This study seeks to push the limits of LC3-50 binders by utilising low-grade kaolinite clays and C-S-H gel nucleation seeding. Four commercially-available kaolinite clays (i.e. kaolinite contents similar to 20 wt%) have been studied by X-ray fluorescence, X-ray powder diffraction and thermal analysis. The clays were thermally activated and milled to D-v,D-50 = 11 +/- 2 mu m. The activated clays showed low pozzolanic performances, as determined by ASTM C1897-20 standard. The heat flows ranged 200-230 J/g calcined clay and the bound waters 4.3-5.7 %. The LC3-50 pastes were characterised by calorimetry, X-ray powder diffraction and the Rietveld method, thermal analysis, and porosimetry to evaluate pozzolanic reactivity and the seeding effect. LC3 mortars, w/b = 0.40, have relatively low compressive strengths, especially at one day, but these values were increased by 64 % on average at one day by seeding. At 1 day, three LC3 mortars showed 11 MPa which increased to 18-20 MPa by seeding. A fourth mortar showed a much higher compressive strength, 16 MPa, that increased to 23 MPa, by seeding. A tested concrete, w/b = 0.50, also showed a high increase of 37 % at 1 day. The improvements at 28 days were maintained but quantitatively lower, 12 and 14 % for the mortars and the concrete, respectively. Insights into the pozzolanic reactions and C-S-H seeding are obtained from the quantitative study of the pastes. For instance, it is proven the pozzolanic reaction at 1 day from the portlandite consumption. Also shown is the enhanced formation of carboaluminates when the strength enhancing admixture is added.

Cucumber green mottle mosaic virus (CGMMV; Tobamovirus viridimaculae, Virgaviridae) is a mechanically transmitted plant virus that poses a major threat to cucurbit (cucumber, watermelon, melon and squash, among others) production worldwide. Its virions are rigid, non-enveloped, rod-shaped particles (~300 nm & times; 18 nm) composed of helically arranged monomers of the coat protein (CP) which encapsidate a positive-sense (+) single-stranded RNA genome (~6.4 kb). The CGMMV (+) RNA encodes two replication-associated proteins, a movement protein, and the CP. CGMMV virions are extremely stable and can persist for extended periods in plant debris and on contaminated surfaces. The virus is primarily associated with Cucurbitaceae, but it can infect plants from other families. Two major genetic types are recognized: Clade I and Clade II, often assimilated to European (EU) and Asian (AS) types, respectively, with Clade II isolates typically causing more severe symptoms and spreading globally. Transmission occurs mainly via mechanical contact, including through contaminated soil and tools, irrigation water, and infected seed, with seed-to-seedling transmission ranging widely from <0.1% to ~70%. Infected plants display stunting, foliar mosaic and deformation, and fruit discoloration and malformation, leading to severe economic losses. Resistances are available in commercial cultivars but do not abolish virus multiplication. Effective control requires integrated management combining prevention, rapid detection, and containment. CGMMV also serves as a valuable model for studying molecular interactions between cucurbits and viruses, and for gene functional studies in this plant family.

Abstract Tomato brown rugose fruit virus ( Tobamovirus fructirugosum ) is an emerging virus that affects tomatoes, capsicum, and chili. Since its first detection in Jordan in 2015, the virus was reported in more than 40 countries across all the continents. In Morocco, the virus was reported for the first time in October 2021. However, its genetic diversity remains unexplored. In this work, we used a collection of tomato fruits from local markets to investigate the variability of the virus in the country. We explored the different pressures acting on the N-terminus of the RNA-dependent RNA polymerase, the movement protein, and the coat protein genes. Then, we used haplotype network analyses to reveal the population structure within the Moroccan isolates and studied their relationships with the ones from the world. We found that genetic diversity is low, which is consistent with the global situation. No signatures of diversifying selection were detected across the analyzed genes. However, the virus sequences from Morocco showed a clear geographic structure, suggesting that geographic factors probably combined with agricultural practices may contribute to shaping the population structure of ToBRFV in Morocco.

