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1.
J Theor Biol ; 581: 111747, 2024 03 21.
Article in English | MEDLINE | ID: mdl-38278344

ABSTRACT

Fat cells, called adipocytes, are designed to regulate energy homeostasis by storing energy in the form of lipids. Adipocyte size distribution is assumed to play a role in the development of obesity-related diseases. These cells that do not have a characteristic size, indeed a bimodal size distribution is observed in adipose tissue. We propose a model based on a partial differential equation to describe adipocyte size distribution. The model includes a description of the lipid fluxes and the cell size fluctuations and using a formulation of a stationary solution fast computation of bimodal distribution is achieved. We investigate the parameter identifiability and estimate parameter values with CMA-ES algorithm. We first validate the procedure on synthetic data, then we estimate parameter values with experimental data of 32 rats. We discuss the estimated parameter values and their variability within the population, as well as the relation between estimated values and their biological significance. Finally, a sensitivity analysis is performed to specify the influence of parameters on cell size distribution and explain the differences between the model and the measurements. The proposed framework enables the characterization of adipocyte size distribution with four parameters and can be easily adapted to measurements of cell size distribution in different health conditions.


Subject(s)
Models, Biological , Models, Theoretical , Rats , Animals , Adipocytes , Adipose Tissue , Cell Size
2.
Obes Surg ; 33(12): 4017-4025, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37924465

ABSTRACT

INTRODUCTION: Obesity is associated with low-grade inflammation, including intestinal inflammation based on fecal or serum calprotectin (FC-SC) measurement. Roux-en-Y gastric bypass (RYGB) improves obesity-related parameters. However, the association between FC-SC levels and postoperative course and the link with metabolic and inflammatory phenotypes before and after RYGB remains unclear. METHODS: We determined SC levels in 48 patients before (T0) and 6 months after (T6M) RYGB. We then analyzed postoperative changes in FC-SC levels and the relationship with inflammation and metabolic status. RESULTS: Twenty-three patients (48%) had elevated SC levels (˃2.9 µg/mL) at T0 and T6M. Six of 29 patients (20.7%) had elevated FC concentrations (>50 µg/g) at T0 vs. 16 of 17 patients (94.1%) at T6M (p=0.006). At T0, FC levels correlated with BMI (Rho=0.63; p=0.001) and systemic inflammation (CRP: Rho=0.66, p=0.0006; IL-6: Rho=0.48, p=0.03; haptoglobin: Rho=0.75; p= 0.0006). SC tended to be positively associated with triglyceride levels (Rho=0.34; p=0.08), BMI (Rho=0.34; p=0.08), and inflammatory markers (CRP: Rho=0.33; p=0.09; IL-6: Rho=0.36; p=0.06). FC levels were associated with increased jejunal IL-17+CD8+ T-cell densities (Rho:0.90; p=0.0002). FC and SC were correlated together at T0 (Rho=0.83; p<0.001) but not at T6M. At T6M, SC decreased by 53.6%, whereas FC increased by 79.7%. SC and FC were not associated with any of the variables studied at T6M. CONCLUSION: FC is a surrogate marker of systemic and intestinal inflammation and adiposity, whereas SC only tends to correlate with systemic inflammation. At 6 months after RYGB, SC-based systemic inflammation decreased, whereas FC-based intestinal inflammation increased. FC and SC levels follow different trajectories and are unrelated to improvements following bariatric surgery.


Subject(s)
Gastric Bypass , Obesity, Morbid , Humans , Obesity, Morbid/surgery , Leukocyte L1 Antigen Complex , Prospective Studies , Interleukin-6 , Obesity/surgery , Inflammation
3.
Article in English | MEDLINE | ID: mdl-37646578

ABSTRACT

Combination therapies targeting multiple organs and metabolic pathways are promising therapeutic options to combat obesity progression and/or its comorbidities. The alterations in the composition of the gut microbiota initially observed in obesity have been extended recently to functional alterations. Bacterial functions involve metabolites synthesis that may contribute to both the gut microbiota and the host physiology. Among them are B vitamins, whose metabolism at the systemic, tissue or microbial level are dysfunctional in obesity. We previously reported that the combination of oral supplementation of a prebiotic (fructo-oligosaccharides, FOS) and vitamin B7/B8 (biotin) impedes fat mass accumulation and hyperglycemia in mice with established obesity. This was associated with an attenuation of dysbiosis with improved microbial vitamin metabolism. We now extend this study by characterizing whole-body energy metabolism along with adipose tissue transcriptome and histology in this mouse model. We observed that FOS resulted in increased caloric excretion in parallel with down-regulation of genes and proteins involved in jejunal lipid transport. The combined treatments also strongly inhibited the accumulation of subcutaneous fat mass, with a reduced adipocyte size and expression of lipid metabolism genes. Down-regulation of inflammatory and fibrotic genes and proteins was also observed in both visceral and brown adipose tissues and liver by combined FOS and biotin supplementation. In conclusion, oral administration of a prebiotic and biotin has a beneficial impact on the metabolism of key organs involved in the pathophysiology of obesity, which could have promising translational applications.

