Discrete Pathways Research Articles

Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling

Abstract A majority of human genes produce non-protein-coding RNA (ncRNA), and some have roles in development and disease. Neither ncRNA nor human skeletal muscle is ideally studied using short-read sequencing, so we used a customised RNA pipeline and network modelling to study cell-type specific ncRNA responses during muscle growth at scale. We completed five human resistance-training studies (n = 144 subjects), identifying 61% who successfully accrued muscle-mass. We produced 288 transcriptome-wide profiles and found 110 ncRNAs linked to muscle growth in vivo, while a transcriptome-driven network model demonstrated interactions via a number of discrete functional pathways and single-cell types. This analysis included established hypertrophy-related ncRNAs, including CYTOR – which was leukocyte-associated (FDR = 4.9×10−7). Novel hypertrophy-linked ncRNAs included PPP1CB-DT (myofibril assembly genes, FDR = 8.15×10−8), and EEF1A1P24 and TMSB4XP8 (vascular remodelling and angiogenesis genes, FDR = 2.77×10−5). We also discovered that hypertrophy lncRNA MYREM shows a specific myonuclear expression pattern in vivo. Our multi-layered analyses established that single-cell-associated ncRNA are identifiable from bulk muscle transcriptomic data and that hypertrophy-linked ncRNA genes mediate their association with muscle growth via multiple cell types and a set of interacting pathways.

Revitalizing the heart: cutting-edge nucleic acid therapies in cardiac regeneration

Heart failure (HF) arises from cardiac injury and subsequent loss of contractile cells. While some organisms can regenerate cardiac tissue through cardiomyocyte proliferation, the adult mammalian heart has limited regenerative capacity due to cardiomyocyte replication ceasing shortly after birth. To enhance proliferation in the adult heart, we aim to identify master regulators of proliferation. In Professor Mauro Giacca’s laboratory, human-specific microRNAs (miRNAs) like miR199a-3p or miR-1825 have been identified as potential enhancers of cardiomyocyte proliferation. My PhD will evaluate these miRNAs using different delivery methods, comparing viral vectors with lipid nanoparticle (SNALP) technology. Additionally, I will adapt CycleTrack, a tool for labelling mitotic cells, to study cardiomyocyte replication accurately in response to these miRNAs. By assessing these approaches in human myocardial slices, this work seeks to uncover the molecular mechanisms of pro-proliferative miRNAs and pave the way for future clinical interventions targeting heart regeneration. In this Student Focus article, I also highlight another aspect: the framework used to address complex biological questions is crucial in shaping the answers we seek. What intrigues me most about my research is the interplay between elucidating discrete molecular pathways and employing holistic approaches to understand cardiac proliferation.

Assembling bacterial puzzles: piecing together functions into microbial pathways.

Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in the KEGG database. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.

Periplasmic electron transfer network in Geobacter sulfurreducens revealed by biomolecular interaction studies

AbstractMultiheme cytochromes located in different compartments are crucial for extracellular electron transfer in the bacterium Geobacter sulfurreducens to drive important environmental processes and biotechnological applications. Recent studies have unveiled that for particular sets of electron terminal acceptors, discrete respiratory pathways selectively recruit specific cytochromes from both the inner and outer membranes. However, such specificity was not observed for the abundant periplasmic cytochromes, namely the triheme cytochrome family PpcA‐E. In this work, the distinctive NMR spectroscopic signatures of these proteins in different redox states were explored to monitor pairwise interactions and electron transfer reactions between each pair of cytochromes. The results showed that the five proteins interact transiently and can exchange electrons between each other revealing intra‐promiscuity within the members of this family. This discovery is discussed in the light of the establishment of an effective electron transfer network by this pool of cytochromes. This network is advantageous to the bacteria as it enables the maintenance of the functional working potential redox range within the cells.

TGF-β ligand cross-subfamily interactions in the response of Caenorhabditis elegans to a bacterial pathogen.

