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Results for “molecular biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 343 records · Page 19Linked to original sources

bioRxiv2026

Polo-like kinase 1 controls activation of adult neural stem cells and represents a druggable entry-point to boost adult neurogenesis

Neural stem cells (NSCs) persist in the mammalian brain after development, but their potential for replacing neural populations lost in brain damage is dramatically restricted. Quiescence, or the ability to transition in and out of the cell cycle is a hallmark of adult NSCs. It deepens as the organism ages and is regarded as a strategy to protect the reservoirs of NSC for the long term. Deciphering the molecular code of dormancy is a major interest in cellular and molecular biology of ageing and in regenerative medicine since it has important implications for potentially manipulating NSCs to improve tissular homeostasis. In this work we have identified the mitotic kinase Polo like kinase 1 (Plk1) as a novel intrinsic regulator of the dynamic transition between NSC quiescence and activation in adult neurogenic niches. Using quantitative phosphoproteomics to pinpoint mechanistical mediators of the role of Plk1, we have identified the quiescence/activation molecular switch formed by E3 ubiquitin ligase Huwe1 and its target, the transcription factor Ascl1/Mash1, as novel effectors of Plk1 in NSCs. We discover that Plk1 restrains the accumulation of Ascl1/Mash1 by acting upstream of Huwe1, providing a direct molecular connection between completion of the cell cycle and the re-establishment of a low activation state following NSC division, which supports the concept that quiescence is an actively maintained state. Moreover we demonstrate that pharmacological inhibition of Plk1 is sufficient to enhance adult neurogenesis in vivo, identifying Plk1 as a viable target to acutely boost endogenous stem cell activation.

neuroscience↗

bioRxiv2018

Modulating CRISPR gene drive activity through nucleocytoplasmic localization of Cas9 in S. cerevisiae

The bacterial CRISPR/Cas genome editing system has provided a major breakthrough in molecular biology. One use of this technology is within a nuclease-based gene drive. This type of system can install a genetic element within a population at unnatural rates. Combatting of vector-borne diseases carried by metazoans could benefit from a delivery system that bypasses traditional Mendelian laws of segregation. Recently, laboratory studies in fungi, insects, and even mice, have demonstrated successful propagation of CRISPR gene drives and the potential utility of this type of mechanism. However, current gene drives still face challenges including evolved resistance, containment, and the consequences of application in wild populations. In this study, we use an artificial gene drive system in budding yeast to explore mechanisms to modulate nuclease activity of Cas9 through its nucleocytoplasmic localization. We examine non-native nuclear localization sequences on Cas9 fusion proteins in vivo and demonstrate that appended signals can titrate gene drive activity and serve as a potential molecular safeguard.

synthetic biology↗

bioRxiv2021

Genomes contain relics of a triplet code connecting the origins of primordial RNA synthesis to the origins of genetically coded protein synthesis

