Biology subjects

Marin, M.

Publications and source records attributed to Marin, M..

At least 19 recordsLinked to original sources

bioRxiv2026

p21(CIP1/WAF1)-mediated partial senescence supports steroidogenesis and therapy resistance in primary prostate cancer cultures

BackgroundProgression of prostate cancer to castration-resistant disease is driven by early adaptive mechanisms that remain poorly defined. Increasing evidence suggests that senescence-associated programs and intratumoral steroidogenesis may contribute to therapeutic resistance, but their functional interplay in hormone-naive disease is unclear. MethodsHormone-naive primary prostate cancer cultures (hnPCs) were established from diagnostic biopsies and characterized for proliferation, therapeutic response, senescence markers, and steroidogenic gene expression. Functional relevance of CDKN1A was assessed by knockdown experiments. Public transcriptomic datasets from ETS fusion-negative, AR signaling inhibitor-naive metastatic castration-resistant prostate cancer (mCRPC) were interrogated for clinical validation. ResultshnPCs exhibited low proliferative capacity yet intrinsic resistance to androgen deprivation therapy and docetaxel. Most cultures displayed coordinated overexpression of CDKN1A/p21CIP1 together with steroidogenic enzymes, particularly AKR1C3, alongside p16INK4a expression and SA-{beta}-galactosidase activity, consistent with a partial senescence-like state. CDKN1A depletion selectively reduced AKR1C3 expression and increased proliferation in a subset of cultures, indicating that p21 maintains specific senescence-associated features while permitting adaptive plasticity. Analysis of ETS fusion-negative, ARSI-naive mCRPC tumors revealed positive correlations between CDKN1A and steroidogenic genes, supporting the translational relevance of this program. ConclusionsThese findings identify a previously underrecognized CDKN1A-associated partial senescence program that supports steroidogenic reprogramming, survival, and early therapeutic resistance in aggressive prostate cancer. This adaptive state may predispose tumors to progression toward castration resistance and represents a potential biomarker and therapeutic vulnerability in high-risk, ETS-negative disease.

cancer biology↗

bioRxiv2025

SERINC5 co-expressed with HIV-1 Env or present in a target membrane destabilizes small fusion pores leading to their collapse

SERINC5 is a multipass membrane protein that reduces infectivity of retroviruses and other enveloped viruses through incorporation into budding virions and inhibiting viral fusion. Several modes of anti-HIV activity of SERINC5 have been reported, including binding to Env glycoprotein, induction of conformational changes and destabilization of Env, as well as disruption of trans-membrane asymmetry of viral envelope. All these reported anti-HIV mechanisms involve SERINC5 incorporation into progeny virions, while there is very little information regarding a potential antiviral activity of SERINC5 in target cells. Here, we show that SERINC5 expressed in target cells efficiently inhibits fusion with cells expressing sensitive but not resistant HIV-1 strains. We show that this activity does not result from downregulation of CD4 or coreceptors on target cells or interference with the formation of ternary Env/CD4/coreceptor complexes. We further demonstrate that SERINC5 destabilizes small fusion pores causing their collapse and that this block can be rescued by incorporation of phosphatidylserine to either effector (Env-expressing) or target cells. Interestingly, we did not detect a significant reduction of HIV-1 pseudovirus fusion with SERINC5 expressing target cells, while virus-mediated cell-cell fusion (fusion-from-without) was inhibited, suggesting a potential role of virus entry pathway in SERINC5 restriction. Collectively, our results reveal a novel mechanism of inhibition of HIV-1 fusion by SERINC5 through destabilization of small fusion pores in a manner that depends on lipid composition. ImportanceSERINC5 incorporates into virions produced by infected cells and inhibits viral fusion with target cells through a poorly understood mechanism. Here, we show that SERINC5 blocks HIV-1 Env mediated cell fusion when expressed in either effector (Env-expressing) or target cells. Inhibition of Env-mediated fusion by SERINC5 expressed in target cells is not through reduction in receptor or coreceptor expression or interference with Envs ability to engage a requisite number of receptors and coreceptors. We demonstrate that the block of fusion is at a post-hemifusion stage of small fusion pores that collapse when SERINC5 is present in effector or target membrane and that this block is rescued by incorporation of specific anionic lipids, such as phosphatidylserine. These findings reveal a previously unappreciated mode of HIV-1 restriction through destabilization of small fusion pores that occurs irrespective of SERINC5 localization in either of fusing membranes.