TAXONOMY:Pepino mosaic virus (PepMV); species: Potexvirus pepini; family: Alphaflexiviridae; order: Tymovirales. VIRION AND GENOME PROPERTIES:PepMV virions are rod-shaped, non-enveloped, and flexuous particles. They encapsidate a monopartite, single-stranded, positive-sense RNA genome of approximately 6.4 kb, that encodes, in the sense orientation, a replicase, three triple gene block proteins, and the coat protein. HOST RANGE:PepMV is widespread and causes a major disease in intensive tomato crops. Natural infections have also been reported in kachuma (also known as cachum or pepino dulce; Solanum muricatum), basil, wild tomato species, and weeds from various families growing near affected tomato crops. Experimentally, PepMV can infect plants of virtually all Solanaceae species. DIVERSITY:Seven genetic types of PepMV are currently recognised: the original Peruvian (LP), European (EU), American US1, American US2, Chilean (CH2), the new Peruvian (PES), and Europe and the Asia-Pacific region (EAP). TRANSMISSION:PepMV is efficiently transmitted through mechanical means and shows a low rate of seed transmission. Insects, contaminated water, and agricultural tools have also been implicated in viral spread. SYMPTOMATOLOGY:PepMV infections can range from asymptomatic to severe. Common symptoms in tomato plants include leaf blistering, chlorosis, mosaic patterns, and fruit bleaching, flaming, and marbling. Severe cases may exhibit necrosis in leaves, stems, and fruits. Symptom severity depends on the viral isolate, tomato cultivar, timing of infection, and environmental conditions. CONTROL:No PepMV-resistant tomato varieties are currently available commercially. Therefore, preventive measures are commonly used strategies against PepMV. Cross-protection has proven highly effective and is widely employed for disease management.

Cucumber green mottle mosaic virus (CGMMV) is a tobamovirus that causes disease in cucumber crops worldwide, leading to significant economic losses. To study the variability of CGMMV in southeastern Spain, partial genome sequences were obtained from isolates collected in 2017 and 2020 from cucumber crops. Phylogenetic analyses revealed that isolates clustered into two major groups, Asian (AS)-like and European (EU)-like CGMMV isolates. These two groups coexisted in the same area, crops, and even individual plants, although the AS type predominated. The accumulation and symptom expression of molecularly cloned isolates from these two groups were assessed in two cucumber cultivars (resistant and susceptible) under both summer and winter conditions. An in planta antagonistic interaction was detected between the AS and EU isolates, in which the accumulation of CGMMV-EU was suppressed during mixed infections. A multivariate analysis did not identify statistically significant differences because of variations in environmental conditions. Unlike CGMMV-EU, CGMMV-AS did not show significant differences in accumulation based on the plant genotype. To further investigate this, the response to CGMMV-AS infection was analyzed in additional susceptible and resistant cultivars. All cultivars appeared to be similarly susceptible to CGMMV-AS, in contrast to CGMMV-EU, which accumulated to a much lower extent in resistant compared with susceptible plants. These results reinforce the need to continue epidemiological surveillance, identify new sources of resistance, and implement strict control of infected seed trade, given the growing threat that CGMMV-AS isolates pose to cucumber cultivation.

Despite its various applications, robotic manipulation of deformable objects in agriculture has experienced limited development so far. This is due to the specific challenges in this domain, i.e., the variety of objects in this field is wide, and the deformation properties of the objects cannot be easily recognized in advance. In addition, deformable objects generally have complex dynamics and high-dimensional configuration space. In this paper, the manipulation of deformable linear objects (DLOs) is addressed by considering these challenges. Concretely, anew indirect adaptive control method is proposed to manipulate DLOs by controlling their shape in 3-D space towards previously defined targets, with a specific focus on agricultural applications. The proposed method can follow a desired dynamic evolution of the shape with a smooth deformation that brings about a stable gripper motion. This property of the method can protect the object from possible damages, even under large deformations, which is crucial in agricultural scenarios. An adaptation law is leveraged for estimating the system parameters, and Lyapunov analysis is employed to study the validity of the proposed control scheme. The scheme can be applied to diverse objects that can be modeled as linear, including tree branches or other rod-like structures. The effectiveness of the scheme is demonstrated through various experiments where, using shape feedback obtained from a 3-D camera, a robotic arm controls the shape of a flexible foam rod and of branches of different plants.

The family Alphaflexiviridae comprises plant- and fungus-infecting viruses with single-stranded, positive-sense RNA genomes ranging from 5.4 to 9 kb. Their virions are flexuous and filamentous, measuring 470–800 nm in length and 12–13 nm in diameter. The family includes 72 recognized species, classified into six genera: Allexivirus, Lolavirus, Platypuvirus, Potexvirus (plant-infecting), and Botrexvirus and Sclerodarnavirus (fungus-infecting). The genus Potexvirus is the largest, with 52 species, including Potexvirus ecspotati (potato virus X), an important crop pathogen and plant virology model. The genera are distinguished by genome organization and host range, while species differentiation relies on nucleotide and protein sequence identity thresholds. In this review, we summarize the current knowledge on the genomic structure, conserved genes, and phylogenetic relationships within Alphaflexiviridae, with a particular focus on the replicase and coat protein genes as signature markers. Additionally, we update the model of cellular remodeling driven by the triple gene block proteins, which are essential for virus movement, among other viral functions. Beyond their biological significance, alphaflexiviruses serve as valuable models for studying virus–host dynamics and hold potential applications in plant disease control and biotechnology. This review provides an updated framework for understanding Alphaflexiviridae and their broader impact on plant virology.