4.
BMC Bioinformatics ; 24(1): 61, 2023 Feb 23.
Article in English | MEDLINE | ID: mdl-36823548

ABSTRACT

BACKGROUND: Current clinical routines rely more and more on "omics" data such as flow cytometry data from host and microbiota. Cohorts variability in addition to patients' heterogeneity and huge dimensions make it difficult to understand underlying structure of the data and decipher pathologies. Patients stratification and diagnostics from such complex data are extremely challenging. There is an acute need to develop novel statistical machine learning methods that are robust with respect to the data heterogeneity, efficient from the computational viewpoint, and can be understood by human experts. RESULTS: We propose a novel approach to stratify cell-based observations within a single probabilistic framework, i.e., to extract meaningful phenotypes from both patients and cells data simultaneously. We define this problem as a double clustering problem that we tackle with the proposed approach. Our method is a practical extension of the Latent Dirichlet Allocation and is used for the Double Clustering task (LDA-DC). We first validate the method on artificial datasets, then we apply our method to two real problems of patients stratification based on cytometry and microbiota data. We observe that the LDA-DC returns clusters of patients and also clusters of cells related to patients' conditions. We also construct a graphical representation of the results that can be easily understood by humans and are, therefore, of a big help for experts involved in pre-clinical research.


Subject(s)
Bayes Theorem , Humans , Cluster Analysis
5.
Mol Metab ; 61: 101512, 2022 07.
Article in English | MEDLINE | ID: mdl-35550189

ABSTRACT

BACKGROUND/PURPOSE: Adipose tissue contains progenitor cells that contribute to beneficial tissue expansion when needed by de novo adipocyte formation (classical white or beige fat cells with thermogenic potential). However, in chronic obesity, they can exhibit an activated pro-fibrotic, extracellular matrix (ECM)-depositing phenotype that highly aggravates obesity-related adipose tissue dysfunction. METHODS: Given that progenitors' fibrotic activation and fat cell browning appear to be antagonistic cell fates, we have examined the anti-fibrotic potential of pro-browning agents in an obesogenic condition. RESULTS: In obese mice fed a high fat diet, thermoneutral housing, which induces brown fat cell dormancy, increases the expression of ECM gene programs compared to conventionally raised animals, indicating aggravation of obesity-related tissue fibrosis at thermoneutrality. In a model of primary cultured murine adipose progenitors, we found that exposure to ß-hydroxybutyrate selectively reduced Tgfß-dependent profibrotic responses of ECM genes like Ctgf, Loxl2 and Fn1. This effect is observed in both subcutaneous and visceral-derived adipose progenitors, as well as in 3T3-L1 fibroblasts. In 30 patients with obesity eligible for bariatric surgery, those with higher circulating ß-hydroxybutyrate levels have lower subcutaneous adipose tissue fibrotic scores. Mechanistically, ß-hydroxybutyrate limits Tgfß-dependent collagen accumulation and reduces Smad2-3 protein expression and phosphorylation in visceral progenitors. Moreover, ß-hydroxybutyrate induces the expression of the ZFP36 gene, encoding a post-transcriptional regulator that promotes the degradation of mRNA by binding to AU-rich sites within 3'UTRs. Importantly, complete ZFP36 deficiency in a mouse embryonic fibroblast line from null mice, or siRNA knock-down in primary progenitors, indicate that ZFP36 is required for ß-hydroxybutyrate anti-fibrotic effects. CONCLUSION: These data unravel the potential of ß-hydroxybutyrate to limit adipose tissue matrix deposition, a finding that might exploited in an obesogenic context.


