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The complex zygomorphic flowers of the early-diverging eudicot Delphinium provide an opportunity to explore intriguing evolutionary, developmental, and genetic questions. The dorsal perianth organs, consisting of a spurred sepal and the nectar-bearing spurred petal(s) in Delphinium, contribute to the dorsoventralization and zygomorphic flower morphology. The seamless integration of the two or three dorsal petaloid spurred organs is considered a synorganization, and the resulting organ complex is referred to as a hyperorgan. The hyperorgan shows variability within the tribe due to variation in the number, size, and shape of the spurs. Research in recent decades within this tribe has enhanced our understanding of morphological evolution of flowers. More recently, functional studies using the RNAi approach of Virus-Induced Gene Silencing (VIGS) have unraveled interesting results highlighting the role of gene duplication in the functional diversification of organ identity and symmetry genes. Research in this early-diverging eudicot genus bridges the gaps in understanding the morphological innovations that are mostly studied in model grass and core eudicot clades. This first comprehensive review synthesizes ecoevo-devo research on Delphinium, developing a holistic understanding of recent advancements and establishing the genus as an exceptional model for addressing fundamental questions in developmental genetics, particularly in the evolution of complex flowers. This progress highlights Delphinium's significant potential for future studies in this field. [ABSTRACT FROM AUTHOR]

In organisms with complex life cycles, life stages that are most susceptible to environmental stress may determine species persistence in the face of climate change. Early embryos of Drosophila melanogaster are particularly sensitive to acute heat stress, yet tropical embryos have higher heat tolerance than temperate embryos, suggesting adaptive variation in embryonic heat tolerance. We compared transcriptomic responses to heat stress among tropical and temperate embryos to elucidate the gene regulatory basis of divergence in embryonic heat tolerance. The transcriptomes of tropical and temperate embryos differed in both constitutive and heat-stress-induced responses of the expression of relatively few genes, including genes involved in oxidative stress. Most of the transcriptomic response to heat stress was shared among all embryos. Embryos shifted the expression of thousands of genes, including increases in the expression of heat shock genes, suggesting robust zygotic gene activation and demonstrating that, contrary to previous reports, early embryos are not transcriptionally silent. The involvement of oxidative stress genes corroborates recent reports on the critical role of redox homeostasis in coordinating developmental transitions. By characterizing adaptive variation in the transcriptomic basis of embryonic heat tolerance, this study is a novel contribution to the literature on developmental physiology and developmental genetics. [ABSTRACT FROM AUTHOR]

Summary: The homology of the single cotyledon of grasses and the ontogeny of the scutellum and coleoptile as the initial, highly modified structures of the grass embryo are investigated using leaf developmental genetics and targeted transcript analyses in the model grass Zea mays subsp. mays.Transcripts of leaf developmental genes are identified in both the initiating scutellum and the coleoptile, while mutations disrupting mediolateral leaf development also disrupt scutellum and coleoptile morphology, suggesting that these grass‐specific organs are modified leaves.Higher‐order mutations in WUSCHEL‐LIKE HOMEOBOX3 (WOX3) genes, involved in mediolateral patterning of plant lateral organs, inform a model for the fusion of coleoptilar margins during maize embryo development.Genetic, RNA‐targeting, and morphological evidence supports models for cotyledon evolution where the scutellum and coleoptile, respectively, comprise the distal and proximal domains of the highly modified, single grass cotyledon. [ABSTRACT FROM AUTHOR]

Background Heterozygous variants in Transient receptor potential melastatin type 7 (TRPM7), encoding an essential and ubiquitously expressed cation channel, may cause hypomagnesemia, but current evidence is insufficient to draw definite conclusions and it is unclear whether any other phenotypes can occur. Methods Individuals with unexplained hypomagnesemia underwent whole-exome sequencing which identified TRPM7 variants. Pathogenicity of the identified variants was assessed by combining phenotypic, functional and in silico analyses. Results We report three new heterozygous missense variants in TRPM7 (p.Met1000Thr, p.Gly1046Arg, p.Leu1081Arg) in individuals with hypomagnesemia. Strikingly, autism spectrum disorder and developmental delay, mainly affecting speech and motor skills, was observed in all three individuals, while two out of three also presented with seizures. The three variants are predicted to be severely damaging by in silico prediction tools and structural modeling. Furthermore, these variants result in a clear loss-of-function of TRPM7-mediated magnesium uptake in vitro , while not affecting TRPM7 expression or insertion into the plasma membrane. Conclusions This study provides additional evidence for the association between heterozygous TRPM7 variants and hypomagnesemia and adds developmental delay to the phenotypic spectrum of TRPM7 -related disorders. Considering that the TRPM7 gene is relatively tolerant to loss-of-function variants, future research should aim to unravel by what mechanisms specific heterozygous TRPM7 variants can cause disease. [ABSTRACT FROM AUTHOR]

Components of the Hippo kinase module are present in some unicellular organisms, and unicellular orthologs of the Hippo pathway kinase Warts have the capability to phosphorylate Yorkie, despite the absence of Yorkie in many of these organisms. A complete core Hippo pathway, including the transcriptional coactivator Yorkie, predated the origin of animals, and is present in the closest unicellular relatives of animals. Functional studies in unicellular organisms and early-branching animals suggest that an ancestral function of the Hippo pathway was regulation of the actomyosin cytoskeleton, and that the pathway was subsequently co-opted for tissue size regulation in the lineage leading to bilaterian animals. Acquisition of the ability of Yorkie to regulate cell proliferation and tissue size regulation may have coincided with the evolutionary emergence of distal enhancer-mediated gene regulation in animals. Decades of work in developmental genetics has given us a deep mechanistic understanding of the fundamental signaling pathways underlying animal development. However, little is known about how these pathways emerged and changed over evolutionary time. Here, we review our current understanding of the evolutionary emergence of the Hippo pathway, a conserved signaling pathway that regulates tissue size in animals. This pathway has deep evolutionary roots, emerging piece by piece in the unicellular ancestors of animals, with a complete core pathway predating the origin of animals. Recent functional studies in close unicellular relatives of animals and early-branching animals suggest an ancestral function of the Hippo pathway in cytoskeletal regulation, which was subsequently co-opted to regulate proliferation and animal tissue size. Decades of work in developmental genetics has given us a deep mechanistic understanding of the fundamental signaling pathways underlying animal development. However, little is known about how these pathways emerged and changed over evolutionary time. Here, we review our current understanding of the evolutionary emergence of the Hippo pathway, a conserved signaling pathway that regulates tissue size in animals. This pathway has deep evolutionary roots, emerging piece by piece in the unicellular ancestors of animals, with a complete core pathway predating the origin of animals. Recent functional studies in close unicellular relatives of animals and early-branching animals suggest an ancestral function Hippo pathway of cytoskeletal regulation, which was subsequently co-opted to regulate proliferation and animal tissue size. [ABSTRACT FROM AUTHOR]

In light of the post-genomic era, epigenetics brings about an opportunity to better understand how the molecular machinery works and is led by a complex dynamic set of mechanisms, often intricate and complementary in many aspects. In particular, epigenetics links developmental biology and genetics, as well as many other areas of knowledge. The present work highlights substantial scopes and relevant discoveries related to the development of the term from its first notions. To our understanding, the concept of epigenetics needs to be revisited, as it is one of the most relevant and multifaceted terms in human knowledge. To redirect future novel experimental or theoretical efforts, it is crucial to compile all significant issues that could impact human and ecological benefit in the most precise and accurate manner. In this paper, the reader can find one of the widest compilations of the landmarks and epistemic considerations of the knowledge of epigenetics across the history of biology from the earliest epigenetic formulation to genetic determinism until the present. In the present work, we link the current body of knowledge and earlier pre-genomic concepts in order to propose a new definition of epigenetics that is faithful to its regulatory nature. [ABSTRACT FROM AUTHOR]

LIM homeobox 4 (LHX4) is a transcription factor crucial for anterior pituitary (AP) development. Patients with LHX4 mutation suffer from combined pituitary hormone deficiency (CPHD), short statures, reproductive and metabolic disorders and lethality in some cases. Lhx4-knockout (KO) mice fail to develop a normal AP and die shortly after birth. Here, we characterize a zebrafish lhx4-KO model to further investigate the importance of LHX4 in pituitary gland development and regulation. At the embryonic and larval stages, these fish express lower levels of tshb mRNA compared with their wildtype siblings. In adult lhx4-KO fish, the expressions of pituitary hormone-encoding transcripts, including growth hormone (gh), thyroid stimulating hormone (tshb), proopiomelanocortin (pomca) and follicle stimulating hormone (fshb), are reduced, the pomca promoter-driven expression in corticotrophs is dampened and luteinizing hormone (lhb)-producing gonadotrophs are severely depleted. In contrast to Lhx4-KO mice, Lhx4-deficient fish survive to adulthood, but with a reduced body size. Importantly, lhx4-KO males reach sexual maturity and are reproductively competent, whereas the females remain infertile with undeveloped ovaries. These phenotypes, which are reminiscent of those observed in CPHD patients, along with the advantages of the zebrafish for developmental genetics research, make this lhx4-KO fish an ideal vertebrate model to study the outcomes of LHX4 mutation. [ABSTRACT FROM AUTHOR]

Medaka fish (Oryzias latipes) is a powerful model to study genetics underlying the developmental and functional traits of the vertebrate visual system. We established a simple and high-throughput optomotor response (OMR) assay utilizing medaka larvae to study visual functions including visual acuity and contrast sensitivity. Our assay presents multiple adjustable stripes in motion to individual fish in a linear arena. For that the OMR assay employs a tablet display and the Fish Stripes software to adjust speed, width, color, and contrast of the stripes. Our results demonstrated that optomotor responses were robustly induced by black and white stripes presented from below in the linear-pool-arena. We detected robust strain specific differences in the OMR when comparing long established medaka inbred strains. We observed an interesting training effect upon the initial exposure of larvae to thick stripes, which allowed them to better respond to narrower stripes. The OMR setup and protocol presented here provide an efficient tool for quantitative phenotype mapping, addressing visual acuity, trainability of cortical neurons, color sensitivity, locomotor response, retinal regeneration and others. Our open-source setup presented here provides a crucial prerequisite for ultimately addressing the genetic basis of those processes. [ABSTRACT FROM AUTHOR]

The historical challenges to bridge the gaps between developmental biology and population or statistical genetics under the explanatory dominance of the Modern Evolutionary Synthesis during the 20th century have been thoroughly documented. However, although several attempts to integrate these fields have been made, most have been deemed unsuccessful. As an example of those efforts, in this paper I discuss the work of James Meadows Rendel, a student of J. B. S. Haldane and disciple of Conrad Hal Waddington. I present his largely forgotten or unrecognized, but innovative, ideas about canalization and the role of development in phylogeny as a valuable piece to connect these fields that could still have important ramifications for today's evolutionary biology. In fact, it is expected that the legacy of J. M. Rendel will be rediscovered, and more importantly, incorporated and extended by future researchers, in light of the growth of evolutionary developmental biology in the last decades. What is more, this case offers a chance to critically revisit standard historiographies about the dichotomy between developmental and population genetics research frameworks in 20th century biology. • Rendel's theory integrated various developmental and evolutionary processes. • Rendel's theoretical work is generally omitted or unrecognized in the literature. • J. M. Rendel can be seen as a forerunner for contemporary Evo-Devo approaches. [ABSTRACT FROM AUTHOR]

Understanding plant sex chromosomes involves studying interactions between developmental and physiological genetics, genome evolution, and evolutionary ecology. We focus on areas of overlap between these. Ideas about how species with separate sexes (dioecious species, in plant terminology) can evolve are even more relevant to plants than to most animal taxa because dioecy has evolved many times from ancestral functionally hermaphroditic populations, often recently. One aim of studying plant sex chromosomes is to discover how separate males and females evolved from ancestors with no such genetic sex-determining polymorphism, and the diversity in the genetic control of maleness vs femaleness. Different systems share some interesting features, and their differences help to understand why completely sex-linked regions may evolve. In some dioecious plants, the sex-determining genome regions are physically small. In others, regions without crossing over have evolved sometimes extensive regions with properties very similar to those of the familiar animal sex chromosomes. The differences also affect the evolutionary changes possible when the environment (or pollination environment, for angiosperms) changes, as dioecy is an ecologically risky strategy for sessile organisms. Dioecious plants have repeatedly reverted to cosexuality, and hermaphroditic strains of fruit crops such as papaya and grapes are desired by plant breeders. Sex-linked regions are predicted to become enriched in genes with sex differences in expression, especially when higher expression benefits one sex function but harms the other. Such trade-offs may be important for understanding other plant developmental and physiological processes and have direct applications in plant breeding. Plant sex chromosomes can add to understanding of sex chromosomes generally, including regular absence of recombination near the sex-determining loci, and repeated expansion of sex-linked regions. [ABSTRACT FROM AUTHOR]