Life on earth relies on three types of information polymers-DNA, RNA and proteins. In all organisms and viruses, these molecules are synthesized by the copying of pre-existing templates. A triplet-based code known as the genetic code guides the synthesis of proteins by complex enzymatic machines that decode genetic information in RNA sequences. The origin of the genetic code is one of the most fundamental questions in biology. In this study, computational analysis of about 5,000 species level metagenomes using techniques for the analysis of human language suggests that the genomes of extant organisms contain relics of a distinct triplet code that potentially predates the genetic code. This code defines the relationship between adjacent triplets in DNA/RNA sequences, whereby these triplets predominantly differ by a single base. Furthermore, adjacent triplets encode amino acids that are thought to have emerged around the same period in the earths early history. The results suggest that the order of triplets in primordial RNA sequences was associated with the availability of specific amino acids, perhaps due to a coupling of a triplet-based primordial RNA synthesis mechanism to a primitive mechanism of peptide bond formation. Together, this coupling could have given rise to early nucleic acid sequences and a system for encoding amino acid sequences in RNA, i.e. the genetic code. Thus, the central role of triplets in biology potentially extends to the primordial world, contributing to both the origins of genomes and the origins of genetically coded protein synthesis. SignificanceOne of the most intriguing discoveries in biology is that the order of amino acids in each protein is determined by the order of nucleotides (commonly represented by the letters A, U, G, C) in a biological molecule known as RNA. The genetic code serves as a dictionary that maps each of the 64 triplets words in RNA to the 20 amino acids, thereby specifying how information encoded in RNA is decoded into sequences of amino acids (i.e., proteins). The deciphering of the genetic code was one of the greatest discoveries of the 20th century (1968 Nobel Prize in Medicine and Physiology) and is central to modern molecular biology. Yet, how it came to be that the order of triplets in RNA encodes the sequence of the protein synthesized remains one of the most important enigmas of biology. Paradoxically, in all life forms proteins cannot be synthesized without RNA and RNA itself cannot also be synthesized without proteins, presenting a chicken and egg dilemma. By analyzing thousands of microbial genomes using approaches drawn from the field of natural language processing, this study finds that the order of triplets across genomes contains relics of an ancient triplet code, distinct from but closely connected to the genetic code. Unlike the genetic code which specifies the relationship between information in RNA and the sequence of proteins, this ancient code describes the relationship between adjacent triplets in extant genome sequences, whereby such triplets are often different from each other by a single letter. Triplets that are closely related by this ancient code encode amino acids that are thought to have emerged around the same period in the earths early history. In other words, a fossil record of the chronological order of appearance of amino acids on early earth appears written in genome sequences. This potentially demonstrates that the process by which RNA sequences were synthesized in the primordial world relied on triplets and was coupled to amino acids available at the time. Hence, the connections between primordial RNA synthesis and a primitive mechanism for linking amino acids to form peptides could have enabled one type of molecule (RNA) to code for the other (protein), facilitating the emergence of the genetic code.

evolutionary biology↗

bioRxiv2017

A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells

Intrinsic and/or acquired resistance represents one of the great challenges in targeted cancer therapy. A deeper understanding of the molecular biology of cancer has resulted in more efficient strategies, where one or multiple drugs are adopted in novel therapies to tackle resistance. This beneficial effect of using combination treatments has also been observed in colorectal cancer patients harboring the BRAF(V600E) mutation, whereby dual inhibition of BRAF(V600E) and EGFR increases antitumor activity. Notwithstanding this success, it is not clear whether this combination treatment is the only or most effective treatment to block intrinsic resistance to BRAF inhibitors. Here, we investigate molecular responses upon single and multi-target treatments, over time, using BRAF(V600E) mutant colorectal cancer cells as a model system. Through integration of transcriptomic, proteomic and phosphoproteomics data we obtain a comprehensive overview, revealing both known and novel responses. We primarily observe widespread upregulation of receptors tyrosine kinases and metabolic pathways upon BRAF inhibition. These findings point to mechanisms by which the drug-treated cells switch energy sources and enter a quiescent-like state as a defensive response, while additionally reactivating the MAPK pathway.

cancer biology↗

bioRxiv2022

End-to-end protein-ligand complex structure generation with diffusion-based generative models

Three-dimensional structures of protein-ligand complexes provide valuable insights into their interactions and are crucial for molecular biological studies and drug design. However, their high-dimensional and multimodal nature hinders end-to-end modeling, and earlier approaches depend inherently on existing protein structures. To overcome these limitations and expand the range of complexes that can be accurately modeled, it is necessary to develop efficient end-to-end methods. We introduce an equivariant diffusion-based generative model that learns the joint distribution of ligand and protein conformations conditioned on the molecular graph of a ligand and the sequence representation of a protein extracted from a pre-trained protein language model. Benchmark results show that this protein structure-free model is capable of generating diverse structures of protein-ligand complexes, including those with correct binding poses. Further analyses indicate that the proposed end-to-end approach is particularly effective when the ligand-bound protein structure is not available. The present results demonstrate the effectiveness and generative capability of our end-to-end complex structure modeling framework with diffusion-based generative models. We suppose that this framework will lead to better modeling of protein-ligand complexes, and we expect further improvements and wide applications.

bioinformatics↗

bioRxiv2018

Integrative pathway enrichment analysis of multivariate omics data

Multi-omics datasets quantify complementary aspects of molecular biology and thus pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple omics datasets using a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes. We demonstrate its utility by analyzing coding and non-coding mutations from 2,583 whole cancer genomes, revealing frequently mutated hallmark pathways and a long tail of known and putative cancer driver genes. We also studied prognostic molecular pathways in breast cancer subtypes by integrating genomic and transcriptomic features of tumors and tumor-adjacent cells and found significant associations with immune response processes and anti-apoptotic signaling pathways. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

bioinformatics↗

bioRxiv2018

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol.

Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.

evolutionary biology↗

bioRxiv2022

Creating a thermostable beta-glucuronidase switch for homogeneous immunoassay by disruption of conserved salt bridges at diagonal interfaces

The Escherichia coli beta-glucuronidase (GUS) has been used as a reporter enzyme in molecular biology and has been engineered to enzyme switches for the development of homogeneous biosensors. Here, we developed a thermostable GUS enzyme switch from a thermostable GUS mutant TR3337 by disrupting a conserved salt bridge (H514-E523) between the diagonal subunits of its homotetramer. A combinatorial library (240 variants) was screened by a novel high-throughput strategy, and a mutant DLW (H514D/M516L/Y517W) was found to be a functional enzyme switch in a caffeine-recognizing immunosensor. The molecular dynamics simulations were performed to predict the topology change around position 514, and the sidechain flip of D514 (repulsion with E523) was observed in the DLW mutant. Up to 1.8-fold of the signal-to-background ratio was confirmed when measured at 45 {degrees}C, which makes the DLW mutant a versatile tool for developing the thermostable immunosensors for in vitro and in cellulo applications. Table of contents graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioengineering↗

bioRxiv2023

Identification of Hub Genes and Functional Annotation of Glaucoma Using Bioinformatic Analysis

Glaucoma is a common eye condition that damages the optic nerve, leading to vision loss and potential blindness if not treated. It affects around 80 million people worldwide and is a major cause of irreversible blindness. This study aims to identify key genes and their functions in glaucoma using bioinformatic analysis. The research follows a five-step approach, including data retrieval, processing, identification of differentially expressed genes (DEGs), protein interaction analysis, functional enrichment analysis, and identification of hub genes. Three GSE datasets (GSE 4316, GSE 53985, and GSE 7144) were selected, resulting in a total of 632 upregulated and 625 downregulated genes. Analysis using the DAVID server revealed significant biological processes related to gene regulation, transcription, and cell adhesion. The protein networks for upregulated and downregulated genes consisted of 581 nodes and 1713 edges, and 575 nodes and 2428 edges, respectively. The Cytohubba plugin identified 10 significant genes for each group. The upregulated genes included PTPRC, INS, SRC, CXCR, FN1, TNF, ACTB, AKT1, ALB, and PECAM1, while the downregulated genes included VEGFA, FN1, TP53, ACTB, AKT1, CCND1, CTNNB1, MYC, CD44, and EGFR. These findings enhance our understanding of glaucomas molecular biology and provide valuable insights for prognosis prediction and the development of treatments and medications.

bioinformatics↗

bioRxiv2019

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

English Wikipedia, containing more than five millions articles, has approximately eleven thousands web pages devoted to proteins or genes most of which were generated by the Gene Wiki project. These pages contain information about interactions between proteins and their functional relationships. At the same time, they are interconnected with other Wikipedia pages describing biological functions, diseases, drugs and other topics curated by independent, not coordinated collective efforts. Therefore, Wikipedia contains a directed network of protein functional relations or physical interactions embedded into the global network of the encyclopedia terms, which defines hidden (indirect) functional proximity between proteins. We applied the recently developed reduced Google Matrix (REGOMAX) algorithm in order to extract the network of hidden functional connections between proteins in Wikipedia. In this network we discovered tight communities which reflect areas of interest in molecular biology or medicine. Moreover, by comparing two snapshots of Wikipedia graph (from years 2013 and 2017), we studied the evolution of the network of direct and hidden protein connections. We concluded that the hidden connections are more dynamic compared to the direct ones and that the size of the hidden interaction communities grows with time. We recapitulate the results of Wikipedia protein community analysis and annotation in the form of an interactive online map, which can serve as a portal to the Gene Wiki project.

