Synchrotron-based X-ray Fluorescence Ghost Imaging

X-ray Fluorescence Ghost Imaging (XRF-GI) was recently demonstrated for x-ray lab sources. It has the potential to reduce acquisition time and deposited dose by choosing their trade-off with spatial resolution, while alleviating the focusing constraints of the probing beam. Here, we demonstrate the realization of synchrotron-based XRF-GI: We present both an adapted experimental setup and its corresponding required computational technique to process the data. This not only extends the above-mentioned advantages to synchrotron XRF imaging, it also presents new possibilities for developing strategies to improve precision in nano-scale imaging measurements

Insulin-like growth factor - Oestradiol crosstalk and mammary gland tumourigenesis

Development and differentiation of the mammary gland are dependent on the appropriate temporal expression of both systemically acting hormones and locally produced growth factors. A large body of evidence suggests that molecular crosstalk between these hormonal and growth factor axes is crucial for appropriate cell and tissue function. Two of the most important trophic factors involved in this process are the oestrogen (E) and insulin-like growth factor (IGF) molecular axes. The reciprocal crosstalk that exists between these pathways occurs at transcriptional/post-transcriptional and translational/post-translational levels regulate the expression and activity of genes involved in this process. In a clinical context an important consequence of such crosstalk in the mammary gland is the role which it may play in the aetiology, maintenance and development of breast tumours. Although oestradiol (E2) acting through oestrogen receptors α and β (ERα/β) is important for normal mammary gland function it can also provide a mitogenic drive to ER+ breast tumours. Therefore over several years anti-oestrogen therapeutic regimens in the form of selective oestrogen receptor modulators (SERMs - e.g. tamoxifen), aromatase inhibitors (AI e.g. anastrozole) or selective oestrogen receptor down regulators (SERDs - e.g. fulvestrant) have been used in an adjuvant setting to control tumour growth. Although initial response is usually encouraging, large cohorts of patients eventually develop resistance to these treatments leading to tumour recurrence and poor prognosis. There are potentially many routes by which breast cancer (BC) cells could escape anti-oestrogen based therapeutic strategies and one of the most studied is the possible growth factor mediated activation of ER(s). Because of this, growth factor modulation of ER activity has been an intensively studied route of molecular crosstalk in the mammary gland. The insulin-like growth factors (IGF-1 and -2) are amongst the most potent mitogens for mammary epithelial cells and there is accumulating evidence that they interact with the E2 axis to regulate mitogenesis, apoptosis, adhesion, migration and differentiation of mammary epithelial cells. Such interactions are bi-directional and E2 has been shown to regulate the expression and activity of IGF axis genes with the general effect of sensitising breast epithelial cells to the actions of IGFs and insulin. In this short review we discuss the evidence for the involvement of crosstalk between the insulin-like growth factor (IGF) and oestrogen axes in the mammary gland and comment on the relevance of such studies in the aetiology and treatment of BC

The SuperCam Instrument Suite on the Mars 2020 Rover: Science Objectives and Mast-Unit Description

On the NASA 2020 rover mission to Jezero crater, the remote determination of the texture, mineralogy and chemistry of rocks is essential to quickly and thoroughly characterize an area and to optimize the selection of samples for return to Earth. As part of the Perseverance payload, SuperCam is a suite of five techniques that provide critical and complementary observations via Laser-Induced Breakdown Spectroscopy (LIBS), Time-Resolved Raman and Luminescence (TRR/L), visible and near-infrared spectroscopy (VISIR), high-resolution color imaging (RMI), and acoustic recording (MIC). SuperCam operates at remote distances, primarily 2-7 m, while providing data at sub-mm to mm scales. We report on SuperCam's science objectives in the context of the Mars 2020 mission goals and ways the different techniques can address these questions. The instrument is made up of three separate subsystems: the Mast Unit is designed and built in France; the Body Unit is provided by the United States; the calibration target holder is contributed by Spain, and the targets themselves by the entire science team. This publication focuses on the design, development, and tests of the Mast Unit; companion papers describe the other units. The goal of this work is to provide an understanding of the technical choices made, the constraints that were imposed, and ultimately the validated performance of the flight model as it leaves Earth, and it will serve as the foundation for Mars operations and future processing of the data.In France was provided by the Centre National d'Etudes Spatiales (CNES). Human resources were provided in part by the Centre National de la Recherche Scientifique (CNRS) and universities. Funding was provided in the US by NASA's Mars Exploration Program. Some funding of data analyses at Los Alamos National Laboratory (LANL) was provided by laboratory-directed research and development funds

LEMMI: a continuous benchmarking platform for metagenomics classifiers

Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the method's release and its adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side-by-side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort where method developers can showcase novel approaches and get unbiased benchmarks for publications, while users can make informed choices and obtain standardized and easy-to-use tools

BUSCO: assessing genome assembly and annotation completeness

Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results

BUSCO Update : Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity. This update of the underlying data to over 18 000 prokaryotes and almost 2000 eukaryotes with over 100 million genes propels the coverage to another level. This achievement also demonstrates the scalability of the underlying OrthoLoger software for delineation of orthologs, freely available from https://orthologer.ezlab.org. In addition to the ab-initio computations of gene orthology used for the OrthoDB release, the OrthoLoger software allows mapping of novel gene sets to precomputed orthologs and thereby links to their annotations. The LEMMI-style benchmarking of OrthoLoger ensures its state-of-the-art performance and is available from https://lemortho.ezlab.org. The OrthoDB web interface has been further developed to include a pairwise orthology view from any gene to any other sampled species. OrthoDB-computed evolutionary annotations as well as extensively collated functional annotations can be accessed via REST API or SPARQL/RDF, downloaded or browsed online from https://www.orthodb.org

Synchrotron-based X-ray Fluorescence Ghost Imaging

International audienceX-ray Fluorescence Ghost Imaging (XRF-GI) was recently demonstrated for x-ray lab sources. It has the potential to reduce acquisition time and deposited dose by choosing their trade-off with spatial resolution, while alleviating the focusing constraints of the probing beam. Here, we demonstrate the realization of synchrotron-based XRF-GI: We present both an adapted experimental setup and its corresponding required computational technique to process the data. This not only extends the above-mentioned advantages to synchrotron XRF imaging, it also presents new possibilities for developing strategies to improve precision in nano-scale imaging measurements

BUSCO applications from quality assessments to gene prediction and phylogenomics

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment datasets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and datasets are now also available for nematodes, protists, and plants. Here we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics datasets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics