The potential of earth observations to capture patterns of biodiversity - OBEF-Accross2

The following section summarizes the scientific and technical achievements and contributions accomplished during the entire duration of OBEF-Accross2. We have successfully reached most of the scheduled objectives and goals and made unexpected and very relevant contributions. Furthermore, we exceeded project expectations in the context of methodological development and evaluation. These achievements can be summarized as follow: 1) We have developed robust simulation frameworks that allowed us to evaluate several methodological approaches for remote estimation of plant functional diversity at different scales. The frameworks’ plausibility was validated using remote sensing (RS) and field observations. 2) For the first time, we have answered four relevant questions regarding the potential and limitations of remote sensing of plant functional diversity in a robust and generalizable way: 1) which functional diversity metrics (FDMs) can capture plant functional diversity from space? 2) Can spectral traits (e.g., reflectance factors) or optical traits (plant trait estimates) capture plant functional diversity? 3) Can single-image analyses infer plant functional diversity in a way comparable at local and global scales? and 4) How do the different RS features (i.e., spectral configuration, spatial resolution, and uncertainty) affect the estimation of plant functional diversity? 3) We have developed a global normalization method that provides directly comparable FDMs for different RS missions and field datasets. In addition, the new approach allowed using equivalent number metrics in RS for the first time, providing unbiased partitioning of biodiversity at different scales (alpha, beta, and gamma) using FDMs. 4) We have evaluated the role of different plant traits in the relationships between plant functional and spectral diversity using machine learning and model analysis techniques. 5) We have processed spaceborne imagery from DESIS and Sentinel-2 MSI sensors to generate functional diversity maps of the FunDivEUROPE network and compared them with field data. Moreover, we have extended Sentinel-2 time series analysis to map plant functional diversity in eddy-covariance stations in support of biodiversity-ecosystem function analyses. In this context, we have explored ways to improve the characterization and interpretation of the temporal variability of plant functional diversity. 6) We have conceptualized a processing chain to map functional diversity from Sentinel-2 imagery and identified the remaining challenges to achieve an operational setup. 7) We have analyzed the relationships between functional diversity and ecosystem functional responses, proving the capability of remote sensing to explain ecosystem functional properties and its increasing role in ecosystem stability in arid environments

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone

Plant cell wall composition is important for regulating growth rates, especially in roots. However, neither analyses of cell wall composition nor transcriptomes on their own can comprehensively reveal which genes and processes are mediating growth and cell elongation rates. This study reveals the benefits of carrying out multiple analyses in combination. Sections of roots from five anatomically and functionally defined zones in Arabidopsis thaliana were prepared and divided into three biological replicates. We used glycan microarrays and antibodies to identify the major classes of glycans and glycoproteins present in the cell walls of these sections, and identified the expected decrease in pectin and increase in xylan from the meristematic zone (MS), through the rapid and late elongation zones (REZ, LEZ) to the maturation zone and the rest of the root, including the emerging lateral roots. Other compositional changes included extensin and xyloglucan levels peaking in the REZ and increasing levels of arabinogalactan-proteins (AGP) epitopes from the MS to the LEZ, which remained high through the subsequent mature zones. Immuno-staining using the same antibodies identified the tissue and (sub)cellular localization of many epitopes. Extensins were localized in epidermal and cortex cell walls, while AGP glycans were specific to different tissues from root-hair cells to the stele. The transcriptome analysis found several gene families peaking in the REZ. These included a large family of peroxidases (which produce the reactive oxygen species (ROS) needed for cell expansion), and three xyloglucan endo-transglycosylase/hydrolase genes (XTH17, XTH18, and XTH19). The significance of the latter may be related to a role in breaking and re-joining xyloglucan cross-bridges between cellulose microfibrils, a process which is required for wall expansion. Knockdowns of these XTHs resulted in shorter root lengths, confirming a role of the corresponding proteins in root extension growth

Evalutating the potential of desis to infer plant taxonomical and functional diversities in europwean forests

