Possible New Candidates Involved to Thalidomide-Related Limbs and Cardiac Defects: A Systems Biology Approach.

Thalidomide is a known teratogen that causes malformations especially in heart and limbs. Its mechanism of teratogenicity is still not fully elucidated. Recently, a new target of thalidomide was described, TBX5, and was observed a new interaction between HAND2 and TBX5 that is disrupted in the presence of thalidomide. Therefore, our study aimed to raise potential candidates for thalidomide teratogenesis, through systems biology, evaluating HAND2 and TBX5 interaction and heart and limbs malformations of thalidomide. Genes and proteins related to TBX5 and HAND2 were selected through TF2DNA, REACTOME, Human Phenotype Ontology, and InterPro databases. Networks were assembled using STRING © database. Network analysis were performed in Cytoscape © and R v3.6.2. Differential gene expression (DGE) analysis was performed through gene expression omnibus. We constructed a network for HAND2 and TBX5 interaction; a network for heart and limbs malformations of TE; and the two joined networks. We observed that EP300 protein seemed to be important in all networks. We also looked for proteins containing C2H2 domain in the assembled networks. ZIC3, GLI1, GLI3, ZNF148, and PRDM16 were the ones present in both heart and limbs malformations of TE networks. Furthermore, in the DGE analysis after treatment with thalidomide, we observed that FANCB, ESCO2, and XRCC2 were downregulated and present both in heart and limbs networks. Through systems biology, we were able to point to different new proteins and genes, and selected specially EP300, which was important in all the analyzed networks, to be further evaluated in the TE teratogenicity.

Whole-Mount Histochemical Protocols in Zebrafish for a Hands-On Developmental Biology Practical Course in Ecuador.

Research-based education at the undergraduate level is ideal for fostering the training of future scientists. In an undergraduate Developmental Biology course, this learning strategy requires the availability of model species and enough research reagents, not only for technique training but also for the development of student original projects. This might be challenging in most countries, where resources are limited. Hence, there is a need to develop low-cost solutions for use in the classroom. In this study, we describe the optimization and use of two low-cost protocols in zebrafish embryos for hands-on practical sessions and project-based learning in a Developmental Biology undergraduate course in Ecuador. These protocols were designed for the practical and experimental learning of vertebrate meroblastic cleavage, gastrulation, and neural crest differentiation. The proposed protocols have been previously described in the literature and use silver nitrate and alcian blue, two relatively inexpensive reagents, to label cell membranes and cartilage. The silver nitrate protocol allows the study of cell contact formation during cleavage and the identification of cellular changes during gastrulation, including yolk internalization and epiboly. The alcian blue staining allows the analysis of cranial mesenchymal differentiation into cartilage. These protocols are ideal for practical sessions due to their ease of application, quick results, adaptability to the class schedule, and robustness in the hands of beginning researchers. Finally, these protocols are adaptable for research-based class projects.

Pollination syndromes and the origins of floral traits.

BACKGROUND: A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. SCOPE: The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. CONCLUSIONS: The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.

The ring-legged earwig Euborellia annulipes as a new model for oogenesis and development studies in insects.

Insects are the dominant group of animals on Earth. Despite this abundance, most of our knowledge about many aspects of their biology and development come from a unique model, the vinegar fly, Drosophila melanogaster. Nevertheless, in the last years, the advances in molecular tools and imaging techniques have allowed the emergence of new insect models, adding valuable information to decipher the morphogenetic bases behind the formation and evolution of the vast diversity of shapes, sizes, and patterns that characterize them. Earwigs belong to Dermaptera which is a small order clustered in the Polyneopteran group. They are hemimetabolous insects with a flattened body, characteristic abdominal pincers, and maternal care behavior. This last feature and their role in agroecosystems have been studied in cosmopolitan species such as Forficula auricularia and Euborellia annulipes; however, their reproduction and embryonic development have been poorly addressed in laboratory conditions. In response, here we describe the ring-legged earwig Euborellia annulipes embryogenesis and life cycle from nymphal to adult stages, its reproduction, and essential morphological and behavioral characters. Additionally, using confocal and transmission electron microscopy we analyzed in detail the morphogenesis of its peculiar meroistic polytrophic ovary. Our aim is to provide an emerging model system to perform comparative studies on insect oogenesis, development, and morphological evolution.