microbiology↗

bioRxiv2025

Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales

Ethological behaviours are a powerful tool for neuroscience since they leverage the robust neural computations shaped by the species evolution to study the neural basis of cognitive functions. However, such behaviours are often transitory and dependent on factors that vary over space, time and number of individuals, making them difficult to capture with standard laboratory tasks. Here we present Aeon, an open-source platform designed for continuous, long-term study of self-guided behaviours in multiple mice and simultaneous recording of brain activity within large, customizable habitats. By integrating specialized modules for navigation, nesting and sleeping, escaping, foraging, and social interaction, Aeon enables the expression of key ethological behaviours while achieving experimental control and multi-dimensional quantifications from sub-millisecond to month-long durations. Its software architecture ensures robust data acquisition via many synchronized data streams and delivers a new standardised, unified data format that yields seamless, integrated analysis pipelines. Using assays such as digging-to-threshold and social foraging, Aeon reveals how mice adapt strategies in a changing environment and in response to conspecifics. Aeon bridges ecological relevance with rigorous experimental control to advance our understanding of how neural circuit activity gives rise to a range of highly conserved and adaptive behaviours.

neuroscience↗

bioRxiv2024

Proteostasis and metabolic dysfunction in a distinct subset of storage-induced senescent erythrocytes targeted for clearance

Although refrigerated storage slows the metabolism of volunteer donor RBCs, cellular aging still occurs throughout this in vitro process, which is essential in transfusion medicine. Storage-induced microerythrocytes (SMEs) are morphologically-altered senescent RBCs that accumulate during storage and which are cleared from circulation following transfusion. However, the molecular and cellular alterations that trigger clearance of this RBC subset remain to be identified. Using a staining protocol that sorts long-stored SMEs (i.e., CFSEhigh) and morphologically-normal RBCs (CFSElow), these in vitro aged cells were characterized. Metabolomics analysis identified depletion of energy, lipid-repair, and antioxidant metabolites in CFSEhigh RBCs. By redox proteomics, irreversible protein oxidation primarily affected CFSEhigh RBCs. By proteomics, 96 proteins, mostly in the proteostasis family, had relocated to CFSEhigh RBC membranes. CFSEhigh RBCs exhibited decreased proteasome activity and deformability; increased phosphatidylserine exposure, osmotic fragility, and endothelial cell adherence; and were cleared from the circulation during human spleen ex vivo perfusion. Conversely, molecular, cellular, and circulatory properties of long-stored CFSElow RBCs resembled those of short-stored RBCs. CFSEhigh RBCs are morphologically and metabolically altered, have irreversibly oxidized and membrane-relocated proteins, and exhibit decreased proteasome activity. In vitro aging during storage selectively alters metabolism and proteostasis in SMEs, targeting these senescent cells for clearance.

cell biology↗

bioRxiv2024

PD-1 blockade enhances HIV-1 vaccine-induced CD8+ T-cell responses in PWH early ART-treated