systems biology↗

bioRxiv2022

Retinoic acid signaling modulates smooth muscle cell phenotypic switching in atherosclerosis through epigenetic regulation of gene expression

BACKGROUNDSmooth muscle cells (SMCs) substantially contribute to the development of atherosclerosis through a process called "phenotypic switching." Our previous work identified an SMC-derived intermediate cell type, termed "SEM" cells, which plays a crucial role in SMC transition to other cell types and in lesion development. Activation of retinoic acid (RA) signaling by all-trans retinoic acid (ATRA) attenuates atherosclerosis in mice coincident with suppression of SEM cell formation. However, the effect of RA signaling on advanced disease and the underlying molecular mechanisms by which RA modulates SMC transition to SEM cells are largely unknown. METHODSWe applied SMC lineage tracing atheroprone mice and biochemistry and cell and molecular biology techniques (e.g., RNA sequencing, quantitative reverse transcription PCR, co-immunoprecipitation, and chromatin immunoprecipitation-quantitative PCR) to reveal the regulatory mechanisms of RA signaling in SMC transition to SEM cells. RESULTSActivation of RA signaling with ATRA in established atherosclerosis significantly reduced SEM cells and lesion size while increasing fibrous cap thickness. Mechanistically, retinoic acid receptor alpha (RAR) directly targets the promoters of Ly6a and Ly6c1 in mouse SMCs, and activation of RA signaling recruits EZH2 to the regulatory elements triggering local H3K27me3. Distinct from a molecular model that reported for RA recruitment of HDAC1 during embryogenesis, RAR/EZH2 complex recruits SIRT1 and SIRT6, rather than classical HDACs, to the regulatory regions of key SEM cell marker genes. This subsequently reduces multiple acetylated histone modifications (e.g., H3K27ac, H3K4ac, H3K9ac, H3K14ac, H3K56ac) with recruitment of the transcription corepressor, NCOR1, to repress downstream SEM cell marker genes. CONCLUSIONSOur findings provide novel mechanistic insights into RA modulating SMC phenotypic switching in atherosclerosis, suggesting molecular targets for preventive and therapeutic interventions for atherosclerosis and its clinical complications.

pathology↗

bioRxiv2019

Structural requirements of the phytoplasma effector protein SAP54 for causing homeotic transformation of floral organs

Phytoplasmas are intracellular bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins. One of these effector proteins, termed SECRETED ASTER YELLOWS-WITCHES BROOM PROTEIN 54 (SAP54), leads to the degradation of a specific subset of floral homeotic proteins of the MIKC-type MADS-domain family via the ubiquitin-proteasome pathway. In consequence, the developing flowers show the homeotic transformation of floral organs into vegetative leaf-like structures. The molecular mechanism of SAP54 action involves physical binding to the keratin-like K-domain of MIKC-type proteins, and to some RAD23 proteins, which translocate ubiquitylated substrates to the proteasome. The structural requirements and specificity of SAP54 function are poorly understood, however. Here we report, based on biophysical and molecular biological analyses, that SAP54 folds into -helical structures. We also show that the insertion of helix-breaking mutations disrupts correct folding of SAP54, which interferes with the ability of SAP54 to bind to its target proteins and to cause disease phenotypes in vivo. Surprisingly, dynamic light scattering data together with electrophoretic mobility shift assays suggest that SAP54 preferentially binds to multimeric complexes of MIKC-type proteins rather than to dimers or monomers of these proteins. Together with literature data this finding suggests that MIKC-type proteins and SAP54 constitute multimeric -helical coiled-coils, possibly also involving other partners such as RAD23 proteins. Our investigations clarify the structure-function relationship of an important phytoplasma effector protein and thus may ultimately help to develop treatments against some devastating plant diseases.\n\nSIGNIFICANCE STATEMENTPhytoplasmas are bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins such as SAP54, which leads to the degradation of some floral homeotic proteins. Our study clarifies the structural requirements of SAP54 function and illuminates the molecular mode of interaction and thus may ultimately help to develop treatments against some devastating plant diseases.

plant biology↗

bioRxiv2026

Xanthomonas translucens inhibits defense responses independently of the Type III secretion system and is recognized by cereal the immune system

