding to stress and regulating the expression of virulence factors. Although tRNA modifications are well-characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such asPseudomonas aeruginosa, remains limited. Here we leveraged two orthogonal approaches to build a reference landscape of tRNA modifications inE. coli, which enabled us to identify similar modifications inP. aeruginosa. Our analysis revealed a substantial degree of conservation between the two organisms, while also uncovering potential sites of tRNA modification in P. aeruginosa tRNAs that are not present inE. coli. The mutational signature at one of these sites, position 46 of tRNAGln1(UUG)is dependent on theP. aeruginosahomolog of TapT, the enzyme responsible for the 3-(3-amino-3-carboxypropyl) uridine (acp3U) modification. Identifying which modifications are present on different tRNAs will uncover the pathways impacted by the different tRNA modifying enzymes, some of which play roles in determining virulence and pathogenicity.
Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data
Authors: Marot-Lassauzaie Valérie , Beneyto-Calabuig Sergi , Obermayer Benedikt , Velten Lars , Beule Dieter , Haghverdi Laleh
Published: February 2024

Single cell RNA sequencing (scRNA-seq) data is widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it can be difficult to fully separate these two populations based on transcriptomics alone. If available, somatic single nucleotide variants (SNVs) observed in the scRNA-seq data could be used to identify the cancer population. However, calling somatic SNVs in scRNA-seq data is a challenging task, as most variants seen in the short read data are not somatic, but can instead be germline variants, RNA edits or transcription, sequencing or processing errors. Additionally, only variants present in actively transcribed regions for each individual cell will be seen in the data. To address these challenges, we develop CCLONE (Cancer Cell Labelling On Noisy Expression), an interpretable tool adapted to handle the uncertainty and sparsity of SNVs called from scRNA-seq data. CCLONE jointly identifies cancer clonal populations, and their associated variants. We apply CCLONE on two acute myeloid leukaemia datasets and one lung adenocarcinoma dataset and show that CCLONE captures both genetic clones and somatic events for multiple patients. These results show how CCLONE can be used to gather insight into the course of the disease and the origin of cancer cells in scRNA-seq data.
Emerin deficiency drives MCF7 cells to an invasive phenotype
Authors: Hansen Emily , Rolling Christal , Wang Matthew , Holaska James M.
Published: February 2024

During metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer cells showed similar results. Supporting the clinical relevance of emerin reduction in cancer progression, our analysis of 192 breast cancer patient samples showed emerin expression inversely correlates with cancer invasiveness. We conclude emerin loss is an important driver of invasive transformation and has utility as a biomarker for tumor progression.
Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH
Authors: Troyer Zach , Gololobova Olesia , Koppula Aakash , Liao Zhaohao , Horns Felix , Elowitz Michael B , Tosar Juan Pablo , Batish Mona , Witwer Kenneth W.
Published: February 2024

Interest in using nanoparticles for delivery of therapeutic RNA has been steadily growing, provoking a need to precisely understand their structure and contents. Single-particle and single-molecule analysis techniques provide snapshots of single biological nanoparticles, including viruses, liposomes, and extracellular vesicles (EVs). While existing methods primarily focus on protein detection, RNA delivery is becoming increasingly prevalent. A method to simultaneously detect protein and internal RNA in the same particle would reveal variability in size, structure, and RNA packaging efficiency, enabling optimization of nanoparticle delivery. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor (SP-IRIS) with single-molecule fluorescence in-situ hybridization (smFISH). Using SPIRFISH, we detect HIV-1 envelope protein and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNA within EVs. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles.

