Biology subjects

Simon, S.

Publications and source records attributed to Simon, S..

35 records · Page 2Linked to original sources

bioRxiv2022

Computational Analysis of Effects of Clot Length on Acute Ischemic Stroke Recanalization under Different Cyclic Aspiration Loading Conditions

Acute ischemic stroke, the second leading cause of death worldwide, results from occlusion of a cerebral artery by a blood clot. Application of cyclic aspiration using an aspiration catheter is a current therapy for the removal of lodged clots. In this study, we perform finite element simulations to analyze deformation of long clots, having length to radius ratio of 2 to 10, which corresponds to clot-length of 2.85-14.25 mm, under peak-to-peak cyclic aspiration pressures of 10 to 50mmmHg, and frequencies of 0.5, 1 and 2 Hz. Our computational system comprises of a nonlinear viscoelastic solid clot, a hyperelastic artery, and a nonlinear viscoelastic cohesive zone, the latter modeling the clot-artery interface. We observe that clots having length-to-radius ratio approximately greater than two separate from the inner arterial surface somewhere between the axial and distal ends, irrespective of the cyclic aspiration loading conditions. The stress distribution within the clot shows large tensile stresses in the clot interior, indicating the possibility of simultaneous fragmentation of the clot. Thus, this study shows us the various failure mechanisms simultaneously present in the clot during cyclic aspiration. Similarly, the stress distribution within the artery implies a possibility of endothelial damage to the arterial wall near the end where the aspiration pressure is applied. This framework provides a foundation for further investigation to clot fracture and adhesion characterization.

bioengineering↗

bioRxiv2022

Dual blockade of misfolded alpha-sarcoglycan degradation by bortezomib and givinostat combination

Limb-girdle muscular dystrophy type R3 (LGMD R3) is a rare genetic disorder characterized by a progressive proximal muscle weakness and caused by mutations in the SGCA gene encoding alpha-sarcoglycan (-SG). Here, we report the results of a mechanistic screening ascertaining the molecular mechanisms involved in the degradation of the most prevalent misfolded R77C--SG protein. We performed a combinatorial study to identify drugs potentializing the effect of a low dose of the proteasome inhibitor bortezomib on the R77C--SG degradation inhibition. Analysis of the screening associated to artificial intelligence-based predictive ADMET characterization of the hits led to identification of the HDAC inhibitor givinostat as potential therapeutical candidate. Functional characterization revealed that givinostat effect was related to autophagic pathway inhibition, unveiling new theories concerning degradation pathways of misfolded SG proteins. Beyond the identification of a new therapeutic option for LGMD R3 patients, our results shed light on the potential repurposing of givinostat for the treatment of other genetic diseases sharing similar protein degradation defects such as LGMD R5 and cystic fibrosis.

pharmacology and toxicology↗

bioRxiv2021

Deep Mutational Engineering of broadly-neutralizing and picomolar affinity nanobodies to accommodate SARS-CoV-1 & 2 antigenic polymorphism

We report in this study the molecular engineering of nanobodies that bind with picomolar affinity to both SARS-CoV-1 and SARS-CoV-2 Receptor Binding Domains (RBD) and are highly neutralizing. We applied Deep Mutational Engineering to VHH72, a nanobody initially specific for SARS-CoV-1 RBD with little cross-reactivity to SARS-CoV-2 antigen. We first identified all the individual VHH substitutions that increase binding to SARS-CoV-2 RBD and then screened highly focused combinatorial libraries to isolate engineered nanobodies with improved properties. The corresponding VHH-Fc molecules show high affinities for SARS-CoV-2 antigens from various emerging variants and SARS-CoV-1, block the interaction between ACE2 and RBD and neutralize the virus with high efficiency. Its rare specificity across sarbecovirus relies on its peculiar epitope outside the immunodominant regions. The engineered nanobodies share a common motif of three amino acids, which contribute to the broad specificity of recognition. These nanobodies appears as promising therapeutic candidates to fight SARS-CoV-2 infection.

