The Quest for Orthologs orthology benchmark service in 2022.

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

Global leaf and root transcriptome in response to cadmium reveals tolerance mechanisms in Arundo donax L.

The expected increase of sustainable energy demand has shifted the attention towards bioenergy crops. Due to their know tolerance against abiotic stress and relatively low nutritional requirements, they have been proposed as election crops to be cultivated in marginal lands without disturbing the part of lands employed for agricultural purposes. Arundo donax L. is a promising bioenergy crop whose behaviour under water and salt stress has been recently studied at transcriptomic levels. As the anthropogenic activities produced in the last years a worrying increase of cadmium contamination worldwide, the aim of our work was to decipher the global transcriptomic response of A. donax leaf and root in the perspective of its cultivation in contaminated soil. In our study, RNA-seq libraries yielded a total of 416 million clean reads and 10.4 Gb per sample. De novo assembly of clean reads resulted in 378,521 transcripts and 126,668 unigenes with N50 length of 1812 bp and 1555 bp, respectively. Differential gene expression analysis revealed 5,303 deregulated transcripts (3,206 up- and 2,097 down regulated) specifically observed in the Cd-treated roots compared to Cd-treated leaves. Among them, we identified genes related to "Protein biosynthesis", "Phytohormone action", "Nutrient uptake", "Cell wall organisation", "Polyamine metabolism", "Reactive oxygen species metabolism" and "Ion membrane transport". Globally, our results indicate that ethylene biosynthesis and the downstream signal cascade are strongly induced by cadmium stress. In accordance to ethylene role in the interaction with the ROS generation and scavenging machinery, the transcription of several genes (NADPH oxidase 1, superoxide dismutase, ascorbate peroxidase, different glutathione S-transferases and catalase) devoted to cope the oxidative stress is strongly activated. Several small signal peptides belonging to ROTUNDIFOLIA, CLAVATA3, and C-TERMINALLY ENCODED PEPTIDE 1 (CEP) are also among the up-regulated genes in Cd-treated roots functioning as messenger molecules from root to shoot in order to communicate the stressful status to the upper part of the plants. Finally, the main finding of our work is that genes involved in cell wall remodelling and lignification are decisively up-regulated in giant reed roots. This probably represents a mechanism to avoid cadmium uptake which strongly supports the possibility to cultivate giant cane in contaminated soils in the perspective to reserve agricultural soil for food and feed crops.

The Quest for Orthologs benchmark service and consensus calls in 2020.

The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.

Psychometric Properties of the Spanish Short Version of the Inventory of Personality Organization (IPO-18) in a Nonclinical Sample.

This report supports validation for the Spanish 18-item short version of the Inventory of Personality Organization (IPO), a self-reported instrument for the assessment of personality organization, according to Kernberg's object-relation based model. The IPO is used to depict personality structure types, using three scales: psychological defense mechanisms, degree of identity integration and reality testing. The review of the literature suggests alternatively factorial solutions. Accordingly, this study, using a nonclinical sample (N = 315), tested the fit of several factorial models (2- and 3- factor solution) via the maximum likelihood approach. Confirmatory Factor Analysis revealed a better fit for the 2-factor solution (CFI = .97, TLI = .96, RMSEA = .037, AIC = 311.06), in accordance with Kernberg's theory. Each of the 2 IPO subscales shows good levels of internal consistency, and they are associated with increased negative affect, aggressive dyscontrol as well as depression, anxiety and general level of psychopathological distress in line with theoretical expectations. Our results suggest that the Spanish short version of the IPO is a reliable and valid tool for the assessment of personality organization following Kernberg's model.

SonicParanoid: fast, accurate and easy orthology inference.

Motivation: Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ. Results: Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets. Availability and implementation: SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid. Supplementary information: Supplementary data are available at Bioinformatics online.

Phytoremediation potential of Arundo donax (Giant Reed) in contaminated soil by heavy metals.