Abstract. Tackling the accelerated human-induced biodiversity loss requires tools able to map biodiversity and its changes globally. Remote sensing (RS) offers unique capabilities of characterizing Earth surfaces; therefore, it could map plant biodiversity continuously and globally. This approach is supported by the Spectral Variation Hypothesis (SVH), which states that spectra and species (taxonomic and trait) diversities are linked through environmental heterogeneity. In this work, we evaluate the capability of the DESIS hyperspectral imager to capture plant diversity patterns as measured in dedicated plots of the network FunDivEUROPE. We computed functional and taxonomical diversity metrics from field taxonomic, structural, and foliar measurements in vegetation plots sampled in Spain and Romania. In addition, we also computed functional diversity metrics both from the DESIS reflectance factors and from vegetation parameters estimated via inversion of a radiative transfer model. Results showed that only metrics computed from spectral reflectance were able to capture taxonomic variability in the area. However, the lack of sensitivity was related to the insufficient plot size and the lack of spatial match between remote sensing and field data, but also the differences between the information contained in the field traits and remote sensing data, and the potential uncertainties in the remote estimates of vegetation parameters. Thus, while DESIS showed some sensitivity to plant diversity, further efforts are needed to deploy suitable biodiversity evaluation and validation plots and networks that support the development of biodiversity remote sensing products

Interventions to reduce peripheral intravenous catheter failure: An international e-Delphi consensus on relevance and feasibility of implementation

Supplementary material is available online at: https://www.sciencedirect.com/science/article/pii/S1876034123003325?via%3Dihub#sec0110 .Copyright .© 2023 The Author(s). Background Around 1 billion peripheral intravenous catheters (PIVC) fail annually worldwide before prescribed intravenous therapy is completed, resulting in avoidable complications, dissatisfaction, and avoidable costs surging to ∼€4bn. We aimed to provide an international consensus on relevance and feasibility of clinical practice guideline recommendations to reduce PIVC failure. Methods e-Delphi study with three rounds through an online questionnaire from March-September 2020 recruiting a multispecialty panel formed by clinicians, managers, academic researchers, and experts in implementation from seven developed and three developing countries, reflecting on experience in PIVC care and implementation of evidence. Further, we included a panel of chronic patients with previous experience in the insert, maintenance, and management of PIVC and intravenous therapy from Ireland and Spain as public and patient involvement (PPI) panel. All experts and patients scored each item on a 4-point Likert scale to assess the relevance and feasibility. We considered consensus descriptor in which the median was 4 with less than or equal to 1,5 interquartile intervals. Findings Over 90% participants (16 experts) completed the questionnaire on all rounds and 100% PPI (5 patients) completed round 1 due to high consensus they achieved. Our Delphi approach included 49 descriptors, which resulted in an agreed 30 across six domains emerged from the related to (i) general asepsis and cutaneous antisepsis (n = 4), (ii) catheter adequacy and insertion (n = 3), (iii) catheter and catheter site care (n = 6), (iv) catheter removal and replacement strategies (n = 4), (v) general principles for catheter management (n = 10), and (vi) organisational environment (n = 3). Conclusion We provide an international consensus of relevant recommendations for PIVC, deemed feasible to implement in clinical settings. In addition, this methodological approach included substantial representation from clinical experts, academic experts, patient and public expertise, mitigating uncertainty during the implementation process with high-value recommendations to prevent PIVC failure based contextual and individual features, and economic resources worldwide.The College of Nurses of the Balearic Islands under award number PI2019/0287

Challenging the link between functional and spectral diversity with radiative transfer modeling and data