Subject(s)
Adipose Tissue, Brown , Adipose Tissue, White , 3-Hydroxybutyric Acid/metabolism , 3-Hydroxybutyric Acid/pharmacology , Adipocytes, Brown/metabolism , Adipose Tissue, Brown/metabolism , Adipose Tissue, White/metabolism , Animals , Fibroblasts/metabolism , Fibrosis , Humans , Mice , Obesity/metabolism , Transforming Growth Factor beta/metabolism , Tristetraprolin/metabolism
6.
Elife ; 112022 03 07.
Article in English | MEDLINE | ID: mdl-35254258

ABSTRACT

Spatiotemporal mechanisms generating neural diversity are fundamental for understanding neural processes. Here, we investigated how neural diversity arises from neurons coming from identical progenitors. In the dorsal thorax of Drosophila, rows of mechanosensory organs originate from the division of sensory organ progenitor (SOPs). We show that in each row of the notum, an anteromedial located central SOP divides first, then neighbouring SOPs divide, and so on. This centrifugal wave of mitoses depends on cell-cell inhibitory interactions mediated by SOP cytoplasmic protrusions and Scabrous, a secreted protein interacting with the Delta/Notch complex. Furthermore, when this mitotic wave was reduced, axonal growth was more synchronous, axonal terminals had a complex branching pattern and fly behaviour was impaired. We show that the temporal order of progenitor divisions influences the birth order of sensory neurons, axon branching and impact on grooming behaviour. These data support the idea that developmental timing controls axon wiring neural diversity.


Subject(s)
Drosophila Proteins , Drosophila , Animals , Axons , Drosophila Proteins/genetics , Neurogenesis/physiology , Neuronal Outgrowth , Sensory Receptor Cells
7.
Obes Surg ; 32(3): 837-844, 2022 03.
Article in English | MEDLINE | ID: mdl-34984630

ABSTRACT

INTRODUCTION: Pathogenic heterozygous MC4R variants are associated with hyperphagia and variable degrees of obesity. Several research groups have reported short-term weight loss outcomes after bariatric surgery in a few patients with MC4R variants, but lack of longer-term data prevents evidence-based clinical decision-making. MATERIALS AND METHODS: Bariatric surgery patients with heterozygous (likely) pathogenic MC4R variants, from three collaborating centers in the Netherlands, France, and the UK, were compared to matched controls (matched 2:1 for age, sex, preoperative BMI, surgical procedure, and diabetes mellitus, but without MC4R mutations). Weight loss and regain outcomes up to 6 years of follow-up were compared. RESULTS: At 60 months of follow-up after RYGB, cases with MC4R variants showed weight regain with a mean of 12.8% (± 10.4 SD) total weight loss (TWL) from nadir, compared to 7.9% (± 10.5 SD) in the controls (p = 0.062). Among patients receiving SG, the cases with MC4R variants experienced inferior weight loss (22.6% TWL) during the first year of follow-up compared to the controls (29.9% TWL) (p = 0.010). CONCLUSIONS: This multicenter study reveals inferior mid-term weight outcomes of cases with MC4R variants after SG, compared to RYGB. Since adequate weight loss outcomes were observed after RYGB, this procedure would appear to be an appropriate surgical approach for this group. However, the pattern of weight regain seen in cases with MC4R variants after both RYGB and SG highlights the need for pro-active lifelong management to prevent relapse, as well as careful expectation management.


Subject(s)
Bariatric Surgery , Gastric Bypass , Obesity, Morbid , Receptor, Melanocortin, Type 4/genetics , Case-Control Studies , Gastric Bypass/methods , Humans , Obesity, Morbid/surgery , Retrospective Studies , Treatment Outcome , Weight Gain , Weight Loss/genetics
8.
J Endocrinol ; 252(1): 31-44, 2021 11 24.
Article in English | MEDLINE | ID: mdl-34647524

ABSTRACT

Changes in dietary habits have occurred concomitantly with a rise of type 2 diabetes (T2D) and obesity. Intestine is the first organ facing nutrient ingestion and has to adapt its metabolism with these dietary changes. HNF-4γ, a transcription factor member of the nuclear receptor superfamily and mainly expressed in intestine, has been suggested to be involved in susceptibility to T2D. Our aim was to investigate the role of HNF-4γ in metabolic disorders and related mechanisms. Hnf4g-/- mice were fed high-fat/high-fructose (HF-HF) diet for 6 weeks to induce obesity and T2D. Glucose homeostasis, energy homeostasis in metabolic cages, body composition and stool energy composition, as well as gene expression analysis in the jejunum were analyzed. Despite an absence of decrease in calorie intake, of increase in locomotor activity or energy expenditure, Hnf4g-/- mice fed with HF-HF are protected against weight gain after 6 weeks of HF-HF diet. We showed that Hnf4g-/- mice fed HF-HF display an increase in fecal calorie loss, mainly due to intestinal lipid malabsorption. Gene expression of lipid transporters, Fatp4 and Scarb1 and of triglyceride-rich lipoprotein secretion proteins, Mttp and ApoB are decreased in gut epithelium of Hnf4g-/- mice fed HF-HF, showing the HNF-4γ role in intestine lipid absorption. Furthermore, plasma GLP-1 and jejunal GLP-1 content are increased in Hnf4g-/- mice fed HF-HF, which could contribute to the glucose intolerance protection. The loss of HNF-4γ leads to a protection against a diet-induced weight gain and to a deregulated glucose homeostasis, associated with lipid malabsorption.