The Transforming Growth Factor beta (TGF-β) family consists of numerous secreted peptide growth factors that play significant roles in cell function, tissue patterning, and organismal homeostasis, including wound repair and immunity. Typically studied as homodimers, these ligands have the potential to diversify their functions through ligand interactions that may enhance, repress, or generate novel functions. In the nematode Caenorhabditis elegans, there are only five TGF-β ligands, providing an opportunity to dissect ligand interactions in fewer combinations than in vertebrates. As in vertebrates, these ligands can be divided into bone morphogenetic protein (BMP) and TGF-β/Activin subfamilies that predominantly signal through discrete signaling pathways. The BMP subfamily ligand DBL-1 has been well studied for its role in the innate immune response in C. elegans. Here we show that all five TGF-β ligands play a role in survival on bacterial pathogens. We also demonstrate that multiple TGF-β ligand pairs act nonredundantly as part of this response. We show that the two BMP-like ligands-DBL-1 and TIG-2 -function independently of each other in the immune response, while TIG2/BMP and the TGF-β/Activin-like ligand TIG-3 function together. Structural modeling supports the potential for TIG-2 and TIG-3 to form heterodimers. Additionally, we identify TIG-2 and TIG-3 as members of a rare subset of TGF-β ligands lacking the conserved cysteine responsible for disulfide linking mature dimers. Finally, we show that canonical DBL1/BMP receptor and Smad signal transducers function in the response to bacterial pathogens, while components of the DAF7 TGF-β/Activin signaling pathway do not play a major role in survival. These results demonstrate a novel potential for BMP and TGF-β/Activin subfamily ligands to interact and may provide a mechanism for distinguishing the developmental and homeostatic functions of these ligands from an acute response such as the innate immune response to bacterial pathogens.

Interictal discharge traveling waves recorded from stereoelectroencephalography electrodes.

Interictal epileptiform discharges (IEDs) are intermittent high-amplitude electrical signals that occur between seizures. They have been shown to propagate through the brain as traveling waves when recorded with epicortical grid-type electrodes and small penetrating microelectrode arrays. However, little work has been done to translate experimental IED analyses to more clinically relevant platforms such as stereoelectroencephalography (SEEG). In this pilot study, the authors aimed to define a computational method to identify and characterize IEDs recorded from clinical SEEG electrodes and leverage the directionality of IED traveling waves to localize the seizure onset zone (SOZ). Continuous SEEG recordings from 15 patients with medically refractory epilepsy were collected, and IEDs were detected by identifying overlapping peaks of a minimum prominence. IED pathways of propagation were defined and compared to the SOZ location determined by a clinical neurologist based on the ictal recordings. For further analysis of the IED pathways of propagation, IED detections were divided into triplets, defined as a set of 3 consecutive contacts within the same IED detection. Univariate and multivariate linear regression models were employed to associate IED characteristics with colocalization to the SOZ. A median (range) of 22.6 (4.4-183.9) IEDs were detected per hour from 15 patients over a mean of 23.2 hours of recording. Depending on the definition of the SOZ, a median (range) of 20.8% (0.0%-54.5%) to 62.1% (19.2%-99.4%) of IEDs per patient traversed the SOZ. IEDs passing through the SOZ followed discrete pathways that had little overlap with those of the IEDs passing outside the SOZ. Contact triplets that occurred more than once were significantly more likely to be detected in an IED passing through the SOZ (p < 0.001). Per our multivariate model, patients with a greater proportion of IED traveling waves had a significantly greater proportion of IEDs that localized to the SOZ (β = 0.64, 95% CI 0.01-1.27, p = 0.045). By using computational methods, IEDs can be meaningfully detected from clinical-grade SEEG recordings of patients with epilepsy. In some patients, a high proportion of IEDs are traveling waves according to multiple metrics that colocalize to the SOZ, offering hope that IED detection, with further refinement, could serve as an alternative method for SOZ localization.

