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We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host’s cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.

The unprecedented growth of universities in recent years has meant that there are more students with learning disabilities attending courses. Consequently, universities have had to adapt, improve and create new resources to ensure greater inclusivity. These resources, their design, and development are managed by inclusion support services, aiming to the full inclusion of students with disabilities and the promotion of community awareness. This article aims to shed light on the current role of inclusion services in supporting students with learning disabilities, and the link these services have with the different university stakeholders, using a thematic analysis from the experiences of this services staff in eight Spanish universities. The results show that: i) there is no uniformity in the support services; and ii) more resources and work are needed to ensure increased inclusion and awareness. The discussion and conclusions drawn highlight the trends, challenges, and opportunities for universities improving their inclusion.

Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.

International audience; The advent of next-generation genome sequencing technologies has allowed approaching the sequencing and analysis of large and complex conifer genomes. Maritime pine (Pinus pinaster Ait.) is an economically and ecologically important conifer species widely distributed in South-West Europe, which shows a significant genetic and adaptive variability. This chapter takes on the task of reviewing the insights into the maritime pine genome sequencing breakthrough and its impact on downstream analysis. Maritime pine genome sequencing and assembly approaches are described along with the impact of related tools. A section of the state-of-the-art research on comparative, functional, structural, and translational genomics aimed at dissecting the genetic basis and the specific regulation of biological processes underlying the expression of traits of interest in maritime pine and other conifers is also described. Perspectives about the impact of these tools as well as additional research approaches are discussed.

Fipronil is a broad-use insecticide with severe toxicity to fish. Biomarkers responses and bioaccumulation were evaluated on Prochilodus lineatus after exposure to environmentally relevant concentrations of fipronil (0.5 μg L−1, 9 μg L−1, and 100 μg L−1) in a prolonged flow-through assay and ex vivo gills short-term exposition. Lipid peroxidation (LPO), oxidatively modified proteins (PO), the activity of superoxide dismutase (SOD), the content of reduced glutathione (GSH), antioxidant capacity against peroxyles (ACAP), and acetylcholinesterase (AChE) were evaluated. Besides, levels of fipronil and metabolites were analyzed by GC-ECD. At the end of the flow-through assay, fipronil, Fp. sulfone and Fp. desulfinyl were detected in fish, being liver the target organ. Fipronil prolonged exposition promoted oxidative damage in lipids and proteins, alterations in the defense system and low-antioxidant capacity in organs of P. lineatus. The brain AChE activity was affected after prolonged exposition. Ex vivo gills exposition to fipronil promoted changes in antioxidant capacity and damage to lipids, providing a fast and suitable test to assess the pesticide exposure in fish. The results revealed that fipronil at environmental concentrations would be an inducer of oxidative stress in this fish, becoming a vulnerable species to the effects of fipronil in aquatic environments.

