Ontogenetic Units Research Articles

Disappearance of Temporal Collinearity in Vertebrates and Its Eventual Reappearance.

Simple SummaryIn 1999 T. Kondo and D. Duboule performed excisions of posterior upstream DNA domains in mouse embryos and they observed that for an extended excision (including Evx gene) the Hox genes of the cluster were simultaneously expressed with the first Hoxd1 gene ‘as if’ Temporal Collinearity (TC) had disappeared. According to a Biophysical Model (BM) during Hox gene expression, Hox clusters behave similar toexpanding elastic springs. For the extended upstream DNA excision, BM predicts the TC disappearance and an experiment is proposed to test this BM prediction. In the chick limb bud C. Tickle et al. observed that the excision of the apical ectodermal ridge (AER) caused the inhibition of HoxA13 expression. However, the implantation of FGF soaked beads at the tip of the limb could surprisingly rescue HoxA13 expression after 24 h so that TC is restored.Brachyury transcription factor (TF) is essential in identifying the targets of this transcription and a chromatin immunoprecipitation microarray chip (ChIP-chip) was produced which can be inserted in the mouse embryonic cells. It is here proposed to insert this chip in the mutant cells where TC has disappeared and compare it to the limb bud case.Is TC restored? It is an important issue worth exploring.It was observed that a cluster of ordered genes (Hox1, Hox2, Hox3…) in the genome are activated in the ontogenetic units (1, 2, 3 …) of an embryo along the Anterior/Posterior axis following the same order of the Hox genes. This Spatial Collinearity (SC) is very strange since it correlates events of very different spatial dimensions. It was later observed in vertebrates, that, in the above ordering, first is Hox1expressed in ontogenetic unit 1, followed later by Hox2 in unit 2 and even later Hox3 in unit 3. This temporal collinearity (TC) is an enigma and even to-day is explored in depth. In 1999 T. Kondo and D. Duboule, after posterior upstream extended DNA excisions, concluded that the Hox cluster behaves ‘as if’ TC disappears. Here the consideration of TC really disappearing is taken face value and its repercussions are analyzed. Furthermore, an experiment is proposed to test TC disappearance. An outcome of this experiment could be the reappearance (partial or total) of TC.

Physical Laws Shape Up HOX Gene Collinearity.

Hox gene collinearity (HGC) is a multi-scalar property of many animal phyla particularly important in embryogenesis. It relates entities and events occurring in Hox clusters inside the chromosome DNA and in embryonic tissues. These two entities differ in linear size by more than four orders of magnitude. HGC is observed as spatial collinearity (SC), where the Hox genes are located in the order (Hox1, Hox2, Hox3 …) along the 3′ to 5′ direction of DNA in the genome and a corresponding sequence of ontogenetic units (E1, E2, E3, …) located along the Anterior—Posterior axis of the embryo. Expression of Hox1 occurs in E1, Hox2 in E2, Hox3 in E3, etc. Besides SC, a temporal collinearity (TC) has been also observed in many vertebrates. According to TC, first Hox1 is expressed in E1; later, Hox2 is expressed in E2, followed by Hox3 in E3, etc. Lately, doubt has been raised about whether TC really exists. A biophysical model (BM) was formulated and tested during the last 20 years. According to BM, physical forces are created which pull the Hox genes one after the other, driving them to a transcription factory domain where they are transcribed. The existing experimental data support this BM description. Symmetry is a physical–mathematical property of matter that was explored in depth by Noether who formulated a ground-breaking theory (NT) that applies to all sizes of matter. NT may be applied to biology in order to explain the origin of HGC in animals developing not only along the A/P axis, but also to animals with circular symmetry.

Hox Gene Collinearity May Be Related to Noether Theory on Symmetry and Its Linked Conserved Quantity

Hox Gene Collinearity (HGC) is a fundamental property that controls the development of many animal species, including vertebrates. In the Hox gene clusters, the genes are located in a sequential order Hox1, Hox2, Hox3, etc., along the 3’ to 5’ direction of the cluster in the chromosome. During Hox cluster activation, the Hox genes are expressed sequentially in the ontogenetic units D1, D2, D3, etc., along the anterior–posterior axis (A-P) of the early embryo. This collinearity, first observed by E.B. Lewis, is surprising because the spatial collinearity of these structures (Hox clusters and embryos) correlates entities that differ by about four orders of magnitude. Biomolecular mechanisms alone cannot explain such correlations. Long-range physical interactions, such as diffusion or electric attractions, should be involved. A biophysical model (BM) was formulated, which, in alignment with the biomolecular processes, successfully describes the existing vertebrate genetic engineering data. One hundred years ago, Emmy Noether made a fundamental discovery in mathematics and physics. She proved, rigorously, that a physical system obeying a symmetry law (e.g., rotations or self-similarity) is followed by a conserved physical quantity. It is argued here that HGC obeys a ‘primitive’ self-similarity symmetry. In this case, the associated primitive conserved quantity is the irreversibly increasing ‘ratchet’-like Hoxgene ordering where some genes may be missing. The genes of a vertebrate Hox clusterare located along a finite straight line. The same order follows the ontogenetic unitsof the vertebrate embryo. Therefore, HGC is a manifestation of a primitive Noether Theory (NT). NT may be applied to other than the vertebrate case, for instance, to animals with a circular topological symmetry. For example, the observed abnormal Hox gene ordering of the echinoderm Hox clusters may be reproduced by a double-strand break of the circular Hox gene ordering and its subsequent incorporation in the flanking chromosome.