Teaser:A new single particle analysis technique simultaneously detects specific RNA and protein in biological nanoparticles.
ConcurrentAscarisinfection modulates host immunity resulting in impaired control ofSalmonellainfection in pigs
Authors: Midha Ankur , Oser Larissa , Schlosser-Brandenburg Josephine , Laubschat Alexandra , Mugo Robert M. , Musimbi Zaneta D. , Höfler Philipp , Kundik Arkadi , Hayani Rima , Adjah Joshua , Groenhagen Saskia , Tieke Malte , Elizalde-Velázquez Luis E. , Kühl Anja A. , Klopfleisch Robert , Tedin Karsten , Rausch Sebastian , Hartmann Susanne
Published: February 2024

Ascarisis one of the most widespread helminth infections of humans and pigs, leading to chronic morbidity in humans and considerable economic losses in pig farming. Additionally, pigs are an important reservoir for the zoonotic bacterial pathogenSalmonella,where pigs can serve as asymptomatic carriers. Here, we investigated the impact of an ongoingAscarisinfection on the immune response toSalmonellain pigs. We observed higher bacterial burdens in experimentally coinfected pigs compared to pigs infected withSalmonellaalone.Ascaris-infected pigs exhibited numerous hallmarks of a type 2 immune response in organs impacted by larval migration, including increased Th2 cells, increased IL-4 production, eosinophilia, and increased expression of CD206, a marker for alternatively activated macrophages. While we observed only mild changes in frequencies of CD4+Treg,Ascaris-infected pigs had increased frequencies of CD8α+Treg. We show that type 2 immune signals enhance susceptibility of macrophages toSalmonellainfectionin vitro. Furthermore,AscarisimpairedSalmonella-induced monocytosis and TNF-α production by myeloid cells. Hence, our data demonstrate widespread immunomodulation during an acuteAscarisinfection that facilitates the microbial spread into gut-associated lymphoid tissue in aSalmonellacoinfection.

Importance

In experimentally infected pigs we show that an ongoing infection with the parasitic wormAscaris suummodulates host immunity to render pigs more susceptible to invadingSalmonella.Both infections are widespread in pig production and the prevalence ofSalmonellais high in endemic regions of human Ascariasis, indicating that this is a clinically meaningful coinfection. We observed a type 2 immune response to be induced during anAscarisinfection correlating with an increased susceptibility of pigs to the concurrent bacterial infection.
Differential functions of the dorsal and intermediate regions of the hippocampus for optimal goal-directed navigation in VR space
Authors: Hwang Hyeri , Jin Seung-Woo , Lee Inah
Published: February 2024

Goal-directed navigation requires the hippocampus to process spatial information in a value-dependent manner, but its underlying mechanism needs to be better understood. Here, we investigated whether the dorsal (dHP) and intermediate (iHP) regions of the hippocampus differentially function in processing place and its associated value information. Rats were trained in a place-preference task involving reward zones with different values in a visually rich VR environment where two-dimensional navigation was possible. Rats learned to use distal visual scenes effectively to navigate to the reward zone associated with a higher reward. Inactivation of both dHP and iHP with muscimol altered the efficiency and precision of wayfinding behavior, but iHP inactivation induced more severe damage, including impaired place preference. Our findings suggest that the iHP is more critical for value-dependent navigation toward higher-value goal locations.
Changes in bird migration phenology over six decades, a perspective from the Neotropical non-breeding grounds
Authors: Gutiérrez-Carrillo Daniel A. , Mateus-Aguilar Bryam , Gómez Camila , Cadena Carlos Daniel
Published: February 2024

Changes in the migration phenology of birds linked to global change are extensively documented. Longitudinal studies from temperate breeding grounds have mostly shown earlier arrivals in the spring and a variety of patterns during fall migration1,2, yet no studies have addressed whether and how migration phenology has changed using data from the tropical non-breeding grounds. Understanding whether changes in migratory phenology are also evident in non-breeding sites is essential to determine the underlying causes of patterns documented in breeding areas. Using data from historical scientific collections and modern repositories of community-science records, we assessed changes in migration phenology of 12 Nearctic-Neotropical long-distance migratory birds in Colombia over six decades. We also explored whether shared breeding and non-breeding climatic niches explained variation in phenological patterns observed among species. All species showed shifts in spring (range −37 – 9 days from peak passage date) or fall (range −26 – 36 days) migration, but patterns differed among species in ways partly attributable to shared breeding or wintering climatic niches. Our results, although not yet broadly generalizable, suggest that birds use cues to time their migration at their non-breeding grounds which are most likely different to those they use on their breeding grounds. To better understand the effects of global change on biodiversity, exploring the underlying drivers of phenological changes with further research integrating more long-term datasets available through scientific collections and community science platforms should be a priority.
The GPI sidechain ofToxoplasma gondiiprevents parasite pathogenesis
Authors: Alvarez Julia A , Gas-Pascual Elisabet , Malhi Sahil , Njume Ferdinand Ngale , Sánchez-Arcila Juan C , van der Wel Hanke , Zhao Yanlin , Ceron Gabriella , Posada Jasmine , Souza Scott P , Yap George S , West Christopher M , Jensen Kirk D C
Published: February 2024

