Biology subjects

Dupont, C.

Publications and source records attributed to Dupont, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Rad55-Rad57 and Srs2 regulate homology search onset, coordination, reach and inactivation

DNA double-strand break (DSB) repair by homologous recombination entails the coordinated search for a homologous dsDNA molecule by two heterotypic Rad51-ssDNA filaments in eukaryotes. How homology search is regulated in cells remains largely unknown. Using genomic and molecular assays to track spatial chromatin organization and early recombination intermediates, we investigated the roles in homology search of two antagonistic regulators of Rad51-ssDNA filaments metabolism in S. cerevisiae: the Rad51 paralogs Rad55-Rad57 and the 3'-5' ssDNA translocase Srs2. Srs2 promoted the coordinated search between filaments on each DSB ends and inactivated homology search following homology identification. Rad55-Rad57 both stimulated the formation of Rad51-ssDNA filaments and protected them against disruption by Srs2. Together, Rad55-Rad57 and Srs2 enacted a structural proof-reading that resulted in stiffer Rad51-ssDNA filaments competent for genome-wide homology search. This work reveals multiple ways by which the control of Rad51-ssDNA filament metastability by the individual and joint activities of Rad55-Rad57 and Srs2 regulate homology search onset, coordination, reach and inactivation.

molecular biology↗

bioRxiv2026

Phosphatase-mediated mitigation of rare earth element toxicity to Pseudomonas putida

Anthropogenic activities are driving an increasing flux of rare earth elements (REE) into environmental compartments, raising concerns about their biological impact, particularly on microorganisms that sustain ecosystem functioning. Here, we provide a systematic assessment of the toxicity of all 16 REE toward Pseudomonas putida KT2440, a soil bacterium that can use these metals as enzyme cofactors. Dose-response growth inhibition assays revealed high sensitivity to light REE. Toxicity correlated strongly with ionic radius, with IC50 values ranging from 0.3 uM for lanthanum to 10 uM for scandium. Serial propagation of P. putida under gradually increasing REE stress yielded resistant populations, from which two stably resistant strains were isolated. Genome resequencing showed that both strains carried a single mutation in uxpB, encoding an alkaline phosphatase. Gene deletion and overexpression experiments, together with phosphatase activity measurements, confirmed the involvement of uxpB in REE resistance. Our findings reveal a previously unrecognized mechanism of tolerance to REE, suggesting that mutations enhancing phosphatase activity promote phosphate release from organic phosphorus compounds and REE immobilization, thereby mitigating toxicity.

microbiology↗

bioRxiv2026

Molecular determinants of Bcl-xL membrane insertion - Structural plasticity exploration in solution and in nanodiscs identifies IsoAsp deamidation as a loss-of function mechanism in vivo.

Multi-domain Bcl-2 family proteins share the ability to form dimers and oligomers, regardless of their pro- or anti-apoptotic activity. Homotypic interactions (pro-pro and anti-anti) and heterotypic interactions (pro-anti) are well-documented, but the role of higher-order organization in their survival/death functions and membrane interactions remains largely unresolved. Looking into anti-apoptotic Bcl-xL, essentially engineered/truncated proteoforms lacking the disordered loop and/or the hydrophobic C-terminal helix, have been used as proxies of the full-length (FL) protein, to elaborate on structural transitions and intermediate states between monomers and homooligomers prior to membrane insertion. Using a minimalist approach with recombinant FL-Bcl-xL (aa 1-233) and artificial nano-membranes, we demonstrate that both the loop and the C-terminal helix are potent contributors to Bcl-xL structural plasticity. Unlike 3D domain swapping (3DDS) dimers resolved with the C-terminal truncated protein, FL-Bcl-xL organized in solution as dimers bridging the unique Cys151 from two monomers. This spontaneous fold indicates that the C-terminal helix drives FL-Bcl-xL to explore different conformations than truncated Bcl-xL. Yet, dimerization was not a prerequisite for membrane insertion into nanodiscs and Cys151 did not contribute to Bcl-xL survival functions in cells. These data support monomeric Bcl-xL as the minimal functional unit in membranes. Further exploring the frequently deleted disordered loop, we discovered that deamidation of Asn52 and Asn66 in IsoAsp, but not in Asp, impairs membrane insertion into nanodiscs. Thus, this reductionist biochemical approach clarifies the loss of tumorigenic function we observed for deamidated Bcl-xL in xenograft experiments in vivo.