Background: Neuropathic pain is a complex condition characterized by sensory, cognitive and affective symptoms that magnify the perception of pain. The underlying pathogenic mechanisms are largely unknown and there is an urgent need for the development of novel medications. The endocannabinoid system modulates pain perception and drugs targeting the cannabinoid receptor type 2 (CB2) devoid of psychoactive side effects could emerge as novel analgesics. An interesting model to evaluate the mechanisms underlying resistance to pain is the fragile X mental retardation protein knockout mouse (Fmr1KO), a model of fragile X syndrome that exhibits nociceptive deficits and fails to develop neuropathic pain. Methods: A partial sciatic nerve ligation was performed to wild-type (WT) and Fmr1KO mice having (HzCB2 and Fmr1KO-HzCB2, respectively) or not (WT and Fmr1KO mice) a partial deletion of CB2 to investigate the participation of the endocannabinoid system on the pain-resistant phenotype of Fmr1KO mice. Results: Nerve injury induced canonical hypersensitivity in WT and HzCB2 mice, whereas this increased pain sensitivity was absent in Fmr1KO mice. Interestingly, Fmr1KO mice partially lacking CB2 lost this protection against neuropathic pain. Similarly, pain-induced depressive-like behaviour was observed in WT, HzCB2 and Fmr1KO-HzCB2 mice, but not in Fmr1KO littermates. Nerve injury evoked different alterations in WT and Fmr1KO mice at spinal and supra-spinal levels that correlated with these nociceptive and emotional alterations. Conclusions: This work shows that CB2 is necessary for the protection against neuropathic pain observed in Fmr1KO mice, raising the interest in targeting this receptor for the treatment of neuropathic pain. Significance: Neuropathic pain is a complex chronic pain condition and current treatments are limited by the lack of efficacy and the incidence of important side effects. Our findings show that the pain-resistant phenotype of Fmr1KO mice against nociceptive and emotional manifestations triggered by persistent nerve damage requires the participation of the cannabinoid receptor CB2, raising the interest in targeting this receptor for neuropathic pain treatment. Additional multidisciplinary studies more closely related to human pain experience should be conducted to explore the potential use of cannabinoids as adequate analgesic tools. This work was supported by research grants from the Spanish Ministry of Science and Innovation (#SAF2017-84060-R-AEI/FEDER-UE), the European Commission-DG Research (PainFact, #H2020-SC1-2019-2-RTD-848099), the Instituto de Salud Carlos III-RETICS (RTA, #RD16/0017/0020), the Spanish Ministerio de Sanidad, Servicios Sociales e Igualdad-Plan Nacional Sobre Drogas (#PNSD-2017I068) to RM; and the Catalan Government-AGAUR (#SGR2017-669 and ICREA Academia Award 2015 to RM and SGR2017-138 to RdlT). AR-L is the recipient of a FI predoctoral fellowship (Generalitat de Catalunya-AGAUR).

Silver nanoparticles (AgNPs) are one of the most produced nanoproducts due to their unique biocide properties. The natural organic matter has an important impact on nanoparticle's dispersion as it may alter their fate and transport, as well as their bioavailability and toxicity. Therefore, this study aimed to evaluate the mitigatory effect of humic acids (HAs) on AgNP toxicity. For this purpose, we carried out an ex vivo exposure of gill of Piaractus mesopotamicus fish to 100 μg L-1 of AgNPs or AgNO3, alone and in combination with 10 mg L-1 of HAs. In parallel, a complete AgNP characterization in the media, including the presence of HAs, was provided, and the Ag+ release was measured. We analyzed Ag bioaccumulation, antioxidant enzymes activities, lipid peroxidation, antioxidant capacity against peroxyl radicals, and reduced glutathione levels in fish tissue. Our results indicated the Ag+ release from AgNPs decreased 28% when the HAs were present in the media. The Ag accumulation in gill tissue exposed to AgNPs alone was higher than the AgNO3 exposure, and sixfold higher than the treatment with the HA addition. Moreover, after both Ag forms, the catalase enzyme augmented its activity. However, those responses were mitigated when the HAs were present in the media. Then, our results suggested the mitigation by HAs under the exposure to both Ag forms, providing valuable information about the fate and behavior of this emergent pollutant.

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

This study describes an intervention carried out in the course on Statistics within the Bachelors’ Degree in Business Administration, and Marketing and Digital Communication. Prior to it, problems related to attention in class and low motivation were identified. A game-based activity was designed aiming at boosting students’ attention and encouraging autonomous study habits, which in turn, positively impact on their grades. To assess the effectiveness of the activity we tracked the grades and satisfaction of 153 students. Critical aspects highlighted by students in a focus group were also analysed. Evidences show the usefulness of the activity in improving students’ grades and, to some extent, in changing their habits.