Tomato leaf curl New Delhi virus (ToLCNDV) causes significant yield and fruit quality losses in cucurbit crops, particularly in the Mediterranean region. Sources of resistance to ToLCNDV have been identified in various cucurbits, including cucumber, where quantitative trait loci (QTLs) have been mapped to chromosomes 1, 2, and 6. A candidate gene encoding RNA-dependent RNA polymerase 3 (CsRDR3) has been identified and functionally validated in QTL1, and a candidate gene encoding heat shock factor A2 (CsHSFA2) has been identified in QTL2. We performed a field screening of cucumber accessions and identified ABS.PE.045 as potentially resistant to ToLCNDV. Since prototype Mediterranean isolates (ToLCNDV-ES) induce only mild symptoms in cucumber, we cloned ToLCNDV-CsES, an aggressive isolate from cucumber. The proteins from ToLCNDV-ES and ToLCNDV-CsES differ by only 10 amino acids; however, ToLCNDV-CsES induces severe symptoms in cucumber plants of the Wisconsin cultivar. We used ToLCNDV-CsES to phenotype ABS.PE.045, Wisconsin, and their F1 and F2,3 progenies. ABS.PE.045 plants were highly resistant, F1 plants showed symptoms and virus progression similar to those of Wisconsin plants, and F2 individuals segregated, suggesting the involvement of two or more genes in resistance determination. A bulk segregant analysis coupled with RNA-Seq suggested the involvement of four QTLs in resistance, with defined intervals on cucumber chromosomes 1, 2, 6, and 7. Our analysis suggested that CsRDR3 and CsHSF2A are bona fide candidates for QTLs 1 and 2, in agreement with previous studies. We propose CsaV3_7G022160, annotated as encoding a CCCH zinc finger protein, as a candidate for QTL7. The new marker and cloned ToLCNDV-CsES represent important tools for breeding resistance to this virus in cucumber.

Introduction:Microorganisms are emerging as key agents in sustainable agriculture due to their ability to enhance crop productivity while reducing environmental impact. Among them, Pseudomonas spp. are well known for promoting plant growth through mechanisms such as phytohormone production and improved nutrient availability. This study describes the characterization of the strain ABP-B9, isolated from the rhizosphere of commercial lettuce crops. Materials and methods:ABP-B9 was evaluated under both field and controlled conditions to assess its plant growth-promoting effects. Parameters such as root development, photosynthetic efficiency, flavonoid content, nitrogen status, and the production of indole-3-acetic acid (IAA) and siderophores were measured. Whole-genome sequencing and phylogenetic analysis were also performed. Results:Field trials showed that ABP-B9 enhanced crop yield in lettuce, spinach, and celery, improving root development, photosynthetic efficiency, flavonoid levels, and nitrogen status. The production of IAA and siderophores was confirmed in vitro. Plant responses were observed as early as five days after application. Genomic analysis revealed that ABP-B9 belongs to the Pseudomonas genus and is closely related to P. seleniipraecipitans. Its genome (4,602,210 bp; 61.46% GC content) includes 4,247 protein-coding genes, 12 rRNAs, and 66 tRNAs. Discussion:ABP-B9 is a novel, non-pathogenic Pseudomonas strain with clear biostimulant activity. Its ability to enhance plant growth and increase crop yield, combined with its safety profile, supports its potential use in sustainable agriculture. Future studies should explore its application across different crops and environmental conditions.

