Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications

We investigated how the two rounds of whole genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic regulatory blocks, GRBs). We showed that the majority of GRBs identified in the last common ancestor of chordates have been maintained as a single copy in humans. We found evidence that dismantling of the duplicated GRB copies occurred early in vertebrate evolution often through the differential retention of the regulatory gene but loss of the bystander gene's exonic sequences. Despite the large evolutionary scale, the presence of duplicated highly conserved non-coding regions provided unambiguous proof for this scenario for multiple ancient GRBs. Remarkably, the dismantling of ancient GRB duplicates has contributed to the creation of large gene deserts associated with regulatory genes in vertebrates, providing a potentially widespread mechanism for the origin of these enigmatic genomic traits

Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers

The pancreas is a central organ for human diseases. Most alleles uncovered by genome-wide association studies of pancreatic dysfunction traits overlap with non-coding sequences of DNA. Many contain epigenetic marks of cis-regulatory elements active in pancreatic cells, suggesting that alterations in these sequences contribute to pancreatic diseases. Animal models greatly help to understand the role of non-coding alterations in disease. However, interspecies identification of equivalent cis-regulatory elements faces fundamental challenges, including lack of sequence conservation. Here we combine epigenetic assays with reporter assays in zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. Among other potential disease-relevant enhancers, we identify a zebrafish ptf1a distal-enhancer whose deletion causes pancreatic agenesis, a phenotype previously found to be induced by mutations in a distal-enhancer of PTF1A in humans, further supporting the causality of this condition in vivo. This approach helps to uncover interspecies functionally equivalent cis-regulatory elements and their potential role in human disease.This study was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC-2015-StG-680156-ZPR and ERC-2016-AdG-740041-EvoLand to J.L.G.-S.). J.B. is supported by an FCT CEEC grant (CEECIND/03482/2018). J.L.G.-S. is supported by the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P), the Marató TV3 Fundacion (Grant 201611) and the institutional grant Unidad de Excelencia María de Maeztu (MDM-2016-0687). R.B.C. was funded by FCT (ON2201403-CTO-BPD), IBMC (BIM/04293-UID991520-BPD) and EMBO (Short-Term Fellowship). J.Tx. (SFRH/BD/126467/2016), M.D. (SFRH/BD/135957/2018), A.E. (SFRH/BD/147762/2019), and F.J.F. (PD/BD/105745/2014) are PhD fellows from FCT. M.G. was supported by the EnvMetaGen project via the European Union’s Horizon 2020 research and innovation programme (grant 668981). This work was funded by National Funds through FCT—Fundação para a Ciência e a Tecnologia, I.P., under the project UIDB/04293/2020”

Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

Trabajo presentado en EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021

An evaluation for the standardization of the Allium cepa test as cytotoxicity and genotoxicity assay

A general report on the use of the Allium test as cytotoxicological and genotoxicological assay is proposed, with particular emphasis about the standardization of the test in several common applications. The intraspecific variation in Allium cepa has been overlooked, as in most investigations no mention is made about origin and denomination of the onion cultivar used. A standardization of the used material would allow a better generalization of the results, since we cannot be sure that all cultivars would give the same response. A more frequent use of transmission electron microscopy (TEM) investigation is proposed. Even if relatively time consuming and not available in all laboratories, it may help to better understand the mechanism of cytotoxicity, since many morphological characters may appear similar but be arisen from different processes observable only with TEM. About statistical testing, tests other than chi-squared may be used in case of a lower amount of data. The most commonly used statistical tests are the parametric tests ANOVA and Student’s t, and the nonparametric tests Kruskal–Wallis and Mann–Whitney U, for analysis of variance. Tests should be used also to assess the minimal sample dimension for obtaining significance, since data collection (microscope observation) appears to be one of the main bottle necks of the test. Also the use of the Allium test for testing liposomes and other nanovectors for drug delivery is proposed, in order to assess the cytotoxicity of these types of medium and the possible increase in cytotoxicity of the associated drug

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayfly Cloeon dipterum and its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects

A high-quality annually laminated sequence from Lake Belau, Northern Germany: Revised chronology and its implications for palynological and tephrochronological studies

The annually laminated record of Lake Belau offers an exceptional opportunity to investigate with high temporal resolution Holocene environmental change, aspects of climate history and human impact on the landscape. A new chronology based on varve counts, 14C-datings and heavy metal history has been established, covering the last 9400 years. Based on multiple varve counting on two core sequences, the easily countable laminated section spans about 7850 varve years (modelled age range c. 9430 to 1630 cal. BP). Not all of the record is of the same quality but approximately 69% of the varves sequence is classified to be of high quality and only c. 5% of low quality. The new chronology suggests dates generally c. 260 years older than previously assumed for the laminated section of the record. The implications for the vegetation and land-use history of the region as well as revised datings for pollen stratigraphical events are discussed. Tephra analysis allowed the identification of several cryptotephra layers. New dates for volcanic eruptions are presented for the Lairg B event (c. 6848 cal. BP, 2s range 6930–6713 cal. BP), the Hekla 4 event (c. 4396 cal. BP, 2s range 4417–4266 cal. BP), and Hekla 3 eruption (c. 3095 cal. BP, 2s range 3120–3068 cal. BP)

Late-glacial and Holocene European pollen data

peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=tjom2

Objective comparison of methods to decode anomalous diffusion

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers. Deviations from Brownian motion leading to anomalous diffusion are ubiquitously found in transport dynamics but often difficult to characterize. Here the authors compare approaches for single trajectory analysis through an open competition, showing that machine learning methods outperform classical approaches

Objective comparison of methods to decode anomalous diffusion

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers

Hip joint articular soft tissues of non-dinosaurian Dinosauromorpha and early Dinosauria: evolutionary and biomechanical implications for Saurischia

Dinosauromorphs evolved a wide diversity of hind limb skeletal morphologies, suggesting highly divergent articular soft tissue anatomies. However, poor preservation of articular soft tissues in fossils has hampered any follow-on functional inferences. We reconstruct the hip joint soft tissue anatomy of non-dinosaurian dinosauromorphs and early dinosaurs using osteological correlates derived from extant sauropsids and infer trends in character transitions along the theropod and sauropodomorph lineagues. Femora and pelves of 107 dinosauromorphs and outgroup taxa were digitized using 3D imaging techniques. Key transitions were estimated using maximum likelihood ancestral state reconstruction. The hips of dinosauromorphs possessed wide a disparity of soft tissue morphologies beyond the types and combinations exhibited by extant archosaurs. Early evolution of the dinosauriform hip joint was characterized by the retention of a prominent femoral hyaline cartilage cone in post-neonatal individuals, with the cartilage cone independently reduced within theropods and sauropodomorphs. The femur of Dinosauriformes possessed a fibrocartilage sleeve on the metaphysis, which surrounded a hyaline core. The acetabulum of Dinosauriformes possessed distinct labrum and antitrochanter structures. In sauropodomorphs, hip congruence was maintained by thick hyaline cartilage on the femoral head, whereas theropods relied on acetabular tissues such as ligaments and articular pads. In particular, the craniolaterally ossified hip capsule of non- Avetheropoda neotheropods permitted mostly parasagittal femoral movements. These data indicate that the dinosauromorph hip underwent mosaic evolution within the saurischian lineage and that sauropodomorphs and theropods underwent both convergence and divergence in articular soft tissues, correlated with transitions in body size, locomotor posture, and joint loading