biochemistry↗

bioRxiv2025

Verapamil limits inflammation by restoring VGCC-driven epithelial Ca2+ in models of cystic fibrosis

RationaleIn cystic fibrosis (CF), caused by mutations in the CFTR gene, excessive neutrophilic inflammation drives lung damage and premature mortality. Current anti-inflammatory therapies have limited efficacy, partly due to an incomplete understanding of the mechanisms underlying CF-associated inflammation. Increased epithelial Ca{superscript 2} signaling has been implicated, but how CFTR dysfunction perturbs the CFTR/Ca{superscript 2} axis to promote inflammation remains unclear. ObjectivesUsing Cftr-depleted zebrafish and human approaches, we sought to i) define how CFTR dysfunction alters epithelial Ca{superscript 2} signaling and promotes inflammation, and ii) assess whether Ca{superscript 2} channel antagonists can attenuate inflammatory damage in CF. Methods and ResultsWe generated a transgenic zebrafish line expressing the Ca{superscript 2} reporter GCaMP6 under an epithelial promoter to dynamically map epithelial Ca{superscript 2} activity in vivo. Cftr-depleted zebrafish exhibited exaggerated epithelial Ca{superscript 2} elevations following injury compared with wild-type animals. Genetic or pharmacological inhibition of L-type voltage-gated Ca{superscript 2} channels (VGCCs) normalized epithelial Ca{superscript 2} responses and reduced both oxidative stress and neutrophil recruitment. Among FDA-approved VGCCs antagonists tested, only verapamil promoted resolution of neutrophilic inflammation and improved tissue repair in CF zebrafish. Mechanistically, verapamil reduced aberrant epithelial Ca{superscript 2} fluxes, ROS generation and NF-{kappa}B activation. These effects were confirmed in the human CF epithelial cell CFBE41o-, where verapamil reduced Ca2+ and oxidative stress. ConclusionsThese findings establish dysregulated Ca{superscript 2} signaling via L-type VGCCs as a pathogenic driver of inflammation in CF and identify verapamil as a promising therapeutic candidate. By restoring Ca{superscript 2} and oxidative homeostasis, verapamil alleviates inflammatory damage, supporting its repurposing as a candidate anti-inflammatory therapy in CF.

immunology↗

bioRxiv2025

Achromobacter xylosoxidans modulates Pseudomonas aeruginosa virulence through a multi-target mechanism of competition