Abstract 3064: Distinct Regulatory Programs Govern Smooth Muscle Cell Fate In Atherosclerosis

Introduction: During atherosclerosis, some vascular smooth muscle cells (SMCs) undergo phenotypic modulation, de-differentiating and adopting a fibroblast-like (FMC) or a chondrocyte/osteoblast-like phenotype (CMC). Although FMCs and CMCs appear to occur in succession in single-cell RNAseq data, they occupy distinct locations within the lesion and are associated with protective and deleterious plaque features, respectively. Hypothesis: Smooth muscle cell transitions to FMC and CMC occur via discrete transcriptional pathways during atherosclerosis. Methods: We performed single-cell RNA-sequencing (scRNAseq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq) on lineage-traced vascular SMCs isolated from the aortic root of ApoE mice (n=3). Our analysis included pseudotime and RNA velocity analyses of the scRNAseq data, which independently identified a subgroup of Vcam+Cd74+ modulated SMCs as a potential cell state from which FMCs and CMCs appear to originate, each following distinct trajectories. We explored lineage-specific gene expression using the TradeSeq R package and conducted Ingenuity Pathway Analysis on differentially expressed genes to identify relevant upstream transcription factors, which were assayed for lineage-specific motif accessibility. Results: Our analysis showed profound changes in gene expression between the two trajectories as well as differential activation and chromatin accessibility of specific transcription factors at the point where FMCs diverge from CMCs. Within the CMC lineage, we noted heightened activation and chromatin accessibility of transcription factors associated with cellular stress and inflammatory responses, including Tp53, Foxo4, and Irf1. In stark contrast, these factors exhibited diminished activity within the FMC lineage during the same pseudotime interval. Furthermore, coronary artery disease GWAS transcription factors Twist1 and Tcf21 displayed differential motif accessibility over the FMC and CMC trajectories. Conclusions: Our study provides valuable insights into the regulatory mechanisms governing SMC phenotypic transitions in atherosclerosis, and further underscores the importance of GWAS genes in influencing these transitions.

Differential Cell Types in the Thick Ascending Limb of the Kidney: Insights into Functionally Distinct TAL Claudin 10 and TAL Claudin 16 Cells

Study objective, hypothesis: The Thick Ascending Limb (TAL) in the kidney is crucial for reabsorbing Na+ and divalent cations like Ca2+ and Mg2+. This reabsorption depends on the apical cotransporter NKCC2, encoded by the Slc12a1 gene. The TAL extends from the outer medulla to the cortex. While typically considered a single functional cell type, recent evidence suggests the presence of two distinct TAL cell types, distinguished by the expression of Claudin 10 and Claudin 16 (PMID: 28028216). Despite these insights, the lack of correlation with functional and morphological data and the absence of a comprehensive model for the cooperative regulation of NaCl and Ca2+/Mg2+ transport remain significant knowledge gaps. Our objective is to couple immunohistochemistry with single nuclei (sn) RNA sequencing technology to uncover unique cell features that are obscure, when a single approach is employed. Methodology: Immunofluorescence analysis was performed on samples from mice, rats, and humans. Additionally, Slc12a1-positive cells were analyzed using sn-RNA sequencing datasets that contained spatial information about cell localization. These datasets were sourced from published studies on mouse (PMID: 31689386) and human samples (PMID: 37468583). Data Immunofluorescence images from mice, rats, and humans revealed mutually exclusive expression patterns of Kir4.1 and ROMK. Apical ROMK was observed only in cells that express Claudin 10, while Kir4.1 was expressed only in cells that express Claudin 16. phospho NKCC2 and CaSR displayed a mosaic pattern, with expression in the Claudin 16 cells throughout the entire TAL and, in both Claudin 10 and Claudin 16 cells only in the cortex. Unsupervised clustering of mouse sn-RNA seq data identified two distinct clusters, TAL Cldn10 and TAL Cldn16, present in both the cortex and medulla. Key Differentially Expressed Genes (DEG) for TAL Cld10 included Avp2r, Wnk4, Spak, Kcnt1 (encoding KCa4.1 or Slo2.2), and genes related to arachidonic acid signaling such as Ptger3 (encoding Ep3), Pla2g7, Cox7a1. Kcnj1 (encoding ROMK) transcripts were found in both clusters, even though ROMK is located apically only in TAL Claudin 10 cells. TAL Claudin 16 cells showed a higher expression of calcium-related genes, including Casr, Pth1r, Vdr, Kl (encoding Klotho), as well as transcripts for Kcnj10 (encoding Kir4.1), Kcnj16 (encoding Kir5.1), Wnk1, Clcnkb, and Bsnd (encoding Barttin). This transcriptional heterogeneity was also observed in human TAL cells. Summary of results Combining morphological and transcriptomic analyses identified two functionally distinct cell types within the TAL, present in both cortex and medulla. Each cell type appears to be associated with specific transport pathways: TAL Claudin 10 cells, express ROMK apically and are thus responsible for generating the transepithelial voltage and for paracellular Na+ reabsorption. They also express more Na+ transport-regulatory genes, including Avp2r and Wnk4, along with genes related to arachidonic acid signaling. TAL Claudin 16 cells mediate Ca2+ &amp; Mg2+ transport via the paracellular pathway, driven by the voltage generated by claudin 10 cells; they express calcium-regulatory genes, including Casr, Pth1r, and Vdr. Interestingly, they also express genes associated with transcellular Na+, K+, and Cl− transport, including Kcnj10 (Kir4.1), Kcnj16 (Kir5.1), Wnk1, and Clcnkb. Together, these results present a new model of discrete but coupled ion transport pathways in the TAL. NIH DK51496 | NIH DK054983 | VA 1I01BX002228 | Global Research Network of Excellence, Leducq Foundation. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Single-cell NAD(H) levels predict clonal lymphocyte expansion dynamics.

