The complete genome sequence of elite bread wheat cultivar, "Sonmez".

High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low-irrigation conditions, which further improves upon irrigation. Additionally, Sonmez-2001 is resilient against certain biotic stressors, particularly soil-borne pathogens. Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling 13.3 gigabase-pairs in length. Additionally, a de novo assembly of an additional 1.05 gigabase-pairs was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. Within this de novo assembly, we identified 35 gene models, of which 11 were high-confidence, that may contribute to the favorable traits of this high-performing variety. We identified up to 24 million sequence variants, of which up to 2.4% reside in coding sequences, that can be used to develop molecular markers that should be of immediate use to the cereal community.

Crystalglobulin-Associated Kidney Disease: A Case Report and Literature Review.

The kidney is commonly involved in multiple myeloma and other disorders producing monoclonal immunoglobulins. Crystalglobulinemia is a rare condition characterized by spontaneous crystallization and deposition of monoclonal immunoglobulins within the microvasculature of the kidney and other organs, leading to inflammation, ischemia, and end-organ damage. The present case and literature review highlight the clinical spectrum, diagnostic challenges, management, and outcomes of this underrecognized complication of monoclonal gammopathy. Crystalglobulin-associated kidney disease should be suspected in patients with rapidly progressive kidney disease associated with hematuria, proteinuria, extrarenal lesions (ie, skin and joints), and monoclonal gammopathy. Kidney biopsy is critical to the diagnosis, which relies on the identification by ultrastructural analysis of electron-dense crystalline structures composed of a monoclonal immunoglobulin within the kidney microvasculature. Conventional immunofluorescence on frozen tissue frequently fails to detect monoclonal protein deposits, and pronase-based antigen retrieval on paraffin-embedded material or immunoelectron microscopy is required to unmask antigenic epitopes located within crystalline inclusions. Early intervention combining treatment of clonal cell proliferation and plasma exchanges is warranted to reduce the burden of this rare but dramatic complication of monoclonal gammopathy.

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.

BACKGROUND: The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. RESULTS: Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. CONCLUSIONS: We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

DNAPL flow and complex electrical resistivity evolution in saturated porous media: A coupled numerical simulation.

Induced Polarization (IP) is a non-intrusive geophysical method to monitor Dense Non-Aqueous Phase Liquid (DNAPL) contamination and remediation processes underground. In this study, an advanced numerical code simulating DNAPL flow and complex electrical resistivity is presented. The model was validated against existing IP results and image measurements that were carried out previously in a series of 2D tank experiment. Multiphase flow modeling in porous media is coupled with electrical current modeling to simulate the process of DNAPL migration and the associated IP response. This brings a broader view of the contamination in space and time compared to surface and borehole measurements, especially when the results are supported by field measurements or laboratory experiments. The simulations are developed in 3D and are performed in COMSOL Multiphysics®. The simulations using petrophysical relationships for in-phase and quadrature resistivity and the results of the experiments are in complete accordance with each other in the parts of the tank where the saturation of DNAPL is relatively low (i.e. especially in the cone of depression in the pumping scenario). However, the parts associated with high saturation of DNAPL show high errors between the in-phase resistivity simulations and the results from experiments. The present work can be regarded as a preliminary study toward further applications of coupled IP-multiphase flow for more accurate detection and monitoring of DNAPLs. It is suggested that the choice of tool/approach in this study be extended to larger-scale studies for further investigation.

Predictive surface complexation model of the calcite-aqueous solution interface: The impact of high concentration and complex composition of brines.

Electrochemical interactions at calcite-water interface are characterized by the zeta potential and play an important role in many subsurface applications. In this work we report a new physically meaningful surface complexation model that is proven to be efficient in predicting calcite-water zeta potentials for a wide range of experimental conditions. Our model uses a two-stage optimization for matching experimental observations. First, equilibrium constants are optimized, and the Stern layer capacitance is optimized in the second stage. The model is applied to a variety of experimental sets that correspond to intact natural limestones saturated with equilibrated solutions of low-to-high salinity, and crushed Iceland Spar sample saturated with NaCl at non-equilibrium conditions. The proposed linear correlation of the Stern layer capacitance with the ionic strength is the main novel contribution to our surface complexation model without which high salinity experiments cannot be modelled. Our model is fully predictive given accurately known conditions. Therefore, the reported parameters and modelling protocol are of significant importance for improving our understanding of the complex calcite-water interfacial interactions. The findings provide a robust tool to predict electrochemical properties of calcite-water interfaces, which are essential for many subsurface applications including hydrology, geothermal resources, CO2 sequestration and hydrocarbon recovery.