biochemistry↗

bioRxiv2021

The effect of mating complexity on gene drive dynamics

Gene drive technology promises to deliver on some of the global challenges humanity faces to-day in healthcare, agriculture and conservation. However, there is a limited understanding of the consequences of releasing self-perpetuating transgenic organisms into the wild populations under complex ecological conditions. In this study, we analyze the impact of three such complexities, mate-choice, mating systems and spatial mating network, on the population dynamics for two distinct classes of modification gene drive systems. All three factors had a high impact on the modelling outcome. First, we demonstrate that distortion based gene drives appear to be more robust against the mate-choice than viability-based gene drives. Second, we find that gene drive spread is much faster for higher degrees of polygamy. Including a fitness cost, the drive is fastest for intermediate levels of polygamy. Finally, the spread of gene drive is faster and more effective when the individuals have fewer connections in a spatial mating network. Our results highlight the need to include mating complexities while modelling the properties of gene drives such as release thresholds, timescales and population-level consequences. This inclusion will enable a more confident prediction of the dynamics of engineered gene drives and possibly even inform on the origin and evolution of natural gene drives.

evolutionary biology↗

bioRxiv2021

Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control

BackgroundThe genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed from > 130 host plants including several economically important crops. ResultsThe 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long read data and Illumina short read), a high-quality genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS, 18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression in combination with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed potential Spodoptera-specific genes of interest such as mg7 and REPAT46 upregulated during 1st and 3rd instar larval stages for targeted pest-outbreak management. ConclusionsThe beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provides critical insights into the biology of this devastating polyphagous insect pest species with a worldwide distribution. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.

genomics↗

bioRxiv2020

Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

AO_SCPLOWBSTRACTC_SCPLOWWith frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may also be involved in or affected by colonization processes, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its microbiota. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the ones from Morocco and North America that are likely the result of recent colonization events. Coalescent-based inferences revealed high levels of gene flow among populations during the colonization but did not allow determining the sequence of colonization of Europe, North America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. We found that D. plantaginea rarely hosts other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play an important role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

evolutionary biology↗

bioRxiv2020

Pluripotent stem cell derived models of neurological diseases reveal early transcriptional heterogeneity

BackgroundMany neurodegenerative diseases (NDs) develop only later in life, when cells in the nervous system lose their structure or function. In genetic forms of NDs, this late onset phenomenon remains largely unexplained. ResultsAnalyzing single cell RNA sequencing (scRNA-seq) from Alzheimers disease (AD) patients, we find increased transcriptional heterogeneity in AD excitatory neurons. We hypothesized that transcriptional heterogeneity precedes ND pathologies. To test this idea experimentally, we used juvenile forms (72Q; 180Q) of Huntingtons disease (HD) iPSCs, differentiated them into committed neuronal progenitors, and obtained single cell expression profiles. We show a global increase in gene expression variability in HD. Autophagy genes become more stable, while energy and actin-related genes become more variable in the mutant cells. Knocking-down several differentially-variable genes resulted in increased aggregate formation, a pathology associated with HD. We further validated the increased transcriptional heterogeneity in CHD8+/- cells, a model for autism spectrum disorder. ConclusionsOverall, our results suggest that although NDs develop over time, transcriptional regulation imbalance is present already at very early developmental stages. Therefore, an intervention aimed at this early phenotype may be of high diagnostic value.

molecular biology↗

bioRxiv2020

Rapid Detection of VanA/B-Producing Vancomycin-Resistant enterococci using Lateral Flow Immunoassay from colonies and blood culture

Vancomycin-resistant enterococci (VRE) have become one of the most important nosocomial pathogens worldwide associated with increased treatment costs, prolonged hospital stay, and high mortality. Rapid detection is crucial to reduce their spread and prevent infections and outbreaks. The lateral flow immunoassay NG-Test VanB (NG Biotech) was evaluated for the rapid detection of VanB-producing vancomycin-resistant enterococci (VanB-VRE) using 104 well-characterized enterococcal isolates. The sensitivity and specificity were both 100%, when bacterial cells were grown in the presence of vancomycin used as VanB inducer. The NG-Test VanB is an efficient, rapid, and easy to implement assay in clinical microbiology laboratories for the confirmation of VanB-VREs either from colonies or from positive blood cultures. Together with the NG-Test VanA, they could complete/replace the already existing panel of tests available for confirmation of acquired vancomycin resistance in enterococci, especially from selective media (rectal screenings) or from antibiograms (infections), with a sensitivity and specificity of both of 100%. The rapid detection in less than 15 minutes will result in more efficient management of carriers and infected patients.