The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells.

Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the 'pluripotency core' and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.

Lung evolution in vertebrates and the water-to-land transition.

A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian 419-359 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for the first time, lung morphology in extensive developmental series of key living lunged osteichthyans using synchrotron x-ray microtomography and histology. Our results shed light on the primitive state of vertebrate lungs as unpaired, evolving to be truly paired in the lineage towards the tetrapods. The water-to-land transition confronted profound physiological challenges and paired lungs were decisive for increasing the surface area and the pulmonary compliance and volume, especially during the air-breathing on land.

All life on Earth started out under water. However, around 400 million years ago some vertebrates, such as fish, started developing limbs and other characteristics that allowed them to explore life on land. One of the most pivotal features to evolve was the lungs, which gave vertebrates the ability to breathe above water. Most land-living vertebrates, including humans, have two lungs which sit on either side of their chest. The lungs extract oxygen from the atmosphere and transfer it to the bloodstream in exchange for carbon dioxide which then gets exhaled out in to the atmosphere. How this important organ first evolved is a hotly debated topic. This is largely because lung tissue does not preserve well in fossils, making it difficult to trace how the lungs of vertebrates changed over the course of evolution. To overcome this barrier, Cupello et al. compared the lungs of living species which are crucial to understand the early stages of the water-to-land transition. This included four species of lunged bony fish which breathe air at the water surface, and a four-legged salamander that lives on land. Cupello et al. used a range of techniques to examine how the lungs of the bony fish and salamander changed shape during development. The results suggested that the lungs of vertebrates started out as a single organ, which became truly paired later in evolution once vertebrates started developing limbs. This anatomical shift increased the surface area available for exchanging oxygen and carbon dioxide so that vertebrates could breathe more easily on land. These findings provide new insights in to how the lung evolved into the paired structure found in most vertebrates alive today. It likely that this transition allowed vertebrates to fully adapt to breathing above water, which may explain why this event only happened once over the course of evolution.

The big potential of the small frog Eleutherodactylus coqui.

The Puerto Rican coquí frog Eleutherodactylus coqui is both a cultural icon and a species with an unusual natural history that has attracted attention from researchers in a number of different fields within biology. Unlike most frogs, the coquí frog skips the tadpole stage, which makes it of interest to developmental biologists. The frog is best known in Puerto Rico for its notoriously loud mating call, which has allowed researchers to study aspects of social behavior such as vocal communication and courtship, while the ability of coquí to colonize new habitats has been used to explore the biology of invasive species. This article reviews existing studies on the natural history of E. coqui and discusses opportunities for future research.

Utilización de la herramienta chroma key para el estudio de la morfología y la fisiología espermática en entornos virtuales / Use of the chroma key to study sperm morphology and physiology in virtual environments

RESUMEN: Uno de los retos en el uso de nuevas metodologías y tecnologías durante la crisis sanitaria causada por el virus SARS-CoV-2 ha sido mantener la motivación del alumnado en entornos virtuales. Por ello, el objetivo de este trabajo fue valorar la utilidad de materiales audiovisuales creados con chroma key en la metodología flipped classroom para impartir algunos conceptos teóricos en la asignatura de Biología del Desarrollo en el Grado en Biología de la Universidad de Alicante. Para ello, el profesorado de la asignatura elaboró vídeos utilizando la tecnología chroma key, los cuales fueron visualizados por parte del alumnado antes de las sesiones teóricas online. Durante dichas sesiones, el alumnado puso en práctica los conceptos comentados en los vídeos a través de la realización de actividades. La percepción del estudiantado sobre la metodología empleada se obtuvo mediante un cuestionario de opinión, en el cual el 90 % de los encuestados/as manifestaron que el uso combinado del flipped classroom con chroma key facilitaba el aprendizaje al adaptarse al ritmo y necesidades educativas de cada estudiante. Asimismo, destacaron que el uso de escenografía virtual con chroma key hizo más amena y atrayente la docencia online. En conclusión, el chroma key constituye una herramienta eficaz para realizar materiales educativos en flipped classroom que, además, resulta llamativo y motivador para el alumnado.