The colonization and persistence of Pseudomonas aeruginosa in chronically diseased lungs are driven by the production of various virulence factors. However, pulmonary infections in cystic fibrosis (CF) patients are predominantly polymicrobial. While Achromobacter xylosoxidans is an opportunistic pathogen in these patients, its impact on P. aeruginosa virulence during co-infection remains largely unknown. This study investigated the interaction between P. aeruginosa and two clonally related A. xylosoxidans strains, Ax 198 and Ax 200, co-isolated from a CF patient sputum. We found that the interaction between P. aeruginosa and co-isolated A. xylosoxidans was strain-dependent, with the Ax 200 strain significantly reducing P. aeruginosa virulence in a zebrafish model, providing the first in vivo evidence of interaction between these two species during co-infection. Proteomic analysis revealed that the P. aeruginosa proteome was differently impacted by the two A. xylosoxidans strains, with Ax 200 altering proteins involved in biofilm formation, swimming motility, iron acquisition, and secretion systems. These proteomic findings were further validated by phenotypic assays, which confirmed that A. xylosoxidans affected major P. aeruginosa virulence phenotypes, including biofilm formation, swimming motility, and siderophore production. Genetic analysis also confirmed that distinct regulatory mechanisms, including mechanisms involved in the iron cycle, may account for the strain-dependent interaction effects of A. xylosoxidans with P. aeruginosa. These findings reveal a novel multi-target competitive mechanism through which A. xylosoxidans significantly disrupts P. aeruginosa virulence. IMPORTANCEPseudomonas aeruginosa, a major human pathogen, is a leading cause of mortality in cystic fibrosis (CF) patients. Understanding its virulence mechanisms is critical for developing effective infection management strategies. Given the polymicrobial nature of CF infections, it is essential to investigate interspecies interactions that may influence bacterial virulence. While A. xylosoxidans is recognized as an opportunistic pathogen in CF, its impact on P. aeruginosa virulence during co-infection remains largely unexplored. Deciphering the molecular basis of P. aeruginosa virulence in polymicrobial settings could reveal novel and specific therapeutic targets to improve treatment strategies.

microbiology↗

bioRxiv2024

Decoding primitive endoderm - epiblast interactions using mouse ICM embryoids

Stem cell-based embryo models are promising alternatives for investigating early embryogenesis. We introduce two distinct models to replicate the dynamics between extra-embryonic endoderm and epiblast during mouse embryonic development. Inducible Gata6 (iGata6) embryoid bodies (EBs), exclusively derived from iGata6 embryonic stem (ES) cells, are valuable for modeling the position-dependent development of the primitive endoderm. Inner cell mass (ICM) embryoids, conversely, efficiently formed by aggregating wild-type and iGata6 ES cells, accurately and at a comparable pace simulate in vivo development from E3.5 to E7.5. Notably, ICM embryoids model cell sorting and through a rosette-like stage, the transition of the epiblast from naive to primed pluripotency. Furthermore, the absence of extra-embryonic ectoderm-like cells in this model, directs both the epiblast and visceral endoderm towards an anterior developmental fate. As such, iGata6 EBs and ICM embryoids are powerful tools for advancing our understanding of cell fate decisions during early embryonic development in mice.

developmental biology↗

bioRxiv2024

Condensin loop extrusion properties, roadblocks, and role in homology search in S. cerevisiae

The in vivo mechanism, cis-acting roadblocks, and biological functions of loop extrusion by eukaryotic SMC complexes are incompletely defined. Here, we identify condensin-dependent Hi-C contact stripes at the Recombination Enhancer (RE) and the rDNA in S. cerevisiae. The RE is an autonomous condensin loading site only active in MATa cells from which oriented, unidirectional loop extrusion proceeds with an estimated processivity [~]150-250 kb and a density [~]0.04-0.18 that varies across the cell cycle. Centromeres, replication forks and highly-transcribed RNA PolII-dependent genes are roadblocks for condensin. Cohesin is not an obstacle for condensin while Top2 promotes its loop extrusion activity. A DNA double-strand break at MAT blocks loop extrusion, resulting in the establishment of a [~]170 kb-long RE-MAT loop. The RE and the DSB are required and sufficient to form this site-specific loop, which promotes RE-proximal homology identification in the early stages of recombinational DNA break repair. We propose that the juxtaposition of the broken MATa site and its target HML donor is the relevant structure by which condensin promotes MATa-to- switching.

molecular biology↗

bioRxiv2024

The multifunction Coxiella effector Vice stimulates macropinocytosis and interferes with the ESCRT machinery