Adaptive immunity requires the expansion of high-affinity lymphocytes from a heterogeneous pool. Whereas current models explain this through signal transduction, we hypothesized that antigen affinity tunes discrete metabolic pathways to license clonal lymphocyte dynamics. Here, we identify nicotinamide adenine dinucleotide (NAD) biosynthesis as a biochemical hub for the T cell receptor affinity-dependent metabolome. Through this central anabolic role, we found that NAD biosynthesis governs a quiescence exit checkpoint, thereby pacing proliferation. Normalizing cellular NAD(H) likewise normalizes proliferation across affinities, and enhancing NAD biosynthesis permits the expansion of lower affinity clones. Furthermore, single-cell differences in NAD(H) could predict division potential for both T and B cells, before the first division, unmixing proliferative heterogeneity. We believe that this supports a broader paradigm in which complex signaling networks converge on metabolic pathways to control single-cell behavior.

Data-Driven Characterization of Metabolome Reprogramming during Early Development of Sorghum Seedlings.

Specialized metabolites are produced via discrete metabolic pathways. These small molecules play significant roles in plant growth and development, as well as defense against environmental stresses. These include damping off or seedling blight at a post-emergence stage. Targeted metabolomics was followed to gain insights into metabolome changes characteristic of different developmental stages of sorghum seedlings. Metabolites were extracted from leaves at seven time points post-germination and analyzed using ultra-high performance liquid chromatography coupled to mass spectrometry. Multivariate statistical analysis combined with chemometric tools, such as principal component analysis, hierarchical clustering analysis, and orthogonal partial least squares-discriminant analysis, were applied for data exploration and to reduce data dimensionality as well as for the selection of potential discriminant biomarkers. Changes in metabolome patterns of the seedlings were analyzed in the early, middle, and late stages of growth (7, 14, and 29 days post-germination). The metabolite classes were amino acids, organic acids, lipids, cyanogenic glycosides, hormones, hydroxycinnamic acid derivatives, and flavonoids, with the latter representing the largest class of metabolites. In general, the metabolite content showed an increase with the progression of the plant growth stages. Most of the differential metabolites were derived from tryptophan and phenylalanine, which contribute to innate immune defenses as well as growth. Quantitative analysis identified a correlation of apigenin flavone derivatives with growth stage. Data-driven investigations of these metabolomes provided new insights into the developmental dynamics that occur in seedlings to limit post-germination mortality.