Bacterial leaf streak disease (BLS), caused by Xanthomonas translucens, is a re-emerging disease of cereals with few effective control measures. Although the disease was identified over 100 years ago, the fundamental molecular biology and mechanisms governing host-pathogen interactions, colonization, host responses, and disease development are poorly understood. To address these knowledge gaps, we studied the early stages of host-microbe interactions between cereal hosts (wheat and barley) and X. translucens pv. undulosa (Xtu). We found that, while the Type III Secretion System (T3SS) is essential for disease and is associated with a 12- or 150-fold increase in bacterial populations in barley and wheat, respectively, the T3SS is not sufficient for disease development. Xanthan, an Xtu-derived exopolysaccharide, strongly contributes to symptom development by suppressing the host immune response. However, in the absence of xanthan, bacterial populations in wheat are unaffected, and in barley xanthan only accounts for a 4-fold difference compared to the wildtype Xtu. Pathogen-associated molecular pattern (PAMP) inhibition bioassays that prime the plant immune response for subsequent infections revealed that xanthan suppresses defense priming. We also found that, in the absence of xanthan, the host immune system recognizes a potentially novel, unidentified microbe-associated molecular pattern (MAMP) of proteinaceous nature present in both X. translucens pathovars, undulosa (Xtu) and translucens (Xtt). Together, our work reveals both conserved and distinct X. translucens plant immune responses and pathogen elicitors, providing key insights into the host-pathogen interaction.

plant biology↗

bioRxiv2024

A novel toolbox of GATEWAY-compatible vectors for rapid functional gene analysis in soybean composite plants

The generation of transgenic plants is essential for plant biology research to investigate plant physiology, pathogen interactions and gene function. However, producing stable transgenic plants for plants such as soybean is a laborious and time-consuming process, which can impede research progress. Composite plants consisting of wild-type shoots and transgenic roots are an alternative method for generating transgenic plant tissues that can facilitate functional analysis of genes-of-interest involved in root development or root-microbe interactions. In this report, we introduce a novel set of GATEWAY-compatible vectors that enable a wide range of molecular biology uses in roots of soybean composite plants. These vectors incorporate in-frame epitope fusions of green fluorescent protein, 3x-HA, or miniTurbo-ID, which can be easily fused to a gene-of-interest using the GATEWAY cloning system. Moreover, these vectors allow for the identification of transgenic roots using either mCherry fluorescence or the RUBY marker. We demonstrate the functionality of these vectors by expressing subcellular markers in soybean, providing evidence of their effectiveness in generating protein fusions in composite soybean plants. Furthermore, we show how these vectors can be used for gene function analysis by expressing the bacterial effector, AvrPphB in composite roots, enabling the identification of soybean targets via immunoprecipitation followed by mass spectrometry. Additionally, we demonstrate the successful expression of stable miniTurbo-ID fusion proteins in composite roots. Overall, this new set of vectors is a powerful tool that can be used to assess subcellular localization and perform gene function analyses in soybean roots without the need to generate stable transgenic plants. Key MessageWe developed a set of GATEWAY vectors to accelerate gene function analysis in soybean composite plants to rapidly screen transgenic roots and investigate subcellular localization, protein-protein interactions, and root-pathogen interactions.

plant biology↗

bioRxiv2026

Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates

Phylogenomic-scale studies of the same clades using different markers and methods often support highly confident yet different species trees, obscuring many phylogenetic relationships and hampering comparative studies. Among reptiles, the >11,000 extant species of squamates (Order Squamata: lizards, snakes, and amphisbaenians) comprise a highly diverse and well-studied clade, yet many unresolved questions about squamate origins remain, including the root of the squamate phylogeny and the relationships of snakes to other toxicoferans. To understand biological, molecular, and methodological sources of phylogenomic heterogeneity in squamates, we analyzed four genome-scale marker datasets, including thousands of protein-coding genes, anchored hybrid enrichment loci, and ultra-conserved elements. We applied standardized alignment, filtering, and tree-building methods across marker sets, analyzed patterns in substitutional saturation and codon positions, and measured gene tree-species tree discordance across all data partitions. We found that many contentious relationships in squamate phylogenetics are driven by conflicts stemming from input data quality, incorrect model fit, and sampling bias, and that biological drivers of heterogeneity include both incomplete lineage sorting and introgression. We account for these sources of heterogeneity and strengthen resolution of the squamate phylogeny. Using a simulation approach, we find that current ultra-conserved element datasets for squamates deviate the most from phylogenetic expectations among marker types. Our work demonstrates that identifying sources of phylogenomic heterogeneity while accounting for input data limitations can resolve phylogenetic conflicts.