Intracellular bacterial pathogens divert multiple cellular pathways to establish their niche and persist inside their host. Coxiella burnetii, the causative agent of Q fever, secretes bacterial effector proteins via its Type 4 secretion system to generate a Coxiella-containing vacuole (CCV). Manipulation of lipid and protein trafficking by these effectors is essential for bacterial replication and virulence. Here, we have characterized the lipid composition of CCVs and discovered that the effector Vice interacts with phosphoinositides and membranes enriched in phosphatidylserine (PS) and lysobisphosphatidic acid (LBPA). Remarkably, eukaryotic cells ectopically expressing Vice present compartments that resemble early CCVs in both morphology and composition. We discovered that the biogenesis of these compartments relies on the double function of Vice. The effector protein initially localizes at the plasma membrane of eukaryotic cells where it triggers the internalization of large vacuoles by macropinocytosis. Then, Vice stabilizes these compartments by perturbing the ESCRT machinery and inhibiting the formation of intraluminal vesicles (ILVs). Collectively, our results reveal that Vice is an essential C. burnetii effector protein capable of hijacking two major cellular pathways to shape the bacterial replicative niche. Significance statementCoxiella burnetii is a unique bacterial pathogen that secretes more than a hundred effector proteins to manipulate cellular processes and establish a replicative niche, the Coxiella-containing vacuole (CCV). Our study identified host cell lipids that are actively recruited by the bacterium to the CCV. Using a library of effector mutants, we identified the protein Vice (for Vacuole-inducing Coxiella effector) as the first bacterial effector capable of interacting with lysobisphosphatydic acid-enriched membranes and accumulating this lipid to CCVs. We show that Vice is also capable of stimulating macropinocytosis and inhibiting the ESCRT machinery. Together, our data show how a single bacterial effector can manipulate different cellular processes to favor the biogenesis of a bacterial pathogens niche.

microbiology↗

bioRxiv2023

Host-Microbiome Associations in Saliva Predict COVID-19 Severity

Established evidence indicates that oral microbiota plays a crucial role in modulating host immune responses to viral infection. Following Severe Acute Respiratory Syndrome Coronavirus 2 - SARS-CoV-2 - there are coordinated microbiome and inflammatory responses within the mucosal and systemic compartments that are unknown. The specific roles that the oral microbiota and inflammatory cytokines play in the pathogenesis of COVID-19 are yet to be explored. We evaluated the relationships between the salivary microbiome and host parameters in different groups of COVID-19 severity based on their Oxygen requirement. Saliva and blood samples (n = 80) were collected from COVID-19 and from non-infected individuals. We characterized the oral microbiomes using 16S ribosomal RNA gene sequencing and evaluated saliva and serum cytokines using Luminex multiplex analysis. Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. The hierarchical classification of COVID-19 status and respiratory severity using multiple modalities separately (i.e., microbiome, salivary cytokines, and systemic cytokines) and simultaneously (i.e., multi-modal perturbation analyses) revealed that the microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity, followed by the multi-modal. Our findings suggest that oral microbiome and salivary cytokines may be predictive of COVID-19 status and severity, whereas atypical local mucosal immune suppression and systemic hyperinflammation provide new cues to understand the pathogenesis in immunologically naive populations. Significance StatementThe oral mucosa is one of the first sites encountered by bacterial and viral infections, including SARS-CoV-2. It consists of a primary barrier occupied by a commensal oral microbiome. The primary function of this barrier is to modulate immunity and provide protection against invading infection. The occupying commensal microbiome is an essential component that influences the immune systems function and homeostasis. The present study showed that the host oral immune response performs unique functions in response to SARS-CoV-2 when compared to systemic responses during the acute phase. We also demonstrated that there is a link between oral microbiome diversity and COVID-19 severity. Additionally, the salivary microbiome was predictive of not only disease status but also severity.

immunology↗

bioRxiv2022

Novel uAUG creating variants in the 5UTR of ENG causing Hereditary Hemorrhagic Telangiectasia