Paradise fish (Macropodus opercularis) is an air‐breathing freshwater fish species with a signature labyrinth organ capable of extracting oxygen from the air that helps these fish to survive in hypoxic environments. The appearance of this evolutionary innovation in anabantoids resulted in a rewired circulatory system, but also in the emergence of species‐specific behaviors, such as territorial display, courtship and parental care in the case of the paradise fish. Early zoologists were intrigued by the structure and function of the labyrinth apparatus and a series of detailed descriptive histological studies at the beginning of the 20th century revealed the ontogenesis and function of this specialized system. A few decades later, these fish became the subject of numerous ethological studies, and detailed ethograms of their behavior were constructed. These latter studies also demonstrated a strong genetic component underlying their behavior, but due to lack of adequate molecular tools, the fine genetic dissection of the behavior was not possible at the time. The technological breakthroughs that transformed developmental biology and behavioral genetics in the past decades, however, give us now a unique opportunity to revisit these old questions. Building on the classic descriptive studies, the new methodologies will allow us to follow the development of the labyrinth apparatus at a cellular resolution, reveal the genes involved in this process and also the genetic architecture behind the complex behaviors that we can observe in this species. Research Highlights: Paradise fish are air‐breathers, living in hypoxic freshwater environments and displaying complex innate behaviors. To help with gas exchange they have evolved a labyrinth organ which makes them a prime subject for evo‐devo studies, too. [ABSTRACT FROM AUTHOR]

Kryptolebias marmoratus (Kmar), a teleost fish of the order Cyprinodontiformes, has a suite of unique phenotypes and behaviors not observed in other fishes. Many of these phenotypes are discrete and highly plastic—varying over time within an individual, and in some cases reversible. Kmar and its interfertile sister species, K. hermaphroditus, are the only known self‐fertile vertebrates. This unusual sexual mode has the potential to provide unique insights into the regulation of vertebrate sexual development, and also lends itself to genetics. Kmar is easily adapted to the lab and requires little maintenance. However, its internal fertilization and small clutch size limits its experimental use. To support Kmar as a genetic model, we compared alternative husbandry techniques to maximize recovery of early cleavage‐stage embryos. We find that frequent egg collection enhances yield, and that protease treatment promotes the greatest hatching success. We completed a forward mutagenesis screen and recovered several mutant lines that serve as important tools for genetics in this model. Several will serve as useful viable recessive markers for marking crosses. Importantly, the mutant kissylips lays embryos at twice the rate of wild‐type. Combining frequent egg collection with the kissylips mutant background allows for a substantial enhancement of early embryo yield. These improvements were sufficient to allow experimental analysis of early development and the successful mono‐ and bi‐allelic targeted knockout of an endogenous tyrosinase gene with CRISPR/Cas9 nucleases. Collectively, these tools will facilitate modern developmental genetics in this fascinating fish, leading to future insights into the regulation of plasticity. Research Highlights: A forward genetic screen in the self‐fertile fish, Kryptolebias marmoratus, identified useful mutants for use as markers and to enhance egg output.Optimization of husbandry further improved egg yield for embryo manipulation.New resources enabled targeted gene knockout in K. marmoratus using CRISPR/Cas9. [ABSTRACT FROM AUTHOR]

The article discusses the battle between the "biometricians" led by W.F.R. Weldon and the "Mendelian" allies led by William Bateson in England in the early 1900s. The author, Gregory Radick, argues that Weldon's untimely death prevented his case from being fully made, but his theory could have had a significant impact on the future of genetics. Radick explores the similarities and differences between Weldon and Bateson's theories, highlighting Weldon's emphasis on complex interactions of hereditary factors with the environment and developmental processes. The article also discusses the counterfactual scenario of what might have happened if Weldon's theory had prevailed over Mendelism, suggesting that it could have led to a different understanding of genetics without genetic determinism. However, the counterfactual story is met with objections, including the empirical distinguishability of the theories and the potential for other responses to Mendelism. The article concludes by acknowledging the need to correct misconceptions about genetic determinism and genes for traits, but questions the value of rehabilitating Weldon's theory or re-fighting the dispute with Bateson. [Extracted from the article]

The differentiation and developmental trajectory of fish gonads, significantly important for fish breeding, culture, and production, has long been a focal point in the fields of fish genetics and developmental biology. However, the mechanism of gonadal differentiation in leopard coral grouper (Plectropomus leopardus) remains unclear. This study investigates the 17β-Hydroxysteroid Dehydrogenase (Hsd17b) gene family in P. leopardus, with a focus on gene characterization, expression profiling, and functional analysis. The results reveal that the P. leopardus's Hsd17b gene family comprises 11 members, all belonging to the SDR superfamily. The amino acid similarity is only 12.96%, but conserved motifs, such as TGxxxGxG and S-Y-K, are present in these genes. Hsd17b12a and Hsd17b12b are unique homologs in fish, and chromosomal localization has confirmed that they are not derived from different transcripts of the same gene, but rather are two independent genes. The Hsd17b family genes, predominantly expressed in the liver, heart, gills, kidneys, and gonads, are involved in synthesizing or metabolizing sex steroid hormones and neurotransmitters, with their expression patterns during gonadal development categorized into three distinct categories. Notably, Hsd17b4 and Hsd17b12a were highly expressed in the testis and ovary, respectively, suggesting their involvement in the development of reproductive cells in these organs. Fluorescence in situ hybridization (FISH) further indicated specific expression sites for these genes, with Hsd17b4 primarily expressed in germ stem cells and Hsd17b12a in oocytes. This comprehensive study provides foundational insights into the role of the Hsd17b gene family in gonadal development and steroidogenesis in P. leopardus, contributing to the broader understanding of fish reproductive biology and aquaculture breeding. [ABSTRACT FROM AUTHOR]

The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata , the sister species of C. elegans , is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. F ST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions. [ABSTRACT FROM AUTHOR]