Glycosylphosphatidylinositols (GPIs) are highly conserved anchors for eukaryotic cell surface proteins. The apicomplexan parasite,Toxoplasma gondii, is a widespread intracellular parasite of warm-blooded animals whose plasma membrane is covered with GPI-anchored proteins, and free GPIs called GIPLs. While the glycan portion is conserved, species differ in sidechains added to the triple mannose core. The functional significance of the Glcα1,4GalNAcβ1-sidechain reported inToxoplasma gondiihas remained largely unknown without an understanding of its biosynthesis. Here we identify and disrupt two glycosyltransferase genes and confirm their respective roles by serology and mass spectrometry. Parasites lacking the sidechain on account of deletion of the first glycosyltransferase, PIGJ, exhibit increased virulence during primary and secondary infections, suggesting it is an important pathogenesis factor. Cytokine responses, antibody recognition of GPI-anchored SAGs, and complement binding to PIGJ mutants are intact. In contrast, the scavenger receptor CD36 shows enhanced binding to PIGJ mutants, potentially explaining a subtle tropism for macrophages detected early in infection. Galectin-3, which bind GIPLs, exhibits a slight enhancement of binding to PIGJ mutants, and the protection of galectin-3 knockout mice from lethality suggests thatΔpigjparasite virulence in this context is sidechain dependent. Parasite numbers are not affected byΔpigjearly in the infection in wildtype mice, suggesting a breakdown of tolerance. However, increased tissue cysts in the brains of mice infected withΔpigjparasites indicate an advantage over wildtype strains. Thus, the GPI sidechain ofT. gondiiplays a crucial and diverse role in regulating disease outcome in the infected host.

The functional significance of sidechain modifications to the GPI anchor is yet to be determined because the glycosyltransferases responsible for these modifications have not been identified. Here we present identification and characterization of bothT.gondiiGPI sidechain-modifying glycosyltransferases. Removal of the glycosyltransferase that adds the first GalNAc to the sidechain results in parasites without a sidechain on the GPI, and increased parasite virulence. Loss of the second glycosyltransferase results in a sidechain with GalNAc alone, and no glucose added, and has negligible effect on parasite virulence. This indicates GPI sidechains as fundamental to host-parasite interactions.
Symplasmic phloem loading and subcellular transport in storage roots are key factors for carbon allocation in cassava
Authors: Rüscher David , Vasina Viktoriya V. , Knoblauch Jan , Bellin Leo , Pommerrenig Benjamin , Alseekh Saleh , Fernie Alisdair R. , Neuhaus H. Ekkehard , Knoblauch Michael , Sonnewald Uwe , Zierer Wolfgang
Published: February 2024

Cassava is a deciduous woody perennial shrub that stores large amounts of carbon and water in its storage roots. Previous studies have shown that assimilate unloading into storage roots happens symplasmically once secondary anatomy is established. However, mechanisms controlling phloem loading and overall carbon partitioning to different cassava tissues remain unclear. Here we used a combination of histological, transcriptional, and biochemical analyses on different cassava tissues and timepoints to better understand source-sink carbon allocation. We find that cassava likely utilizes a predominantly passive symplasmic phloem loading strategy, indicated by the lack of expression of genes coding for key players of sucrose transport, the existence of branched plasmodesmata in the companion cell/bundle sheath interface of minor leaf veins, and very high leaf sucrose concentrations. Furthermore, we show that tissue-specific changes in anatomy and NSC contents are associated with tissue-specific modification in gene expression for sucrose cleavage/synthesis, as well as subcellular compartmentalization of sugars. Overall, our data suggest that carbon allocation during storage root filling is mostly facilitated symplasmically, and is likely mostly regulated by local tissue demand and subcellular compartmentalization.
Mutational Analysis of an Antimalarial Drug TargetPfATP4
Authors: Rachuri Swaksha , Nepal Binod , Shukla Anurag , Ramanathan Aarti , Morrisey Joanne M. , Daly Thomas , Mather Michael W. , Bergman Lawrence W. , Kortagere Sandhya , Vaidya Akhil B.
Published: February 2024