This study explores the feasibility of using calcined bentonitic clays in LC3-50 binders. Four commercially available bentonite rocks were thermally activated and milled to a Dv,50 of 12 +/- 2 mu m. Their pozzolanic activities were assessed using the R3 method, yielding total heat released values between 190 and 378 J/g-SCM, exceeding the minimum requirements for supplementary cementitious materials (SCMs). The incorporation of superplasticisers (SP) in bentonitic LC3 mortars was optimized, requiring dosages between 0.7 and 1.1 wt% (by the weight of binder) to achieve an initial slump of 200 +/- 20 mm, with flow maintained for 1 h in three of them. These results dispel concerns regarding the use of SP in LC3 containing calcined bentonites. Early-age hydration reactions were accelerated using C-S-H nucleation seeding technology, which increased bentonite LC3 mortar compressive strength by 50 % at one day. The compressive mechanical strengths at 28 days of the seeded mortars were also enhanced by 15 %. To elucidate the effects of C-S-H nucleation seeding, LC3 pastes were analysed, confirming the occurrence of pozzolanic reactions at one day of hydration. The portlandite contents, determined by Rietveld quantitative phase analysis and thermal analysis, were lower than expected based on the alite hydration degree at the analysed times. Furthermore, the strength enhancing admixture systematically increased the formation of AFm-type phases, such as hemicarboaluminate, and refined the pore microstructure at one day of hydration.

Tracking the 3D shape of a deforming object using only monocular 2D vision is a challenging problem. This is because one should (i) infer the 3D shape from a 2D image, which is a severely underconstrained problem, and (ii) implement the whole solution pipeline in real time. The pipeline typically requires feature detection and matching, mismatch filtering, 3D shape inference and feature tracking algorithms. We propose ROBUSfT, a conventional pipeline based on a template containing the object's rest shape, texture map and deformation law. ROBUSfT is ready-to-use, wide-baseline, capable of handling large deformations, fast up to 30 fps, free of training, and robust against partial occlusions and discontinuities. It outperforms the state-of-the-art methods in challenging video datasets. ROBUSfT is implemented as a publicly available C++ library. We provide the code, a tutorial on how to use it, and a supplementary video of our experiments at https://github.com/mrshetab/ROBUSfT.

In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA samples. The pipeline is designed for the analysis of short reads generated using an Illumina platform and free-available software tools. First, we provide advice for high-quality total RNA purification, library preparation, and sequencing. The bioinformatics pipeline begins with the raw reads obtained from the sequencing machine and performs some curation steps to obtain long contigs. Contigs are blasted against a local database of reference nucleotide viral sequences to identify the viruses in the samples. Then, the search is refined by applying specific filters. We also provide the code to re-map the short reads against the viruses found to get information on sequencing depth and read coverage for each virus. No previous bioinformatics background is required, but basic knowledge of the Unix command line and R language is recommended.

The most effective approach to mitigating the environmental impact of cement production is through the utilisation of pozzolanic materials to prepare blended cement. Calcined kaolinitic clays are one of the most promising materials to be used as supplementary cementitious materials (SCM) due to their final performances. However, there are locations where kaolinitic rocks are not available. This work presents the study of two dioctahedral smectite standards from the Clay Minerals Society (CMS), SWy-3 and SAu-1, to be used as references. After thermal activation optimisation, their pozzolanic performances are compared with those of lowgrade kaolinitic clay. On the one hand, raw SWy-3 has an amorphous content of -80 wt%, considered montmorillonite, with quartz and feldspars. The optimum calcination temperature was 800 degrees C, at which the smectite is fully dehydroxylated (as determined by thermal analysis) but not completely amorphized (as shown by powder diffraction). After calcination (800 degrees C), with a median particle size by volume (Dv,50) of -11 mu m, -480 J/g were released at 7 days in the R3 test. On the other hand, SAu-1 has a higher amount of amorphous content, -96 wt%, which includes interstratified illite/smectite. The optimum calcination temperature was found to be 750 degrees C. This sample (Dv,50 -10 mu m) gave 452 J/g at 7 days in the R3 test. The optimised active smectites gave a pozzolanic activity comparable to clay with 30-35 % kaolinite, as determined, for the first time, by the R3 test. This work has established descriptors for the activation of natural smectites/bentonites and reference values for the resulting smectite-based SCMs.

The hydration processes of Portland cements (PC) and blends are complicated as there are many components with great heterogeneity at different length scales. Thus, 3D nanoimaging techniques with high spatial resolution and scanning large fields of view are needed. Here, synchrotron X-ray near-field ptychographic tomography is used to investigate four pastes within 0.2 mm thick capillaries: PC with CaCl2, PC hydration enhanced by C-S-H nucleation seeding, PC partly substituted with metakaolin, and PC partly substituted with metakaolin and limestone. Data analysis emphasis has been placed on the characterization of amorphous components: (i) C-S-H and C-A-S-H gels; (ii) iron aluminium siliceous hydrogarnets; (iii) metakaolin; and (iv) aluminium carboaluminate, AFm-like. Synchrotron ptychotomography yields electron density and absorption coefficient tomograms and the resulting bivariate plots are instrumental for characterising these amorphous components. The attained spatial resolution, similar to 220 nm, with very good contrast allowed us to determine nanofeatures including mass densities and spatial distributions of amorphous components. For instance, the C-S-H gel mass density differences between the two type of accelerated pastes are detailed.