Soil pollution from heavy metals poses a serious risk for environment and public health. Phytoremediation is an eco-friendly and cheaper alternative compared to chemical-physical techniques. We carried out in vitro tests where three microorganisms Trichoderma harzianum, Saccharomyces cerevisiae and Wickerhamomyces anomalus were exposed to eight different heavy metals (one metal at a time) in order to evaluate resistance, growth and bioaccumulation capability for each metal (Ni, Cd, Cu, V, Zn, As, Pb, Hg). Taking into account the natural characteristics of T. harzianum, (resistance to environmental stress, resistance to pathogenic fungi, ability to establish symbiotic relationships with superior green plants) and the good bioaccumulation capacity for V, As, Cd, Hg, Pb shown after in vitro tests, it was chosen as a microorganism to be used in greenhouse tests. Controlled exposure tests were performed in greenhouse, where Arundo donax and mycorrhized Arundo donax with T. harzianum were exposed for 7 months at two different doses (L1 and L2) of a heavy metal mix, so as to assess whether the symbiotic association could improve the bioaccumulation capability of the superior green plant A. donax. Heavy metals were determined with ICP-MS. The average bioaccumulation percentage values of A. donax for L1 and L2 were, respectively: Ni (31%, 26%); Cd (35%, 50%); Cu (30%, 35%); As (19%, 27%); Pb (18%, 14%); Hg (42%, 45%); V (39%, 26%); Zn (23%, 9%). The average bioaccumulation percentage values of mycorrhized A. donax with T. harzianum for L1 and L2 were, respectively: Ni (27%, 38%); Cd (44%, 42%); Cu (36%, 29%); As (17%, 23%); Pb (37%, 54%); Hg (44%, 60%); V (16%, 20%); Zn (14%, 7%). A. donax showed the highest BAF (bioaccumulation factor) for Cd (0.50), Cu (0.35), As (0.27) and Hg (0.45) after exposure to L2; mycorrhized A. donax with T. harzianum showed the highest BAF for Ni (0.38), Cd (0.42), Pb (0.54) and Hg (0.60) after exposure to L2. A. donax showed the highest TF (translocation factor) values for Cd (0.28) and Hg (0.26) after exposition at L1 and L2 respectively; A. donax mycorrhized with T. harzianum showed the highest TF values for Cd (0.70), As (0.56), V (0.24), Pb (0.18) after exposition at L2, and Zn (0.30) after exposition at L1. Our study showed a good growth capability in contaminated soils and a good bioaccumulation capability of heavy metals, both for A. donax and mycorrhized A. donax with T. harzianum. Furthermore, for three metals (Ni, Pb and Hg) the bioaccumulation capability was improved by the symbiosis of T. harzianum with A. donax. So, these results proved the suitability both for A. donax and mycorrhized A. donax with T. harzianum for phytoremediation processes.

RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress.

BACKGROUND: To compensate for the lack of information about the molecular mechanism involved in Arundo donax L. response to salt stress, we de novo sequenced, assembled and analyzed the A. donax leaf transcriptome subjected to two levels of long-term salt stress (namely, S3 severe and S4 extreme). RESULTS: The picture that emerges from the identification of differentially expressed genes is consistent with a salt dose-dependent response. Hence, a deeper re-programming of the gene expression occurs in those plants grew at extreme salt level than in those subjected to severe salt stress, probably representing for them an "emergency" state. In particular, we analyzed clusters related to salt sensory and signaling, transcription factors, hormone regulation, Reactive Oxygen Species (ROS) scavenging, osmolyte biosynthesis and biomass production, all of them showing different regulation either versus untreated plants or between the two treatments. Importantly, the photosynthesis is strongly impaired in samples treated with both levels of salinity stress. However, in extreme salt conditions, a dramatic switch from C3 Calvin cycle to C4 photosynthesis is likely to occur, this probably being the more impressive finding of our work. CONCLUSIONS: Considered the distinct response to salt doses, genes either involved in severe or in extreme salt response could constitute useful markers of the physiological status of A. donax to deepen our understanding of its biology and productivity in salinized soil. Finally, many of the unigenes identified in the present study have the potential to be used for the development of A. donax varieties with improved productivity and stress tolerance, in particular the knock out of the GTL1 gene acting as negative regulator of water use efficiency has been proposed as good target for genome editing.