Among new antimalarials discovered over the past decade are multiple chemical scaffolds that targetPlasmodium falciparumP-type ATPase (PfATP4). This essential protein is a Na+pump responsible for the maintenance of Na+homeostasis.PfATP4 belongs to the type 2D subfamily of P-type ATPases, for which no structures have been determined. To gain better insight into the structure/function relationship of this validated drug target, we generated a homology model ofPfATP4 based on SERCA, a P2A-type ATPase, and refined the model using molecular dynamics in its explicit membrane environment. This model predicted several residues inPfATP4 critical for its function, as well as those that impart resistance to variousPfATP4 inhibitors. To validate our model, we developed a genetic system involving merodiploid states ofPfATP4 in which the endogenous gene was conditionally expressed, and the second allele was mutated to assess its effect on the parasite. Our model predicted residues involved in Na+coordination as well as the phosphorylation cycle ofPfATP4. Phenotypic characterization of these mutants involved assessment of parasite growth, localization of mutatedPfATP4, response to treatment with knownPfATP4 inhibitors, and evaluation of the downstream consequences of Na+influx. Our results were consistent with modeled predictions of the essentiality of the critical residues. Additionally, our approach confirmed the phenotypic consequences of resistance-associated mutations as well as a potential structural basis for the fitness cost associated with some mutations. Taken together, our approach provides a means to explore the structure/function relationship of essential genes in haploid organisms.

Significance Statement

Plasmodium falciparumATP4 (PfATP4) is a Na+efflux pump and represents an important target for antimalarial drugs with nanomolar potency. However, the structure ofPfATP4 is unknown, prompting the development of new methodologies to investigate the structure/function relationship. Here, we introduce a dynamic homology modeling approach to (a) identify key residues essential forPfATP4 function and (b) provide a structural basis to understand resistance-associated mutations. To validate these predictions, we developed a genetic system to manipulate the PfATP4 gene to assess the phenotypic consequences of such changes. Our results support the utility of combining homology modeling and genetics to gain functional insights into an antimalarial drug target.
Mutations iniclRincrease evolvability by facilitating compensation that exposes cryptic beneficial mutations in experimental populations ofEscherichia coli
Authors: Staples Rachel K , Cooper Tim F.
Published: February 2024

Evolvability describes the potential of a population to generate beneficial variation. Several mechanisms that increase evolvability have been demonstrated, including the action of systems that reveal accumulated beneficial variants following an environmental shift. We examine the basis of an increase in the evolvability ofEscherichia colilines that were first selected in an environment supplemented with glucose as sole carbon source and then transferred to an otherwise identical lactose supplemented environment. These lines increased in fitness significantly more quickly in the lactose environment, and reached a higher final fitness, than did naïve ancestral lines. In four of six lines this increased evolvability can be explained by mutations iniclRthat were selected in glucose but were significantly deleterious in lactose, masking the effect of other generally beneficial mutations. Secondary mutations that compensated for this cost resulted in large fitness increases. We did not detect any consistent genetic signature associated with the compensation, suggesting that different pathways were responsible and, therefore, that it can occur at a relatively high rate. That mutations selected in one environment will become deleterious following an environmental shift, so that compensation provides potential for a large subsequent fitness increase represents a potentially common and general mechanism of evolvability in changing environments.
Development of novel tools for dissection of central versus peripheral dopamine D2-like receptor signaling in dysglycemia
Authors: Bonifazi Alessandro , Ellenberger Michael , Farino Zachary J. , Aslanoglou Despoina , Rais Rana , Pereira Sandra , Mantilla-Rivas José O. , Boateng Comfort A. , Eshleman Amy J. , Janowsky Aaron , Hahn Margaret K. , Schwartz Gary J. , Slusher Barbara S. , Newman Amy Hauck , Freyberg Zachary
Published: February 2024