Current HIV-1 therapeutic vaccines do not generate T-cell immune responses in people with HIV-1 (PWH) able to eradicate the virus or to broadly control viral replication. The expression of inhibitory receptors (IRs) may limit vaccine efficacy by reducing specific effector functions in vaccine-induced T-cells. Recently, the clinical use of antibodies targeting IRs or immune checkpoint blockade (ICB) has demonstrated remarkable success in cancer remission. Therefore, there is a potential benefit of using ICB in PWH to improve the effectiveness of vaccine-induced T-cell responses. Here, we evaluated functional changes in vaccine-induced HIV-specific CD8 T-cell responses by in-vitro PD-1 and TIM-3 blockade during immune stimulation in PWH early ART-treated and vaccinated (Etvac). We compared Etvac to PWH early ART-treated (Et) and chronic ART-treated PWH (Chro). Our results demonstrate a significant increase in the functional responses of vaccine-induced HIV-1-specific CD8 T-cells upon PD-1 but not TIM-3 blockade in cellular proliferation, IFN{gamma} production, and activation. Although no effect was found in Et, similar findings were obtained in HIV-1-specific CD8 T-cells in Chro for combined PD-1/TIM-3 blockade. Moreover, we identify in Etvac a direct association between PD-1 expression in CD8+ T cells and in vitro response to anti-PD-1 treatment. Our findings support the potential adjuvant effect of PD-1 blockade to improve HIV-1 therapeutic vaccine efficacy in early ART-treated PWH for future human studies.

immunology↗

bioRxiv2024

Analysis of high-molecular-weight proteins using MALDI-TOF MS and Machine Learning for the differentiation of clinically relevant Clostridioides difficile ribotypes

Clostridioides difficile is the main cause of antibiotic related diarrhea and some ribotypes (RT), such as RT027, RT181 or RT078, are considered high risk clones. A fast and reliable approach for C. difficile ribotyping is needed for a correct clinical approach. This study analyses high-molecular-weight proteins for C. difficile ribotyping with MALDI-TOF MS. Sixty-nine isolates representative of the most common ribotypes in Europe were analyzed in the 17,000-65,000 m/z region and classified into 4 categories (RT027, RT181, RT078 and Other RTs). Five supervised Machine Learning algorithms were tested for this purpose: K-Nearest Neighbors, Support Vector Machine, Partial Least Squares-Discriminant Analysis, Random Forest and Light-Gradient Boosting Machine. All algorithms yielded cross-validation results >70%, being RF and Light-GBM the best performing, with 88% of agreement. Area under the ROC curve of these two algorithms was >0.9. RT078 was correctly classified with 100% accuracy and isolates from the RT181 category could not be differentiated from RT027.

microbiology↗

bioRxiv2024

The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference

The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulence, and antibiotic resistance. While it is known that within-MTBC diversity is characterised by large deletions found only in certain lineages (regions of difference [RDs]), a comprehensive pangenomic analysis incorporating both coding and non-coding regions remains unexplored. We utilised a curated dataset representing various MTBC genomes, including under-represented lineages, to quantify the full diversity of the MTBC pangenome. The MTBC was found to have a small, closed pangenome with distinct genomic features and RDs both between lineages (as previously known) and between sub-lineages. The accessory genome was identified to be a product of genome reduction, showing both divergent and convergent deletions. This variation has implications for traits like virulence, drug resistance, and metabolism. The study provides a comprehensive understanding of the MTBC pangenome, highlighting the importance of genome reduction in its evolution, and underlines the significance of genomic variations in determining the pathogenic traits of different MTBC lineages.

evolutionary biology↗

bioRxiv2024

Evaluating generalizability of artificial intelligence models for molecular datasets