The effect of summer drought on the yield of Arundo donax is reduced by the retention of photosynthetic capacity and leaf growth later in the growing season.

BACKGROUND AND AIMS: The development of Arundo donax as a biomass crop for use on drought-prone marginal lands in areas with warm to hot climates is constrained by the lack of variation within this species. We investigated the effect of morphological and physiological variation on growth and tolerance to drought under field conditions in three ecotypes of A. donax collected from habitats representing a climate gradient: a pre-desert in Morocco, a semi-arid Mediterranean climate in southern Italy and a warm sub-humid region of central Italy. METHODS: The three A. donax ecotypes were grown under irrigated and rain-fed conditions in a common garden field trial in a region with a semi-arid Mediterranean climate. Physiological and morphological characteristics, and carbohydrate metabolism of the ecotypes were recorded to establish which traits were associated with yield and/or drought tolerance. KEY RESULTS: Variation was observed between the A. donax ecotypes. The ecotype from the most arid habitat produced the highest biomass yield. Stem height and the retention of photosynthetic capacity later in the year were key traits associated with differences in biomass yield. The downregulation of photosynthetic capacity was not associated with changes in foliar concentrations of sugars or starch. Rain-fed plants maintained photosynthesis and growth later in the year compared with irrigated plants that began to senescence earlier, thus minimizing the difference in yield. Effective stomatal control prevented excessive water loss, and the emission of isoprene stabilized photosynthetic membranes under drought and heat stress in A. donax plants grown under rain-fed conditions without supplementary irrigation. CONCLUSIONS: Arundo donax is well adapted to cultivation in drought-prone areas with warm to hot climates. None of the A. donax ecotypes exhibited all of the desired traits consistent with an 'ideotype'. Breeding or genetic (identification of quantitative trait loci) improvement of A. donax should select ecotypes on the basis of stem morphology and the retention of photosynthetic capacity.

Benchmarking of methods for genomic taxonomy.

One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.

Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by time-consuming all-versus-all alignments and the existence of proteins with complex domain architectures. Here, we present a substantial update of SonicParanoid, where a gradient boosting predictor halves the execution time and a language model doubles the recall. Application to empirical large-scale and standardized benchmark datasets shows that SonicParanoid2 is much faster than comparable methods and also the most accurate. SonicParanoid2 is available at https://gitlab.com/salvo981/sonicparanoid2 and https://zenodo.org/doi/10.5281/zenodo.11371108 .

Harnessing Lignocellulosic Crops for Phytomanagement of Contaminated Soils: A Multi-Country Study.