Dopamine (DA) D2-like receptors in both the central nervous system (CNS) and the periphery are key modulators of metabolism. Moreover, disruption of D2-like receptor signaling is implicated in dysglycemia. Yet, the respective metabolic contributions of CNS versus peripheral D2-like receptors including D2(D2R) and D3(D3R) receptors remain poorly understood. To address this, we developed new pharmacological tools, D2-like receptor agonists with diminished and delayed blood-brain barrier capability, to selectively manipulate D2R/D3R signaling in the periphery. We designated bromocriptine methiodide (BrMeI), a quaternary methiodide analogue of D2/3R agonist and diabetes drug bromocriptine, as our lead compound based on preservation of D2R/D3R binding and functional efficacy. We then used BrMeI and unmodified bromocriptine to dissect relative contributions of CNS versus peripheral D2R/D3R signaling in treating dysglycemia. Systemic administration of bromocriptine, with unrestricted access to CNS and peripheral targets, significantly improved both insulin sensitivity and glucose tolerance in obese, dysglycemic micein vivo. In contrast, metabolic improvements were attenuated when access to bromocriptine was restricted either to the CNS through intracerebroventricular administration or delayed access to the CNS via BrMeI. Our findings demonstrate that the coordinated actions of both CNS and peripheral D2-like receptors are required for correcting dysglycemia. Ultimately, the development of a first-generation of drugs designed to selectively target the periphery provides a blueprint for dissecting mechanisms of central versus peripheral DA signaling and paves the way for novel strategies to treat dysglycemia.
A doubly stochastic renewal framework for partitioning spiking variability
Authors: Aghamohammadi Cina , Chandrasekaran Chandramouli , Engel Tatiana A.
Published: February 2024

The firing rate is a prevalent concept used to describe neural computations, but estimating dynamically changing firing rates from irregular spikes is challenging. An inhomogeneous Poisson process, the standard model for partitioning firing rate and spiking irregularity, cannot account for diverse spike statistics observed across neurons. We introduce a doubly stochastic renewal point process, a flexible mathematical framework for partitioning spiking variability, which captures the broad spectrum of spiking irregularity from periodic to super-Poisson. We validate our partitioning framework using intracellular voltage recordings and develop a method for estimating spiking irregularity from data. We find that the spiking irregularity of cortical neurons decreases from sensory to association areas and is nearly constant for each neuron under many conditions but can also change across task epochs. A spiking network model shows that spiking irregularity depends on connectivity and can change with external input. These results help improve the precision of estimating firing rates on single trials and constrain mechanistic models of neural circuits.
A site-wise reliability analysis of the ABCD diffusion fractional anisotropy and cortical thickness: impact of scanner platforms
Authors: Pan Yezhi , Hong L. Elliot , Acheson Ashley , Thompson Paul M. , Jahanshad Neda , Zhu Alyssa H. , Yu Jiaao , Chen Chixiang , Ma Tianzhou , Liu Ho-Ling , Veraart Jelle , Fieremans Els , Karcher Nicole R. , Kochunov Peter , Chen Shuo
Published: February 2024

The Adolescent Brain and Cognitive Development (ABCD) project is the largest study of adolescent brain development. ABCD longitudinally tracks 11,868 participants aged 9-10 years from 21 sites using standardized protocols for multi-site MRI data collection and analysis. While the multi-site and multi-scanner study design enhances the robustness and generalizability of analysis results, it may also introduce non-biological variances including scanner-related variations, subject motion, and deviations from protocols. ABCD imaging data were collected biennially within a period of ongoing maturation in cortical thickness and integrity of cerebral white matter. These changes can bias the classical test-retest methodologies, such as intraclass correlation coefficients (ICC). We developed a site-wise adaptive ICC (AICC) to evaluate the reliability of imaging-derived phenotypes while accounting for ongoing brain development. AICC iteratively estimates the population-level age-related brain development trajectory using a weighted mixed model and updates age-corrected site-wise reliability until convergence. We evaluated the test-retest reliability of regional fractional anisotropy (FA) measures from diffusion tensor imaging and cortical thickness (CT) from structural MRI data for each site. The mean AICC for 20 FA tracts across sites was 0.61±0.19, lower than the mean AICC for CT in 34 regions across sites, 0.76±0.12. Remarkably, sites using Siemens scanners consistently showed significantly higher AICC values compared to those using GE/Philips scanners for both FA (AICC=0.71±0.12 vs 0.46±0.17, p<0.001) and CT (AICC=0.80±0.10 vs 0.69±0.11, p<0.001). These findings demonstrate site-and-scanner related variations in data quality and underscore the necessity for meticulous data curation in subsequent association analyses.
Metabolic Quadrivalency in RSeT Human Embryonic Stem Cells
Authors: Chen Kevin G. , Park Kyeyoon , Maric Dragan , Johnson Kory R. , Robey Pamela G. , Mallon Barbara S.
Published: February 2024