The medaka fish (Oryzias latipes) is a vertebrate model used in developmental biology and genetics. Here we explore its suitability as a model for investigating the molecular mechanisms of human myopathies caused by mutations in sarcomeric proteins. To this end, the relevant mechanical parameters of the intact skeletal muscle of wild-type medaka are determined using the transparent tail at larval stage 40. Tails were mounted at sarcomere length of 2.1 μm in a thermoregulated trough containing physiological solution. Tetanic contractions were elicited at physiological temperature (10C–30C) by electrical stimulation, and sarcomere length changes were recorded with nanometer-microsecond resolution during both isometric and isotonic contractions with a striation follower. The force output has been normalized for the actual fraction of the cross section of the tail occupied by the myofilament lattice, as established with transmission electron microscopy (TEM), and then for the actual density of myofilaments, as established with X-ray diffraction. Under these conditions, the mechanical performance of the contracting muscle of the wild-type larva can be defined at the level of the half-thick filament, where ~300 myosin motors work in parallel as a collective motor, allowing a detailed comparison with the established performance of the skeletal muscle of different vertebrates. The results of this study point out that the medaka fish larva is a suitable model for the investigation of the genotype/phenotype correlations and therapeutic possibilities in skeletal muscle diseases caused by mutations in sarcomeric proteins. NEW & NOTEWORTHY The suitability of the medaka fish as a model for investigating the molecular mechanisms of human myopathies caused by mutations of sarcomeric proteins is tested by combining structural analysis and sarcomere-level mechanics of the skeletal muscle of the tail of medaka larva. The mechanical performance of the medaka muscle, scaled at the level of the myosin-containing thick filament, together with its reduced genome duplication makes this model unique for investigations of the genotype/phenotype correlations in human myopathies. [ABSTRACT FROM AUTHOR]

Premise of research. The maintenance of mixed selfing and outcrossing is an enduring mystery in evolutionary biology. Cleistogamy, in which individuals produce both potentially outcrossing chasmogamous (CH) and obligately selfing cleistogamous (CL) flowers, provides an ideal framework in which to study the evolutionary forces maintaining mixed mating. Despite their promise for providing insight into mating system evolution, few studies of cleistogamous species have comprehensively investigated the relative costs and benefits of CL selfing. Methodology. We quantified the necessary components to calculate the relative energetic cost of reproduction of each flower type—CH and CL—in a greenhouse study using three populations of the perennial Ruellia humilis Nutt (Acanthaceae). These components included flower dry mass, fertility (i.e., fruit set), seed mass per fruit, and number of seeds per fruit. We also measured pollen-ovule ratios for both flower types as another measure of relative energetic investment. Last, we tracked phenology of the two flower types and used the proportion of CH flowers to estimate maximum potential outcrossing rates. Pivotal results. We found that the energetic cost of reproduction via CL flowers was four to 10 times lower than that of reproduction via CH flowers. This energetic economy derived both from the reduced mass and from the increased fertility of CL flowers. Pollen-ovule ratios in CL flowers were one-third to one-half those of CH flowers, providing additional support for their energetic economy. Maximum potential outcrossing rates in these populations based on CH flower production were between 43% and 61%, but CH flowers can autogamously self at rates between 33% and 75%. Conclusions. These results suggest that selection should favor only CL flowers due to their greater energetic economy. Additional work in this species demonstrates that neither inbreeding depression nor heterosis can provide an advantage strong enough to overcome the energetic benefits of CL reproduction. Further research on the developmental genetics of the two flower types and potential genetic constraints on the loss of CH flowers is needed. [ABSTRACT FROM AUTHOR]

The article explores the development of a new type of flowering dogwood called 'Erica's Appalachian Sunrise'. It explains that this cultivar was created through a form of asexual reproduction called apomixis, resulting from a breeding attempt between two existing cultivars. The article describes the tree's structure, flower bract shape, and leaf color, highlighting the distinctions between 'Erica's Appalachian Sunrise' and another cultivar called 'Cherokee Brave™'. It also addresses the misconception that 'Erica's Appalachian Sunrise' was the product of self-pollination, providing evidence to support its apomictic origin. The study further discusses the genomic evidence suggesting the occurrence of apomixis in Cornus florida, the species to which the flowering dogwood belongs. The DNA sequences of the maternal plant and the plant derived from apomixis are identical, but there are noticeable differences in their physical characteristics. These differences are attributed to epigenetic factors, such as modifications to DNA or gene expression regulation. This discovery marks the first report of apomixis in C. florida. [Extracted from the article]

Objective·To study the relationship between evolution and the developmental process from the perspective of DNA sequence conservation, and explore their inherent principles.Methods·First, conservation rate (CR) was established by analyzing the conservation of amino acid sequences of coding genes in 100 species to quantify the evolutionary conservation of genes. The relationship between CR and developmental potential was verified by using the feature genes involved in embryonic stem cells pathways. Secondly, cell type-specific genes and their characteristics in conservation were studied by analyzing the RNA sequencing (RNA-seq) data of the three early germ layers (ectoderm, mesoderm and endoderm) and their corresponding mature organs (brain, heart, liver, etc). Then, chromatin immunoprecipitation sequencing (ChIP-seq) data of enhancer histone H3 acetylated at lysine 27 (H3K27ac) from early germ layers and mature organs were collected to search for enhancer sites and identify super enhancers in various cells and tissues by using the ROSE procedure. Functional enrichment and signaling pathway analysis of genes was used to examine the identity correlation between SEs-regulated genes and the corresponding cell characteristics, to clarify whether the SEs identified in this study were consistent with the characteristics reported in previous studies. Finally, PhastCons program was used to calculate the DNA conservation score (CS) of non-coding regulatory regions to study their relationship with developmental potential.Results·In the coding region of DNA, CR was successfully established to quantify the conservation of genes. The gene expression data of early germ layers and mature organs showed that the genes with higher conservation rate were more relevant to the stemness and early developmental process, and the differences between the tissues from early and late development could be distinguished by using CR. In the non-coding regions of DNA, it was found that the conservation of regulatory regions was also correlated with development. The CS of the SE sequences in the early developmental germ layers was significantly higher than that of the SE sequences in the corresponding mature organs. However, cell-specific typical enhancers (TEs) did not show such a trend.Conclusion·During the developmental process, CR of genes expressed in the coding region decreases, and CS of super-enhancer DNA in the non-coding region decreases.