SUMMARY: One of the challenges in the use of new methodologies and technologies during the health crisis caused by the SARS-CoV-2 virus has been to keep students motivated in virtual environments. Therefore, the objective of this work was to assess the usefulness of audiovisual materials created with chroma key in the flipped classroom methodology to teach some theoretical concepts in the subject of Developmental Biology in the Degree in Biology at the University of Alicante. For this, the teaching staff of the subject produced videos using chroma key technology, which were viewed by the students before the online theoretical sessions. During these sessions, the students put into practice the concepts discussed in the videos by carrying out activities. The students' perception of the methodology used was obtained through an opinion questionnaire, in which 90 % of the respondents stated that the combined use of the flipped classroom with chroma key facilitated learning by adapting to the rhythm and educational needs of each student. They also highlighted that the use of virtual scenery with chroma key made online teaching more enjoyable and attractive. In conclusion, the chroma key is an effective tool for creating educational materials in the flipped classroom that is also attractive and motivating for students.

Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism.

The developmental strategies used by progenitor cells to allow a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here, we uncovered a mechanism of progenitor cell allocation that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the superficial epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-lasting apical contacts that enable the epithelial layer to pull a subset of progenitors on their way to the vegetal pole. The remaining delaminated cells follow the movement of apically attached progenitors by a protrusion-dependent cell-cell contact mechanism, avoiding sequestration by the adjacent endoderm, ensuring their collective fate and allocation at the site of differentiation. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development.

Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration.

Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Albors et al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rost et al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modeling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during ~85 hours after amputation within ~830 µm of the injury. We adapted Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding bona fide spinal cord regeneration.

What we can learn from embryos to understand the mesenchymal-to-epithelial transition in tumor progression.

Epithelial plasticity involved the terminal and transitional stages that occur during epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET), both are essential at different stages of early embryonic development that have been co-opted by cancer cells to undergo tumor metastasis. These processes are regulated at multiple instances, whereas the post-transcriptional regulation of key genes mediated by microRNAs is gaining major attention as a common and conserved pathway. In this review, we focus on discussing the latest findings of the cellular and molecular basis of the less characterized process of MET during embryonic development, with special attention to the role of microRNAs. Although we take in consideration the necessity of being cautious when extrapolating the obtained evidence, we propose some commonalities between early embryonic development and cancer progression that can shed light into our current understanding of this complex event and might aid in the design of specific therapeutic approaches.

Early ontogeny of Pimelodus blochii Valenciennes, 1840 (Siluriformes: Pimelodidae): Neotropical catfish.

Larval ontogeny of the long-whiskered catfish Pimelodus blochii Valenciennes, 1840 is described, providing useful characters for identification and determining the growth pattern throughout its development. Eighty-nine larvae classified in three stages (preflexion, flexion and postflexion) and 30 juveniles were analyzed, totaling 119 individuals. The specimens were collected monthly from January 2013 to May 2019 in the lower Amazon river. A suite of morphological, morphometric, and meristic data was used to describe the stages of development. Three analytical regression models were used: simple linear, quadratic and piecewise regressions. The larvae are characterized by small to moderate eyes, subinferior mouth, and long barbels (maxillary larger than the mental barbels), triangular-shaped adipose fin, and the final part of the intestine reaching half the body. Pigmentation consists of dendritic chromatophores distributed irregularly in the body, ventral region and head, intensifying in the flanks and dorsal region throughout development. The total number of myomeres has a mode of 42 muscle bundles, ranging from 40 to 42 (15 to 16 pre-and 25 to 26 post-anal) and the number of fin segments corresponded to: pectoral = I + 9, pelvic = 6, dorsal = I + 6 and anal = 11-12. All body variables showed discontinuous isometric growth, indicating a deceleration in the structural modeling of the body, between the flexion/post-flexion stages and acceleration in post-flexion/early juvenile period. Precisely when the formation of the fin rays, muscles and organs of the digestive system and ossification are observed, suggesting low morphological variation during ontogenetic development. Pimelodus blochii differs from other congeneric species in the lower Amazon river by meristic characters, which helps to correctly identify individuals in early stages of development.