genomics↗

bioRxiv2022

Cytocapsulae and cytocapsular tubes are golden targets for precise, effective and efficient cancer diagnosis and therapy in 307 kinds of liquid and solid cancers

Cancer is a leading cause of human lethality worldwide. A cancer cell is not only the cytoplasm and nucleus enclosed in the cell membrane. A malignant tumor is not only a mass of cancer cells. Cancer in a patient is not only isolated tumors distributed in tissues and organs. The comprehensive understanding of the complete structural compartments and their biological functions of cancer cells, malignant tumors and tumor systems in patients in vivo is an indispensable prerequisite for effective drug development and efficient clinical cancer pharmacotherapies. However, there remains an open question for a long time: what are the complete structural compartments of cancer cells, malignant tumors and tumor systems in the patient body? Here, we comprehensively and systematically investigated the complete structural compartments of cancer cells, malignant tumors and cytocapsular tube (CCT) network-tumor system (CNTS) of 307 types/subtypes of cancers in 33 kinds of tissues and organs by biochemistry and molecular biology assays with 9,811 clinical cancer tissue specimens from 9,637 cancer patients and >110,000 immunohistochemistry (IHC) fluorescence staining images. We discovered the complete structural compartments of cancer cells, malignant tumors and CNTSs in 307 kinds of cancers, elucidated mechanisms of cytocapsular growth and CCT elongation, and identified the comprehensive procedures of cancer evolution in patients. This study paves avenues for curing all kinds of cancers.

cancer biology↗

bioRxiv2024

Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells

The central dogma at the core of molecular biology states that information flows from DNA to RNA and then to protein. Our research seeks to introduce a conceptually novel approach towards synthetic life by leveraging RNA origami, as an alternative to proteins, requiring only a single copying step between genetic information and function. Here, we report the genetic encoding and expression of an RNA origami cytoskeleton-mimic within giant unilamellar lipid vesicles (GUVs). We design the first RNA origami tiles which fold co-transcriptionally from a DNA template and self-assemble into higher-order 3D RNA origami nanotubes at constant 37{whitebullet} C in GUVs, where they reach several micrometers in length. Unlike pre-formed and encapsulated DNA cytoskeletons, these GUVs produce their own molecular hardware in an out-of-equilibrium process fuelled by nucleotide feeding. To establish genotype-phenotype correlations, we investigate how sequence mutations govern the contour and persistence length of the RNA origami nanotubes with experiments and coarse-grained molecular-dynamics simulations, realizing a phenotypic transition to closed rings. Finally, we achieve RNA origami cortex formation and GUV deformation without chemical functionalization by introducing RNA aptamers into the tile design.Altogether, this work pioneers the expression of RNA origami-based hardware in vesicles as a new approach towards active, evolvable and RNA-based synthetic cells.

synthetic biology↗

bioRxiv2021

New detection of SARS-CoV-2 in two cats height months after COVID-19 outbreak appearance in France

Although there are several reports in the literature of SARS-CoV-2 infection in cats, few SARS-CoV-2 sequences from infected cats have been published. In this report, SARS-CoV-2 infection was evaluated in two cats by clinical observation, molecular biology (qPCR and NGS), and serology (Microsphere immunoassay and seroneutralization). Following the observation of symptomatic SARS-CoV-2-infection in two cats, infection status was confirmed by RT-qPCR and, in one cat, serological analysis for antibodies against N-protein and S-protein, as well as neutralizing antibodies. Comparative analysis of five SARS-CoV-2 sequence-fragments obtained from one of the cats showed that this infection was not with one of the three recently emerged variants of SARS-CoV-2. This study provides additional information on the clinical, molecular, and serological aspects of SARS-CoV-2 infection in cats.

microbiology↗