Are there discrete recombination pathways in the case of semi-localized thermoluminescence transitions: The significance of thermal treatments towards their discrimination

This study explores an advanced luminescence protocol, aiming to reveal recombination mechanisms behind stimulated luminescence in MgB4O7: Dy, Na (MBO), and BeO: Cr, Mg, Sn (BeOR). The two-stage protocol integrates elements from prior methodologies. In the initial phase, materials undergo precise annealing at varying temperatures, followed by Thermoluminescence (TL) measurements. The second stage involves repeating annealing procedures with a single high dose. Materials exhibit localized peaks within dosimetric regions. The analysis reveals MBO's two distinct excited states, valuable for understanding recombination mechanisms and potential transitions. While BeOR undergoes a complete transition, MBO shows indications of a similar transformation. The confirmed presence of two distinct excited states within MBO establishes a fundamental premise. Validation includes peak shape methods (PSM), initial rise (IR), and prompt isothermal decay (PID). This approach enhances the understanding of stimulated luminescence phenomena, providing insights into trapping parameters and transitions between states in the studied materials.

Transcriptional consequences of trisomy 21 on neural induction.

Down syndrome, caused by trisomy 21, is a complex developmental disorder associated with intellectual disability and reduced growth of multiple organs. Structural pathologies are present at birth, reflecting embryonic origins. A fundamental unanswered question is how an extra copy of human chromosome 21 contributes to organ-specific pathologies that characterize individuals with Down syndrome, and, relevant to the hallmark intellectual disability in Down syndrome, how trisomy 21 affects neural development. We tested the hypothesis that trisomy 21 exerts effects on human neural development as early as neural induction. Bulk RNA sequencing was performed on isogenic trisomy 21 and euploid human induced pluripotent stem cells (iPSCs) at successive stages of neural induction: embryoid bodies at Day 6, early neuroectoderm at Day 10, and differentiated neuroectoderm at Day 17. Gene expression analysis revealed over 1,300 differentially expressed genes in trisomy 21 cells along the differentiation pathway compared to euploid controls. Less than 5% of the gene expression changes included upregulated chromosome 21 encoded genes at every timepoint. Genes involved in specific growth factor signaling pathways (WNT and Notch), metabolism (including oxidative stress), and extracellular matrix were altered in trisomy 21 cells. Further analysis uncovered heterochronic expression of genes. Trisomy 21 impacts discrete developmental pathways at the earliest stages of neural development. The results suggest that metabolic dysfunction arises early in embryogenesis in trisomy 21 and may affect development and function more broadly.

2P-FLIM unveils time-dependent metabolic shifts during osteogenic differentiation with a key role of lactate to fuel osteogenesis via glutaminolysis identified

BackgroundHuman mesenchymal stem cells (hMSCs) utilize discrete biosynthetic pathways to self-renew and differentiate into specific cell lineages, with undifferentiated hMSCs harbouring reliance on glycolysis and hMSCs differentiating towards an osteogenic phenotype relying on oxidative phosphorylation as an energy source.MethodsIn this study, the osteogenic differentiation of hMSCs was assessed and classified over 14 days using a non-invasive live-cell imaging modality—two-photon fluorescence lifetime imaging microscopy (2P-FLIM). This technique images and measures NADH fluorescence from which cellular metabolism is inferred.ResultsDuring osteogenesis, we observe a higher dependence on oxidative phosphorylation (OxPhos) for cellular energy, concomitant with an increased reliance on anabolic pathways. Guided by these non-invasive observations, we validated this metabolic profile using qPCR and extracellular metabolite analysis and observed a higher reliance on glutaminolysis in the earlier time points of osteogenic differentiation. Based on the results obtained, we sought to promote glutaminolysis further by using lactate, to improve the osteogenic potential of hMSCs. Higher levels of mineral deposition and osteogenic gene expression were achieved when treating hMSCs with lactate, in addition to an upregulation of lactate metabolism and transmembrane cellular lactate transporters. To further clarify the interplay between glutaminolysis and lactate metabolism in osteogenic differentiation, we blocked these pathways using BPTES and α-CHC respectively. A reduction in mineralization was found after treatment with BPTES and α-CHC, demonstrating the reliance of hMSC osteogenesis on glutaminolysis and lactate metabolism.ConclusionIn summary, we demonstrate that the osteogenic differentiation of hMSCs has a temporal metabolic profile and shift that is observed as early as day 3 of cell culture using 2P-FLIM. Furthermore, extracellular lactate is shown as an essential metabolite and metabolic fuel to ensure efficient osteogenic differentiation and as a signalling molecule to promote glutaminolysis. These findings have significant impact in the use of 2P-FLIM to discover potent approaches towards bone tissue engineering in vitro and in vivo by engaging directly with metabolite-driven osteogenesis.Graphical