The dwindling availability of agricultural land, caused by factors such as rapid population growth, urban expansion, and soil contamination, has significantly increased the pressure on food production. To address this challenge, cultivating non-food crops on contaminated land has emerged as a promising solution. This approach not only frees up fertile soil for food production but also mitigates human exposure to contaminants. This work aimed to examine the impact of soil contamination with Cd, Pb, Ni, and Zn on the growth, productivity, metal accumulation, and the tolerance of five lignocellulosic non-food crops: switchgrass (Panicum virgatum L.), biomass sorghum (Sorghum bicolor L. Moench), giant reed (Arundo donax L.), African fodder cane (Saccharum spontaneum L. spp. aegyptiacum Willd. Hackel), and miscanthus (Miscanthus × giganteus Greef et Deu.). A two-year pot experiment was conducted in Greece, Italy, and Portugal, following the same protocols and applying various levels of metals: Cd (0, 4, 8 mg kg-1), Pb and Zn (0, 450, 900 mg kg-1), and Ni (0, 110, 220 mg kg-1). The experimental design was completely randomized, with three replicates for each treatment. The results showed that switchgrass and sorghum generally maintained their height and productivity under Cd and Pb stress but were adversely affected by high Zn and Ni concentrations. Giant reed and African fodder cane showed reduced height and productivity at higher Ni and Zn levels. Miscanthus exhibited resilience in height but experienced productivity reductions only at the highest Zn concentration. Heavy metal uptake varied among crops, with switchgrass and sorghum showing high Cd and Pb uptake, while giant reed accumulated the most Cd and Zn. Miscanthus had the highest Ni accumulation. The tolerance indices indicated that switchgrass and sorghum were more tolerant to Cd and Zn at lower concentrations, whereas miscanthus had lower tolerance to Cd but a higher tolerance to Zn at higher concentrations. Giant reed and African fodder cane demonstrated stable tolerance across most heavy metals. Accumulation indices highlighted the effectiveness of switchgrass and sorghum in Cd and Pb uptake, while miscanthus excelled in Ni and Zn accumulation. The cluster analysis revealed similar responses to heavy metal stress between African fodder cane and giant reed, as well as between sorghum and miscanthus, with switchgrass displaying distinct behavior. Overall, the study highlights the differential tolerance and accumulation capacities of these crops, indicating the potential for phytoremediation applications and biomass production in heavy metal-contaminated soils.

Quest for Orthologs in the Era of Biodiversity Genomics.

The era of biodiversity genomics is characterised by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g., by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialised methods for the identification of orthologs to short proteins and non-coding RNAs, and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the FAIR principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution.

Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years.

It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.

Perennial biomass cropping and use: Shaping the policy ecosystem in European countries.

Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023-27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&D and education for positive environmental, economic and social sustainability impacts.

Multilocus sequence typing of total-genome-sequenced bacteria.

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Identification of acquired antimicrobial resistance genes.

OBJECTIVES: Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data. METHODS: We developed a web-based method, ResFinder that uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de-novo-sequenced isolates. RESULTS: When testing the 1862 GenBank files, the method identified the resistance genes with an ID = 100% (100% identity) to the genes in ResFinder. Agreement between in silico predictions and phenotypic testing was found when the method was further tested on 23 isolates of five different bacterial species, with available phenotypes. Furthermore, ResFinder was evaluated on WGS chromosomes and plasmids of 30 isolates. Seven of these isolates were annotated to have antimicrobial resistance, and in all cases, annotations were compatible with the ResFinder results. CONCLUSIONS: A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created. ResFinder can be accessed at www.genomicepidemiology.org. ResFinder will continuously be updated as new resistance genes are identified.

Relative Water Content, Proline, and Antioxidant Enzymes in Leaves of Long Shelf-Life Tomatoes under Drought Stress and Rewatering.

Some physiological, oxidative, and antioxidant enzymatic patterns were assessed in plants of three local Sicilian landraces of long shelf-life tomatoes ('Custonaci', 'Salina', and 'Vulcano'), as compared to the commercial tomato hybrid 'Faino' (control). Three water treatments were considered in open-field: DRY (no irrigation); IRR (long-season full irrigation); REW (drought/rewatering cycles). During the growing season, soil water deficit (SWD) was estimated, and relative water content (RWC), specific leaf area (SLA), proline and malondialdehyde (MDA) content, and glutathione peroxidase (GPX), catalase (CAT), and superoxide dismutase (SOD) activities were measured in leaves. Differently from control, RWC in local landraces exhibited a similar pattern in REW and DRY, indicating a low capacity to re-hydrate after rewatering. Positive correlation of proline content vs. SWD in all local landraces highlights an osmotic adjustment occurring in these tomatoes in response to limited soil water content. Long shelf-life tomatoes suffered minor oxidative stress due to severe soil water deficit, as revealed by the lower levels of MDA with respect to the control. Significant correlation of CAT vs. SWD for all tomatoes indicates that this antioxidant enzyme, among those analyzed, may be considered as a biomarker for a water stress condition more than for oxidative stress due to water deficit.

