Spatially unique Shh-Fgf8 distribution in regenerating limb guarantees consistent limb morphogenesis in different limb sizes and contributes to axolotl specific digit patterning.

Limb regeneration in Ambystoma mexicanum occurs in various sizes of fields and can recreate consistent limb morphology. It was not known what mechanism supports such stable limb morphogenesis regardless of size. Limb regeneration in urodele amphibians has been basically considered to recapitulate the limb developmental processes. Many molecules in the limb developmental processes are conserved with other tetrapods. SHH and FGF8 play important roles in the morphogenesis of limbs among them. Focusing on these two factors, we investigated the detailed expression pattern of Shh and Fgf8 in the various sizes of blastema in axolotl limb regeneration. Fgf8 is expressed in the anterior side of a blastema and Shh is expressed in the posterior side. These are maintained in a mutually dependent manner. We also clarified that the size of Shh and Fgf8 expression domains were scaled as the size of the blastemas increased. However, it was found that the secretion and working range of SHH were kept constant. We also found that the consistent SHH secretion range contributed to promoting cell proliferation and the first digital cartilage differentiation near the Shh expression domain. This would be a reasonable system to guarantees constant limb morphogenesis regardless of the blastema size. We also showed that the Shh-Fgf8 expression domain was shifted posteriorly as the digital differentiation progressed. Consistently, slowing the timing of blocking Shh signaling resulted in morphological defects that could be observed in only posterior digits. The revealed posteriorly shifting Shh-Fgf8 domain might explain urodele specific digit formation, in which digits are added posteriorly.

The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing

N6-methyladenosine (m6A) and its regulatory components play critical roles in various developmental processes in mammals(1-5). However, the landscape and function of m6A in the maternal-to-zygotic transition (MZT) remain unclear due to limited materials. Here, by developing an ultralow-input MeRIP-seq method, we revealed the dynamics of the m6A RNA methylome during the MZT process in mice. We found that more than 1/3 maternal decay and 2/3 zygotic mRNAs were modified by m6A. Moreover, m6As are highly enriched in the RNA of transposable elements MTA and MERVL, which are highly expressed in oocytes and 2-cell embryos, respectively. Notably, maternal depletion of Kiaa1429, a component of the m6A methyltransferase complex, leads to a reduced abundance of m6A-marked maternal RNAs, including both genes and MTA, in GV oocytes, indicating m6A-dependent regulation of RNA stability in oocytes. Interestingly, when the writers were depleted, some m6A-marked 2-cell specific RNAs, including Zscan4 and MERVL, appeared normal at the 2-cell stage but failed to be decayed at later stages, suggesting that m6A regulates the clearance of these transcripts. Together, our study uncovered that m6As function in context-specific manners during MZT, which ensures the transcriptome stability of oocytes and regulates the stage specificity of zygotic transcripts after fertilization.

Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress responses, and aging

The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode Caenorhabditis elegans have shown that the Axin homolog PRY-1 plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Knocking down eight of the genes (spp-1, clsp-1, ard-1, rpn-7, cpz-1, his-7, cdk-1, and rnr-1) via RNA interference efficiently suppressed the multivulva phenotype of pry-1 mutants. In all cases, the ectopic induction of P3.p vulval precursor cell was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that in addition to their role in vulval development, these genes participate in one or more pry-1-mediated biological events. Whereas four of them (cpz-1, his-7, cdk-1, and rnr-1) function in both stress response and aging, two (spp-1 and ard-1) are specific to stress response. Altogether, these findings demonstrate the important role of pry-1 suppressors in regulating developmental and post-developmental processes in C. elegans. Given that the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin in metazoans.

Growth rate as a modulator of tooth patterning during adaptive radiations

The discovery of mechanistic rules that underlie phenotypic variation has been a longstanding goal of evolutionary biology. Developmental processes offer a potential source for such rules because they translate genomic variation into the population-scale phenotypic variation. However, our understanding of developmental rules is based on a handful of well-established model species which hindered identifying rules and investigating their evolution. Recent methodological advances, such as µCT scanning on soft tissues, two-photon imaging and modelling have facilitated the study of how developmental processes shape phenotypic variation in diverse, non-traditional model species. Here, we use the outstanding dental diversity of bats to investigate how the interplay between developmental processes can explain the morphological diversity in teeth. We find that the inhibitory cascade model, which has been used to predict the proportions of teeth and other serial organs, poorly predicts the variation in tooth number and size in bats. Instead, by tinkering with reaction/diffusion processes, we identify jaw growth as a key driver of the phenotypic evolution of tooth number and size critical to the different diets. By studying developmental processes in the context of adaptive evolution, we are able to discover a new developmental rule that explain and predict interspecific variation in serial organ number and proportion.