Subject(s)
Hepatocyte Nuclear Factor 4/genetics , Intestinal Absorption/genetics , Lipid Metabolism/genetics , Obesity/genetics , Animals , Cells, Cultured , Diet, High-Fat/adverse effects , Female , Fructose/adverse effects , Gene Deletion , Glucose Intolerance/etiology , Glucose Intolerance/genetics , Glucose Intolerance/metabolism , Intestines/metabolism , Malabsorption Syndromes/genetics , Malabsorption Syndromes/metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Obesity/etiology , Obesity/metabolism , Triglycerides/metabolism , Weight Gain/genetics
9.
Curr Biol ; 31(21): 4762-4772.e5, 2021 11 08.
Article in English | MEDLINE | ID: mdl-34529937

ABSTRACT

Survival of animals is dependent on the correct selection of an appropriate behavioral response to competing external stimuli. Theoretical models have been proposed and underlying mechanisms are emerging to explain how one circuit is selected among competing neural circuits. The evolutionarily conserved forebrain to midbrain habenulo-interpeduncular nucleus (Hb-IPN) pathway consists of cholinergic and non-cholinergic neurons, which mediate different aversive behaviors. Simultaneous calcium imaging of neuronal cell bodies and of the population dynamics of their axon terminals reveals that signals in the cell bodies are not reflective of terminal activity. We find that axon terminals of cholinergic and non-cholinergic habenular neurons exhibit stereotypic patterns of spontaneous activity that are negatively correlated and localize to discrete subregions of the target IPN. Patch-clamp recordings show that calcium bursts in cholinergic terminals at the ventral IPN trigger excitatory currents in IPN neurons, which precede inhibition of non-cholinergic terminals at the adjacent dorsal IPN. Inhibition is mediated through presynaptic GABAB receptors activated in non-cholinergic habenular neurons upon GABA release from the target IPN. Together, the results reveal a hardwired mode of competition at the terminals of two excitatory neuronal populations, providing a physiological framework to explore the relationship between different aversive responses.


Subject(s)
Habenula , Presynaptic Terminals , Animals , Calcium/metabolism , Cholinergic Agents/metabolism , Habenula/physiology , Presynaptic Terminals/metabolism , gamma-Aminobutyric Acid/metabolism
10.
Am J Physiol Endocrinol Metab ; 321(3): E417-E432, 2021 09 01.
Article in English | MEDLINE | ID: mdl-34338041

ABSTRACT

Carbohydrates and sweeteners are detected by the sweet taste receptor in enteroendocrine cells (EECs). This receptor is coupled to the gustducin G-protein, which α-subunit is encoded by GNAT3 gene. In intestine, the activation of sweet taste receptor triggers a signaling pathway leading to GLP-1 secretion, an incretin hormone. In metabolic diseases, GLP-1 concentration and incretin effect are reduced while partly restored after Roux-en-Y gastric bypass (RYGB). We wondered if the decreased GLP-1 secretion in metabolic diseases is caused by an intestinal defect in sweet taste transduction pathway. In our RNA-sequencing of EECs, GNAT3 expression is decreased in patients with obesity and type 2 diabetes compared with normoglycemic obese patients. This prompted us to explore sweet taste signaling pathway in mice with metabolic deteriorations. During obesity onset in mice, Gnat3 expression was downregulated in EECs. After metabolic improvement with enterogastro anastomosis surgery in mice (a surrogate of the RYGB in humans), the expression of Gnat3 increased in the new alimentary tract and glucose-induced GLP-1 secretion was improved. To evaluate if high-fat diet-induced dysbiotic intestinal microbiota could explain the changes in the expression of sweet taste α-subunit G-protein, we performed a fecal microbiota transfer in mice. However, we could not conclude if dysbiotic microbiota impacted or not intestinal Gnat3 expression. Our data highlight that metabolic disorders were associated with altered gene expression of sweet taste signaling in intestine. This could contribute to impaired GLP-1 secretion that is partly rescued after metabolic improvement.NEW & NOTEWORTHY Our data highlighted 1) the sweet taste transduction pathway in EECs plays pivotal role for glucose homeostasis at least at gene expression level; 2) metabolic disorders lead to altered gene expression of sweet taste signaling pathway in intestine contributing to impaired GLP-1 secretion; and 3) after surgical intestinal modifications, increased expression of GNAT3, encoding α-gustducin contributed to metabolic improvement.