Hereditary Hemorrhagic Telangiectasia (HHT) is a rare vascular disorder causing abnormal vessel formation and characterized by autosomal dominant transmission. The associated considerable variability in symptoms and clinical severity complicate the management of the disease. In clinical routine, 3 main genes, ACVRL1 (also known as ALK1), ENG and SMAD4 are screened for pathogenic variants at the origin of HHT. About 80% of HHT cases are caused by pathogenic coding variants in ACVRL1 and ENG. However, at least 15% remain with no molecular explanations in the 3 main genes. We here report the identification of 2 never reported variants, c.-79C>T and c.-68G>A, in the 5UTR of ENG in 2 unrelated HHT patients. These 2 variants are predicted to create upstream AUGs (uAUGs) in the 5UTR, which are in frame with a stop codon located within the CoDing Sequence (CDS), thus generating Overlapping upstream Open reading frames (uoORFs). In other cases, uAUGs can lead to fully upstream ORFs (uORFs) when associated with stop codons located within the 5UTR or to elongated CDS (eCDS) when in frame with the CDS and associated with the main stop codon. In order to assess the pathogenicity of these ENG variants, we performed in vitro functional assays based on the expression of wild-type and mutant constructs in human cells. We found that these 5UTR ENG variants were associated with a decrease of protein levels in HeLa and HUVEC cells. They were also associated with a decreased ability to activate BMP9-stimulated ALK1 receptor in a BMP-response element (BRE) assay. This assay is a mandatory element before providing a definitive molecular diagnosis and has been so far applied only on coding ENG variants. We applied the same experimental workflow on 3 additional uoORF-creating variants (c.-142A>T, c.-127C>T and c.-10C>T) and one eCDS-creating variant (c.-9G>A) in the 5UTR of ENG previously reported in HHT patients. We found that all the analysed uoORF-creating variants alter endoglin levels and function. A comparison of our experimental results with patients clinical characteristics suggests that uoORF-creating variants leading to ENG protein levels [≤] 40% in vitro would be associated with HHT. Additional experiments relying on an artificial deletion in our mutated constructs show that created uAUGs predicted to create uoORFs are able to initiate the translation indicating that the associated effect is likely caused by an alteration of the translation mechanism. Overall, we here identified two never reported 5UTR ENG variations in HHT patients and shed new lights on the role of upstream ORFs on ENG regulation. Our findings contribute to the amelioration of molecular diagnosis in HHT.

molecular biology↗

bioRxiv2021

Variation in colour signals among Sarracenia pitcher plants and the potential role of areoles in the attraction of flying Hymenoptera

Sarracenia insectivorous plants show a diversity of visual features in their pitchers but their perception by insects and their role in attraction, have received little attention. They also vary in prey composition, with some species trapping more flying Hymenoptera, such as bees. To test the hypothesis of a link between visual signal variability and prey segregation ability, and to identify which signal could attract flying Hymenoptera, we characterised, the colour patterns of 32 pitchers belonging to four taxa, modelled their perception by flying Hymenoptera, and examined the prey they trapped. The pitchers of the four taxa differed in colour patterns, with notably two long-leaved taxa displaying clear areoles, which contrasted strongly in colour and brightness with the vegetative background and with other pitcher areas in the eyes of flying Hymenoptera. These taxa trapped high proportion of flying hymenoptera. This suggests that contrasting areoles may act as a visual lure for flying Hymenoptera, making plants particularly visible to these insects. Prey capture also differed according to pitcher stage, morphology, season and visual characteristics. Further studies on prey visitation are needed to better understand the link between prey capture and attraction feature.

ecology↗

bioRxiv2021

Roscovitine exacerbates Mycobacterium abscessus infection by reducing NADPH oxidase-dependent neutrophil trafficking

