Nitric oxide pathway in lower metazoans

The presence of nitric oxide (NO) pathway has been well demonstrated in the main invertebrate groups, showing parallel findings on the role of NO in vertebrates and invertebrates. Noteworthy is the example of the role played by the nitrergic pathway in the sensorial functions, mainly in olfactory-like systems. On the other hand, the emerging molecular information about NOSs from lower metazoans (Porifera, cnidarians up to higher invertebrates) suggests that NO pathways might represent examples of a parallel evolution of the NOS prototypes in different animal lineages. Nevertheless, increasing evidence suggests that NO is one of the earliest and most widespread signaling molecules in living organisms.Here, we attempt to provide a survey of current knowledge of the synthesis and possible roles of NO and the related signaling pathway in lower metazoans (i.e., Porifera and Cnidaria), two phyla forming a crucial bridge spanning the evolutionary gap between the protozoans and higher metazoans. From the literature data here reported, it emerges that future research on the biological roles of NO in basal metazoans is likely to be very important for understanding the evolution of signaling systems.     

Neurogenetics: advancing the "next-generation" of brain research

There can be little doubt that genetics has transformed our understanding of mechanisms mediating brain disorders. The last two decades have brought tremendous progress in terms of accurate molecular diagnoses and knowledge of the genes and pathways that are involved in a large number of neurological and psychiatric disorders. Likewise, new methods and analytical approaches, including genome array studies and "next-generation" sequencing technologies, are bringing us deeper insights into the subtle complexities of the genetic architecture that determines our risks for these disorders. As we now seek to translate these discoveries back to clinical applications, a major challenge for the field will be in bridging the gap between genes and biology. In this Overview of Neuron's special review issue on neurogenetics, we reflect on progress made over the last two decades and highlight the challenges as well as the exciting opportunities for the future.     

Variations on the topic of the "histone code"

Histones are the fundamental structural proteins intimately associated with eukaryotic DNA to form a highly ordered and condensed nucleoproteic complex termed chromatin. They are the targets of various posttranslational modifications including acetylation, methylation, phosphorylation and ubiquitination that modulate the structure/function of chromatin. The combinatorial nature of histone modifications is hypothesized to define a "histone code" that considerably extends the information potential of the genetic code, giving rise to epigenetic information. Moreover, most core histones consist of several nonallelic variants that can mark specific loci and could play an important role in establishment and maintenance of epigenetic memory. Here we will briefly present our current knowledge about histone posttranslational modifications and their implications in the regulation of epigenetic information. We will next describe core histone variants, insisting on their mode of incorporation into chromatin to discuss their epigenetic function and inheritance.     

An epithelial tissue in Dictyostelium challenges the traditional origin of metazoan multicellularity

We hypothesize that aspects of animal multicellularity originated before the divergence of metazoans from fungi and social amoebae. Polarized epithelial tissues are a defining feature of metazoans and contribute to the diversity of animal body plans. The recent finding of a polarized epithelium in the non-metazoan social amoeba Dictyostelium discoideum demonstrates that epithelial tissue is not a unique feature of metazoans, and challenges the traditional paradigm that multicellularity evolved independently in social amoebae and metazoans. An alternative view, presented here, is that the common ancestor of social amoebae, fungi, and animals spent a portion of its life cycle in a multicellular state and possessed molecular machinery necessary for forming an epithelial tissue. Some descendants of this ancestor retained multicellularity, while others reverted to unicellularity. This hypothesis makes testable predictions regarding tissue organization in close relatives of metazoans and provides a novel conceptual framework for studies of early animal evolution. Editor's suggested further reading in BioEssays Searching for Eve: Basal metazoans and the evolution of multicellular complexity Abstract.     