Subject(s)
Diabetes Mellitus, Type 2/metabolism , Obesity/metabolism , Signal Transduction , Taste , Transducin/metabolism , Animals , Dysbiosis/metabolism , Enteroendocrine Cells/metabolism , Gastrointestinal Microbiome , Humans , Male , Mice, Inbred C57BL
11.
Sci Rep ; 11(1): 12192, 2021 06 09.
Article in English | MEDLINE | ID: mdl-34108539

ABSTRACT

In this manuscript, we propose a novel approach to assess relationships between environment and metabolic networks. We used a comprehensive dataset of more than 5000 prokaryotic species from which we derived the metabolic networks. We compute the scope from the reconstructed graphs, which is the set of all metabolites and reactions that can potentially be synthesized when provided with external metabolites. We show using machine learning techniques that the scope is an excellent predictor of taxonomic and environmental variables, namely growth temperature, oxygen tolerance, and habitat. In the literature, metabolites and pathways are rarely used to discriminate species. We make use of the scope underlying structure-metabolites and pathways-to construct the predictive models, giving additional information on the important metabolic pathways needed to discriminate the species, which is often absent in other metabolic network properties. For example, in the particular case of growth temperature, glutathione biosynthesis pathways are specific to species growing in cold environments, whereas tungsten metabolism is specific to species in warm environments, as was hinted in current literature. From a machine learning perspective, the scope is able to reduce the dimension of our data, and can thus be considered as an interpretable graph embedding.

12.
Int J Obes (Lond) ; 45(1): 170-183, 2021 01.
Article in English | MEDLINE | ID: mdl-33037328

ABSTRACT

OBJECTIVES: Altered enteroendocrine cell (EEC) function in obesity and type 2 diabetes is not fully understood. Understanding the transcriptional program that controls EEC differentiation is important because some EEC types harbor significant therapeutic potential for type 2 diabetes. METHODS: EEC isolation from jejunum of obese individuals with (ObD) or without (Ob) type 2 diabetes was obtained with a new method of cell sorting. EEC transcriptional profiles were established by RNA-sequencing in a first group of 14 Ob and 13 ObD individuals. EEC lineage and densities were studied in the jejunum of a second independent group of 37 Ob, 21 ObD and 22 non obese (NOb) individuals. RESULTS: The RNA seq analysis revealed a distinctive transcriptomic signature and a decreased differentiation program in isolated EEC from ObD compared to Ob individuals. In the second independent group of ObD, Ob and NOb individuals a decreased GLP-1 cell lineage and GLP-1 maturation from proglucagon, were observed in ObD compared to Ob individuals. Furthermore, jejunal density of GLP-1-positive cells was significantly reduced in ObD compared to Ob individuals. CONCLUSIONS: These results highlight that the transcriptomic signature of EEC discriminate obese subjects according to their diabetic status. Furthermore, type 2 diabetes is associated with reduced GLP-1 cell differentiation and proglucagon maturation leading to low GLP-1-cell density in human obesity. These mechanisms could account for the decrease plasma GLP-1 observed in metabolic diseases.


Subject(s)
Diabetes Mellitus, Type 2 , Enteroendocrine Cells/metabolism , Jejunum/cytology , Obesity , Adult , Cells, Cultured , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/epidemiology , Diabetes Mellitus, Type 2/metabolism , Enteroendocrine Cells/cytology , Female , Humans , Male , Middle Aged , Obesity/complications , Obesity/epidemiology , Obesity/metabolism
13.
Mol Metab ; 39: 101007, 2020 09.
Article in English | MEDLINE | ID: mdl-32360426