One of the most important properties of human embryonic stem cells (hESCs) is related to their pluripotent states. In our recent study, we identified a previously unrecognized pluripotent state induced by RSeT medium. This state makes primed hESCs resistant to conversion to naïve pluripotent state. In this study, we have further characterized the metabolic features in these RSeT hESCs, including metabolic gene expression, metabolomic analysis, and various functional assays. The commonly reported metabolic modes include glycolysis or both glycolysis and oxidative phosphorylation (i.e., metabolic bivalency) in pluripotent stem cells. However, besides the presence of metabolic bivalency, RSeT hESCs exhibited a unique metabolome with additional fatty acid oxidation and imbalanced nucleotide metabolism. This metabolic quadrivalency is linked to hESC growth independent of oxygen tension and restricted capacity for naïve reprogramming in these cells. Thus, this study provides new insights into pluripotent state transitions and metabolic stress-associated hPSC growthin vitro.
Single-molecule Mapping of Amyloid-β Oligomer Insertion into Lipid Bilayers
Authors: Dey Arpan , Patil Abhsihek , Arumugam Senthil , Maiti Sudipta
Published: February 2024

The interaction of disease-causing amyloid oligomers with lipid membranes is implicated in their toxicity. However, understanding the membrane interaction of different oligomers, and each constituent monomer in a given oligomer, has remained a challenge. Here we employed a recently developed single-molecule technique, called QSLIP, which can simultaneously determine the stoichiometry and membrane location of individual fluorescent labels on oligomeric membrane proteins. Using QSLIP, we measured the membrane insertion of small amyloid-beta (Aβ) oligomers of three different isoforms at the single-molecule level, and found that their toxicity is correlated with the depth of penetration of their amino-terminal into the bilayer. Such single-molecule maps provide a detailed assay for measuring the effect of any drug candidate on oligomer-membrane interactions.
Incomplete remyelination via endogenous or therapeutically enhanced oligodendrogenesis is sufficient to recover visual cortical function
Authors: Nunes Gustavo Della-Flora , Osso Lindsay A , Haynes Johana A , Morris Amanda , Conant Lauren , Stockton Michael E , Thornton Michael A , Vivian Jeffrey A , Gandhi Rohan , Denman Daniel J , Hughes Ethan G
Published: February 2024

Myelin loss induces deficits in action potential propagation that result in neural dysfunction and contribute to the pathophysiology of neurodegenerative diseases, injury conditions, and aging. Because remyelination is often incomplete, better understanding endogenous remyelination and developing remyelination therapies that seek to restore neural function are clinical imperatives. Here, we usedin vivotwo-photon microscopy and electrophysiology to study the dynamics of endogenous and therapeutic-induced cortical remyelination and functional recovery after cuprizone-mediated demyelination in mice. We focused on the visual pathway, which is uniquely positioned to provide insights into structure-function relationships during de/remyelination. We show that endogenous remyelination is driven by recent oligodendrocyte loss and is highly efficacious following mild demyelination, but fails to restore the oligodendrocyte population when high rates of oligodendrocyte loss occur too quickly. Testing a novel thyromimetic compared to clemastine fumarate, we find it better enhances oligodendrocyte gain during remyelination and hastens recovery of neuronal function. Surprisingly, its therapeutic benefit was temporally restricted, and it acted exclusively following moderate to severe demyelination to eliminate endogenous remyelination deficits. However, complete remyelination is unnecessary as partial oligodendrocyte restoration was sufficient to recover visual neuronal function. These findings advance our understanding of remyelination and its impact on functional recovery to inform future therapeutic strategies.
Salivary metabolomics in the family environment: A large-scale study investigating oral metabolomes in children and their parental caregivers
Authors: Rothman Jason A. , Piccerillo Hillary L. , Riis Jenna L. , Granger Douglas A. , Thomas Elizabeth A. , Whiteson Katrine L.
Published: February 2024

