Work in Process: Inhabiting Matter in Time

The typical American house is conceived of and constructed as a permanent and singular object. This method of permanent design and construction is not conducive to sustainable resource and material protection. The permanent connections and material customizations used in construction disallow most C&D (construction and demolition) materials from being salvaged, reused or recycled once the house has reached its end-of-life. As a result, residential demolition in America produces for over 19 million tons of material waste each year (US EPA 6). Deconstruction offers a valid alternative to demolition but is not commonly practiced for two main reasons. First, deconstruction remains a more expensive alternative. Second, the perception of the house as a singular and permanent object undermines the reusability of its material constituents. The following thesis includes research of typical construction design and methodology, a proposed construction design and methodology, a precedent analysis of architectural projects designed for deconstruction, and a design case study testing the validity of the proposed construction design and methodology. The research of typical construction design and methodology analyses those aspects that prohibit deconstruction as a viable method for dealing with the end-of-life of residential structures. The subsequent proposed construction design and methodology outlines a design hypothesis that would promote deconstruction over demolition. The precedent research analyzes past architectural projects that were designed with the intention of later being disassembled rather than demolished. The proposed construction design and methodology research is tested through the design process of the two case studies. These studies employ and develop design principles focused on creating a dynamic architectural design system that can adapt to changes in the needs of its inhabitants. The design utilizes locally bought materials that can be reused or recycled completely after use

Identification of long non-coding RNAs in insects genomes

International audienceThe development of high throughput sequencing technologies (HTS) has allowed researchers to better assess the complexity and diversity of the transcriptome. Among the many classes of non-coding RNAs (ncRNAs) identified the last decade, long non-coding RNAs (lncRNAs) represent a diverse and numerous repertoire of important ncRNAs, reinforcing the view that they are of central importance to the cell machinery in all branches of life. Although lncRNAs have been involved in essential biological processes such as imprinting, gene regulation or dosage compensation especially in mammals, the repertoire of lncRNAs is poorly characterized for many non-model organisms. In this review, we first focus on what is known about experimentally validated lncRNAs in insects and then review bioinformatic methods to annotate lncRNAs in the genomes of hexapods

On the recirculating flow of three-dimensional asymmetric bluff bodies

Abstract The paper investigates the role of geometrical asymmetric modifications of a rectangular flat-backed body on the properties of the recirculating flow at a Reynolds number $$Re=1.8\times 10^5$$ R e = 1.8 × 10 5 . The reference model has two reflectional symmetries denoted $$s_y$$ s y and $$s_z$$ s z in both spanwise directions. The flow is subjected to the static instability that leads to two mirrored wake states breaking the symmetry $$s_y$$ s y . Two families of geometrical variation of the fore-body and after-body are studied, each breaking one of the reflectional symmetries of the reference model. Geometrical modifications that preserve $$s_y$$ s y evidence possibilities of bistable dynamics suppression although the static instability persists. Geometrical modifications that do not preserve $$s_y$$ s y produces a large unbalance of both wake states in accordance to recent observations on real cars (Bonnavion et al. in J Wind Eng Ind Aerodyn 184:77–89, 2019). Results offer perspectives for potential drag reduction induced by appropriate coupling of bluff body geometry and wake state selection. Graphic abstract </jats:sec

Human immortalized chondrocytes carrying heterozygous FGFR3 mutations: An in vitro model to study chondrodysplasias

AbstractAchondroplasia and thanatophoric dysplasia are human chondrodysplasias caused by mutations in the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed an immortalized human chondrocyte culture model to study the regulation of chondrocyte functions. One control and eight mutant chondrocytic lines expressing different FGFR3 heterozygous mutations were obtained. FGFR3 signaling pathways were modified in the mutant lines as revealed by the constitutive activation of the STAT pathway and an increased level of P21WAF1/CIP1 protein. This model will be useful for the study of FGFR3 function in cartilage studies and future therapeutic approaches in chondrodysplasias

LRez: C++ API and toolkit for analyzing and managing Linked-Reads data

International audienceLinked-Reads technologies, such as 10x Genomics, Haplotagging, stLFR and TELL-Seq, partition and tag high-molecular-weight DNA molecules with a barcode using a microfluidic device prior to classical short-read sequencing. This way, Linked-Reads manage to combine the high-quality of the short reads and a long-range information which can be inferred by identifying distant reads belonging to the same DNA molecule with the help of the barcodes. This technology can thus efficiently be employed in various applications, such as structural variant calling, but also genome assembly, phasing and scaffoling. To benefit from Linked-Reads data, most methods first map the reads against a reference genome, and then rely on the analysis of the barcode contents of genomic regions, often requiring to fetch all reads or alignments with a given barcode. However, despite the fact that various tools and libraries are available for processing BAM files, to the best of our knowledge, no such tool currently exists for managing Linked-Reads barcodes, and allowing features such as indexing, querying, and comparisons of barcode contents. LRez aims to address this issue, by providing a complete and easy to use API and suite of tools which are directly compatible with various Linked-Reads sequencing technologies. LRez provides various functionalities such as extracting, indexing and querying Linked-Reads barcodes, in BAM, FASTQ, and gzipped FASTQ files (Table 1). The API is compiled as a shared library, helping its integration to external projects. Moreover, all functionalities are implemented in a thread-safe fashion. Our experiments show that, on a 70 GB Haplotagging BAM file from Heliconius erato [1], index construction took an hour, and resulted in an index occupying 11 GB of RAM. Using this index, querying time per barcode reached an average of 11 ms. In comparison, using a naive approach without a barcode-based index, querying time per barcode reached an hour