In a context of accelerated human-induced biodiversity loss, remote sensing (RS) is emerging as a promising tool to map plant biodiversity from space. Proposed approaches often rely on the Spectral Variation Hypothesis (SVH), linking the heterogeneity of terrestrial vegetation to the variability of the spectroradiometric signals. Yet, due to observational limitations, the SVH has been insufficiently tested, remaining unclear which metrics, methods, and sensors could provide the most reliable estimates of plant biodiversity. Here we assessed the potential of RS to infer plant biodiversity using radiative transfer simulations and inversion. We focused specifically on “functional diversity,” which represents the spatial variability in plant functional traits. First, we simulated vegetation communities and evaluated the information content of different functional diversity metrics (FDMs) derived from their optical reflectance factors (R) or the corresponding vegetation “optical traits,” estimated via radiative transfer model inversion. Second, we assessed the effect of the spatial resolution, the spectral characteristics of the sensor, and signal noise on the relationships between FDMs derived from field and remote sensing datasets. Finally, we evaluated the plausibility of the simulations using Sentinel-2 (multispectral, 10 m pixel) and DESIS (hyperspectral, 30 m pixel) imagery acquired over sites of the Functional Significance of Forest Biodiversity in Europe (FunDivEUROPE) network. We demonstrate that functional diversity can be inferred both by reflectance and optical traits. However, not all the FDMs tested were suited for assessing plant functional diversity from RS. Rao's Q index, functional dispersion, and functional richness were the best-performing metrics. Furthermore, we demonstrated that spatial resolution is the most limiting RS feature. In agreement with simulations, Sentinel-2 imagery provided better estimates of plant diversity than DESIS, despite the coarser spectral resolution. However, Sentinel-2 offered inaccurate results at DESIS spatial resolution. Overall, our results identify the strengths and weaknesses of optical RS to monitor plant functional diversity. Future missions and biodiversity products should consider and benefit from the identified potentials and limitations of the SVH.JPL, MMi, and MMa acknowledge the German Aerospace Center (DLR) project OBEF-Accross2 “The Potential of Earth Observations to Capture Patterns of Biodiversity” (Contract No. 50EE1912, German Aerospace Center). JPL, MMi, AH, CW, MMa, GK, FJB, and UW acknowledge the German Aerospace Center (DLR) for providing DESIS imagery through the Announcement of Opportunity “EBioIDEA: Enhancing Biodiversity Inventories with DESIS Imagery Analysis”. FunDivEUROPE data collection was supported by the European Union Seventh Framework Programme (FP7/2007-2013) (grant agreement number: 265171) and the EU H2020 project Soil4Europe (Bioidversa 2017-2019). The in-situ plant traits data collected over Romanian and Spanish sites were supported by a Marie-Curie Fellowship (DIVERFOR, FP7-PEOPLE-2011-IEF. No. 302445) to R. Benavides. OB acknowledges funding from project 10PFE/2021 Ministry of Research, Innovation and Digitalization within Program 1 - Development of national research and development system, Subprogram 1.2 - Institutional Performance - RDI excellence funding projects. XM was supported by the National Natural Science Foundation of China (42171305), the Director Fund of the International Research Center of Big Data for Sustainable Development Goals (CBAS2022DF006), and the Open Fund of State Key Laboratory of Remote Sensing Science (OFSLRSS202229)N

Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data

<p>Abstract</p> <p>Background</p> <p>Long terminal repeat (LTR) retrotransposons are a class of mobile genetic element capable of autonomous transposition via an RNA intermediate. Their large size and proliferative ability make them important contributors to genome size evolution, especially in plants, where they can reach exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. Using a phylogenetic approach, we characterize dynamics of proliferation events of <it>Ty3/gypsy</it>-like LTR retrotransposons that led to massive genomic expansion in three <it>Helianthus </it>(sunflower) species of ancient hybrid origin. The three hybrid species are independently derived from the same two parental species, offering a unique opportunity to explore patterns of retrotransposon proliferation in light of reticulate evolutionary events in this species group.</p> <p>Results</p> <p>We demonstrate that <it>Ty3/gypsy</it>-like retrotransposons exist as multiple well supported sublineages in both the parental and hybrid derivative species and that the same element sublineage served as the source lineage of proliferation in each hybrid species' genome. This inference is based on patterns of species-specific element numerical abundance within different phylogenetic sublineages as well as through signals of proliferation events present in the distributions of element divergence values. Employing methods to date paralogous sequences within a genome, proliferation events in the hybrid species' genomes are estimated to have occurred approximately 0.5 to 1 million years ago.</p> <p>Conclusion</p> <p>Proliferation of the same retrotransposon major sublineage in each hybrid species indicates that similar dynamics of element derepression and amplification likely occurred in each hybrid taxon during their formation. Temporal estimates of these proliferation events suggest an earlier origin for these hybrid species than previously supposed.</p

History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations

Modelling of interactions for the recognition of activities in groups of people

In this research study we adopt a probabilistic modelling of interactions in groups of people, using video sequences, leading to the recognition of their activities. Firstly, we model short smooth streams of localised movement. Afterwards, we partition the scene in regions of distinct movement, by using maximum a posteriori estimation, by fitting Gaussian Mixture Models (GMM) to the movement statistics. Interactions between moving regions are modelled using the Kullback–Leibler (KL) divergence between pairs of statistical representations of moving regions. Such interactions are considered with respect to the relative movement, moving region location and relative size, as well as to the dynamics of the movement and location inter-dependencies, respectively. The proposed methodology is assessed on two different data sets showing different categories of human interactions and group activities