microbiology↗

bioRxiv2020

Discordant transcriptional signatures of mitochondrial genes in Parkinson's disease human myeloid cells

An increasing number of identified Parkinsons disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their potential role in pathological mechanisms is not obvious. We have generated transcriptomic profiles of CD14+ monocytes from 230 individuals with sporadic PD and age-matched healthy subjects. We identified dysregulation of genes involved in mitochondrial and proteasomal function. We also generated transcriptomic profiles of primary microglia from autopsied brains of 55 PD and control subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified PD susceptibility genes, whose expression, relative to each risk allele, is altered in monocytes. These findings reveal that transcriptomic mitochondrial alterations are detectable in PD monocytes and are distinct from brain microglia, and facilitates efforts to understand the roles of myeloid cells in PD.

neuroscience↗

bioRxiv2020

Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Here we reveal, in the plant model Arabidopsis thaliana, that the PIN7 gene, which encodes a polarly localized transporter for the phytohormone auxin, produces two evolutionary-conserved transcripts. These isoforms PIN7a and PIN7b, differing in a 4 amino acid motif, are present at nearly equal levels in most cells. Although both variants do not differ in the subcellular localization and transport auxin with similar capacity, they closely associate and mutually influence their stability within the plasma membrane. Phenotypic complementation tests reveal that the functional contribution of PIN7b per se is minor but it markedly attenuates the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. These results establish alternative splicing of the PIN family as a conserved, functionally-relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.

plant biology↗

bioRxiv2020

Vpr Co-assembles with Gag during HIV-1 Assembly

The HIV-1 accessory protein Vpr is packaged into new virions at a 7:1 ratio of Gag/Vpr. Previous biochemical and genetic analysis has shown that Vpr gets packaged into virions via an LXXLF motif on the p6 domain of the Gag structural polyprotein. The kinetics of Vpr packaging compared to Gag assembly was previously unknown. Here, we confirm via biochemistry and imaging that fluorescently tagged Vpr gets packaged into virus-like particles only when the LXXLF motif is intact. When the LXXLF motif is mutated, Vpr is no longer recruited to Gag assemblies. When Vpr and Gag assembly are imaged together, we see that Vpr co-assembles with a slight delay compared to Gag suggesting that Vpr is not being recruited to the membrane with Gag but is instead being recruited to actively assembling Gag. ImportanceHIV-1 affects over 30 million people around the globe, and although we have good treatments, there is still no cure. The virus encodes 15 distinct proteins, and four of those proteins are known as accessory proteins. Vpr is one of the accessory proteins that is packaged into HIV-1 by interacting with the Gag structural protein. Without Vpr, HIV-1 is not as infectious. Our research shows that Vpr is packaged into new viruses as the virus is being formed rather than being put in towards the end of the assembly of a virus. Getting a clearer view of each step in the process of assembling each virion will help inform future treatments and help with overall comparisons between the assembly of different viruses.

microbiology↗

bioRxiv2019

Can genome-based analysis be the new gold-standard for routine Salmonella serotyping?

Salmonella enterica is the second most reported bacterial cause of food-borne infections in Europe. Therefore molecular surveillance activities based on pathogen subtyping are an important measure of controlling Salmonellosis by public health agencies. In Germany, at the federal level, this work is carried out by the National Reference Center for Salmonella and other Bacterial Enteric Pathogens (NRC). With rise of next generation sequencing techniques, the NRC has introduced whole-genome-based typing methods for S. enterica in 2016. In this study we report on the feasibility of genome-based in silico serotyping in the German setting using raw sequence reads. We found that SeqSero and seven gene MLST showed 98% and 95% concordance, respectively, with classical serotyping for the here evaluated serotypes, including the most common German serotypes S. Enteritidis and S. Typhimurium as well as less frequently found serotypes. The level of concordance increased to >99% when the results of both in silico methods were combined. However, both tools exhibited misidentification of monophasic variants, in particular monophasic S. Typhimurium and therefore need to be fine-tuned for reliable detection of this epidemiologically important variant. We conclude that with adjustments Salmonella genome-based serotyping might become the new gold standard.