Physical Forces May Cause the HoxD Gene Cluster Elongation.

Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains. A Biophysical Model of physical forces was proposed which can bridge the intermediate space and explain the results of genetic engineering experiments. Recent progress in constructing instruments and achieving high resolution imaging (e.g., 3D DNA FISH, STORM etc.) enable the assessment of the geometric structure of the chromatin during the different phases of Hox gene activation. It is found that the mouse HoxD gene cluster is elongated up to 5–6 times during Hox gene transcription. These unexpected findings agree with the BM predictions. It is now possible to measure several physical quantities inside the nucleus during Hox gene activation. New experiments are proposed to test further this model.

Finding the "prism": Understanding Vygotsky's perezhivanie as an ontogenetic unit of child consciousness

The concept of perezhivanie, Vygotsky's last word on psychology, has been among the most difficult of his theoretical constructs to define and operationalise in research. Drawing on close analysis of key texts, this article identifies and examines three defining attributes of perezhivanie found throughout Vygotsky's works. The attributes are: perezhivanie as a prism of psychological development, as a unit of human consciousness, and as perception of one's environment. In contrast with common understandings of perezhivanie as emotional experience, privileging it as affect, this article highlights the intellectual basis of perezhivanie in Vygotsky's writings with particular reference to his notions of generalised and intelligent perception. The article argues that perezhivanie is best understood, psychologically, as an intellectual gestalt reflecting the intellectualisation of perception and, ontologically, as an apperceptual organ of selection of consciousness and personality refracting the child's individual social situation of development.International Research in Early Childhood Education, vol. 7, no. 1, p. 5-33

Hox Gene Collinearity: From A-P Patterning to Radially Symmetric Animals.

Hox gene collinearity relates the gene order of the Hox cluster in the chromosome (telomeric to centromeric end) with the serial activation of these genes in the ontogenetic units along the Anterior-Posterior embryonic axis. Although this collinearity property is well respected in bilaterians (e.g. vertebrates), it is violated in other animals. The A-P axis is established in the early embryo of the sea urchin. Subsequently, rotational symmetry is superimposed when the vestibula larva is formed. In analogy to the linear A-P case, it is here hypothesized that the circular topology of the ontogenetic modules is associated to the architectural restructuring of the Hox loci where the two discrete ends of the Hox cluster approach each other so that an almost circular DNA contour is created. In the evolutionary process the circular mode undergoes double strand breaks and the generated cluster ends are attached to the open ends of the flanking chromosome. This event may lead to a novel gene ordering associated with an evolutionary innovation. For example, the loss of Hox4 is followed by the formation of a shorter gene circular arrangement. The opening of this contour at the missing Hox4 location and its connection to the chromosomal flanking ends leads to a new diversification namely the creation of the unusual gene order of the sea urchin Hox cluster.

Evolution of gnathostome lateral line ontogenies.

An outgroup analysis of multiple ontogenies provides the most robust approach to understanding phylogeny. Such an analysis of the lateral line system among extinct and extant gnathostomes reveals that lateral line placodes constitute the basic ontogenetic unit responsible for the development of this system. Six pairs of lateral line placodes appear to have existed in the earliest gnathostomes, and eight stages (stages A-H) can be recognized in their differentiation. Terminal truncation (heterochronic changes) in the primitive sequence of placodal development has occurred in one or more placodes in each gnathostome radiation, with the most extensive truncations occurring in arthrodire placoderms, lepidosirenid lungfishes and extant amphibians. The most extensive nonterminal changes in the primitive sequence of placodal development involve the failure of electroreceptors to form within the lateral zones of the elongatiang sensory ridges of the placodes. This nonterminal change appears to have occurred independently in ancestral neopterygian bony fishes, in many amphibians and, possibly, in the extinct acanthodians. At least two teleost radiations, osteoglossomorphs and ostariophysines, have re-evolved electroreceptors which may represent additional nonterminal changes in placodal patterning or, possibly, a change in the embryonic source of these receptors.

Pattern formation in the developing superior colliculus: ontogeny of the periodic architecture in the intermediate layers.