Deep learning has made rapid advances in modeling molecular sequencing data. Despite achieving high performance on benchmarks, it remains unclear to what extent deep learning models learn general principles and generalize to previously unseen sequences. Benchmarks traditionally interrogate model generalizability by generating metadata based (MB) or sequence-similarity based (SB) train and test splits of input data before assessing model performance. Here, we show that this approach mischaracterizes model generalizability by failing to consider the full spectrum of cross-split overlap, i.e., similarity between train and test splits. We introduce SPECTRA, a spectral framework for comprehensive model evaluation. For a given model and input data, SPECTRA plots model performance as a function of decreasing cross-split overlap and reports the area under this curve as a measure of generalizability. We apply SPECTRA to 18 sequencing datasets with associated phenotypes ranging from antibiotic resistance in tuberculosis to protein-ligand binding to evaluate the generalizability of 19 state-of-the-art deep learning models, including large language models, graph neural networks, diffusion models, and convolutional neural networks. We show that SB and MB splits provide an incomplete assessment of model generalizability. With SPECTRA, we find as cross-split overlap decreases, deep learning models consistently exhibit a reduction in performance in a task- and model-dependent manner. Although no model consistently achieved the highest performance across all tasks, we show that deep learning models can generalize to previously unseen sequences on specific tasks. SPECTRA paves the way toward a better understanding of how foundation models generalize in biology.

bioinformatics↗

bioRxiv2024

Rapid, automatic typing of Clostridioides difficile Ribotypes Using MALDI-TOF MS

Clostridioides difficile is a major cause of hospital-acquired diarrhea, posing significant clinical challenges due to its high morbi-mortality rates and its involvement in nosocomial outbreaks. Detecting its toxigenic ribotypes rapidly and accurately is crucial for effective outbreak control. This study aimed to create a rapid diagnostic methodology based on MALDI-TOF MS and Machine Learning algorithms to differentiate toxigenic C. difficile RTs. MALDI-TOF spectra were acquired from 379 clinical isolates sourcing from 10 Spanish hospitals and analysed using Clover MSDAS, a specific software for MALDI-TOF spectra analysis, considered as the state-of-the-art tool for this purpose, and AutoCdiff, an ad hoc software developed in this study. Seven biomarker peaks were found to differentiate epidemic RT027 and RT181 strains from other RTs (2463, 3353, 4933, 4993, 6187, 6651 and 6710 m/z). Two peaks (2463 and 4993 m/z) were specifically found in RT027 isolates while combinations of the other 5 peaks allowed the differentiation of RT181 from other ribotypes. Automatic classification tools developed in Clover MSDAS and AutoCdiff using the specific peaks and the entire protein spectra, respectively, showed up to 100% balanced accuracy. Both methods allowed correct ribotype assignment for isolates sourcing from real-time outbreaks. The developed models, available from Clover MSDAS and the AutoCdiff website -https://bacteria.id-offer researchers a valuable tool for quick C. difficile ribotype determination based on MALDI-TOF spectra analysis. Although further validation of the models is still required, they represent rapid and cost-effective methods for standardized C. difficile ribotype assignment.

microbiology↗

bioRxiv2024

Developmental Reprogramming of Hypothalamic-Pituitary Axis in Mice by Common Environmental Pollutants

Humans are exposed to a large number of endocrine disrupting chemicals (EDCs). Many studies demonstrated that exposures to EDCs during critical windows of development can permanently affect endocrine health outcomes. Most of experimental studies address changes in secretion of hormones produced by gonads, thyroid gland and adrenals, and little is known about the ability of EDCs to produce long-term changes in the hypothalamic-pituitary (HP) control axes. Here, we examined the long-term effects of three common EDCs on male mouse HP gene expression, following developmental exposures. Pregnant mice were exposed to 0.2 mg/ml solutions of bisphenol S (BPS), 2,2,4,4-tetrabromodiphenyl ether (BDE-47), or 3,3,5,5-tetrabromobisphenol A (TBBPA) from pregnancy day 8 through lactation day 21 (weaning day). Male offspring were left untreated until postnatal day 140, where pituitaries and hypothalami were collected. Pituitaries were assed for gene expression via RNA sequencing, while specific genes were assessed for expression in hypothalami via RT-qPCR. Differential expression, as well as gene enrichment and pathway analysis, indicated that all three chemicals induced long-term changes, (mostly suppression) in pituitary genes involved in its endocrine function. BPS and BDE-47 produced effects overlapping significantly at the level of effected genes and pathways. All three chemicals altered genes and pathways of gonad and liver HP axes, while BPS altered HP-adrenal and BDE-47 altered HP-thyroid pathways specifically. All three chemicals also reduced expression of immune genes in the pituitaries. Targeted gene expression in the hypothalamus indicates a down regulation of hypothalamic endocrine control genes by BPS and BDE-47 groups, concordant with changes in the pituitary and suggests that these chemicals suppress the overall HP endocrine function. Interestingly, all three chemicals altered pituitary genes of GPCR-mediated intracellular signaling molecules, many of which are key signalers common to many pituitary responses to hormones. The results of this study show that developmental exposures to common and ubiquitous EDCs have long-term impacts on hormonal feedback control at the hypothalamic-pituitary level.