Introduction: The Multidimensional Weight Locus of Control Scale (MWLCS) measures a person's beliefs regarding the locus of control or lack of locus of control over his/her body weight. Purpose: We aim to evaluate the factorial structure and psychometric properties of the MWLCS with Spanish normal weight, overweight and obese samples. Methods: The research was carried out in two different studies. The first included a sample of 140 normal weight participants, selected out of a 274 sample recruited with an online survey. Study 2 was carried out in a sample of 633 participants recruited from the PREDIMED-Plus study. Out of them, 558 participants fulfilled the weight criteria and were categorized into: overweight (BMI 25 - < 29.99; N = 170), obese class I (BMI 30 - < 34.99; N = 266), and obese class II (BMI 35 - < 39.99; N = 122). Exploratory (EFA) and confirmatory (CFA) factor analyses were used to evaluate the factor structure of the MWLCS, and reliabilities and Spearman's correlations were estimated. Invariance measurement was tested across the three subgroups of weight in Study 2. Results: A three-factor structure indicating weight locus of control factors (internal, chance, and powerful others) was supported, both via EFA in the normal weight sample and CFA in the overweight and obese samples. In the normal weight sample, the powerful others dimension was positively related to BMI and the dimensions of the Dutch Eating Behaviors Questionnaire. Additionally, the scale showed evidence of scalar invariance across the groups with different weight conditions. Conclusions: This scale seems to be a psychometrically appropriate instrument and its use is highly recommended when designing interventions for overweight or obese individuals. Level of evidence: Level V, descriptive study. CIBEROBN is an initiative of the ISCIII (Instituto de Salud Carlos III, Spain). We thank the PREDIMEDPLUS Biobank Network, part of the National Biobank Platform of Instituto de Salud Carlos III for storing and managing biological samples. We thank to Research Council (Grant 340918) and PROMETEO Grant (17/2017) from the Generalitat Valenciana.

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

SUMMARYDrought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate GWAS methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western US – coast redwood and giant sequoia – using ten drought-related physiological and anatomical traits and genome-wide sequence-capture SNPs. Population level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.Significance StatementClimate change brings more frequent and severe drought events that challenge the survival of natural populations of plants. While most of our knowledge about drought tolerance comes from annual and domesticated plants, the genomic basis of drought tolerance in long-generation trees is poorly understood. Here, we aim to fill this gap by identifying candidate genes in two conifer species, coast redwood and giant sequoia.

BackgroundTocilizumab (TCZ) has shown to be effective for large vessel vasculitis including giant cell arteritis (GCA) and Takayasu arteritis (TAK) (1-5). However, LVV-GCA and TAK show different demographic and clinical features that may influence on TCZ therapeutic response.ObjectivesTo compare the effectiveness of TCZ in patients with LVV-GCA and patients with TAK.MethodsObservational multicenter study of patients with LVV-GCA and TAK who received TCZ. Outcome variables were: a) proportion of patients who achieved complete clinical improvement along with normalization of laboratory markers (CRP ≤0.5mg/dL and/or ESR ≤ 20 mm/1st hour) at 12 months b) complete improvement in imaging techniques. A comparative study between patients with LVV-GCA and TAK was performed.ResultsWe evaluated 70 LVV-GCA and 57 TAK patients who received TCZ. Main clinical and demographic characteristic are described in Table 1. Patients with TAK were younger, had longer disease duration, had received more commonly previous biologic therapy and were receiving higher doses of prednisone at baseline. TCZ intravenous administration was more common in TAK patients (80.7% vs 48.6%; pTable 1.LVV-GCA (n=70)TAK (n=57)pGeneral featuresAge (years), mean ± SD67.2 ± 10.540.5 ± 16.3< 0.01Sex (female), n (%)51 (72.9)49 (86)0.07Disease evolution before TCZ onset (months), median [IQR]5 [2-15]12 [3-37]Baseline laboratory parametersESR (mm/1st hour), median [IQR]32 [12.5-54.7]31 [10-52]0.82CRP (mg/dL), median [IQR]1.4 [0.5-2.4]1.4 [0.5-3.5]0.41Baseline prednisone dose (mg/day), median [IQR]15 [10-20]30 [15-50]< 0.01Previous therapyConventional DMARDs, n(%)45 (64.3)44(77.2)0.51Biologic therapy, n (%)0(0)12 (21.1)TCZ therapyIntravenous, n (%)34 (48.6)46 (80.7)< 0.01Combined with MTX, n(%)24 (34.3)24 (42.1)0.37Follow-up time after TCZ onset, median [IQR]20 [10-36]18 [7-41]0.73Complete clinical improvement and ESR/CRP normalization at 12 months, n/N (%)35/47 (74.4)30/39 (76.9)0.79Complete improvement in imaging techniques, n/N(%)7/37 (18.9)8/38 (21.1)0.85CRP: C-reactive protein; DMARDs: Disease-modifying anti-rheumatic drugs ESR: erythrocyte sedimentation rate; GCA: giant cell arteritis; IQR: interquartile range; LVV: large vessel; MTX: methotrexate; n: Number of patients; N: total number of patients: TCZ: tocilizumab; TAK:takayasuFigure 1.ConclusionThe effectiveness of TCZ was similar in patients with LVV-GCA and TAK, despite a more refractory disease in TAK patients. A discordance between clinical and imaging activity improvement was observed in both LVV-GCA and TAK, as reported in previous studies (3).References[1]Calderón-Goercke M, et al. Semin Arthritis Rheum 2019; 49:126-35. https://doi.org/10.1016/j.semarthrit.2019.01.003[2]Prieto-Peña D et al. Ther Adv Musculoskelet Dis. 2021;13:175. PMID: 34211589.[3]Prieto Peña D et al. Clin Exp Rheumatol. 2021;39 Suppl 129:69-75. PMID: 33253103.[4]González-Gay MA, et al. Expert Opin Biol Ther. 2019;19:65-72. doi: 10.1080/14712598.2019.1556256.[5]Prieto-Peña D, et al. Semin Arthritis Rheum. 2019;48(4):720-727. doi: 10.1016/j.semarthrit.2018.05.007Disclosure of InterestsNone declared

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.

Triclosan (TCS) is an antimicrobial and antimycotic agent widely used in personal care products. In aquatic environments, both TCS and its biomethylated more persistent form, methyl-triclosan (MeTCS), are usually detected in wastewater effluents and rivers, where are commonly adsorbed to suspended solids and sediments. The aim of this study was to evaluate biochemical and physiological effects in Danio rerio after a short term (2 days) and prolonged (21 days) exposures to sediment spiked with TCS acting as the source of the pollutant in the assay. The activities of catalase (CAT), glutathione-s transferase (GST) and superoxide dismutase (SOD), lipid peroxidation levels (LPO), total capacity against peroxyl radicals (ACAP), and acetylcholinesterase enzymatic activity (AChE) were measured in liver, gills, and brain. Most of TCS on the spiked sediment was biotransformed to MeTCS and promoted different adverse effects on D. rerio. Gills were the most sensitive organ after 2 day-exposure, showing lipid damage and increased SOD activity. After 21 days of exposure, liver was the most sensitive organ, showing lower ACAP, increased LPO levels, and SOD and CAT activities. This is the first study reporting the effects on biochemical markers in D. rerio from a MeTCS sink resulting from sediment spiked with TCS.