Substrate Sequestration and Chain Flipping in Human Mitochondrial Acyl Carrier Protein.

Outside of their involvement in energy production, mitochondria play a critical role for the cell through their access to a discrete pathway for fatty acid biosynthesis. Despite decades of study in bacterial fatty acid synthases (the putative evolutionary mitochondrial precursor), our understanding of human mitochondrial fatty acid biosynthesis remains incomplete. In particular, the role of the key carrier protein, human mitochondrial acyl carrier protein (mACP), which shuttles the substrate intermediates through the pathway, has not been well-studied in part due to challenges in protein expression and purification. Herein, we report a reliable method for recombinant Escherichia coli expression and purification of mACP. Fundamental characteristics, including substrate sequestration and chain-flipping activity, are demonstrated in mACP using solvatochromic response. This study provides an efficient approach toward understanding the fundamental protein-protein interactions of mACP and its partner proteins, ultimately leading to a molecular understanding of human mitochondrial diseases such as mitochondrial fatty acid oxidation deficiencies.

Pan-tissue mitochondrial phenotyping reveals lower OXPHOS expression and function across cancer types

Targeting mitochondrial oxidative phosphorylation (OXPHOS) to treat cancer has been hampered due to serious side-effects potentially arising from the inability to discriminate between non-cancerous and cancerous mitochondria. Herein, comprehensive mitochondrial phenotyping was leveraged to define both the composition and function of OXPHOS across various murine cancers and compared to both matched normal tissues and other organs. When compared to both matched normal tissues, as well as high OXPHOS reliant organs like heart, intrinsic expression of the OXPHOS complexes, as well as OXPHOS flux were discovered to be consistently lower across distinct cancer types. Assuming intrinsic OXPHOS expression/function predicts OXPHOS reliance in vivo, these data suggest that pharmacologic blockade of mitochondrial OXPHOS likely compromises bioenergetic homeostasis in healthy oxidative organs prior to impacting tumor mitochondrial flux in a clinically meaningful way. Although these data caution against the use of indiscriminate mitochondrial inhibitors for cancer treatment, considerable heterogeneity was observed across cancer types with respect to both mitochondrial proteome composition and substrate-specific flux, highlighting the possibility for targeting discrete mitochondrial proteins or pathways unique to a given cancer type.