Cystic proliferation of germline stem cells is necessary to reproductive success and normal mating behavior in medaka.

The production of an adequate number of gametes is necessary for normal reproduction, for which the regulation of proliferation from early gonadal development to adulthood is key in both sexes. Cystic proliferation of germline stem cells is an especially important step prior to the beginning of meiosis; however, the molecular regulators of this proliferation remain elusive in vertebrates. Here, we report that ndrg1b is an important regulator of cystic proliferation in medaka. We generated mutants of ndrg1b that led to a disruption of cystic proliferation of germ cells. This loss of cystic proliferation was observed from embryogenic to adult stages, impacting the success of gamete production and reproductive parameters such as spawning and fertilization. Interestingly, the depletion of cystic proliferation also impacted male sexual behavior, with a decrease of mating vigor. These data illustrate why it is also necessary to consider gamete production capacity in order to analyze reproductive behavior.

Age-Related Metabolic Pathways Changes in Dental Follicles: A Pilot Study.

Aging is not a matter of choice; it is our fate. The "time-dependent functional decline that affects most living organisms" is coupled with several alterations in cellular processes, such as cell senescence, epigenetic alterations, genomic instability, stem cell exhaustion, among others. Age-related morphological changes in dental follicles have been investigated for decades, mainly motivated by the fact that cysts and tumors may arise in association with unerupted and/or impacted teeth. The more we understand the physiology of dental follicles, the more we are able to contextualize biological events that can be associated with the occurrence of odontogenic lesions, whose incidence increases with age. Thus, our objective was to assess age-related changes in metabolic pathways of dental follicles associated with unerupted/impacted mandibular third molars from young and adult individuals. For this purpose, a convenience sample of formalin-fixed paraffin-embedded (FFPE) dental follicles from young (<16 y.o., n = 13) and adult (>26 y.o., n = 7) individuals was selected. Samples were analyzed by high-performance liquid chromatography-mass spectrometry (HPLC-MS)-based untargeted metabolomics. Multivariate and univariate analyses were conducted, and the prediction of altered pathways was performed by mummichog and Gene Set Enrichment Analysis (GSEA) approaches. Dental follicles from young and older individuals showed differences in pathways related to C21-steroid hormone biosynthesis, bile acid biosynthesis, galactose metabolism, androgen and estrogen biosynthesis, starch and sucrose metabolism, and lipoate metabolism. We conclude that metabolic pathways differences related to aging were observed between dental follicles from young and adult individuals. Our findings support that similar to other human tissues, dental follicles associated with unerupted tooth show alterations at a metabolic level with aging, which can pave the way for further studies on oral pathology, oral biology, and physiology.

Genetics of Transposition of Great Arteries: Between Laterality Abnormality and Outflow Tract Defect.

Transposition of great arteries (TGA) is a complex congenital heart disease whose etiology is still unknown. This defect has been associated, at least in part, with genetic abnormalities involved in laterality establishment and heart outflow tract development, which suggest a genetic heterogeneity. In animal models, the evidence of association with certain genes is strong but, surprisingly, genetic anomalies of its human orthologues are found only in a low proportion of patients and in nonaffected subjects, so that the underlying causes remain as an unexplored field. Evidence related to TGA suggests different pathogenic mechanisms involved between patients with normal organ disposition and isomerism. This article reviews the most important genetic abnormalities related to TGA and contextualizes them into the mechanism of embryonic development, comparing them between humans and mice, to comprehend the evidence that could be relevant for genetic counseling. Graphical abstract.

Dynamical patterning modules and network motifs as joint determinants of development: Lessons from an aggregative bacterium.