microbiology↗

bioRxiv2019

Phylogenetic synecdoche demonstrates optimality of subsampling and improves recovery of the Blaberoidea phylogeny

Phylogenomics seeks to use next-generation data to robustly infer an organisms evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this goal by designing an optimized subsample of data with an experimental design whose results are determined on the basis of phylogenetic synecdoche - a comparison of phylogenies inferred from a subsample to phylogenies inferred from the entire dataset. We examine locus mutation rate, saturation, evolutionary divergence, rate heterogeneity, selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean cockroaches and 22 outgroup species. High phylogenetic utility is demonstrated by loci with high mutation rate, low saturation, low sequence distance, low rate heterogeneity, and low selection. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction and improved statistical support. In sum, optimized subsampling can improve tree quality while reducing data collection costs and yielding 4-6x improvements to computation time in tree inference and bootstrapping.

evolutionary biology↗

bioRxiv2018

Structures of the PKA RIα holoenzyme with the FLHCC driver J-PKAcα or wild type PKAcα

Fibrolamellar hepatocellular carcinoma (FLHCC) is driven by J-PKAc, a kinase fusion chimera of the J-domain of DnaJB1 with PKAc, the catalytic subunit of Protein Kinase A (PKA). Here we report the crystal structures of the chimeric fusion RI2:J-PKAc2 holoenzyme formed by J-PKAc and the PKA regulatory (R) subunit RI, and the wild type (wt) RI2:PKAc2 holoenzyme. The chimeric and wt RI holoenzymes have quaternary structures different from the previously solved wt RI{beta} and RII{beta} holoenzymes. The chimeric holoenzyme shows an isoform-specific interface dominated by antiparallel interactions between the N3A-N3A motifs of RI that serves as an anchor for RI structural rearrangements during cAMP activation. The wt RI holoenzyme showed the same configuration as well as a distinct second conformation. In the structure of the chimeric fusion RI2:J-PKAc2 holoenzyme, the presence of the J-domain does not prevent formation of the holoenzymes, and is positioned away from the symmetrical interface between the two RI:J-PKAc heterodimers in the holoenzyme. The J-domains have significantly higher temperature factors than the rest of the holoenzyme, implying a large degree of conformational flexibility. Furthermore molecular dynamics simulations were applied to analyze the conformational states of chimeric fusion and wt RI holoenzymes, and showed an ensemble of conformations in the majority of which the J-domain was dynamic and rotated away from the R:J-PKAc interface. Thus, rather than affecting the interactions with the regulatory subunits, the fusion of the J-domain to the PKAc alters the conformational landscape of the chimeric fusion holoenzymes and potentially, as result, the interactions with other molecules. The structural and dynamic features of these holoenzymes enhance our understanding of the fusion chimera protein J-PKAc that drives FLHCC as well as the isoform specificity of PKA.

biochemistry↗

bioRxiv2018

Base-pairing requirements for small RNA mediated gene silencing of recessive self incompatibility alleles in Arabidopsis halleri.

Small non-coding RNAs are central regulators of genome activity and stability. Their regulatory function typically involves sequence similarity with their target sites, but understanding the criteria by which they specifically recognize and regulate their targets across the genome remains a major challenge in the field, especially in the face of the diversity of silencing pathways involved. The dominance hierarchy among self-incompatibility alleles in Brassicaceae is controlled by interactions between a highly diversified set of small non-coding RNAs produced by dominant S-alleles and their corresponding target sites on recessive S-alleles. By controlled crosses, we created numerous heterozygous combinations of S-alleles in Arabidopsis halleri and developed an RT-qPCR assay to compare allele-specific transcript levels for the pollen determinant of self-incompatibility (SCR). This provides the unique opportunity to evaluate the precise base-pairing requirements for effective transcriptional regulation of this target gene. We found strong transcriptional silencing of recessive SCR alleles in all heterozygote combinations examined. A simple threshold model of base-pairing for the sRNA-target interaction captures most of the variation in SCR transcript levels. For a subset of S-alleles, we also measured allele-specific transcript levels of the determinant of pistil specificity (SRK) and found sharply distinct expression dynamics throughout flower development between SCR and SRK. In contrast to SCR, both SRK alleles were expressed at similar levels in the heterozygote genotypes examined, suggesting no transcriptional control of dominance for this gene. We discuss the implications for the evolutionary processes associated with the origin and maintenance of the dominance hierarchy among self-incompatibility alleles.

