Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

Background: Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. Results: Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. Conclusions: These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms

Dynamic and Differential Regulation of Stem Cell Factor FoxD3 in the Neural Crest Is Encrypted in the Genome

The critical stem cell transcription factor FoxD3 is expressed by the premigratory and migrating neural crest, an embryonic stem cell population that forms diverse derivatives. Despite its important role in development and stem cell biology, little is known about what mediates FoxD3 activity in these cells. We have uncovered two FoxD3 enhancers, NC1 and NC2, that drive reporter expression in spatially and temporally distinct manners. Whereas NC1 activity recapitulates initial FoxD3 expression in the cranial neural crest, NC2 activity recapitulates initial FoxD3 expression at vagal/trunk levels while appearing only later in migrating cranial crest. Detailed mutational analysis, in vivo chromatin immunoprecipitation, and morpholino knock-downs reveal that transcription factors Pax7 and Msx1/2 cooperate with the neural crest specifier gene, Ets1, to bind to the cranial NC1 regulatory element. However, at vagal/trunk levels, they function together with the neural plate border gene, Zic1, which directly binds to the NC2 enhancer. These results reveal dynamic and differential regulation of FoxD3 in distinct neural crest subpopulations, suggesting that heterogeneity is encrypted at the regulatory level. Isolation of neural crest enhancers not only allows establishment of direct regulatory connections underlying neural crest formation, but also provides valuable tools for tissue specific manipulation and investigation of neural crest cell identity in amniotes

Artificial intelligence effectivity in fracture detection

The scientific study aimed to explore the practical implementation of artificial intelligence (AI) technologies in radiology and traumatology for fracture detection, as well as evaluate their overall effectiveness in modern medicine. In recent years, AI has gained significant traction in the healthcare industry, enabling the analysis of patients' clinical data and facilitating disease diagnosis, monitoring, risk assessment, and surgical intervention possibilities. The relevance of the scientific work is in the gradual expansion of practical applications of artificial intelligence technologies in medicine, particularly in radiology for diagnosing fractures. The study aimed to investigate the practical effectiveness of AI technology in fracture detection on example of Hospital of Traumatology and Orthopaedics in Riga, Latvia. The methodological approach combined system analysis of AI system implementation in modern medical institutions for creating X-ray images with a clinical study of fracture diagnosis experience at the Hospital of Orthopedics and Traumatology in Riga, Latvia. Fractures were detected by radiologists, attending physicians, and the AI program, with comparisons made between them. Results were analyzed to assess the program's efficacy. The results of the study demonstrated the high effectiveness of AI technologies in fracture detection. The application of these systems in clinical practice led to a significant reduction in diagnostic errors (by 2-3 times) and an increase in diagnostic accuracy (from 78.1% to 85.2%). Moreover, AI systems proved to be capable of detecting fractures that were not initially identified during routine examinations by paramedics and medical practitioners. This emphasized the practicality of expanding the use of these systems in clinical practice. The practical significance of the obtained results is in their potential use in the development of software systems based on AI, aimed at enhancing fracture diagnosis in medical institutions. These findings provided valuable insights for further advancements in AI-based technologies for fracture detectio

Artificial intelligence effectivity in fracture detection

The scientific study aimed to explore the practical implementation of artificial intelligence (AI) technologies in radiology and traumatology for fracture detection, as well as evaluate their overall effectiveness in modern medicine. In recent years, AI has gained significant traction in the healthcare industry, enabling the analysis of patients' clinical data and facilitating disease diagnosis, monitoring, risk assessment, and surgical intervention possibilities. The relevance of the scientific work is in the gradual expansion of practical applications of artificial intelligence technologies in medicine, particularly in radiology for diagnosing fractures. The study aimed to investigate the practical effectiveness of AI technology in fracture detection on example of Hospital of Traumatology and Orthopaedics in Riga, Latvia. The methodological approach combined system analysis of AI system implementation in modern medical institutions for creating X-ray images with a clinical study of fracture diagnosis experience at the Hospital of Orthopedics and Traumatology in Riga, Latvia. Fractures were detected by radiologists, attending physicians, and the AI program, with comparisons made between them. Results were analyzed to assess the program's efficacy. The results of the study demonstrated the high effectiveness of AI technologies in fracture detection. The application of these systems in clinical practice led to a significant reduction in diagnostic errors (by 2-3 times) and an increase in diagnostic accuracy (from 78.1% to 85.2%). Moreover, AI systems proved to be capable of detecting fractures that were not initially identified during routine examinations by paramedics and medical practitioners. This emphasized the practicality of expanding the use of these systems in clinical practice. The practical significance of the obtained results is in their potential use in the development of software systems based on AI, aimed at enhancing fracture diagnosis in medical institutions. These findings provided valuable insights for further advancements in AI-based technologies for fracture detection

Why does entrepreneurial orientation affect company performance?

© 2019 Strategic Management Society Research summary: To better understand why entrepreneurial orientation (EO) is positively associated with company performance, we propose and test a reconceptualization of how the components of EO (risk-taking, innovativeness, proactiveness) combine in driving performance. Drawing on financial economics theory, our conceptualization highlights that all three components positively contribute to performance, but in different ways. Risk-taking has a direct positive relationship with performance, which can be understood through the risk–return tradeoff that is central in financial economics theory. The relationship between risk-taking and performance is conditional on the level of innovativeness and thus innovativeness contributes to performance through its effect on the type of risk-taking. Proactiveness contributes to performance through its positive effect on the level of risk-taking. Managerial summary: This study analyzes three key drivers of company performance: risk-taking, innovativeness, and proactiveness. We show that constructive risk-taking is the central driver of company performance, mirroring the principle of risk and return in financial investment settings. Risk- taking that is associated with innovation has a particularly strong positive relationship with performance, consistent with innovation being a driver of growth and profitability. More proactive firms tend to take on more risk and thus also perform better than less proactive firms

Molecular Characterization of the Gastrula in the Turtle Emys orbicularis: An Evolutionary Perspective on Gastrulation

Due to the presence of a blastopore as in amphibians, the turtle has been suggested to exemplify a transition form from an amphibian- to an avian-type gastrulation pattern. In order to test this hypothesis and gain insight into the emergence of the unique characteristics of amniotes during gastrulation, we have performed the first molecular characterization of the gastrula in a reptile, the turtle Emys orbicularis. The study of Brachyury, Lim1, Otx2 and Otx5 expression patterns points to a highly conserved dynamic of expression with amniote model organisms and makes it possible to identify the site of mesoderm internalization, which is a long-standing issue in reptiles. Analysis of Brachyury expression also highlights the presence of two distinct phases, less easily recognizable in model organisms and respectively characterized by an early ring-shaped and a later bilateral symmetrical territory. Systematic comparisons with tetrapod model organisms lead to new insights into the relationships of the blastopore/blastoporal plate system shared by all reptiles, with the blastopore of amphibians and the primitive streak of birds and mammals. The biphasic Brachyury expression pattern is also consistent with recent models of emergence of bilateral symmetry, which raises the question of its evolutionary significance

A Novel TGFβ Modulator that Uncouples R-Smad/I-Smad-Mediated Negative Feedback from R-Smad/Ligand-Driven Positive Feedback

As some of the most widely utilised intercellular signalling molecules, transforming growth factor β (TGFβ) superfamily members play critical roles in normal development and become disrupted in human disease. Establishing appropriate levels of TGFβ signalling involves positive and negative feedback, which are coupled and driven by the same signal transduction components (R-Smad transcription factor complexes), but whether and how the regulation of the two can be distinguished are unknown. Genome-wide comparison of published ChIP-seq datasets suggests that LIM dom