Human metabolism is complex and dynamic, and is impacted by genetics, diet, health, and countless inputs from the environment. Beyond the genetics shared by family members, cohabitation leads to shared microbial and environmental exposures. Furthermore, metabolism is affected by factors such as inflammation, environmental tobacco smoke (ETS) exposure, metabolic regulation, and exposure to heavy metals.

Metabolomics represents a useful analytical method to assay the metabolism of individuals to find potential biomarkers for metabolic conditions that may not be phenotypically obvious or represent unknown physiological processes. As such, we applied untargeted LC-MS metabolomics to archived saliva samples from a racially diverse group of elementary school-aged children and their caregivers collected during the “90-month” assessment of the Family Life Project. We assayed a total of 1,425 saliva samples of which 1,344 were paired into 672 caregiver/child dyads. We compared the metabolomes of children (N = 719) and caregivers (N = 706) within and between homes, performed population-wide “metabotype” analyses, and measured associations between metabolites and salivary biomeasures of inflammation, antioxidant potential, ETS exposure, metabolic regulation, and heavy metals.

Dyadic analyses revealed that children and their caregivers have largely similar salivary metabolomes. Although there were differences between the dyads at the individual levels of analysis, dyad explained most (62%) of the metabolome variation. At a population level of analysis, our data clustered into two large groups, indicating that people likely share most of their metabolomes, but that there are distinct “metabotypes” across large sample sets. Lastly, individual differences in several metabolites – which were putative oxidative damage-associated or pathological markers – were significantly correlated with salivary measures indexing inflammation, antioxidant potential, ETS exposure, metabolic regulation, and heavy metals. Implications of the effects of family environment on metabolomic variation at the population, dyadic, and individual levels of analyses for health and human development are discussed.
Improving 3D-CINE tTV-regularized whole-heart MRI reconstruction
Authors: Milani Bastien , Roy Christopher , Ledoux Jean-Baptiste , Rotzinger David C. , Masi Ambra , Troxler Renaud , Si-mohamed Salim , Yerly Jerome , Romanin Ludovica , Rutz Tobias , Tenisch Estelle , Prsa Milan , Schwitter Juerg , Stuber Matthias
Published: February 2024

Purpose

To improve the image quality of 3D radial free-running MRI data of the heart through a deliberate and stepwise extension of the XD-GRASP reconstruction.

Methods

Ferumoxytol-enhanced cardiac free-running 3D-radial data were reconstructed using an XD-GRASP reconstruction improved by 4 new developments: motion-compensated temporal-Total-Variation (MC-tTV) regularization for 3D images, a new coil-sensitivity, a new k-space density compensation and a revisited conjugate-gradient-descent (with exact line search) for solving the least-square sub-problem of ADMM. The resulting images were compared quantitatively and qualitatively to reconstructions lacking some of the newly implemented measures. Also, the measurement of ejection-fraction by a threshold-based method on the new reconstruction was compared to a reference standard.

Results

The new reconstruction significantly increased the sharpness of the right coronary artery (4% to 6%, p < 0.05) and the left anterior descending coronary artery (4% to 5% p < 0.05). It also increased blood-myocardium interface sharpness (between 20% and 25%, p < 0.05) and decreases spatial-Total-Variation in the blood-pool (13%, p < 0.05). The qualitative evaluation suggests better anatomical depiction of small structures using the new reconstruction. As compared to a reference standard method, ejection fraction could also be correctly evaluated.