Megaselia scalaris, commonly known as the scuttle fly, is a cosmopolitan species in the family Phoridae. It is an easily cultured fly species that is an emerging model organism in the fields of genetics and developmental biology. Its affinity for carrion and its predictable life cycle makes it useful in the field of forensic science for estimating the post-mortem interval (PMI) of human remains. Cases of human myasis caused by M. scalaris have also been reported in the medical literature. Despite its ubiquitous prevalence and its relevance across multiple fields, its morphology has not been adequately characterized. Here, we report the complete morphological characterization of all lifestages of M. scalaris, ranging from egg to adult. Scanning electron microscopy has enabled us to uncover morphological features and developmental processes that have previously not been reported in the literature. Our data lays the groundwork for future genetic studies: a morphological characterization of the wild type must be performed before mutants displaying different phenotypes can be identified. In this vein, we also report the observation of a acephalic, or 'headless', adult phenotype whose study could yield insights into the process of cephalogenesis. Finally, all morphological features observed have been compiled into an 'atlas' that should be of use to all workers in the field. [ABSTRACT FROM AUTHOR]

How behaviors vary among individuals and covary with other behaviors has been a major topic of interest over the last two decades, particularly in research on animal personality, behavioral syndromes, and trade-offs with life-history traits. Unfortunately, proposed theoretical and conceptual frameworks explaining the seemingly ubiquitous observation of behavioral (co)variation have rarely successfully generalized. For example, the "pace-of-life syndrome hypothesis" proposes that behaviors, life-history, and physiological traits should be correlated in a predictable manner. However, these predictions are not consistently upheld. Two observations perhaps explain this failure: First, phenotypic correlations between behaviors are more strongly influenced by correlated and reversible plastic changes in behavior than by among-individual correlations which stem from the joint effects of genetics and developmental plasticity. Second, while trait correlations are frequently assumed to arise via trade-offs, the observed pattern of correlations is not consistent with simple pair-wise trade-offs. A possible resolution to the apparent inconsistency between observed correlations and a role for trade-offs is provided by state-behavior feedbacks. This is critical because the inconsistency between data and theory represents a major failure in our understanding of behavioral evolution. These two primary observations emphasize the importance of an increased research focus on correlated reversible plasticity in behavior—frequently estimated and then disregarded as within-individual covariances. [ABSTRACT FROM AUTHOR]

Objective·To study the relationship between evolution and the developmental process from the perspective of DNA sequence conservation, and explore their inherent principles. Methods·First, conservation rate (CR) was established by analyzing the conservation of amino acid sequences of coding genes in 100 species to quantify the evolutionary conservation of genes. The relationship between CR and developmental potential was verified by using the feature genes involved in embryonic stem cells pathways. Secondly, cell type-specific genes and their characteristics in conservation were studied by analyzing the RNA sequencing (RNA-seq) data of the three early germ layers (ectoderm, mesoderm and endoderm) and their corresponding mature organs (brain,heart, liver, etc). Then, chromatin immunoprecipitation sequencing (ChIP-seq) data of enhancer histone H3 acetylated at lysine 27 (H3K27ac) from early germ layers and mature organs were collected to search for enhancer sites and identify super enhancers in various cells and tissues by using the ROSE procedure. Functional enrichment and signaling pathway analysis of genes was used to examine the identity correlation between SEs-regulated genes and the corresponding cell characteristics, to clarify whether the SEs identified in this study were consistent with the characteristics reported in previous studies. Finally, PhastCons program was used to calculate the DNA conservation score (CS) of non-coding regulatory regions to study their relationship with developmental potential. Results·In the coding region of DNA, CR was successfully established to quantify the conservation of genes. The gene expression data of early germ layers and mature organs showed that the genes with higher conservation rate were more relevant to the stemness and early developmental process, and the differences between the tissues from early and late development could be distinguished by using CR. In the non-coding regions of DNA, it was found that the conservation of regulatory regions was also correlated with development. The CS of the SE sequences in the early developmental germ layers was significantly higher than that of the SE sequences in the corresponding mature organs. However, cell-specific typical enhancers (TEs) did not show such a trend. Conclusion·During the developmental process, CR of genes expressed in the coding region decreases, and CS of super-enhancer DNA in the non-coding region decreases. [ABSTRACT FROM AUTHOR]

Background: A goal of developmental genetics is to identify functional interactions that underlie phenotypes caused by mutations. We sought to identify functional interactors of Vsx2, which when mutated, disrupts early retinal development. We utilized the Vsx2 loss‐of‐function mouse, ocular retardation J (orJ), to assess interactions based on principles of positive and negative epistasis as applied to bulk transcriptome data. This was first tested in vivo with Mitf, a target of Vsx2 repression, and then to cultures of orJ retina treated with inhibitors of Retinoid‐X Receptors (RXR) to target Rxrg, an up‐regulated gene in the orJ retina, and gamma‐Secretase, an enzyme required for Notch signaling, a key mediator of retinal proliferation and neurogenesis. Results: Whereas Mitf exhibited robust positive epistasis with Vsx2, it only partially accounts for the orJ phenotype, suggesting other functional interactors. RXR inhibition yielded minimal evidence for epistasis between Vsx2 and Rxrg. In contrast, gamma‐Secretase inhibition caused hundreds of Vsx2‐dependent genes associated with proliferation to deviate further from wild‐type, providing evidence for convergent negative epistasis with Vsx2 in regulating tissue growth. Conclusions: Combining in vivo and ex vivo testing with transcriptome analysis revealed quantitative and qualitative characteristics of functional interaction between Vsx2, Mitf, RXR, and gamma‐Secretase activities. Key Findings: The MItf‐mi allele exhibits positive epistasis with the Vsx2‐orJ allele, but Mitf activity only partially accounts for disrupted early retinal development in Vsx2 mutant mice.Rxrg is highly upregulated in the Vsx2 mutant retina, but RXR activity is not a strong driver of the early retinal phenotype.Gamma secretase activity regulates a large cohort of Vsx2‐dependent genes associated with proliferation, providing evidence for convergent negative epistasis, and could account for the continued but slow rate of proliferation in Vsx2 mutant retinal progenitor cells.Bulk RNA sequencing combined with tests of functional interaction can provide sufficient resolution to assess phenotypic changes and epistasis of complex developmental phenotypes [ABSTRACT FROM AUTHOR]