Development and evolution are dynamical processes under the continuous control of organismic and environmental factors. Generic physical processes, associated with biological materials and certain genes or molecules, provide a morphological template for the evolution and development of organism forms. Generic dynamical behaviors, associated with recurring network motifs, provide a temporal template for the regulation and coordination of biological processes. The role of generic physical processes and their associated molecules in development is the topic of the dynamical patterning module (DPM) framework. The role of generic dynamical behaviors in biological regulation is studied via the identification of the associated network motifs (NMs). We propose a joint DPM-NM perspective on the emergence and regulation of multicellularity focusing on a multicellular aggregative bacterium, Myxococcus xanthus. Understanding M. xanthus development as a dynamical process embedded in a physical substrate provides novel insights into the interaction between developmental regulatory networks and generic physical processes in the evolutionary transition to multicellularity.

Alterações idade-dependente nas vias metabólicas de folículos dentários: um estudo piloto / Age-related metabolic pathways changes in dental follicles: a pilot study

Envelhecer não é uma escolha; é nosso destino. O declínio funcional dependente do tempo que afeta a maioria dos organismos vivos está vinculado às alterações em variados processos celulares, incluindo senescência celular, alterações epigenéticas, instabilidade genômica, exaustão de células-tronco, entre outras. As alterações morfológicas relacionadas à idade nos folículos dentários associados a dentes não-erupcionados têm sido investigadas há décadas, principalmente motivado pelo fato de que cistos e tumores podem surgir em associação a dentes inclusos e/ou impactados. Quanto mais entendemos a fisiologia dos folículos dentários, mais nos tornamos capazes de contextualizar eventos biológicos que podem estar associados à ocorrência de lesões odontogênicas cuja incidência aumenta com a idade. Assim, nosso objetivo foi avaliar as alterações metabólicas relacionadas à idade em amostras de folículos dentários associados à terceiros molares inferiores inclusos/impactados de indivíduos adolescentes e adultos. Uma amostra de conveniência de folículos dentários fixados em formalina e embebidos em parafina de indivíduos adolescentes (<16 anos, n= 13) e adultos (>26 anos, n= 7) foi selecionada. As amostras foram preparadas e submetidas à cromatografia líquida de alta eficiência acoplada a espectrometria de massa (HPLC-MS) em análise metabolômica untargeted. Análises uni- e multivariadas foram conduzidas, e a previsão de vias alteradas foi realizada pelas abordagens mummichog e GSEA. Folículos dentários de indivíduos adolescentes e adultos mostraram diferenças nas vias relacionadas à biossíntese do hormônio esteróide C21, biossíntese dos ácidos biliares, metabolismo da galactose, biossíntese de androgênio e estrogênio, metabolismo do amido e sacarose e metabolismo do lipoato. Nossos achados sugerem que, assim como outros tecidos humanos, os folículos dentários associados a dentes não erupcionados apresentam, durante o envelhecimento, alterações em nível metabólico, o que pode abrir caminho para novos estudos sobre biologia, fisiologia e patologia oral.

Aging is not a matter of choice; it is our fate. The 'time-dependent functional decline that affects most living organisms' is coupled with several alterations in cellular processes, including cell senescence, epigenetic alterations, genomic instability, stem cell exhaustion, amongst others. Age-related morphological changes in dental follicles have been investigated for decades, mainly motivated by the fact that cysts and tumors may arise in association with a unerupted and/or impacted teeth. The more we understand dental follicles' physiology, the more we become able to contextualize biological events that can be associated with the occurrence of odontogenic lesions which incidence increases with age. Thus, our objective was to assess age-related changes in metabolic pathways of dental follicles associated with unerupted/impacted mandibular third molars from young and adult individuals. For this purpose, a convenience sample of formalin-fixed paraffin-embedded dental follicles from young (<16 y.o., n = 13) and adult (>26 y.o., n = 7) individuals was selected. Samples were analyzed by high-performance liquid chromatography-mass spectrometry (HPLC-MS)-based untargeted metabolomics. Multivariate and univariate analyses were conducted, and the prediction of altered pathways was performed by mummichog and GSEA approaches. Dental follicles from young and older individuals showed differences in pathways related to C21-steroid hormone biosynthesis, bile acid biosynthesis, galactose metabolism, androgen and estrogen biosynthesis, starch and sucrose metabolism and lipoate metabolism. Our findings support that similar to other human tissues, dental follicles associated with unerupted tooth show alterations at a metabolic level with aging, which can pave the way for further studies on oral pathology, oral biology and physiology.