ABSTRACT

OBJECTIVE: Obesity is characterized by systemic and low-grade tissue inflammation. In the intestine, alteration of the intestinal barrier and accumulation of inflammatory cells in the epithelium are important contributors of gut inflammation. Recent studies demonstrated the role of the aryl hydrocarbon receptor (AhR) in the maintenance of immune cells at mucosal barrier sites. A wide range of ligands of external and local origin can activate this receptor. We studied the causal relationship between AhR activation and gut inflammation in obesity. METHODS: Jejunum samples from subjects with normal weight and severe obesity were phenotyped according to T lymphocyte infiltration in the epithelium from lamina propria and assayed for the mRNA level of AhR target genes. The effect of an AhR agonist was studied in mice and Caco-2/TC7 cells. AhR target gene expression, permeability to small molecules and ions, and location of cell-cell junction proteins were recorded under conditions of altered intestinal permeability. RESULTS: We showed that a low AhR tone correlated with a high inflammatory score in the intestinal epithelium in severe human obesity. Moreover, AhR activation protected junctional complexes in the intestinal epithelium in mice challenged by an oral lipid load. AhR ligands prevented chemically induced damage to barrier integrity and cytokine expression in Caco-2/TC7 cells. The PKC and p38MAPK signaling pathways were involved in this AhR action. CONCLUSIONS: The results of these series of human, mouse, and cell culture experiments demonstrate the protective effect of AhR activation in the intestine targeting particularly tight junctions and cytokine expression. We propose that AhR constitutes a valuable target to protect intestinal functions in metabolic diseases, which can be achieved in the future via food or drug ligands.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , Intestinal Mucosa/metabolism , Obesity/metabolism , Receptors, Aryl Hydrocarbon/metabolism , Adiposity/genetics , Adult , Aged , Aged, 80 and over , Animals , Basic Helix-Loop-Helix Transcription Factors/genetics , Biomarkers , Cell Line , Comorbidity , Cytokines/metabolism , Epithelial Cells/metabolism , Female , Humans , Intestinal Mucosa/immunology , Intestinal Mucosa/pathology , Jejunum/metabolism , Lipid Metabolism , MAP Kinase Signaling System , Male , Mice , Middle Aged , Models, Biological , Obesity/etiology , Obesity/pathology , Permeability , Receptors, Aryl Hydrocarbon/genetics , Signal Transduction , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Tight Junctions/drug effects , Tight Junctions/metabolism
14.
BMC Bioinformatics ; 20(1): 499, 2019 Oct 15.
Article in English | MEDLINE | ID: mdl-31615420

ABSTRACT

BACKGROUND: Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to study fluxes through the reactions, or to relate the graph structure to environmental characteristics and phenotypes. About ten years ago, Takemoto et al. (2007) stated that the structure of prokaryotic metabolic networks represented as undirected graphs, is correlated to their living environment. Although metabolic networks are naturally directed graphs, they are still usually analysed as undirected graphs. RESULTS: We implemented a pipeline to reconstruct metabolic networks from genome data and confirmed some of the results of Takemoto et al. (2007) with today data using up-to-date databases. However, Takemoto et al. (2007) used only a fraction of all available enzymes from the genome and taking into account all the enzymes we fail to reproduce the main results. Therefore, we introduce three robust measures on directed representations of graphs, which lead to similar results regardless of the method of network reconstruction. We show that the size of the largest strongly connected component, the flow hierarchy and the Laplacian spectrum are strongly correlated to the environmental conditions. CONCLUSIONS: We found a significant negative correlation between the size of the largest strongly connected component (a cycle) and the optimal growth temperature of the considered prokaryotes. This relationship holds true for the spectrum, high temperature being associated with lower eigenvalues. The hierarchy flow shows a negative correlation with optimal growth temperature. This suggests that the dynamical properties of the network are dependant on environmental factors.


Subject(s)
Bacteria/metabolism , Computational Biology , Metabolic Networks and Pathways , Models, Biological , Temperature , Enzymes
15.
PLoS Comput Biol ; 15(8): e1006795, 2019 08.
Article in English | MEDLINE | ID: mdl-31425510

ABSTRACT

Astrocytes, a glial cell type of the central nervous system, have emerged as detectors and regulators of neuronal information processing. Astrocyte excitability resides in transient variations of free cytosolic calcium concentration over a range of temporal and spatial scales, from sub-microdomains to waves propagating throughout the cell. Despite extensive experimental approaches, it is not clear how these signals are transmitted to and integrated within an astrocyte. The localization of the main molecular actors and the geometry of the system, including the spatial organization of calcium channels IP3R, are deemed essential. However, as most calcium signals occur in astrocytic ramifications that are too fine to be resolved by conventional light microscopy, most of those spatial data are unknown and computational modeling remains the only methodology to study this issue. Here, we propose an IP3R-mediated calcium signaling model for dynamics in such small sub-cellular volumes. To account for the expected stochasticity and low copy numbers, our model is both spatially explicit and particle-based. Extensive simulations show that spontaneous calcium signals arise in the model via the interplay between excitability and stochasticity. The model reproduces the main forms of calcium signals and indicates that their frequency crucially depends on the spatial organization of the IP3R channels. Importantly, we show that two processes expressing exactly the same calcium channels can display different types of calcium signals depending on the spatial organization of the channels. Our model with realistic process volume and calcium concentrations successfully reproduces spontaneous calcium signals that we measured in calcium micro-domains with confocal microscopy and predicts that local variations of calcium indicators might contribute to the diversity of calcium signals observed in astrocytes. To our knowledge, this model is the first model suited to investigate calcium dynamics in fine astrocytic processes and to propose plausible mechanisms responsible for their variability.