Evolutionary origin of synapses and neurons – Bridging the gap

The evolutionary origin of synapses and neurons is an enigmatic subject that inspires much debate. Non‐bilaterian metazoans, both with and without neurons and their closest relatives already contain many components of the molecular toolkits for synapse functions. The origin of these components and their assembly into ancient synaptic signaling machineries are particularly important in light of recent findings on the phylogeny of non‐bilaterian metazoans. The evolution of synapses and neurons are often discussed only from a metazoan perspective leaving a considerable gap in our understanding. By taking an integrative approach we highlight the need to consider different, but extremely relevant phyla and to include the closest unicellular relatives of metazoans, the ichthyosporeans, filastereans and choanoflagellates, to fully understand the evolutionary origin of synapses and neurons. This approach allows for a detailed understanding of when and how the first pre‐ and postsynaptic signaling machineries evolved.     

CHARACIOCHLORIS AND CHARACIOSIPHON FORM A SISTER GROUP TO THE "DUNALIELLA" LINEAGE

This presentation will review the 1976 discovery of the enzyme complex in cellulose biosynthesis in Oocystis apiculata. A linear terminal complex (TC) was found to be associated with a microfibril, and from other freeze fracture applications, TCs have been found in many different algal genera. In fact, the algae have the most diverse and complex TCs among all organisms. TC diversity in terms of the evolution of cellulose biogenesis will be discussed. Combining the latest information from biochemistry and molecular genetics, the multiplicity of cellulose biogenesis will be reviewed. Cellulose molecular weight, crystalline structure, and mode of glycosylation for polymer formation all indicate that cellulose biogenesis is an extremely complex process. Major questions still remain, and the enzymes for cellulose biosynthesis have yet to be crystallized and their structure elucidated; however, the wealth of new information on cellulose structure and biosynthesis from algae to vascular plants, including bacteria and tunicates, all point to a very exciting and useful area of research. The algae have played key roles in our understanding of nature's most abundant macromolecule.     

Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages

Understanding the nature and timing of metazoan origins is oneof the most important, yet elusive, questions in evolutionarybiology. Fossil data provide the most tangible evidence forthe origin of early animal lineages, although additional evidencefrom molecular phylogenetics, molecular clock studies, and developmenthas contributed to our current understanding. We review severallines of evidence to explore the nature and timing of earlymetazoan evolution and discuss how these data, when consideredtogether, provide a more cohesive picture of the origin of animaldiversity. We discuss how trace fossils and biomarkers providecompelling evidence for the origins of Bilateria and siliceoussponges. Using a molecular phylogenetic framework for metazoans,we discuss how fossils can be used to date the origin of clades.We use these fossil dates to perform a relaxed molecular clockanalysis for estimating dates of nodes when no fossils are available.We also discuss current data from developmental biology thatsuggest that early metazoans possessed a sophisticated moleculartoolkit for building complex body plans. We conclude that thebest evidence for the origin of major metazoan lineages liesin the careful interpretation of the fossil record and thatthese data, when considered with phylogenetic and developmentalevidence, support the notion that the Cambrian radiation isa real phenomenon that marks a critically important time inthe history of life.     

Cellular and molecular processes leading to embryo formation in sponges: evidences for high conservation of processes throughout animal evolution

The emergence of multicellularity is regarded as one of the major evolutionary events of life. This transition unicellularity/pluricellularity was acquired independently several times (King 2004). The acquisition of multicellularity implies the emergence of cellular cohesion and means of communication, as well as molecular mechanisms enabling the control of morphogenesis and body plan patterning. Some of these molecular tools seem to have predated the acquisition of multicellularity while others are regarded as the acquisition of specific lineages. Morphogenesis consists in the spatial migration of cells or cell layers during embryonic development, metamorphosis, asexual reproduction, growth, and regeneration, resulting in the formation and patterning of a body. In this paper, our aim is to review what is currently known concerning basal metazoans—sponges’ morphogenesis from the tissular, cellular, and molecular points of view—and what remains to elucidate. Our review attempts to show that morphogenetic processes found in sponges are as diverse and complex as those found in other animals. In true epithelial sponges (Homoscleromorpha), as well as in others, we find similar cell/layer movements, cellular shape changes involved in major morphogenetic processes such as embryogenesis or larval metamorphosis. Thus, sponges can provide information enabling us to better understand early animal evolution at the molecular level but also at the cell/cell layer level. Indeed, comparison of molecular tools will only be of value if accompanied by functional data and expression studies during morphogenetic processes.     

Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies.

The unprecedented advances in molecular biology during the last two decades have resulted in a dramatic increase in knowledge about gene structure and function, an immense database of genetic sequence information, and an impressive set of efficient new technologies for monitoring genetic sequences, genetic variation, and global functional gene expression. These advances have led to a new sub-discipline of toxicology: "toxicogenomics". We define toxicogenomics as "the study of the relationship between the structure and activity of the genome (the cellular complement of genes) and the adverse biological effects of exogenous agents". This broad definition encompasses most of the variations in the current usage of this term, and in its broadest sense includes studies of the cellular products controlled by the genome (messenger RNAs, proteins, metabolites, etc.). The new "global" methods of measuring families of cellular molecules, such as RNA, proteins, and intermediary metabolites have been termed "-omic" technologies, based on their ability to characterize all, or most, members of a family of molecules in a single analysis. With these new tools, we can now obtain complete assessments of the functional activity of biochemical pathways, and of the structural genetic (sequence) differences among individuals and species, that were previously unattainable. These powerful new methods of high-throughput and multi-endpoint analysis include gene expression arrays that will soon permit the simultaneous measurement of the expression of all human genes on a single "chip". Likewise, there are powerful new methods for protein analysis (proteomics: the study of the complement of proteins in the cell) and for analysis of cellular small molecules (metabonomics: the study of the cellular metabolites formed and degraded under genetic control). This will likely be extended in the near future to other important classes of biomolecules such as lipids, carbohydrates, etc. These assays provide a general capability for global assessment of many classes of cellular molecules, providing new approaches to assessing functional cellular alterations. These new methods have already facilitated significant advances in our understanding of the molecular responses to cell and tissue damage, and of perturbations in functional cellular systems.As a result of this rapidly changing scientific environment, regulatory and industrial toxicology practice is poised to undergo dramatic change during the next decade. These advances present exciting opportunities for improved methods of identifying and evaluating potential human and environmental toxicants, and of monitoring the effects of exposures to these toxicants. These advances also present distinct challenges. For example, the significance of specific changes and the performance characteristics of new methods must be fully understood to avoid misinterpretation of data that could lead to inappropriate conclusions about the toxicity of a chemical or a mechanism of action. We discuss the likely impact of these advances on the fields of general and genetic toxicology, and risk assessment. We anticipate that these new technologies will (1) lead to new families of biomarkers that permit characterization and efficient monitoring of cellular perturbations, (2) provide an increased understanding of the influence of genetic variation on toxicological outcomes, and (3) allow definition of environmental causes of genetic alterations and their relationship to human disease. The broad application of these new approaches will likely erase the current distinctions among the fields of toxicology, pathology, genetic toxicology, and molecular genetics. Instead, a new integrated approach will likely emerge that involves a comprehensive understanding of genetic control of cellular functions, and of cellular responses to alterations in normal molecular structure and function.     

Evolutionary crossroads in developmental biology: the spider Parasteatoda tepidariorum

Spiders belong to the chelicerates, which is an arthropod group that branches basally from myriapods, crustaceans and insects. Spiders are thus useful models with which to investigate whether aspects of development are ancestral or derived with respect to the arthropod common ancestor. Moreover, they serve as an important reference point for comparison with the development of other metazoans. Therefore, studies of spider development have made a major contribution to advancing our understanding of the evolution of development. Much of this knowledge has come from studies of the common house spider, Parasteatoda tepidariorum. Here, we describe how the growing number of experimental tools and resources available to study Parasteatoda development have provided novel insights into the evolution of developmental regulation and have furthered our understanding of metazoan body plan evolution.     

Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes

Reciprocal crosses between species can yield hybrids with different viabilities. The high frequency of this asymmetric hybrid viability ("Darwin's corollary") places it alongside Haldane's rule and the "large-X effect" as a general feature of postmating reproductive isolation. Recent theory suggests that reciprocal cross asymmetries can arise from stochastic substitutions in uniparentally inherited loci such as mitochondrial genomes, although large systematic differences in mitochondrial substitution rates can also contribute to asymmetries. Although the magnitude of asymmetry will be relatively insensitive to unequal rates of mitochondrial evolution in diverging species, we show here that rate asymmetries can have a large effect on the direction of viability asymmetries. In reciprocal crosses between species, the maternal parent with faster mitochondrial evolution will tend to produce less viable F(1) hybrids owing to an increased probability of mito-nuclear incompatibilities. We test this prediction using data on reciprocal hybrid viability and molecular evolution rates from a clade of freshwater fishes, Centrarchidae. As predicted, species with accelerated mitochondrial evolution tend to be the worse maternal parent for F(1) hybrids, providing the first comparative evidence for a systematic basis to Darwin's corollary. This result is consistent with the hypothesis that mito-nuclear incompatibilities can play an important role in reproductive isolation. Such asymmetrical reproductive isolation may help explain the asymmetrical mitochondrial introgression observed between many hybridizing species. However, as with any comparative study, we cannot rule out the possibility that our results arise from a mutual correlation with a third variable such as body size.     

Choanoflagellates, choanocytes, and animal multicellularity

Abstract. It is widely accepted that multicellular animals (metazoans) constitute a monophyletic unit, deriving from ancestral choanoflagellate‐like protists that gave rise to simple choanocyte‐bearing metazoans. However, a re‐assessment of molecular and histological evidence on choanoflagellates, sponge choanocytes, and other metazoan cells reveals that the status of choanocytes as a fundamental cell type in metazoan evolution is unrealistic. Rather, choanocytes are specialized cells that develop from non‐collared ciliated cells during sponge embryogenesis. Although choanocytes of adult sponges have no obvious homologue among metazoans, larval cells transdifferentiating into choanocytes at metamorphosis do have such homologues. The evidence reviewed here also indicates that sponge larvae are architecturally closer than adult sponges to the remaining metazoans. This may mean that the basic multicellular organismal architecture from which diploblasts evolved, that is, the putative planktonic archimetazoan, was more similar to a modern poriferan larva lacking choanocytes than to an adult sponge. Alternatively, it may mean that other metazoans evolved from a neotenous larva of ancient sponges. Indeed, the Porifera possess some features of intriguing evolutionary significance: (1) widespread occurrence of internal fertilization and a notable diversity of gastrulation modes, (2) dispersal through architecturally complex lecithotrophic larvae, in which an ephemeral archenteron (in dispherula larvae) and multiciliated and syncytial cells (in trichimella larvae) occur, (3) acquisition of direct development by some groups, and (4) replacement of choanocyte‐based filter‐feeding by carnivory in some sponges. Together, these features strongly suggest that the Porifera may have a longer and more complicated evolutionary history than traditionally assumed, and also that the simple anatomy of modern adult sponges may have resulted from a secondary simplification. This makes the idea of a neotenous evolution less likely than that of a larva‐like choanocyte‐lacking archimetazoan. From this perspective, the view that choanoflagellates may be simplified sponge‐derived metazoans, rather than protists, emerges as a viable alternative hypothesis. This idea neither conflicts with the available evidence nor can be disproved by it, and must be specifically re‐examined by further approaches combining morphological and molecular information. Interestingly, several microbial lin°Cages lacking choanocyte‐like morphology, such as Corallochytrea, Cristidiscoidea, Ministeriida, and Mesomycetozoea, have recently been placed at the boundary between fungi and animals, becoming a promising source of information in addition to the choanoflagellates in the search for the unicellular origin of animal multicellularity.     

Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular‐based research in ecology and evolution

Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next‐generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search.     

Shaping time: chromatin structure and the DNA replication programme

DNA is replicated according to a precise and reproducible temporal pattern. The S-phase programme has previously been analyzed in metazoan and yeast cells using different methods: cytological chromosome banding in human cells and DNA isotopic-labeling techniques in yeast. Microarray-based approaches for the analysis of the replication programme and chromatin structure are bringing us closer to a molecular understanding of the factors that determine replication time. In this article, I assess the impact of recent investigations and compare our knowledge of DNA replication-timing controls in yeast with those of metazoans.     

Inflorescence diversification in the "finger millet clade" (Chloridoideae, Poaceae): a comparison of molecular phylogeny and developmental morphology

Within the Poaceae, inflorescence diversification and its bearing on phylogeny and evolution are exceedingly complex. We used phylogenetic information of the "finger millet clade," a group of grasses with digitate inflorescences, to study the inflorescence diversification. This clade appears monophyletic in the morphological and molecular phylogenetic analyses. Three well-supported clades are shown in our cpDNA-derived phylogeny, with clades I and III consisting of species of Chloris and Microchloa, respectively, and clade II including species of Cynodon, Dactyloctenium, and Eleusine. Variation appears at different times throughout development. Changes involving primordium number and arrangement occur very early, changes involving duration of primordium activity occur much later. Characters derived from the comparison of developmental sequences were optimized onto the most parsimonious tree. The developmental characters were congruent with the molecular phylogeny. Two developmental characters may not be homologous in the Chloris subclade and the Cynodon subclade.     

Drosophila melanogaster: a model for the study of DNA damage checkpoint response

The cells of metazoans respond to DNA damage by either arresting their cell cycle in order to repair the DNA, or by undergoing apoptosis. This response is highly conserved across species, and many of the genes involved in this DNA damage response have been shown to be inactivated in human cancers. This suggests the importance of DNA damage response with regard to the prevention of cancer. The DNA damage checkpoint responses vary greatly depending on the developmental context, cell type, gene expression profile, and the degree and nature of the DNA lesions. More valuable information can be obtained from studies utilizing whole organisms in which the molecular basis of development has been well established, such as Drosophila. Since the discovery of the Drosophila p53 orthologue, various aspects of DNA damage responses have been studied in Drosophila. In this review, I will summarize the current knowledge on the DNA damage checkpoint response in Drosophila. With the ease of genetic, cellular, and cytological approaches, Drosophila will become an increasingly valuable model organism for the study of mechanisms inherent to cancer formation associated with defects in the DNA damage pathway.     

The evolution of metazoan axial properties

Renewed interest in the developmental basis of organismal complexity, and the emergence of new molecular tools, is improving our ability to study the evolution of metazoan body plans. The most substantial changes in body-plan organization occurred early in metazoan evolution; new model systems for studying basal metazoans are now being developed, and total-genome-sequencing initiatives are underway for at least three of the four most important taxa. The elucidation of how the gene networks that are involved in axial organization, germ-layer formation and cell differentiation are used differently during development is generating a more detailed understanding of the events that have led to the current diversity of multicellular life.     

Getting a head start: the importance of personal genetics education in high schools

With advances in sequencing technology, widespread and affordable genome sequencing will soon be a reality. However, studies suggest that "genetic literacy" of the general public is inadequate to prepare our society for this unprecedented access to our genetic information. As the current generation of high school students will come of age in an era when personal genetic information is increasingly utilized in health care, it is of vital importance to ensure these students understand the genetic concepts necessary to make informed medical decisions. These concepts include not only basic scientific knowledge, but also considerations of the ethical, legal, and social issues that will arise in the age of personal genomics. In this article, we review the current state of genetics education, highlight issues that we believe need to be addressed in a comprehensive genetics education curriculum, and describe our education efforts at the Harvard Medical School-based Personal Genetics Education Project.