pharmacology and toxicology↗

bioRxiv2023

Apoplastic barrier establishment in roots and nodules of Lotus japonicus is essential for root-shoot signaling and N-fixation

The molecular framework underlying apoplastic root barrier formation has been unveiled in the model species Arabidopsis thaliana where establishment of Casparian strips occurs at an early stage of root development. In legumes, this region overlaps with the area where nitrogen-fixing bacteria can induce nodule formation, termed the susceptible zone. Moreover, while nodules themselves also contain an endodermis spanning their vascular bundles, it is current unknown if Casparian strips serve as a filter for transport across this specialized organ. Here we establish barrier mutants in the symbiosis model Lotus japonicus. We find that the while genetic network controlling Casparian strip formation is conserved in this legume species, formation of functional barriers is crucial for establishment of N-fixing nodules. By probing this in detail, we establish a model where the Casparian strip, via its linked Schengen pathway, converge with long distance N signaling and systemic regulation of nodulation. Moreover, this also reveal that the genetic system for barrier establishment in the root endodermis is shared in nodule vascular endodermis and required for nodule function. Combined, our findings uncover a novel role of apoplastic root barriers and establishes a mutant collection suitable to probe the role of root barriers in symbiotic plant-microbe relationships.

plant biology↗

bioRxiv2023

High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes

BackgroundCombatting the tuberculosis (TB) epidemic caused by Mycobacterium tuberculosis (Mtb) necessitates a better understanding of the factors contributing to patient clinical outcomes and transmission. While host and environmental factors have been evaluated, the impact of Mtb genetic background and phenotypic diversity is underexplored. Previous work has made associations between Mtb genetic lineages and some clinical and epidemiological features, but the bacterial traits underlying these connections are largely unknown. MethodsWe developed a high-throughput functional genomics platform for defining genotype-phenotype relationships across a panel of Mtb clinical isolates. These phenotypic fitness profiles function as intermediate traits which can be linked to Mtb genetic variants and associated with clinical and epidemiological outcomes. We applied this approach to a collection of 158 Mtb strains from a study of Mtb transmission in Ho Chi Minh City, Vietnam. Mtb strains were genetically tagged in multiplicate, which allowed us to pool the strains and assess in vitro competitive fitness using deep sequencing across a set of 14 host-relevant antibiotic and metabolic conditions. Phylogenetic and monogenic associations with these intermediate traits were identified and then associated with clinical outcomes. FindingsMtb clinical strains have a broad range of growth and drug response dynamics that can be clustered by their phylogenetic relationships. We identified novel monogenic associations with Mtb fitness in various metabolic and antibiotic conditions. Among these, we find that mutations in Rv1339, a phosphodiesterase, which were identified through their association with slow growth in glycerol, are further associated with treatment failure. We also identify a previously uncharacterized subclade of Lineage 1 strains (L1.1.1.1) that is phenotypically distinguished by slow growth under most antibiotic and metabolic stress conditions in vitro. This clade is associated with cavitary disease, treatment failure, and demonstrates increased transmission potential. InterpretationHigh-throughput phenogenotyping of Mtb clinical strains enabled bacterial intermediate trait identification that can provide a mechanistic link between Mtb genetic variation and patient clinical outcomes. Mtb strains associated with cavitary disease, treatment failure, and transmission potential display intermediate phenotypes distinguished by slow growth under various antibiotic and metabolic conditions. These data suggest that Mtb growth regulation is an adaptive advantage for host bacterial success in human populations, in at least some circumstances. These data further suggest markers for the underlying bacterial processes that govern these clinical outcomes. FundingNational Institutes of Allergy and Infectious Diseases: P01 AI132130 (SS, SMF); P01 AI143575 (XW, SMF); U19 AI142793 (QL, SMF); 5T32AI132120-03 (SS); 5T32AI132120-04 (SS); 5T32AI049928-17 (SS) Wellcome Trust Fellowship in Public Health and Tropical Medicine: 097124/Z/11/Z (NTTT) National Health and Medical Research Council (NHMRC)/A*STAR joint call: APP1056689 (SJD) The funding sources had no involvement in study methodology, data collection, analysis, and interpretation nor in the writing or submission of the manuscript. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe used different combinations of the words mycobacterium tuberculosis, tuberculosis, clinical strains, intermediate phenotypes, genetic barcoding, phenogenomics, cavitary disease, treatment failure, and transmission to search the PubMed database for all studies published up until January 20th, 2022. We only considered English language publications, which biases our search. Previous work linking Mtb determinants to clinical or epidemiological data has made associations between bacterial lineage, or less frequently, genetic polymorphisms to in vitro or in vivo models of pathogenesis, transmission, and clinical outcomes such as cavitary disease, treatment failure, delayed culture conversion, and severity. Many of these studies focus on the global pandemic Lineage 2 and Lineage 4 Mtb strains due in part to a deletion in a polyketide synthase implicated in host-pathogen interactions. There are a number of Mtb GWAS studies that have led to novel genetic determinants of in vitro drug resistance and tolerance. Previous Mtb GWAS analyses with clinical outcomes did not experimentally test any predicted phenotypes of the clinical strains. Published laboratory-based studies of Mtb clinical strains involve relatively small numbers of strains, do not identify the genetic basis of relevant phenotypes, or link findings to the corresponding clinical outcomes. There are two recent studies of other pathogens that describe phenogenomic analyses. One study of 331 M. abscessus clinical strains performed one-by-one phenotyping to identify bacterial features associated with clearance of infection and another details a competition experiment utilizing three barcoded Plasmodium falciparum clinical isolates to assay antimalarial fitness and resistance. Added value of this studyWe developed a functional genomics platform to perform high-throughput phenotyping of Mtb clinical strains. We then used these phenotypes as intermediate traits to identify novel bacterial genetic features associated with clinical outcomes. We leveraged this platform with a sample of 158 Mtb clinical strains from a cross sectional study of Mtb transmission in Ho Chi Minh City, Vietnam. To enable high-throughput phenotyping of large numbers of Mtb clinical isolates, we applied a DNA barcoding approach that has not been previously utilized for the high-throughput analysis of Mtb clinical strains. This approach allowed us to perform pooled competitive fitness assays, tracking strain fitness using deep sequencing. We measured the replicative fitness of the clinical strains in multiplicate under 14 metabolic and antibiotic stress condition. To our knowledge, this is the largest phenotypic screen of Mtb clinical isolates to date. We performed bacterial GWAS to delineate the Mtb genetic variants associated with each fitness phenotype, identifying monogenic associations with several conditions. We then defined Mtb phenotypic and genetic features associated with clinical outcomes. We find that a subclade of Mtb strains, defined by variants largely involved in fatty acid metabolic pathways, share a universal slow growth phenotype that is associated with cavitary disease, treatment failure and increased transmission potential in Vietnam. We also find that mutations in Rv1339, a poorly characterized phosphodiesterase, also associate with slow growth in vitro and with treatment failure in patients. Implications of all the available evidencePhenogenomic profiling demonstrates that Mtb strains exhibit distinct growth characteristics under metabolic and antibiotic stress conditions. These fitness profiles can serve as intermediate traits for GWAS and association with clinical outcomes. Intermediate phenotyping allows us to examine potential processes by which bacterial strain differences contribute to clinical outcomes. Our study identifies clinical strains with slow growth phenotypes under in vitro models of antibiotic and host-like metabolic conditions that are associated with adverse clinical outcomes. It is possible that the bacterial intermediate phenotypes we identified are directly related to the mechanisms of these outcomes, or they may serve as markers for the causal yet unidentified bacterial determinants. Via the intermediate phenotyping, we also discovered a surprising diversity in Mtb responses to the new anti-mycobacterial drugs that target central metabolic processes, which will be important in considering roll-out of these new agents. Our study and others that have identified Mtb determinants of TB clinical and epidemiological phenotypes should inform efforts to improve diagnostics and drug regimen design.