Subject(s)
Astrocytes/metabolism , Calcium Signaling/physiology , Models, Neurological , Animals , Brain/metabolism , Computational Biology , Computer Simulation , Hippocampus/metabolism , Humans , Inositol 1,4,5-Trisphosphate Receptors/metabolism , Spatio-Temporal Analysis , Stochastic Processes
16.
Behav Processes ; 162: 147-156, 2019 May.
Article in English | MEDLINE | ID: mdl-30825505

ABSTRACT

Seasonally-breeding species experience significant and predictable shifts in vocal behaviour; however, it is unclear to what extent this is true for species that breed opportunistically. The Australian zebra finch is an opportunistically breeding species, which means individuals must time breeding bouts based on many environmental factors. Here we tested the effect of experimental water restriction, which suppresses reproductive readiness in zebra finches, on vocal behaviour of males and females. More specifically, we quantified the effect of water restriction on three parameters of vocal behaviour in pair-bonded zebra finches: vocal activity, patterns of vocal exchanges, and the acoustic structure of vocalisations (calls and male song). We found that water restriction caused a decrease in vocal output (both song and call rate). Additionally, water restriction affected the composition of male songs. However, there was no effect of water restriction on the patterns of calling exchanges for monogamous partners (temporal coordination and turn taking). Finally, water restriction had vocalisation- and sex-specific effects on the acoustic structure of song syllables and calls. Because the direction of these effects were vocalisation- and sex- specific, there may be different mechanisms underlying the effects of water restriction on acoustic structure depending on context. These results contribute to the growing body of research highlighting the rich communicative potential of bird calls. Our current results raise the hypothesis that zebra finches may use changes in vocal behaviour and/or the structure of vocalisations of their conspecifics when making breeding decisions.


Subject(s)
Acoustics , Finches , Reproduction , Vocalization, Animal , Water Resources , Animals , Australia , Female , Male , Pair Bond , Sexual Behavior, Animal , Water , Water Supply
17.
Behav Neurosci ; 132(6): 536-546, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30284861

ABSTRACT

Although steroids are widely known to affect behavior through activation of nuclear/cytosolic receptors ("genomic" effects), steroids can also rapidly affect behavior via modulation of signal transduction pathways ("nongenomic," fast actions, or rapid effects). In zebra finches, there is evidence that sex steroids have context-specific effects on pair-maintenance behavior, on both acute and chronic timescales. Here, we quantified the effects of orally administered testosterone and 17ß-estradiol (E2) on pair-maintenance behavior. We show that E2 rapidly affects female, but not male, affiliative behavior profiles during a partner separation and reunion paradigm. More specifically, E2 rapidly (within 5-15 min of administration) increased females' spatial proximity to a partner. This effect was present regardless of breeding condition (water restriction or water ad libitum). Combined, these results contribute to a growing body of evidence implicating sex steroids in the regulation of prosocial behavior. (PsycINFO Database Record (c) 2018 APA, all rights reserved).


Subject(s)
Estradiol/metabolism , Finches/metabolism , Pair Bond , Sex Characteristics , Testosterone/metabolism , Animals , Estradiol/administration & dosage , Female , Male , Social Behavior , Spatial Behavior/drug effects , Spatial Behavior/physiology , Testosterone/administration & dosage
18.
J Pathol ; 246(2): 217-230, 2018 10.
Article in English | MEDLINE | ID: mdl-29984492