Multi-scale model to study gas transport processes in clay materials

In the field of radioactive waste confinement, the question of gas transfers in clay formations is a crucial issue [1]. A certain amount of gas, such as Hydrogen may be generated during the exploitation phase in the nearfield by the deterioration of the metal components of the system. Since the host medium is characterised by a very low permeability, the mechanisms of gas transport by advection and diffusion within the groundwater remain insufficient to evacuate the gas generated and a free gas phase is formed. If the gas pressure keeps increasing and reaches the minimum principal stress acting on the rock, micro-fractures, known as preferential gas pathways could develop through the rock mass [2], and affect the clay barrier integrity.&#x0D; There is a growing body of experimental evidences [3, 4] that separation planes such as bedding planes or pre-existing fractures and heterogeneities in clay-rich materials represent preferred weaknesses for the process of opening discrete gas-filled pathways. Capturing the related transport mechanisms therefore requires to go from macroscopic to microscopic scale. In this context, the adopted numerical approach would ideally take into account the effect of each constituent of the material microstructure on the macroscopic gas flow. Yet, direct modelling of the entire microstructure using small-scale models is usually not possible due to the huge computational costs it would require at the scale of a repository. Conversely, indirect modelling of the behaviour of all the micro-constituents by collective closed-form macroscopic constitutive equations using large-scale models [5] has also limits in terms of assumptions formulation and parameters identification. Hence, the use of a multi-scale approach that models the micro-scale effects explicitely on their specific length scale and couples their homogenized effects to the macro-scale is proposed in the present work. Based on a periodicity assumption of the microstructure, the physical and geometrical properties of the microstructure are embedded on a Representative Element Volume (REV) which contains a detailed model of the microstructure constituents, i.e. the pore network, the bedding planes and the bridging planes, while eluding a complex description of the whole microstructure over the domain. From this local description of the material, the macroscopic response to loading can be derived using numerical homogenisation techniques [6].&#x0D; The multi-scale model proposed here has been implemented in the finite element code Lagamine, and validated against a well established and documented macro-scale THM coupled model [7]. The size and structure of the REV comes from experimental data acquired from scanning images in clay material, like for instance the Boom Clay formation which is envisaged as a potential host rock for a deep geological disposal in Belgium. Such scans reveal the opening of large aperture with a repeated distance in-between, which make it possible to extrapolate a physical idealisation of the microstructure (Figure 1a), built with one of these fractures corresponding to the bedding planes (red) and the pore network substituted by an assembly of tubes (green). Narrow-aperture fissures, known as the bridging planes (blue) were also identified to contribute to the flow normal to the predominant direction of fissure [4], by connecting the natural discontinuities which were initially closed. These micro-scale constituents are defined in such a way as to satisfy the conditions of pore size distribution, macroporosity and intrinsic permeability. For the mechanical behaviour, a simple linear elastic constitutive law was introduced for the tube network while a non-linear stress-strain relationship was used for the interfaces defining the bedding and bridging planes. Concerning the hydraulic behaviour, gas diffusive fluxes were considered and modelled by a Fick’s law while a channel flow based on the Navier-Stokes equations was used for the multiphase flow in the different constituents.&#x0D; The model has been subsequently applied to simulate a gas injection test parallel and perpendicular to the bedding of initially saturated samples of Boom Clay [4]. This analysis provides a rather good agreement with the experimental results in terms of injection and outflow pressure response, outflow volume and average axial strain along the sample height. In addition, it allows to simulated the creation of a preferential flow pathway along the sample axis (Figure 1b, top), which serves as basis to numerically reproduce the development of random pathway through the sample in plane strain state (Figure 1b, bottom), and aims to improve the mechanistic understanding of the gas transport processes at play in clayey barriers [8].

Nonlinearly tunable Fano resonance in photonic crystal heterostructure with embedded a varactor-loaded split ring resonator

The study explores the Fano-type interference effect in a microstrip photonic crystal (PC) heterostructure integrated with a varactor-loaded split ring resonator (SRR), both experimentally and numerically. This effect capitalizes on the PC heterostructure’s ability to provide a broad continuous spectrum, while the embedded SRR offers a narrow discrete pathway. Through coherent interference between these elements, a sharp asymmetric Fano-type transmission spectrum emerges, accompanied by a notable group delay. Furthermore, the composite configuration exhibits an electric field enhancement at the Fano resonant frequency, enhancing the nonlinear sensitivity of the transmission spectrum. The nonlinear tunability of the Fano resonance is demonstrated by applying distinct input powers, allowing for the realization of a high-performance bistable electromagnetic switch and diode in the microwave regime. The proposed configuration exhibits key features such as significant transmission contrast, low threshold intensity, and relatively high transmission amplitude, all within a compact device volume, thanks to the Fano resonant mechanism in the PC heterostructure. This design paves the way for the implementation of active metamaterials-assisted components in micro- or nano-photonic circuits, with potential applications in advanced optical devices.