Conclusion

Compressed sensing image reconstruction for 3D-radial free-running cardiac acquisition was successfully improved by including MC-tTV regularization, a new density compensation, a new coil-sensitivity and a revisited conjugate-gradient-descent with exact line search. Quantitative and qualitative quality metrics demonstrated significant improvement in image quality when using the new reconstruction, while extracted dynamic information compared favorably with the gold standard.
Perceptions of barriers and facilitators for cervical cancer screening from women and healthcare workers in Ghana: Applying the Dynamic Sustainability Framework
Authors: Boamah Mensah Adwoa Bemah , Konney Thomas Okpoti , Adankwah Ernest , Amuasi John , Nones Madalyn , Okyere Joshua , Boadu Kwame Ofori , Efua Eduah Felicia Maame , Xiong Serena , Moon J. Robin , Virnig Beth , Kulasingam Shalini
Published: February 2024

Cervical cancer screening has reduced cervical cancer-related mortality by over 70% in countries that have achieved high coverage. However, there are significant geographic disparities in access to screening. In Ghana, although cervical cancer is the second most common cancer in women, there is no national-level cervical cancer screening program, and only 2 to 4% of eligible Ghanaian women have ever been screened for cervical cancer. This study used an exploratory, sequential mixed-methods approach to examine barriers and facilitators to cervical cancer screening from women and healthcare workers perspectives, guided by the Dynamic Sustainability Framework. Two convenience samples of 215 women and 17 healthcare personnel were recruited for this study. All participants were from one of three selected clinics (Ejisu Government Hospital, Kumasi South Hospital, and the Suntreso Government Hospital) in the Ashanti region of Ghana. Descriptive analyses were used to group the data by practice setting and ecological system. Statistical differences in means and proportions were used to evaluate women’s barriers to cervical cancer screening. Quantitative findings from the women’s survey informed qualitative, in-depth interviews with the healthcare workers and analyzed using an inductive thematic analysis. The median age of women and healthcare workers was 37.0 years and 38.0 years respectively. Most women (n=194, 90.2%) reported never having been screened. Women who had not been screened were more likely to have no college or university education. Ecologic factors identified were lack of knowledge about available services, distance to a clinic and requiring a spouse’s permission prior to scheduling. Practice setting barriers included long clinic wait times and culturally sensitive issue. The quantitative and qualitative data were integrated in the data collection stage, results, and subsequent discussion. These findings highlight the need for non-clinician-based culturally sensitive tool options for screening such as self-collected HPV tests to increase screening participation in Ghana.
Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population
Authors: Zhang Mingxia , Han Xu , Wang Hui , Sun Junsheng , Guo Baojin , Gao Minggang , Xu Huiyan , Zhang Guizhi , Li Hongna , Cao Xiaofeng , Li Nannan , Xu Yiru , Wu Qun , Wang Chunyang , Zhang Guohua , Yuan Yapei , Man Junxia , Pu Yanyan , Lv Guangde , Qu Chunyan , Sun Jinjie , Cheng Xiyong , Dong Xinjuan , Kong Fanmei , Zhao Yan , An Yanrong , Yuan Yuanyuan , Guo Ying , Li Sishen
Published: February 2024

In wheat (Triticum aestivumL.), yield component traits (YCTs) are the most important yield traits. Only several genes for YCTs have been originally cloned. The efficient cloning of genes for YCTs directly from wheat remains a challenge. Here, we proposed a strategy for cloning genes from quantitative trait loci (QTLs) by sequencing of recombinant inbred lines (RILs) (QTL-Seq-RIL). Using the ‘TN18 × LM6’ RIL population as an example, we identified 138 candidate unigenes (CUGs) for YCTs from 77 stable QTLs. The average of CUGs per QTL was 1.8, which enabled us to confirm the CUGs directly. We have confirmed seven CUGs,TaIFABPL, TaDdRp, TaRLK, TaTD, TaTFC3, TaKMTandTaSPL17, via the CRISPR/Cas9 system. Of these, six genes were found firstly to regulate YCTs in crops except forTaSPL17. Five CUGs (includeTaSPL17) for which orthologous genes have been cloned previously with the same or similar agronomic functions. It is to say, 11 CUGs were preliminarily validated using a single RIL population. QTL-Seq-RIL provides an efficient method for rapid gene cloning using existing RIL populations.