There is converging evidence that 40-Hz auditory steady-state responses (ASSRs) are robustly impaired in schizophrenia and could constitute a potential biomarker for characterizing circuit dysfunctions as well as enable early detection and diagnosis. Here, we provide an overview of the mechanisms involved in 40-Hz ASSRs, drawing on computational, physiological, and pharmacological data with a focus on parameters modulating the balance between excitation and inhibition. We will then summarize findings from electro- and magnetoencephalographic studies in participants at clinical high risk for psychosis, patients with first-episode psychosis, and patients with schizophrenia to identify the pattern of deficits across illness stages, the relationship with clinical variables, and the prognostic potential. Finally, data on genetics and developmental modifications will be reviewed, highlighting the importance of late modifications of 40-Hz ASSRs during adolescence, which are closely related to the underlying changes in GABA (gamma-aminobutyric acid) interneurons. Together, our review suggests that 40-Hz ASSRs may constitute an informative electrophysiological approach to characterize circuit dysfunctions in psychosis that could be relevant for the development of mechanistic biomarkers. [ABSTRACT FROM AUTHOR]

Summary: Molecular quantitative trait loci (QTLs) allow us to understand the biology captured in genome-wide association studies (GWASs). The placenta regulates fetal development and shows sex differences in DNA methylation. We therefore hypothesized that placental methylation QTL (mQTL) explain variation in genetic risk for childhood onset traits, and that effects differ by sex. We analyzed 411 term placentas from two studies and found 49,252 methylation (CpG) sites with mQTL and 2,489 CpG sites with sex-dependent mQTL. All mQTL were enriched in regions that typically affect gene expression in prenatal tissues. All mQTL were also enriched in GWAS results for growth- and immune-related traits, but male- and female-specific mQTL were more enriched than cross-sex mQTL. mQTL colocalized with trait loci at 777 CpG sites, with 216 (28%) specific to males or females. Overall, mQTL specific to male and female placenta capture otherwise overlooked variation in childhood traits.

Summary: Embigin (Gp70), a receptor for fibronectin and an ancillary protein for monocarboxylate transporters, is known to regulate stem cell niches in sebaceous gland and bone marrow. Here, we show that embigin expression is at high level during early mouse embryogenesis and that embigin is essential for lung development. Markedly increased neonatal mortality of Emb−/− mice can be explained by the compromised lung maturation: in Emb−/− mice (E17.5) the number and the size of the small airways and distal airspace are significantly smaller, there are fewer ATI and ATII cells, and the alkaline phosphatase activity in amniotic fluid is lower. Emb−/− lungs show less peripheral branching already at E12.5, and embigin is highly expressed in lung primordium. Thus, embigin function is essential at early pseudoglandular stage or even earlier. Furthermore, our RNA-seq analysis and Ki67 staining results support the idea that the development of Emb−/− lungs is rather delayed than defected.

Summary: Sirt6, a member of the class III histone deacetylases (HDACs), functions in the regulation of genomic stability, DNA repair, cancer, metabolism and aging. Sirt6 deficiency is lethal, and newborn SIRT6-null cynomolgus monkeys show unfinished brain development. After the generation of a cortex-specific Sirt6 conditional knockout mouse model, we investigated the specific deletion of Sirt6 in NPCs at E10.5. This study found that Sirt6 deficiency causes excessive proliferation of neural precursor cells (NPCs) and retards differentiation. The results suggest that endogenous Sirt6 in NPCs regulates histone acetylation and limits stemness-related genes, including Notch1, in order to participate in NPC fate determination. These findings help elucidate Sirt6’s role in brain development and in NPC fate determination while providing data on species generality and differentiation.

Summary: DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, we demonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control.

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. [ABSTRACT FROM AUTHOR]

Thus, as Paul Farber noted, I was among the "three generations of American historians, historians of biology, and biologists" that Gar influenced (Farber [12], p. 625). Historians and philosophers of biology mourn the loss of distinguished scholar and friend Gar Allen on February 10, 2023.[1] Gar had faced health challenges in recent years, but his rapid deterioration due to sepsis caught everyone off guard. Having attended the MBL Embryology Course in 1955, Everett encouraged other historians of biology to visit there (Mendelsohn [18]). There he met Jeff J. W. Baker, and together they authored a series of influential biology textbooks, which reflected Gar's lifelong interest in I teaching i biology. [Extracted from the article]

Summary: Mouse studies continue to help elaborate upon the genetic landscape of mammalian disease and the underlying molecular mechanisms. Here, we have investigated an Embigintm1b allele maintained on a standard C57BL/6N background and on a co-isogenic C57BL/6N background in which the Cdh23ahl allele has been “repaired.” The hypomorphic Cdh23ahl allele is present in several commonly used inbred mouse strains, predisposing them to progressive hearing loss, starting in high-frequency regions. Absence of the neural cell adhesion molecule Embigin on the standard C57BL/6N background leads to accelerated hearing loss and causes sub-viability, brain and cardiac defects. Contrastingly, Embigintm1b/tm1b mice maintained on the co-isogenic “repaired” C57BL/6N background exhibit normal hearing and viability. Thus Embigin genetically interacts with Cdh23. Importantly, our study is the first to demonstrate an effect of the common Cdh23ahl allele outside of the auditory system, which has important ramifications for genetic studies involving inbred strains carrying this allele.

Summary: Double homeobox (DUX) genes are unique to eutherian mammals, expressed transiently during zygotic genome activation (ZGA) and involved in facioscapulohumeral muscular dystrophy (FSHD) and cancer when misexpressed. We evaluate the 3 human DUX genes and the ancestral single homeobox gene sDUX from the non-eutherian mammal, platypus, and find that DUX4 cytotoxicity is not shared with DUXA or DUXB, but surprisingly is shared with platypus sDUX, which binds DNA as a homodimer and activates numerous ZGA genes and long terminal repeat (LTR) elements. DUXA, although transcriptionally inactive, has DNA binding overlap with DUX4, and DUXA-VP64 activates DUX4 targets and is cytotoxic. DUXA competition antagonizes the activity of DUX4 on its target genes, including in FSHD patient cells. Since DUXA is a DUX4 target gene, this competition potentiates feedback inhibition, constraining the window of DUX4 activity. The DUX gene family therefore comprises antagonistic members of opposing function, with implications for their roles in ZGA, FSHD, and cancer.