Data for: In situ synchrotron powder diffraction study of LC3 cement activation at very early ages by C-S-H nucleation seeding

Limestone Calcined Clay Cements (LC3) are attracting considerable attention due to their low CO2 footprints and relatively fast hydration kinetics. LC3-50 formulations (approximately 50 % Portland clinker, 30 % kaolinitic calcined clay, 15 % limestone and 5 % gypsum) are being extensively investigated and the hydration chemistry, rheology, mechanical strength developments and durability performances are starting to be well established. LC3 binders with lower clinker factors are possible, offering an opportunity for further CO2 footprint reduction. However, these blends have been much less studied. This work contributes to fill this gap. Here, a LC3-35 binder (i.e. 35 % Portland clinker content) is investigated and its performances are compared to those of the original Portland cement (PC) and a standard LC3-50 binder. The effects of two superplasticizers and a strength-enhancing admixture are thoroughly investigated in mortars and pastes. Larger calcined clay contents result in an exacerbation of the slump retention problem, but this issue is solved by the use of a new superplasticizer. Moreover, the low mechanical strengths at early ages can be partly mitigated with a C-S-H nucleation seeding admixture. Employing the right admixtures, LC3-35 binders can develop strength values similar to those of neat PC and LC3-50 at 7 and 28 days. The laboratory X-ray powder diffraction results for LC3-35 pastes, when using the strength-enhancing admixture, show that C4AF exhibits an accelerated reaction rate, leading to the formation of larger amounts of AFt and AFm phases. Approximate mass balance calculations are carried out to estimate the metakaolin reaction degree. Finally, an environmental performance indicator is used to place the footprints of the reported binders within the LC3 landscape.

Background and Aims Given the lack of specific studies on floral development in melon (Cucumis melo L.), we carried out an extensive study involving morphological and transcriptomic analyses to characterize floral development in this species. Methods Using an andromonoecious line, we analysed the development of floral buds in male and hermaphrodite flowers with both light microscopy and scanning electron microscopy. Based on flower lengths, we established a correlation between the developmental stages and four main episodes of floral development and conducted an extensive RNA sequencing analysis of these episodes. Key Results We identified 12 stages of floral development, from the appearance of the floral meristems to anthesis. The main structural differences between male and hermaphrodite flowers appeared between stages 6 and 7; later stages of development leading to the formation of organs and structures in both types of flowers were also described. We analysed the gene expression patterns of the four episodes in flower development to find the genes that were specific to each given episode. Among others, we identified genes that defined the passage from one episode to the next according to the ABCDE model of floral development. Conclusions This work combines a detailed morphological analysis and a comprehensive transcriptomic study to enable characterization of the structural and molecular mechanisms that determine the floral development of an andromonoecious genotype in melon. Taken together, our results provide a first insight into gene regulation networks in melon floral development that are crucial for flowering and pollen formation, highlighting potential targets for genetic manipulation to improve crop yield of melon in the future.

Dataset for paper abstract: "It is reported an innovative methodology based on in situ MoKa1 laboratory X-ray powder diffraction (LXRPD) and microtomography (μCT) avoiding any sample conditioning. The pastes are injected in 2.0 mm capillaries and the extremes are just sealed. The measurements take place in the same region of the hydrating paste. Thick capillaries are key to avoiding self-desiccation, which dictates the need of high-energy X-ray radiation for the diffraction study. This approach has been tested with a PC 42.5 R paste having w/c=0.50. μCT data were collected at 12 hours and 1, 3, 7 and 79 days. LXRPD data were acquired at 1, 3, 7 and 77 days. In this proof-of-principle research, the same paste was also cured ex situ. Portlandite contents obtained by thermal analysis, ex situ powder diffraction, in situ mass balance calculation and in situ powder diffraction were 13.8, 13.1, 13.1 and 12.5 wt%, respectively. From the μCT study, the grey value histogram evolution with time showed a crossing point which allowed us to distinguish (appearing) hydrated products from (dissolving) unhydrated cement particles. Segmentations were carried out by global thresholding and the random forest approach (one type of supervised Machine Learning). The comparison of the segmented results for the unhydrated cement fraction and the Rietveld quantitative phase analysis outputs gave an agreement of 2%. The potential of this methodology to deal with more complex binders is also presented."