genetics↗

bioRxiv2018

CagY-dependent regulation of type IV secretion in Helicobacter pylori is associated with alterations in integrin binding

Strains of Helicobacter pylori that cause ulcer or gastric cancer typically express a type IV secretion system (T4SS) encoded by the cag pathogenicity island (PAI). CagY is an ortholog of VirB10 that, unlike other VirB10 orthologs, has a large middle repeat region (MRR) with extensive repetitive sequence motifs, which undergo CD4+ T cell-dependent recombination during infection of mice. Recombination in the CagY MRR reduces T4SS function, diminishes the host inflammatory response, and enables the bacteria to colonize at a higher density. Since CagY is known to bind human 5{beta}1 integrin, we tested the hypothesis that recombination in the CagY MRR regulates T4SS function by modulating binding to 5{beta}1 integrin. Using a cell-free microfluidic assay, we found that H. pylori binding to 5{beta}1 integrin under shear flow is dependent on the CagY MRR, but independent of the presence of the T4SS pili, which are only formed when H. pylori is in contact with host cells. Similarly, expression of CagY in the absence of other T4SS genes was necessary and sufficient for whole bacterial cell binding to 5{beta}1 integrin. Bacteria with variant cagY alleles that reduced T4SS function showed comparable reduction in binding to 5{beta}1 integrin, though CagY was still expressed on the bacterial surface. We speculate that cagY-dependent modulation of H. pylori T4SS function is mediated by alterations in binding to 5{beta}1 integrin, which in turn regulates the host inflammatory response so as to maximize persistent infection.\n\nIMPORTANCEInfection with H. pylori can cause peptic ulcers, and is the most important risk factor for gastric cancer, the third most common cause of cancer death worldwide. The major H. pylori virulence factor that determines whether infection causes disease or asymptomatic colonization is the type IV secretion system (T4SS), a sort of molecular syringe that injects bacterial products into gastric epithelial cells and alters host cell physiology. We previously showed that recombination in CagY, an essential T4SS component, modulates the function of the T4SS. Here we found that these recombination events produce parallel changes in specific binding to 5{beta}1 integrin, a host cell receptor that is essential for T4SS-dependent translocation of bacterial effectors. We propose that CagY-dependent binding to 5{beta}1 integrin acts like a molecular rheostat that alters T4SS function and modulates the host immune response to promote persistent infection.

microbiology↗

bioRxiv2017

Predicted sensory consequences of voluntary actions modulate amplitude and temporal dynamics of preceding readiness potentials

Self-generated, voluntary actions, are preceded by a slow negativity in the scalp electroencephalography (EEG) signal recorded from frontal regions (termed readiness potential; RP). This signal, and its lateralized subcomponent (LRP), is mainly regarded as preparatory motor activity associated with the forthcoming motor act. However, it is not clear whether this neural signature is associated with preparatory motor activity, expectation of its associated sensory consequences, or both. Here we recorded EEG data from 12 healthy subjects while they performed self-paced button presses with their right index and middle fingers. In one condition (motor+sound) these button-presses triggered a sound while in another (motor-only) they did not. Additionally, subjects passively listened to sounds delivered in expected timings (sound-only). We found that the RP amplitude (locked to time of button press) was significantly more negative in the motor+sound compared with motor-only conditions starting ~1.4 seconds prior to button press. Importantly, no signal negativity was observed prior to expected sound delivery in the sound-only condition. Thus, the differences in RP amplitude between motor+sound and motor-only conditions are beyond differences in mere expectation of a forthcoming auditory sound. No significant differences between the two conditions were obtained in the LRP component. Our results suggest that expected auditory consequences are encoded in the early phase of the RP preceding the voluntary actions that generate them.

neuroscience↗