microbiology↗

bioRxiv2023

Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor

Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a "mechanical test" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.

biophysics↗

bioRxiv2021

A promiscuity locus confers Lotus burttii nodulation with rhizobia from five different genera

Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil dwelling organisms and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, where the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity QTL to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for host-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions.

plant biology↗

bioRxiv2021

Rapid and reproducible MALDI-TOF-based method for detection Vancomycin-resistant Enterococcus faecium using classifying algorithms

Vancomycin-resistant Enterococcus faecium has become a health threat over the last 20 years due to its ability to rapidly spread and cause outbreaks in hospital settings. Although MALDI-TOF MS has already demonstrated its usefulness for accurate identification of E. faecium, its implementation for antimicrobial resistance detection is still under evaluation. The reproducibility of MALDI-TOF MS for peak analysis and its performance for correct discrimination of vancomycin susceptible isolates (VSE) from those hosting the VanA and VanB resistance mechanisms was evaluated in this study. For the first goal, intra-spot, inter-spot -technical- and inter-day -biological- reproducibility was assayed. The capability of MALDI-TOF to discriminate VSE isolates from VanA VRE and VanB VRE strains was carried out on protein spectra from 178 E. faecium unique clinical isolates -92 VSE, 31 VanA VRE, 55 VanB VRE-, processed with Clover MS Data Analysis software. Unsupervised (Principal Component Analysis -PCA-) and supervised algorithms (Support Vector Machine -SVM-, Random Forest -RF- and Partial Least Squares-Discriminant Analysis -PLS-DA-) were applied. The reproducibility assay showed lower variability for normalized data (p<0.0001) and for the peaks within the 3000-9000 m/z range. Besides, 80.9%, 79.21% and 77.53% VSE vs VRE (VanA + VanB) discrimination was achieved by applying SVM, RF and PLS-DA, respectively. Correct differentiation of VanA from VanB VRE isolates was obtained by SVM in 86.65% cases. The implementation MALDI-TOF MS and peak analysis could represent a rapid and effective tool for VRE screening. However, further improvements are needed to increase the accuracy of this approach.

microbiology↗

bioRxiv2021

The microbiome of Lotus nodules varies with plant health in a species-specific manner

Nitrogen fixation is carried out inside nodules of legumes by symbiotic rhizobia. Rhizobia dominate the nodule microbiome, however other non-rhizobial bacteria also colonise root nodules. It is not clear whether these less abundant nodule colonisers impact nodule function. In order to investigate the relationship between the nodule microbiome and nodule function as influenced by the soil microbiome, we used a metabarcoding approach to characterise the communities inside Lotus burttii, Lotus japonicus and Lotus corniculatus nodules from plants that were either starved or healthy resulting from inoculations with different soil suspensions in a closed pot experiment. We found that the nodule microbiome of all tested Lotus species differed according to inoculum, but only that of L. burttii varied with plant health. Using a machine learning algorithm, we also found that among the many non-rhizobial bacteria inside the nodule, amplicon sequence variants that were related to Pseudomonas were the most indicative signatures of a healthy plant nodule microbiome. These results support the hypothesis that legume nodule endophytes may play a role in the overall success of root-nodule symbiosis, albeit in a plant host specific manner.