Williams-Beuren syndrome (WBS) is a rare genetic multisystemic disorder characterized by mild to moderate intellectual disability and hypersocial phenotype, while the most life-threatening features are cardiovascular abnormalities. Nowadays, there are no available treatments to ameliorate the main traits of WBS. The endocannabinoid system (ECS), given its relevance for both cognitive and cardiovascular function, could be a potential druggable target in this syndrome. We analyzed the components of the ECS in the complete deletion (CD) mouse model of WBS and assessed the impact of its pharmacological modulation in key phenotypes relevant for WBS. CD mice showed the characteristic hypersociable phenotype with no preference for social novelty and poor object-recognition performance. Brain cannabinoid type-1 receptor (CB1R) in CD male mice showed alterations in density and coupling with no detectable change in main endocannabinoids. Endocannabinoid signaling modulation with sub-chronic (10 d) JZL184, a selective inhibitor of monoacylglycerol lipase (MAGL), specifically normalized the social and cognitive phenotype of CD mice. Notably, JZL184 treatment improved cardiac function and restored gene expression patterns in cardiac tissue. These results reveal the modulation of the ECS as a promising novel therapeutic approach to improve key phenotypic alterations in WBS.

Ivermectin (IVM) is one of the most widely used antiparasitics worldwide. It is a potent and effective drug for treatment and prevention of internal and external parasitic infections of livestock and humans. IVM is excreted unchanged in manure of treated animals. Thus, residues of IVM may reach aquatic systems, affecting non-target organisms such as fish. Although the presence of IVM in aquatic environments has been reported, a multilevel approach (from cellular to behavioral responses) is necessary to determine the health of exposed organisms and the environmental risks associated. The aim of the present study was to investigate the response of the Neotropical fish Prochilodus lineatus, one of the main target species of South American freshwater fisheries, exposed to environmental concentrations of IVM: low (0.5 μg L−1) and high (1.5 μg L−1). Behavioral responses were assessed in juvenile fish and included water column use, routine swimming, total distance travelled, total activity time and Maximum swimming speed achieved during the escape response. Biochemical/oxidative stress responses assessed included brain acetylcholinesterase (AChE), catalase (CAT) and glutathione S-transferase (GST) activities; total antioxidant competence against peroxyl radicals (ACAP) and lipid oxidative damage (TBARs). Hematological biomarker responses included blood glucose levels, hematocrit, hemoglobin concentration, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscular volume. Condition factor and hepatosomatic index were also calculated. The lowest IVM concentration caused a significant decrease in GST activity and maximum swimming speed during the escape response. Multivariate analysis with biochemical/stress and behavioral data revealed overall effects of IVM treatments. This multilevel analysis shows detrimental effects related to swimming behavior and predator avoidance which could affect population size and size-structure of P. lineatus. To our knowledge this is the first attempt to assess the effects of IVM on Neotropical fishes using an integrative approach based on biomarkers from different levels of biological organization.

Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water‐conducting systems, secondary metabolism, stress defense mechanisms, and small RNA‐mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole‐genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.

We investigated the strength of the interactions of the elements of the Estonian network of payments (link weight of payments and volume of payments) by the realization of particular experiments. Specific statistical measures of this network, which combine the topology of the relations of the strength of links and nodes and their specific weights, were studied with the purpose of discovering beyond the topological architecture of our network and revealing aspects of its complex structure. Moreover, scale-free properties between the strengths and the degree values were found. We also identified clear patterns of structural changes in such a network over the analysed period.

The tomato processing industry generates huge quantities of sludge annually (1.5% of the tomato) which represents an environmental problem, especially in the large producing areas such as Extremadura in Spain. The substitution of clayey raw materials for other wastes, in this case tomato sewage sludge, in the production of traditional ceramics, could be cost-effective from the utilization and recycling of these wastes as a secondary raw material. Different quantities of sewage sludge from the tomato processing industry have been added to the body of the clay to produce ceramic materials. It has achieved a ceramic material with greater porosity to improve its thermal and acoustic insulation capacity.

Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance. Whole-genome resequencing data were used to generate high-resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda) natural range. Genome-wide associations were tested with a large phenotypic dataset comprising 409 variables including morphological traits (height, diameter, carbon isotope discrimination, pitch canker resistance), and molecular traits such as metabolites and expression of xylem development genes. Our study identified 2335 new SNP × trait associations for the species, with many SNPs located in physical clusters in the genome of the species; and the genomic location of hotspots for metabolic × genotype associations. We found a highly polygenic basis of quantitative inheritance, with significant differences in number, effects size, genomic location and frequency of alleles contributing to variation in phenotypes in the different traits. While mutation-selection balance might be shaping the genetic variation in metabolic traits, balancing selection is more likely to shape the variation in expression of xylem development genes. Our work contributes to the study of complex traits in nonmodel plant species by identifying associations at a whole-genome level.

The aim of this study was to evaluate simultaneously a battery of biomarkers in Prochilodus lineatus fish in order to obtain a holistic overview of silver nanoparticles (AgNP) toxicity. Juveniles were exposed to 2.5 and 25.0 µgAgNP L−1 for 5 and 15 days. We analyzed silver accumulation in tissues (liver, intestine and brain), morphometric and hematological parameters, oxidative stress markers (antioxidant enzymes, lipid peroxidation, and antioxidant capacity against peroxyl radicals-ACAP-), and metabolic responses in plasma (glucose, proteins, triglycerides and cholesterol), liver and muscle (glycogen, proteins, and lipids). Additionally, after 15-day exposure, the number of colony forming units (CFU) of bacteria living at the skin mucus secretion was analyzed to corroborate the AgNP biocide properties. Tissue Ag accumulation was concentration- and time-dependent: liver > intestine > brain. The hepatosomatic index increased at both periods of exposure at 25.0 µgAgNP L−1. Hematological and plasma biochemical parameters increased after 5 days of exposure to the highest concentration. When fish were exposed for 15 days to 25.0 µgAgNP L−1, many changes were observed: glycogen content increased in liver and muscle, muscle protein concentration decreased, all antioxidant enzymes activities were enhanced and ACAP decreased in liver. The CFU decreased in the mucus of fish exposed to both AgNP treatments when compared to the control group. The multivariate analysis revealed a clear difference in physiological profiles of individuals exposed to the different treatments. Our results showed that AgNP in short and subchronic exposures threaten the health of fish. Fil: Ale, Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina Fil: Rossi, Andrea Silvana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina Fil: Bacchetta, Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina Fil: Gervasio, Susana Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina Fil: de la Torre, Fernando Roman. Universidad Nacional de Luján. Instituto de Ecología y Desarrollo Sustentable. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ecología y Desarrollo Sustentable; Argentina Fil: Cazenave, Jimena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

Natural hybridization occurs in sites where Pinus halepensis Mill. and Pinus brutia Ten. overlap geographically. Studies have shown that these hybrids demonstrate vigorous growth. Currently, there is no efficient method for hybrid identification. In the present study, a transcriptome database that was established from P. halepensis and P. brutia provided 111,388 potential SNP markers for hybrid identification. We selected 295 SNPs that were verified in silico using the Integrative Genomics Viewer (IGV) program. Forty-three SNPs were confirmed in vitro using several methods, including CAPS, HRM, TaqMan, KASP, and direct sequencing. Seven SNPs that were used for genotyping P. brutia trees in three planted sites along the climatic gradient of Israel demonstrated hybrid incidences of 2.5, 6.3, and 9.4%. The trunk volume of the hybrids in these sites was 2.9, 2.4, and 1.2 times larger than that of their P. brutia neighboring trees. Differences among the sites in the hybrid vigorous growth extent might have resulted from several factors, including genetic source, stand age, thinning history, and site conditions. However, the overall vigorous growth of the hybrids that was more pronounced in the arid site highlights the potential of interspecific hybridization as a means for improving the drought resistance of forest trees. This work provides a reliable SNP database for the identification of P. brutia × P. halepensis hybrids for the potential utilization of these hybrids to confront changes in climate.