Early Stages of Aluminum-Doped Zinc Oxide Growth on Silicon Nanowires.

Aluminum-doped zinc oxide (AZO) is an electrically conductive and optically transparent material with many applications in optoelectronics and photovoltaics as well as in the new field of plasmonic metamaterials. Most of its applications contemplate the use of complex and nanosized materials as substrates onto which the AZO forms the coating layer. Its morphological characteristics, especially the conformality and crystallographic structure, are crucial because they affect its opto-electrical response. Nevertheless, it was difficult to find literature data on AZO layers deposited on non-planar structures. We studied the AZO growth on silicon-nanowires (SiNWs) to understand its morphological evolution when it is formed on quasi one-dimensional nanostructures. We deposited by sputtering different AZO thicknesses, leading from nanoclusters until complete incorporation of the SiNWs array was achieved. At the early stages, AZO formed crystalline nano-islands. These small clusters unexpectedly contained detectable Al, even in these preliminary phases, and showed a wurtzite crystallographic structure. At higher thickness, they coalesced by forming a conformal polycrystalline shell over the nanostructured substrate. As the deposition time increased, the AZO conformal deposition led to a polycrystalline matrix growing between the SiNWs, until the complete array incorporation and planarization. After the early stages, an interesting phenomenon took place leading to the formation of hook-curved SiNWs covered by AZO. These nanostructures are potentially very promising for optical, electro-optical and plasmonic applications.

Genetic and Morpho-Agronomic Characterization of Sicilian Tetraploid Wheat Germplasm.

Cereal landraces are a very valuable resource in contemporary agriculture. A renewed focus for breeding purposes could ameliorate some negative consequences of modern agriculture and conventional breeding, such as the loss of genetic diversity. One strategy combining molecular genotyping and characterization of morpho-agronomic traits related to productivity is proposed to assess a group of tetraploid wheat landraces named Bufala, historically cultivated in the mountain areas of Sicily and characterized by adaptability in terms of cold tolerance, ability to grow in marginal soils, weed competitiveness and resistance to diseases. A total of 55 SSR molecular markers were used to detect patterns of diversity in 30 rivet and durum wheat genotypes. Furthermore, phenotyping was then conducted for 8 morpho-agronomic traits. Discriminant analysis of principal components (DAPC), STRUCTURE and phylogenetical analysis allowed to identify three groups, two of them genetically close and including both Bufala and Bufala-related rivet landraces. To the third group, old and more recent durum wheat varieties, constituting the outgroup, were assigned. Clustering was confirmed by Principal Component Analysis (PCA). Finally, a correlation analysis showed that Bufala genotypes are characterized by lower ear density, major ear length and later earing time compared with the other studied genotypes. The levels of diversity and population structure could be an important contribution to parent selection in tetraploid wheat breeding programs, as well as to germplasm conservation and management.

Optimization of Oxygen Evolution Reaction with Electroless Deposited Ni-P Catalytic Nanocoating.

The low efficiency of water electrolysis mostly arises from the thermodynamic uphill oxygen evolution reaction. The efficiency can be greatly improved by rationally designing low-cost and efficient oxygen evolution anode materials. Herein, we report the synthesis of Ni-P alloys adopting a facile electroless plating method under mild conditions on nickel substrates. The relationship between the Ni-P properties and catalytic activity allowed us to define the best conditions for the electroless synthesis of highperformance Ni-P catalysts. Indeed, the electrochemical investigations indicated an increased catalytic response by reducing the thickness and Ni/P ratio in the alloy. Furthermore, the Ni-P catalysts with optimized size and composition deposited on Ni foam exposed more active sites for the oxygen evolution reaction, yielding a current density of 10 mA cm-2 at an overpotential as low as 335 mV, exhibiting charge transfer resistances of only a few ohms and a remarkable turnover frequency (TOF) value of 0.62 s-1 at 350 mV. The present study provides an advancement in the control of the electroless synthetic approach for the design and large-scale application of high-performance metal phosphide catalysts for electrochemical water splitting.