The developmental genetics of reproductive structure control in maize must consider both the staminate florets of the tassel and the pistillate florets of the ear synflorescences. Pistil abortion takes place in the tassel florets, and stamen arrest is affected in ear florets to give rise to the monoecious nature of maize. Gibberellin (GA) deficiency results in increased tillering, a dwarfed plant syndrome, and the retention of anthers in the ear florets of maize. The silkless1 mutant results in suppression of silks in the ear. We demonstrate in this study that jasmonic acid (JA) and GA act independently and show additive phenotypes resulting in androecious dwarf1;silkless1 double mutant plants. The persistence of pistils in the tassel can be induced by multiple mechanisms, including JA deficiency, GA excess, genetic control of floral determinacy, and organ identity. The silkless1 mutant can suppress both silks in the ear and the silks in the tassel of JA‐deficient and AP2 transcription factor tasselseed mutants. We previously demonstrated that GA production was required for brassinosteroid (BR) deficiency to affect persistence of pistils in the tassel. We find that BR deficiency affects pistil persistence by an independent mechanism from the silkless1 mutant and JA pathway. The silkless1 mutant did not prevent the formation of pistils in the tassel by nana plant2 in double mutants. In addition, we demonstrate that there is more to the silkless1 mutant than just a suppression of pistil growth. We document novel phenotypes of silkless1 mutants including weakly penetrant ear fasciation and anther persistence in the ear florets. Thus, the JA/AP2 mechanism of pistil retention in the tassel and silk growth in the ear are similarly sensitive to loss of the SILKLESS1 protein, while the BR/GA mechanism is not. [ABSTRACT FROM AUTHOR]

This article discusses the search for tendril-less cucumbers, which would eliminate the need for labor-intensive removal of tendrils and branches in commercial cucumber production. Researchers have identified a gene called CsTL that is responsible for tendril initiation in cucumbers. They also found that CsTL physically interacts with another gene called CsTEN, which promotes tendril development. This study reveals that cucumber has distinct pathways for regulating branching and tendril formation, and targeting CsTL and CsREV genes could potentially improve cucumber architecture and increase yields. [Extracted from the article]

This document, titled "From the archives: Targeting proteins to plasmodesmata, germination in the desert, and functional diversity of KNOX proteins," provides a summary of three research articles published in the Plant Cell journal. The first article discusses the targeting of proteins to plasmodesmata, which are channels connecting plant cells. The second article explores the unique germination process of date palm seeds in the desert, where the embryo is protected and development is paused until it is safe to emerge. The third article focuses on the functional diversity of KNOX proteins, which are transcription factors involved in plant development. These articles provide valuable insights into various aspects of plant biology and offer potential applications in agriculture. [Extracted from the article]

This article discusses a study conducted on the model legume species Medicago truncatula to understand how plants cope with sudden drops in temperature. The researchers focused on a transcription factor called MtNAC80, which is highly expressed in response to cold stress. They discovered that MtNAC80 undergoes reversible protein lipidation, specifically S-acylation, which allows it to associate with cell membranes. The study also identified the proteins responsible for the acylation and de-acylation of MtNAC80, as well as its target genes involved in reducing oxidative stress. Understanding these mechanisms could have implications for improving crop tolerance to cold snaps. [Extracted from the article]

Summary: Wing polyphenism is found in a variety of insects and offers an attractive model system for studying the evolutionary significance of dispersal. The Forkhead box O (FoxO) transcription factor (TF) acts as a wing-morph switch that directs wing buds developing into long-winged (LW) or short-winged morphs in wing-dimorphic planthoppers, yet the regulatory mechanism of the FoxO module remains elusive. Here, we identified the zinc finger TF rotund as a potential wing-morph regulator via transcriptomic analysis and phenotypic screening in the brown plathopper, Nilaparvata lugens. RNA interference-mediated knockdown of rotund antagonized the LW development derived from in the context of FoxO depletion or the activation of the insulin/insulin-like growth factor signaling cascade, reversing long wings into intermediate wings. In vitro binding assays indicated that rotund physically binds to FoxO to form the FoxO combinatorial code. These findings broaden our understanding of the complexity of transcriptional regulation governing wing polyphenism in insects.

Developmental coordination disorder (DCD) is a developmental disorder characterized by impaired motor coordination, often co-occurring with attention deficit disorder, autism spectrum disorders, and other psychological and behavioural conditions. The aetiology of DCD is believed to involve brain changes and environmental factors, with genetics also playing a role in its pathogenesis. Recent research has identified several candidate genes and genetic factors associated with motor impairment, including deletions, copy number variations, single nucleotide polymorphisms, and epigenetic modifications. This review provides an overview of the current knowledge in genetic research on DCD, highlighting the importance of continued research into the underlying genetic mechanisms. While evidence suggests a genetic contribution to DCD, the evidence is still in its early stages, and much of the current evidence is based on studies of co-occurring conditions. Further research to better understand the genetic basis of DCD could have important implications for diagnosis, treatment, and our understanding of the condition's aetiology. [ABSTRACT FROM AUTHOR]

Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana , the SAM produces small orbicular leaves in the juvenile phase, but gives rise to large elliptical leaves in the adult phase. Previous studies have established that a developmental decline of microRNA156 (miR156) is necessary and sufficient to trigger this leaf shape switch, although the underlying mechanism is poorly understood. Here we show that the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors with age promotes cell growth anisotropy in the abaxial epidermis at the base of the leaf blade, evident by the formation of elongated giant cells. Time-lapse imaging and developmental genetics further revealed that the establishment of adult leaf shape is tightly associated with the longitudinal cell expansion of giant cells, accompanied by a prolonged cell proliferation phase in their vicinity. Our results thus provide a plausible cellular mechanism for heteroblasty in Arabidopsis, and contribute to our understanding of anisotropic growth in plants. [ABSTRACT FROM AUTHOR]

Despite morphological similarity of lemmas and paleas in rice, lemma gene expression is similar to that of glumes, while palea gene expression is similar to that of lodicules and reproductive organs (Zong et al., [17]). Keywords: developmental genetics; evolution of floral development; floral homology; monocots; Poaceae; sepals; tepals EN developmental genetics evolution of floral development floral homology monocots Poaceae sepals tepals 1 4 4 05/03/23 20230401 NES 230401 Plant form is astonishingly diverse. If, for instance, ChINs for bract and sepal identity were defined, they could be compared to genes involved in lemma development to determine whether lemmas rely on the leaf ChIN, sepal ChIN, or a combination of both. [Extracted from the article]