Silver nanoparticles (AgNP) are unique because of their biocide properties. Once released to environment, AgNP interact with the natural organic matter which impact on their fate, dispersion, and ultimate toxicity. We carried out an ex vivo exposure of gill of Corydoras paleatus fish to 100 µg L−1 of AgNP or AgNO3, alone and in combination with 10 mg L−1 of humic acids (HA), with the aim to evaluate the potential mitigation of HA on AgNP toxic effects. We analyzed Ag accumulation and oxidative stress biomarkers. The results showed high bioaccumulation after the AgNO3+HA exposure. An inhibition of glutathione-S-transferase enzymatic activity and depletion of reduced glutathione levels were registered after the AgNO3 exposure, and increased lipid peroxidation levels in the case of AgNP one. Oxidative responses were mitigated when the HA were present in the media. Overall, the knowledge about the fate of this emergent pollutant was deepened through this study.

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species&rsquo, predictions under climate change.

Fipronil is a broad-use insecticide with severe toxicity to fish. Biomarkers responses and bioaccumulation were evaluated on Prochilodus lineatus after exposure to environmentally relevant concentrations of fipronil (0.5 μg L

The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.

Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.

In contrast to flowering plants, the genomes of gymnosperms are still poorly understood. Current knowledge on the genomic architecture, gene space, and macrostructure of gymnosperm genomes mainly comes from Pinaceae species, in which spruce species (genera with most sequenced genomes to date) had played a significant role. Whereas the accumulation of nuclear genomes’ sequence information has followed a slow pace, the sequencing of chloroplast genomes skyrocketed in the last 10 years, with many spruce species sequenced so far. From the comparison of nuclear, mitochondrial, and chloroplast genomes, we can conclude that they all differ in their genomic macrostructure and rates of sequence evolution. The high structural conservation among species, genera, and families is characteristic of nuclear genomes, whereas chloroplast and mitochondrial genomes show less conserved structures due to genomic arrangements. Finally, Picea species follow trends observed in other gymnosperms and angiosperms, in which rates of sequence evolution are the highest in nuclear DNA, followed by chloroplast and then mitochondrial DNA.

The spruce reference genomes (Picea abies, P. glauca, P. glauca x engelmannii) were published eight years after the release of Populus trichocarpa’s genome, the first forest tree species ever sequenced (Science 313:1596–1604 (2006)). Although sequencing these highly complex 20 Gigabases spruce genomes represented a major achievement, the current assemblies present many limitations and a chromosome-level assembly reference in this ecologically and economically important genus is still far from reach (Chaps. 2, 7, 8). Nevertheless, improvements in next-generation sequencing technologies and bioinformatic methods have led to important advancements as outlined in this book (Chap. 3). Increasingly complete and more accurate spruce genome sequences will serve the research community in many aspects. Foremost, they will enable improved annotations in the gene space, new discoveries in plant secondary metabolism, and support new breeding strategies for physiologically active compounds and beyond (Chaps. 5, 9, 12, and 13). An even more uncharted territory is the elucidation of epigenetic memory (Chaps. 4 and 6). In the context of adaptation to future climates, spruces are prime study subjects, as important representatives of boreal ecosystems (Chaps. 10 and 11). Following the example of plant species with less complex genomes, whole-genome resequencing will become state-of-the-art in population genomics of spruces and thus invaluable for finding the most important genetic/genomic variants underlying traits of interest. This volume details the progress of the spruce genome sequencing efforts as a cornerstone for exciting discoveries in gymnosperm genomics.

Reference genomes provide valuable information to study the molecular biology and the genomic architecture of species, and constitute a baseline for applied sciences such as molecular breeding and gene editing. The sequencing of conifer genomes still lags behind other plant and animal species, with only a few available conifers having full sequence genomes to date. This chapter aims to describe details on the sequencing and bioinformatics analysis of the nuclear and organelle genome assemblies of the economically important white spruce (Picea glauca), and closely related Picea species P. sitchensis and P. engelmannii. The chapter finishes by providing some perspectives for future genome assemblies of North American species.