Persistent neutrophilic inflammation associated with chronic pulmonary infection causes progressive lung injury and eventually death in individuals with cystic fibrosis (CF), a genetic disease caused by bi-allelic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We therefore examined whether Roscovitine, a cyclin-dependent kinase inhibitor that (in other conditions) reduces inflammation while promoting host defence, might provide a beneficial effect in the context of CF. Herein, using CFTR-depleted zebrafish larvae as an innovative vertebrate model of CF immuno-pathophysiology, combined with murine and human approaches, we sought to determine the effects of Roscovitine on innate immune responses to tissue injury and pathogens in CF condition. We show that Roscovitine exerts anti-inflammatory and pro-resolution effects in neutrophilic inflammation induced by infection or tail amputation in zebrafish. Roscovitine reduces overactive epithelial ROS-mediated neutrophil trafficking, by reducing DUOX2/NADPH-oxidase activity, and accelerates inflammation resolution by inducing neutrophil apoptosis and reverse migration. Importantly, while Roscovitine efficiently enhances intracellular bacterial killing of Mycobacterium abscessus in human CF macrophages ex vivo, we found that treatment with Roscovitine results in worse infection in mouse and zebrafish models. By interfering with DUOX2/NADPH oxidase-dependent ROS production, Roscovitine reduces the number of neutrophils at infection sites, and consequently compromises granuloma formation and maintenance, favouring extracellular multiplication of M. abscessus and more severe infection. Our findings bring important new understanding of the immune-targeted action of Roscovitine and have significant therapeutic implications for safety targeting inflammation in CF.

microbiology↗

bioRxiv2021

Microbiota and stress: a loop that impacts memory

Chronic stress and the gut microbiota appear to comprise a feed-forward loop, which contributes to the development of depressive disorders. Evidence suggests that memory can also be impaired by either chronic stress or microbiota imbalance. However, it remains to be established whether these could be a part of an integrated loop model and be responsible for memory impairments. To shed light on this, we used a two-pronged approach in Japanese quail: first stress-induced alterations in gut microbiota were characterized, then we tested whether this altered microbiota could affect brain and memory function when transferred to a germ-free host. The cecal microbiota of chronically stressed quails was found to be significantly different from that of unstressed individuals with lower and {beta} diversities and increased Bacteroidetes abundance largely represented by the Alistipes genus, a well-known stress target in rodents and humans. The transfer of this altered microbiota into germ-free quails decreased their spatial and cue-based memory abilities as previously demonstrated in the stressed donors. The recipients also displayed increased anxiety-like behavior, reduced basal plasma corticosterone levels and differential gene expression in the brain. Furthermore, cecal microbiota transfer from a chronically stressed individual was sufficient to mimic the adverse impact of chronic stress on memory in recipient hosts and this action may be related to the Alistipes genus. Our results provide evidence of a feed-forward loop system linking the microbiota-gut-brain axis to stress and memory function and suggest that maintaining a healthy microbiota could help alleviate memory impairments linked to chronic stress.

animal behavior and cognition↗

bioRxiv2021

The Alzheimer's disease genetic risk factor BIN1 induces isoform-dependent neurotoxicity through early endosome defects

The Bridging Integrator 1 (BIN1) gene is a major susceptibility gene for Alzheimers disease (AD). Deciphering its pathophysiological role is challenging due to its numerous isoforms. Here we observed in Drosophila that human BIN1 isoform1 (BIN1iso1) overexpression, contrary to BIN1iso8 and BIN1iso9, induced an accumulation of endosomal vesicles and neurodegeneration. Systematic search for endosome regulators able to prevent BIN1iso1-induced neurodegeneration indicated that a defect at the early endosome level is responsible for the neurodegeneration. In human induced neurons (hiNs) and cerebral organoids, BIN1 knock-out resulted in the narrowing of early endosomes. This phenotype was rescued by BIN1iso1 but not BIN1iso9 expression. Finally, BIN1iso1 overexpression also led to an increase in the size of early endosomes and neurodegeneration in hiNs. Altogether, our data demonstrate that the AD susceptibility gene BIN1, and especially BIN1iso1, contributes to early-endosome size deregulation, which is an early pathophysiological hallmark of AD pathology.

neuroscience↗

bioRxiv2021

Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells.