Engaging Parents in the Development and Testing of a Website to Support Social-Communication and Play Development for Preschoolers with Autism Spectrum Disorder

Preschoolers with autism spectrum disorder (ASD) present with social-communication and play challenges and would benefit from interventions targeting these skills. One way to ensure this is by engaging parents in technological supports to learn about an intervention and increase home-school collaboration. Thus, a website could potentially address both needs. This study describes the initial developmental processes of one such website. Specifically, we describe how engaging parents as stakeholders in the website development enhanced its future usability and feasibility. Data were collected through focus groups, interviews, and surveys to obtain parent feedback about website usability and applicability and about the intervention. Survey data were descriptively analyzed. Focus group and interview data were analyzed using systematic qualitative analysis. Parents perceived the website to be useful in helping them target social-communication and play with their preschoolers with ASD and highlighted specific aspects of the website and intervention they perceived as effective. Child outcomes and parent fidelity to the intervention supported these perceived developmental gains. Findings suggest that engaging parents in developmental processes may help ensure usability and applicability of resources and interventions. Furthermore, findings support the use of technology to help parents learn to use an intervention with their preschoolers with ASD. Implications for research and practice are discussed.

Universal DNA Methylation Age Across Mammalian Tissues

Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, it is difficult to ignore the likelihood that a defined and shared mechanism instead, underlies the aging process. To address this, we generated over 10,000 methylation arrays, each profiling up to 37,000 cytosines in highly-conserved stretches of DNA, from over 59 tissue-types derived from 128 mammalian species. From these, we identified and characterized specific cytosines, whose methylation levels change with age across mammalian species. Genes associated with these cytosines are greatly enriched in mammalian developmental processes and implicated in age-associated diseases. From the methylation profiles of these age-related cytosines, we successfully constructed three highly accurate universal mammalian clocks for eutherians, and one universal clock for marsupials. The universal clocks for eutherians are similarly accurate for estimating ages (r>0.96) of any mammalian species and tissue with a single mathematical formula. Collectively, these new observations support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new and compelling evidence.

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

Independent Acquisition of Carnassial Teeth in Fishes and Mammals

Vertebrates evolved tooth replacement over 400 million years ago. Over 200 million years later, the combination of vertical tooth replacement with thecodont implantation (teeth in bone sockets) has been considered a key morphological innovation in mammal evolution. We discovered that an extinct fish taxon, Serrasalmimus secans, that shows this same innovation in a lineage (Serrasalmimidae) that survived the end Cretaceous mass extinction. Carnassial teeth are known in both mammals and pycnodont fish, but these teeth do not share the same tissues nor developmental processes. Therefore, a serrasalmimid pycnodont fish independently acquired mammal-like tooth replacement and implantation, thus showing that fishes and mammals evolved convergent carnassial dental morphologies at about the same time, around 60 Ma, in separate ecosystems.

Dentine matrix metalloproteinases as potential mediators of dentine regeneration

Matrix metalloproteinases (MMPs) have been implicated not only in the regulation of developmental processes but also in the release of biologically active molecules and in the modulation of repair during tertiary dentine formation. Although efforts to preserve dentine have focused on inhibiting the activity of these proteases, their function is much more complex and necessary for dentine repair than expected. The present review explores the role of MMPs as bioactive components of the dentine matrix involved in dentine formation, repair and regeneration. Special consideration is given to the mechanical properties of dentine, including those of reactionary and reparative dentine, and the known roles of MMPs in their formation. MMPs are critical components of the dentine matrix and should be considered as important candidates in dentine regeneration.

Mutations in DISC1 alter IP3R and Voltage-Gated Ca2+ Channel Functioning: Implications for Major Mental Illness

Disrupted in Schizophrenia 1 (DISC1) participates in a wide variety of developmental processes of central neurons. It also serves critical roles that underlie cognitive functioning in adult central neurons. Here we summarize DISC1’s general properties and discuss its use as a model system for understanding major mental illnesses. We then discuss the cellular actions of DISC1 that involve or regulate Ca2+ signaling in adult central neurons. In particular, we focus on the tethering role DISC1 plays in transporting RNA particles containing Ca2+ channel subunit RNAs, including IP3R1, CACNA1C and CACNA2D1, and in transporting mitochondria into dendritic and axonal processes. We also review DISC1’s role in modulating IP3R1 activity within mitochondria-associated ER membrane. Finally, we discuss DISC1-GSK3b signaling that regulates functional expression at voltage-gated Ca2+ channel at central synapses. In each case, DISC1 regulates the movement of molecules that impact Ca2+ signaling in neurons.