Summary: Cell type-specific expression of the developmental gene is conferred by distinct enhancer elements. Current knowledge about mechanisms in Nkx2-5 transcriptional regulation and its specific roles in multistage heart morphogenesis is limited. We comprehensively interrogate enhancers U1 and U2 in controlling Nkx2-5 transcription during heart development. Serial genomic deletions in mice reveal U1 and U2 function redundantly to confer Nkx2-5 expression at early stages, but U2 instead of U1 supports its expression at later stages. Combined deletions markedly reduce Nkx2-5 dosage as early as E7.5, despite being largely reinstated two days later, displaying heart malformations with precocious differentiation of cardiac progenitors. Cutting-edge low-input chromatin immunoprecipitation sequencing (ChIP-seq) confirmed that not only genomic NKX2-5 occupancy but also its regulated enhancer landscape is mostly disturbed in the double-deletion mouse hearts. Together, we propose a model that the temporal and partially compensatory regulatory function of two enhancers dictates a transcription factor (TF)’s dosage and specificity during development.

The article focuses on the development and application of synthetic gene drives in plants, a technology previously successful in animals but challenging for plant species. Topics include the engineering of Arabidopsis thaliana with genetic payloads inherited by nearly all offspring, potentially transforming weed management by targeting herbicide-resistant species.

The article discusses the interplay between brassinosteroid signaling and the phosphate starvation response in plants. Phosphorus is an essential nutrient for plants, but it is often depleted in intensively farmed soil. Researchers are interested in enhancing plants' innate mechanisms to cope with phosphorus deficiency. The study shows that overactive brassinosteroid signaling amplifies the phosphate starvation response in rice plants, while the central inhibitor of brassinosteroid signaling downregulates the response. The study also identifies a phosphorylation site on a key regulator of the response, which could be a potential target for gene editing to maximize phosphorus uptake in crops. [Extracted from the article]

Summary: Knowledge of RNA molecules regulating testicular development and spermatogenesis in bulls is essential for elite bull selection and an ideal breeding program. Herein, we performed direct RNA sequencing (DRS) to explore the functional characterization of RNA molecules produced in the testicles of 9 healthy Simmental bulls at three testicular development stages (prepuberty, puberty, and postpuberty). We identified 5,043 differentially expressed genes associated with testicular weight. These genes exhibited more alternative splicing at sexual maturity, particularly alternative 3’ (A3) and 5’ (A5) splice sites usage and exon skipping (SE). The expression of hub genes in testicular developmental stages was also affected by both m6A and m5C RNA modifications. We found m5C-mediated splicing events significantly (p

Summary: Various parasitic flatworms infect vertebrates for sexual reproduction, often causing devastating diseases in their hosts. Consequently, flatworms are of great socioeconomic and biomedical importance. Although the cessation of parasitic flatworm sexual reproduction is a major target of anti-parasitic drug design, little is known regarding bioactive compounds controlling flatworm sexual maturation. Using the planarian Dugesia ryukyuensis, we observed that sex-inducing substances found in planarians are also widespread in parasitic flatworms, such as monogeneans and flukes (but not in tapeworms). Reverse-phase HPLC analysis revealed the sex-inducing substance(s) eluting around the tryptophan retention time in the fluke Calicophoron calicophorum, consistent with previous studies on the planarian Bipalium nobile, suggesting that the substance(s) is likely conserved among flatworms. Moreover, six of the 18 ovary-inducing substances identified via transcriptome and metabolome analyses are involved in purine metabolism. Our findings provide a basis for understanding and modifying the life cycles of various parasitic flatworms.

Summary: Clustered protocadherin is a family of cell-surface recognition molecules implicated in neuronal connectivity that has a diverse isoform repertoire and homophilic binding specificity. Mice have 58 isoforms, encoded by Pcdhα, β, and γ gene clusters, and mutant mice lacking all isoforms died after birth, displaying massive neuronal apoptosis and synapse loss. The current hypothesis is that the three specific γC-type isoforms, especially γC4, are essential for the phenotype, raising the question about the necessity of isoform diversity. We generated TC mutant mice that expressed the three γC-type isoforms but lacked all the other 55 isoforms. The TC mutants died immediately after birth, showing massive neuronal death, and γC3 or γC4 expression did not prevent apoptosis. Restoring the α- and β-clusters with the three γC alleles rescued the phenotype, suggesting that along with the three γC-type isoforms, other isoforms are also required for the survival of neurons and individual mice.

Leaves, encountered in the majority of modern tracheophytes, evolved multiple times independently in several lineages. We define leaves as lateral appendages that share a common set of characters: vascularization, determinacy, regular arrangement, bilateral symmetry and, in most cases, adaxial-abaxial (dorsiventral) polarity. In this review we integrate data from developmental genetics and the fossil record to understand how the molecular and cellular mechanisms of leaf development evolved. We show that lycopsid leaves likely evolved once, and earlier, than euphyllophyte leaves, and that euphyllophyte leaves all evolved from lateral branching systems that were produced at regular intervals around the stem. We also show that the mosaic pattern of distribution and tempo of evolution of leaf-defining features (such as bilateral symmetry and dorsiventral polarity) among the different lineages suggests that these features evolved independently. Overall, at the level of the entire tracheophyte clade, integration of developmental, regulatory and fossil data reveals three overarching patterns: (1) the different leaf characters evolved independently throughout tracheophyte phylogeny and their regulatory pathways were assembled independently, only to become tightly integrated with each other later in the evolution of different lineages; (2) bilateral symmetry is a distinct and evolutionarily independent leaf feature from dorsiventral polarity; (3) regular arrangement is the most plesiomorphic and earliest-evolving leaf-defining feature across tracheophytes. • Several leaf-defining characters arose independently throughout evolution. • Leaves evolved multiple times in euphyllophytes and likely once in lycopsids. • Lycopsids and euphyllophytes have different molecular mechanisms of leaf development. • Leaves evolved in euphyllophyte lineages with a regular taxis of leaf precursors. • Seed plants evolved leaves once, but use different cellular mechanisms of leaf blade formation. [ABSTRACT FROM AUTHOR]