ABSTRACT

Obesity and its metabolic complications are characterized by subclinical systemic and tissue inflammation. In rodent models of obesity, inflammation and metabolic impairments are linked with intestinal barrier damage. However, whether intestinal permeability is altered in human obesity remains to be investigated. In a cohort of 122 severely obese and non-obese patients, we analyzed intestinal barrier function combining in vivo and ex vivo investigations. We found tight junction impairments in the jejunal epithelium of obese patients, evidenced by a reduction of occludin and tricellulin. Serum levels of zonulin and LPS binding protein, two markers usually associated with intestinal barrier alterations, were also increased in obese patients. Intestinal permeability per se was assessed in vivo by quantification of urinary lactitol/mannitol (L/M) and measured directly ex vivo on jejunal samples in Ussing chambers. In the fasting condition, L/M ratio and jejunal permeability were not significantly different between obese and non-obese patients, but high jejunal permeability to small molecules (0.4 kDa) was associated with systemic inflammation within the obese cohort. Altogether, these results suggest that intestinal barrier function is subtly compromised in obese patients. We thus tested whether this barrier impairment could be exacerbated by dietary lipids. To this end, we challenged jejunal samples with lipid micelles and showed that a single exposure increased permeability to macromolecules (4 kDa). Jejunal permeability after the lipid load was two-fold higher in obese patients compared to non-obese controls and correlated with systemic and intestinal inflammation. Moreover, lipid-induced permeability was an explicative variable of type 2 diabetes. In conclusion, intestinal barrier defects are present in human severe obesity and exacerbated by a lipid challenge. This paves the way to the development of novel therapeutic approaches to modulate intestinal barrier function or personalize nutrition therapy to decrease lipid-induced jejunal leakage in metabolic diseases. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Diabetes Mellitus, Type 2/metabolism , Inflammation/metabolism , Intestinal Absorption/drug effects , Jejunum/drug effects , Lipids/administration & dosage , Obesity/metabolism , Acute-Phase Proteins , Adult , Aged , Caco-2 Cells , Carrier Proteins/blood , Case-Control Studies , Cholera Toxin/blood , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/physiopathology , Female , Haptoglobins , Humans , Inflammation/complications , Inflammation/physiopathology , Jejunum/metabolism , Jejunum/physiopathology , MARVEL Domain Containing 2 Protein/metabolism , Male , Membrane Glycoproteins/blood , Micelles , Middle Aged , Obesity/complications , Obesity/physiopathology , Occludin/metabolism , Permeability , Protein Precursors , Tight Junctions/metabolism , Young Adult
19.
Biochimie ; 150: 1-7, 2018 Jul.
Article in English | MEDLINE | ID: mdl-29705133

ABSTRACT

p-Cresyl glucuronide (p-CG) is a by-product of tyrosine metabolism that accumulates in patients with end-stage renal disease. p-CG binding to human serum albumin in physiological conditions (37 °C, pH 7.40) was studied by ultrafiltration (MWCO 10 kDa) and data were analyzed assuming one binding site. The estimated value of the association constant was 2.77 × 103 M-1 and a maximal stoichiometry of 3.80 mol per mole. At a concentration relevant for end-stage renal patients, p-CG was 23% bound to albumin. Competition experiments, using fluorescent probes, demonstrated that p-CG did not bind to Sudlow's site I or site II. The p-CG did not interfere with the binding of p-cresyl-sulfate or indoxyl sulfate to serum albumin.


Subject(s)
Cresols/chemistry , Glucuronides/chemistry , Serum Albumin, Human/chemistry , Humans , Protein Binding
20.
Front Psychol ; 7: 1816, 2016.
Article in English | MEDLINE | ID: mdl-27965602

ABSTRACT

Social networks are often inferred from spatial associations, but other parameters like acoustic communication are likely to play a central role in within group interactions. However, it is currently difficult to determine which individual initiates vocalizations, or who responds to whom. To this aim, we designed a method that allows analyzing group vocal network while controlling for spatial networks, by positioning each group member in equidistant individual cages and analyzing continuous vocal interactions semi-automatically. We applied this method to two types of zebra finch groups, composed of either two adult females and two juveniles, or four young adults (juveniles from the first groups). Young often co-occur in the same social group as adults but are likely to have a different social role, which may be reflected in their vocal interactions. Therefore, we tested the hypothesis that the social structure of the group influences the parameters of the group vocal network. We found that groups including juveniles presented periods with higher level of activity than groups composed of young adults. Using two types of analyses (Markov analysis and cross-correlation), we showed that juveniles as well as adults were more likely to respond to individuals of their own age-class (i.e. to call one after another, in terms of turn-taking, and within a short time-window, in terms of time delay). When juveniles turned into adulthood, they showed adult characteristics of vocal patterns. Together our results suggest that vocal behavior changes during ontogeny, and individuals are more strongly connected with individuals of the same age-class within acoustic networks.

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