Rett Syndrome is a neurodevelopmental disorder in girls that is caused by heterozygous inactivation of the chromatin remodeler gene MECP2. Rett Syndrome may therefore be treated by reactivation of the wild type copy of MECP2 from the inactive X chromosome. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model system for monitoring Mecp2 reactivation that is more sensitive and versatile than any bioluminescent and fluorescent system currently available. The model consists of neural stem cells derived from female mice with a dual reporter system where MECP2 is fused to NanoLuciferase and TdTomato on the inactive X chromosome. We show by bioluminescence and fluorescence that Mecp2 is synergistically reactivated by 5-Aza treatment and Xist knockdown. As expected, other genes on the inactive X chromosome are also reactivated, the majority of which overlaps with genes reactivated early during reprogramming of mouse embryonic fibroblasts to iPSCs. Genetic and epigenetic features such as CpG density, SINE elements, distance to escapees and CTCF binding are consistent indicators of reactivation, whereas different higher order chromatin areas are either particularly prone or resistant to reactivation. Our MeCP2 reactivation monitoring system thereby suggests that genetic and epigenetic features on the inactive X chromosome affect reactivation of its genes, irrespective of cell type or procedure of reactivation.

molecular biology↗

bioRxiv2019

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a common syntax has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG)-based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe \"universal Loop\" (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4n-1). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/744854v2_ufig.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@c36f4forg.highwire.dtl.DTLVardef@c0b007org.highwire.dtl.DTLVardef@64c810org.highwire.dtl.DTLVardef@8a94b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2019

The concentration of heterotrophic growth substrates in culture medium is a crucial determinant of the culturability of subsurface soil microbes

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted extracted cells into one of two custom-designed defined growth media that differed only by a 100-fold difference in the concentration of amino acids and organic carbon. Across both media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria. The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria. We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically-divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic-acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and the concentration of substrates in culture medium influences the culturability of specific microbial lineages. ImportanceIsolating environmental microbes and studying their physiology under controlled conditions is an essential aspect of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities--the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.

microbiology↗

bioRxiv2019

Sedentary behavior, physical inactivity and body composition in relation to idiopathic infertility among men and women

BackgroundPhysical activity and sedentary behavior has inconsistent effects on fertility. High body mass index is associated with infertility but to our knowledge, very few studies have explored body composition in association to fertility.\n\nObjectiveTo assess the association between physical inactivity, sedentary behavior, body composition and idiopathic infertility in French men and women.\n\nDesignWe conducted a case-control multicentric observational study. 159 infertile (79 men and 80 women) and 143 fertile (72 men and 71 women) were recorded in four fertility centers.\n\nMain Outcome MeasuresParticipants completed self-administered questionnaires on sociodemographic and lifestyle characteristics, dietary intake, physical activity and sedentary behavior. Anthropometrics were measured, and bioelectrical impedance analysis was used to estimate body composition. Multivariable logistic regression was used to analyze the association of fertility with PA level and sedentary behavior.\n\nResultsIn men, being physically inactive (Odd ratio [OR] 2.20; 95% confidence interval [CI], 1.06, 4.58) and having fat mass greater than the reference values for their age (OR 2.83; 95%CI, 1.31, 6.10) were positively associated with infertility. Sedentary behavior and fat-free mass were not related to infertility in men. In women, sedentary behavior (OR 3.61; 95%CI, 1.58, 8.24), high body fat (OR 3.16; 95%CI, 1.36, 7.37) and low fat-free mass (OR 2.65; 95%CI, 1.10, 6.37) were associated with infertility. PA level was not associated with fertility in women.\n\nConclusionsThis study suggests that sedentary behavior and physical inactivity would represent two independent risk factors associated with fertility. The various elements that make up physical activity (frequency, intensity, time, and type of exercise) and the interrupting time spent sitting should be considered. Body composition variation should be explored further in relation to the biological pathways involved in idiopathic infertility. Moreover, the improvement of lifestyle factors should be considered in infertility treatment.

epidemiology↗