Onset of IgA nephropathy in a patient treated with infliximab for ankylosing spondylitis.

We report the case of a 43-year-old man, suffering from ankylosing spondylitis and treated with Infliximab 5 mg/kg every 2 months, with an excellent disease control. During a follow-up consultation, an incipient renal insufficiency is detected. A urine analysis showed haematuria and proteinuria and a renal puncture-biopsy revealed an image of IgA nephropathy.Several cases of IgA nephropathy have been reported in the literature associated with ankylosing spondylitis. Some of them occur in patients treated with antitumour necrosis factor, but it is unclear whether this pathology is caused by the treatment or whether treatment failed to prevent its occurrence.Our clinical case highlights the importance of regular monitoring of renal function in patients with ankylosing spondylitis, as well as urinary spotting.The question of whether the disease itself, the treatment or other factors such as immune dysregulation could be held responsible for kidney disease will be addressed in the discussion.

Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency.

Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.

Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies.

Russian wheat aphid (RWA) ( Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat ( L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of as the most likely candidate opens an avenue for its validation through functional genomics approaches.

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize.

Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data.

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species.

Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Spectral induced polarization of Na-montmorillonite dispersions.

Montmorillonite (Mt) clays have a high specific surface area and surface charge, which confer them remarkable adsorption properties. Nevertheless, their electrochemical and aggregation behavior are not completely elucidated because of the complexity of their microstructural and interfacial properties. In this work, the conductive and dispersive properties of Na-Mt suspensions of weight fractions 0.5-5.2% were investigated for the first time using the spectral induced polarization method. A four-electrode system was used to reduce errors introduced by electrode polarization and contact resistances. Complex conductivity spectra in the low-frequency range of 0.1Hz to 45kHz were successfully described using a triple layer model of the basal surface of Mt and a complex conductivity model that considers conduction of the diffuse layer and polarization of the Stern layer. Aggregate size distributions were inferred from inverted relaxation time distributions. We found that the negative and permanent surface charge of the basal plane of Na-Mt controls its quadrature (imaginary) conductivity, which is not very sensitive to pH and salinity (NaCl) in the 100Hz to 45kHz frequency range. For lower frequencies, the sudden increase of the quadrature conductivity at the highest salinities was explained by considering coagulation of Na-Mt particles.

Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

Influence of surface conductivity on the apparent zeta potential of calcite.

Zeta potential is a physicochemical parameter of particular importance in describing the surface electrical properties of charged porous media. However, the zeta potential of calcite is still poorly known because of the difficulty to interpret streaming potential experiments. The Helmholtz-Smoluchowski (HS) equation is widely used to estimate the apparent zeta potential from these experiments. However, this equation neglects the influence of surface conductivity on streaming potential. We present streaming potential and electrical conductivity measurements on a calcite powder in contact with an aqueous NaCl electrolyte. Our streaming potential model corrects the apparent zeta potential of calcite by accounting for the influence of surface conductivity and flow regime. We show that the HS equation seriously underestimates the zeta potential of calcite, particularly when the electrolyte is diluted (ionic strength ⩽ 0.01 M) because of calcite surface conductivity. The basic Stern model successfully predicted the corrected zeta potential by assuming that the zeta potential is located at the outer Helmholtz plane, i.e. without considering a stagnant diffuse layer at the calcite-water interface. The surface conductivity of calcite crystals was inferred from electrical conductivity measurements and computed using our basic Stern model. Surface conductivity was also successfully predicted by our surface complexation model.

Evidence for TiO2 nanoparticle transfer in a hard-rock aquifer.