microbiology↗

bioRxiv2021

The late endosome-resident lipid bis(monoacylglycero)phosphate is a cofactor for Lassa virus fusion

Arenavirus entry into host cells occurs through a low pH-dependent fusion with late endosomes that is mediated by the viral glycoprotein complex (GPC). The mechanisms of GPC-mediated membrane fusion and of virus targeting to late endosomes are not well understood. To gain insights into arenavirus fusion, we examined cell-cell fusion induced by the Old World Lassa virus (LASV) GPC complex. LASV GPC-mediated cell fusion is more efficient and occurs at higher pH in cells expressing human LAMP1 compared to cells lacking this cognate receptor, but this receptor is not absolutely required for virus entry. GPC-induced fusion progresses through the same lipid intermediates as fusion mediated by other viral glycoproteins - a lipid curvature-sensitive intermediate upstream of hemifusion and a hemifusion intermediate downstream of acid-dependent steps that can be arrested in the cold. Importantly, GPC-mediated fusion is specifically augmented by an anionic lipid, bis(monoacylglycero)phosphate (BMP), which is highly enriched in late endosomes. We show that BMP promotes late steps of LASV fusion downstream of hemifusion - the formation and enlargement of fusion pores. This lipid also specifically promotes cell fusion mediated by GPC of the unrelated New World Junin arenavirus. The BMP-dependence of post-hemifusion stages of arenavirus fusion suggests that these viruses evolved to use this lipid as a cofactor to direct virus entry to late endosomes. Author SummaryPathogenic arenaviruses pose a serious health threat. The viral envelope glycoprotein GPC mediates attachment to host cells and drives virus entry via endocytosis and low pH-dependent fusion within late endosomes. Understanding the host factors and processes that are essential for arenavirus fusion may identify novel therapeutic targets. To delineate the mechanism of arenavirus entry, we examined cell-cell fusion induced by the Old World Lassa virus GPC proteins at low pH. Lassa virus fusion was augmented by the LAMP1 receptor and progressed through lipid curvature-sensitive intermediates, such as hemifusion (merger of contacting leaflets of viral and cell membrane without the formation of a fusion pore). We found that most GPC-mediated fusion events were off-path hemifusion structures and that the transition from hemifusion to full fusion and fusion pore enlargement were specifically promoted by an anionic lipid, bis(monoacylglycero)phosphate, which is highly enriched in late endosomes. This lipid also specifically promotes fusion of unrelated New World Junin arenavirus. Our results imply that arenaviruses evolved to use bis(monoacylglycero)phosphate to enter cells from late endosomes.

microbiology↗

bioRxiv2021

A hetero-oligomeric remorin-receptor complex regulates plant development

Plant growth and development are modulated by both biotic and abiotic stress. Increasing evidence suggests that cellular integration of the corresponding signals occurs within preformed hubs at the plasma membrane called nanodomains. These membrane sub-compartments are organized by multivalent molecular scaffold proteins, such as remorins. Here, we demonstrate that Group 1 remorins form a hetero-oligomeric complex at the plasma membrane. While these remorins are functionally redundant for some pathways their multivalency also allows the recruitment of specific interaction partners. One of them, the receptor-like kinase REMORIN-INTERACTING RECEPTOR 1 (RIR1), that acts redundantly with the closely related receptor NILR2, is specifically recruited by REM1.2 in a phosphorylation-dependent manner. Overlapping developmental phenotypes suggest that the REM/RIR complex regulates key developmental pathways.

plant biology↗