CGLRs are a diverse family of pattern recognition receptors in innate immunity

Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and invivo analysis in coral and oyster animals, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.

209-LB: Discovery Metabolomics across a Population Scale Study Identifies a Community of Glycerolipids Associated with Incident Type 2 Diabetes

It is well appreciated that changes in metabolic pathways precede the development of overt type 2 diabetes (T2D), but a systematic and unbiased evaluation of such metabolic changes is lacking. Here, we applied a novel high-throughput untargeted liquid chromatography-mass spectrometry (LC-MS) method to the FINRISK 2002 cohort (n=8014) to identify plasma metabolite predictors of incident T2D. We analyzed LC-MS data consisting of 14,615 metabolite features from individuals without prevalent T2D to discover 171 that predicted T2D incidence at a threshold of P&amp;lt;10-6 (Cox regression). To identify discrete molecular pathways, we performed Gaussian graphical modeling to create a network of all detected metabolite features finding that the T2D predictor metabolites were enriched in 11 distinct metabolite communities containing between 6 and 48 interconnected metabolites. Here we highlight one community consisting of 26 plasma diacylglycerols (DAGs) and closely related metabolites. One member of this community, a DAG with carbon:unsaturated bond sum composition of 36:4, predicted T2D incidence (HR = 1.22, p = 7.6×10-10) independently of insulin, glucose and HbA1c, but not 2-hour glucose as measured by OGTT. Thus, this metabolite is a novel predictor of incident T2D that can capture the metabolic dysregulation identifiable by OGTT. In summary, we have identified multiple communities of T2D metabolite biomarkers, representative of distinct pathways that are dysregulated preceding T2D, with potentially clinical useful properties. Disclosure A. Begzati: None. K. P. Godinez Macias: None. J. Watrous: None. T. Long: None. E. Kantz: None. J. Tuomilehto: Stock/Shareholder; Orion pharma. A. S. Havulinna: None. T. Niiranen: Speaker's Bureau; AstraZeneca, Servier Laboratories. P. Jousilahti: None. V. Salomaa: Research Support; Bayer Inc. T. Ideker: None. M. Jain: Employee; Sapient Bioanalytics. A. R. Majithia: None. Funding National Institutes of Health (5R01DK129840-02)

Multistage W-Sn metallogenic processes in the Xitian ore field, South China: Evolution from skarn-type to vein-type mineralization

The Nanling Metallogenic Belt is a major W-Sn province in South China containing numerous ore deposits formed during a complex history of magma emplacement and mineralization. The Xitian ore field in Hunan Province is a typical example of a late magmatic-metallogenic system. In this study, garnets from skarn-type ores in the Xitian ore field yield a U-Pb age of 231.7 ± 1.3 Ma (n = 33), whereas cassiterite grains from quartz vein-type ores give U-Pb ages of 158 to 154 Ma (n = 72) and 140.7 ± 3.3 Ma (n = 6), suggesting three stages of W-Sn mineralization (Late Triassic, Late Jurassic, and Early Cretaceous). In the Late Triassic skarn-type ores, the REE patterns of scheelite change from MREE-enriched to LREE-enriched with time, whereas the REE patterns of scheelite shift from MREE-enriched to MREE-depleted in the Late Jurassic quartz vein-type ores, indicating diverse metallogenic processes. Differences in the Y/Ho ratios and Sr-O isotope compositions of scheelite further confirm discrete metallogenic pathways for the Late Triassic skarn-type W ore and the Late Jurassic quartz vein-type ore, with fluid-rock interaction of the former dominated by magmatic-hydrothermal fluids whereas the latter was influenced by large amounts of meteoric water. A model emphasizing the evolution from skarn-type to vein-type metallogeny is proposed to account for the complex genesis of multistage W–Sn deposits related to the Xitian granite complex. More generally, this study demonstrates that in-situ LA-ICP(MC)-MS U-Pb dating and isotopic analysis of hydrothermal minerals are powerful tools to decipher the nature, timing, and evolution of multistage W-Sn metallogenic systems.