Water flow and TiO2 nanoparticle (NP) transfer in a fractured hard-rock aquifer were studied in a tracer test experiment at a pilot site in Brittany, France. Results from the Br tracer test show that the schist aquifer can be represented by a two-layer medium comprising i) fractures with low longitudinal dispersivity in which water and solute transport is relatively fast, and ii) a network of small fissures with high longitudinal dispersivity in which transport is slower. Although a large amount of NPs was retained within the aquifer, a significant TiO2 concentration was measured in a well 15m downstream of the NP injection well, clearly confirming the potential for TiO2 NPs to be transported in groundwater. The Ti concentration profile in the downstream well was modelled using a two-layer medium approach. The delay used for the TiO2 NPs simulation compared to the Br concentration profiles in the downstream well indicate that the aggregated TiO2 NPs interacted with the rock. Unlike Br, NPs do not penetrate the entire pore network during transfer because of electrostatic interactions between NP aggregates and the rock and also to the aggregate size and the hydrodynamic conditions, especially where the porosity is very low; NPs with a weak negative charge can be attached onto the rock surface, and more particularly onto the positively charged iron oxyhydroxides coating the main pathways due to natural denitrification. Nevertheless, TiO2 NPs are mobile and transfer within fracture and fissure media. Any modification of the aquifer's chemical conditions is likely to impact the groundwater pH and, the nitrate content and the denitrification process, and thus affect NP aggregation and attachment.

Virulence Factors of Streptococcus pneumoniae. Comparison between African and French Invasive Isolates and Implication for Future Vaccines.

BACKGROUND: Many surface proteins thought to promote Streptocococcus pneumoniae virulence have recently been discovered and are currently being considered as future vaccine targets. We assessed the prevalence of 16 virulence genes among 435 S. pneumoniae invasive isolates from France and the "African meningitis belt" region, with particular focus on serotype 1 (Sp1), to compare their geographical distribution, assess their association with site of infection and evaluate their potential interest as new vaccine candidates. METHODS: Detection by PCR of pspA (+families), pspC (+pspC.4), pavA, lytA, phtA,B,D,E, nanA,B,C, rrgA (Pilus-1), sipA (Pilus-2), pcpA and psrp was performed on all isolates, as well as antibiotic resistance testing and MLVA typing (+MLST on 54 representative strains). Determination of ply alleles was performed by sequencing (Sp1 isolates). RESULTS: MLVA and virulence genes profiles segregated Sp1 isolates into 2 groups that followed continent distribution. The ply allele 5 and most of the genes that were variable (nanC, Pilus-2, psrp, pcpA, phtD) were present in the French Sp1 isolates (PMEN clone Sweden(1)-28, ST306) but absent from the African ones. Whereas all African Sp1 isolates clustered into a single MLST CC (CC217), MLVA distinguished two CCs that followed temporal evolution. Pilus-2 and psrp were more prevalent in bacteraemic pneumonia yielded isolates and phtB in meningitis-related isolates. Considering vaccine candidates, phtD was less prevalent than anticipated (50%) and pcpA varied importantly between France and Africa (98% versus 34%). Pilus-1 was carried by 7-11% of isolates and associated with ß-lactams resistance. CONCLUSIONS: Most virulence genes were carried by the European ST306 clone but were lacking on Sp1 isolates circulating in the African meningitis belt, where a more serious pattern of infection is observed. While virulence proteins are now considered as vaccine targets, the geographical differences in their prevalence could affect the efficacy expected from future vaccines.

The electrophoretic mobility of montmorillonite. Zeta potential and surface conductivity effects.

Clay minerals have remarkable adsorption properties because of their high specific surface area and surface charge density, which give rise to high electrochemical properties. These electrochemical properties cannot be directly measured, and models must be developed to estimate the electrostatic potential at the vicinity of clay mineral surfaces. In this context, an important model prediction is the zeta potential, which is thought to be representative of the electrostatic potential at the plane of shear. The zeta potential is usually deduced from electrophoretic measurements but for clay minerals, high surface conductivity decreases their mobility, thereby impeding straightforward interpretation of these measurements. By combining a surface complexation, conductivity and electrophoretic mobility model, we were able to reconcile zeta potential predictions with electrophoretic measurements on montmorillonite immersed in NaCl aqueous solutions. The electrochemical properties of the Stern and diffuse layers of the basal surfaces were computed by a triple-layer model. Computed zeta potentials have considerably higher amplitudes than measured zeta potentials calculated with the Smoluchowski equation. Our model successfully reproduced measured electrophoretic mobilities. This confirmed our assumptions that surface conductivity may be responsible for montmorillonite's low electrophoretic mobility and that the zeta potential may be located at the beginning of the diffuse layer.

Structural and functional partitioning of bread wheat chromosome 3B.

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.