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

National audienceLinked-Reads technologies, popularized by 10x Genomics, combine the highquality and low cost of short-reads sequencing with a long-range information by adding barcodes that tag reads originating from the same long DNA fragment. Thanks to their high-quality and long-range information, such reads are thus particularly useful for various applications such as genome scaffolding and structural variant calling. As a result, multiple structural variant calling methods were developed within the last few years. However, these methods were mainly tested on human data, and do not run well on non-human organisms, for which reference genomes are highly fragmented, or sequencing data display high levels of heterozygosity. Moreover, even on human data, most tools still require large amounts of computing resources. We present LEVIATHAN, a new structural variant calling tool that aims to address these issues, and especially better scale and apply to a wide variety of organisms. Our method relies on a barcode index, that allows to quickly compare the similarity of all possible pairs of regions in terms of amount of common barcodes. Region pairs sharing a sufficient number of barcodes are then considered as potential structural variants, and complementary, classical short reads methods are applied to further refine the breakpoint coordinates. Our experiments on simulated data underline that our method compares well to the state-of-the-art, both in terms of recall and precision, and also in terms of resource consumption. Moreover, LEVIATHAN was successfully applied to a real dataset from a non-model organism, while all other tools either failed to run or required unreasonable amounts of resources. LEVIATHAN is implemented in C++, supported on Linux platforms, and available under AGPL-3.0 License at https://github.com/morispi/LEVIATHAN

Plant-phenotypic changes induced by parasitoid ichnoviruses enhance the performance of both unparasitized and parasitized caterpillars

There is increasing awareness that interactions between plants and insects can be mediated by microbial symbionts. Nonetheless, evidence showing that symbionts associated with organisms beyond the second trophic level affect plant-insect interactions are restricted to a few cases belonging to parasitoid-associated bracoviruses. Insect parasitoids harbour a wide array of symbionts which, like bracoviruses, can be injected into their herbivorous hosts to manipulate their physiology and behaviour. Yet, the function of these symbionts in plant-based trophic webs remains largely overlooked. Here, we provide the first evidence of a parasitoid-associated symbiont belonging to the group of ichnoviruses which affects the strength of plant-insect interactions. A comparative proteomic analysis shows that, upon parasitoid injection of calyx fluid containing ichnovirus particles, the composition of salivary glands of caterpillars changes both qualitatively (presence of two viral-encoded proteins) and quantitatively (abundance of several caterpillar-resident enzymes, including elicitors such as glucose oxidase). In turn, plant phenotypic changes triggered by the altered composition of caterpillar oral secretions affect the performance of herbivores. Ichnovirus manipulation of plant responses to herbivory leads to benefits for their parasitoid partners in terms of reduced developmental time within the parasitized caterpillar. Interestingly, plant-mediated ichnovirus-induced effects also enhance the performances of unparasitized herbivores which in natural conditions may feed alongside parasitized ones. We discuss these findings in the context of ecological costs imposed to the plant by the viral symbiont of the parasitoid. Our results provide intriguing novel findings about the role played by carnivore-associated symbionts on plant-insect-parasitoid systems and underline the importance of placing mutualistic associations in an ecological perspective

Saethre-Chotzen mutations cause TWIST protein degradation or impaired nuclear location

International audienceH-TWIST belongs to the family of basic helix-loop-helix (bHLH) transcription factors known to exert their activity through dimer formation. We have demonstrated recently that mutations in H-TWIST account for Saethre-Chotzen syndrome (SCS), an autosomal dominant craniosynostosis syndrome characterized by premature fusion of coronal sutures and limb abnormalities of variable severity. Although insertions, deletions, nonsense and missense mutations have been identified, no genotype-phenotype correlation could be found, suggesting that the gene alterations lead to a loss of protein function irrespective of the mutation. To assess this hypothesis, we studied stability, dimerization capacities and subcellular distribution of three types of TWIST mutant. Here, we show that: (i) nonsense mutations resulted in truncated protein instability; (ii) missense mutations involving the helical domains led to a complete loss of H-TWIST heterodimerization with the E12 bHLH protein in the two-hybrid system and dramatically altered the ability of the TWIST protein to localize in the nucleus of COS-transfected cells; and (iii) in-frame insertion or missense mutations within the loop significantly altered dimer formation but not the nuclear location of the protein. We conclude that at least two distinct mechanisms account for loss of TWIST protein function in SCS patients, namely protein degradation and subcellular mislocalization