The superior colliculus of mammals contains a striking neurochemical architecture in which histochemically identifiable compartments are distributed in an iterative arrangement in the intermediate layers. We used stains for acetylcholinesterase activity as a compartment marker to trace ontogenesis of this architecture during pre- and postnatal development in the domestic cat. We found that compartmentation in the intermediate collicular layers is virtually absent at birth, and only gradually emerges during the first weeks of postnatal life. Over the same postnatal period, acetylcholinesterase activity shifts from a predominantly perikaryal expression pattern immediately postnatally to a nearly exclusive localization in the neuropil at maturity. Remarkably, a striking compartmentation of the superior colliculus was readily apparent with acetylcholinesterase histochemistry prenatally. The first appearance of a periodic architecture in the superior colliculus was observed at embryonic day 34, a time at which the collicular plate had not yet become laminated. The compartments characterized by high levels of acetylcholinesterase activity then gained in prominence until late in the prenatal period, when they receded and disappeared. The loss of the acetylcholinesterase-positive compartments in the perinatal period did not reflect a loss of compartmentation altogether. Neonatally, there was a distinct compartmental architecture visible with enkephalin immunohistochemistry. The virtual absence of acetylcholinesterase-positive compartments in the superior colliculus at birth therefore reflects developmental regulation of enzyme expression in the compartments, not regulation of the compartments as structural entities. We conclude that the periodic architecture, which characterizes the intermediate collicular layers in the adult cat, arises early in ontogenesis. These observations raise the possibility that the histochemical compartments are ontogenetic units that undergo remodeling as the superior colliculus matures.

Clonally related cortical cells show several migration patterns.

The mammalian cerebral cortex is organized into columns of cells with common functional properties. During embryogenesis, cortical neurons are formed deep, near the lateral ventricles, and migrate radially to their final position. This observation led to the suggestion that the cortex consists of radial, ontogenetic units of clonally related neurons. In the experiments reported here, this hypothesis was tested by studying cell lineage in the rat cortex with a retroviral vector carrying the Escherichia coli beta-galactosidase gene, which can be easily visualized. Labeled, clonally related cortical neurons did not occur in simple columnar arrays. Instead, clonally related neurons entered several different radial columns, apparently by migrating along different radial glial fibers.

Neurogenetics and Behaviour in Insects

ABSTRACT The importance of the genome for behaviour has been amply demonstrated by the tools of population genetics. A deeper understanding of the relationship between genes and behaviour requires an investigation of how they influence brain development and neuronal function. This is the objective of neurogenetics. Rigid genetic control of brain structure in insects is indicated by bilateral symmetry and by the similarity of isogenic brains (in locust). In large parts of the brain (e.g. optic lobes) the role of developmental variability seems to be as limited as in nematodes, but at closer inspection, the growth of at least some brain structures (e.g. mushroom bodies) is influenced by experience, similar to the growth of some vertebrate systems. The role of individual genes for brain development and brain function is being studied in Drosophila melanogaster. Here, many single gene mutations affecting the brain and behaviour have been isolated. They either alter the development of neural circuits or modify cellular functions of neurones. Mutations of both categories are often remarkably specific (i.e. they influence only certain functional subsystems, leaving others unaffected). Therefore, functional subsystems are to some degree ontogenetic units under independent genetic control. Telling examples are sexual dimorphisms of behaviour and brain structure. The already peripheral separation of functional pathways in the brain seems to be partially due to the selective advantage of independent genetic modifiability of functions.

Chemospecificity of ontogenetic units in the striatum: demonstration by combining [3H]thymidine neuronography and histochemical staining.

Neurons being generated in the striatum of 10 fetal cats were pulse labeled by injection of [3H]thymidine directly into the maternal uterus at times ranging between the 22nd and 30th days (E22-E30) of the 65-day gestational period. Many of the striatal neurons labeled during this interval were found, at adolescence, to form 100- to 600-mum-wide cell clusters in the caudate nucleus. In E24-E30 specimens, we compared the distributions of these cell clusters with the locations of patches of low acetylcholinesterase activity and high enkephalin immunoreactivity (the "striosomes') visualized in serially adjoining sections. We found precise matches between most of the cell clusters and the acetylcholinesterase-poor enkephalin-rich zones, regardless of the embryonic age at which exposure to the [3H]thymidine had occurred. We conclude that the histochemically distinct striosomal patch-works observed in the acetylcholinesterase and enkephalin preparations correspond to ontogenetic units of the striatum.

DNA, RNA, Protein, and Free Amino Acids During Ontogenesis of Rainbow Trout (Salmo gairdneri)

During the first 2 wk of incubation, the pattern of change in DNA concentration tended to precede similar changes in RNA concentration. Unfertilized eggs contained 23.2 and 77.2 μg of DNA and RNA, respectively. DNA concentration rose from 155.8 μg/fry (after 23 days of incubation) to 326.6 μg/larva (14 days after hatching), while RNA increased from 238.8 to 693.3 μg during the same period. Protein per ontogenetic unit was relatively constant during the prehatching stages but dropped markedly just prior to hatching. Of the protein in the unfertilized egg, approximately 20% was retained in the fry at hatching and approximately 50% was retained in the larva following yolk absorption. Total free amino acid concentrations declined just after fertilization, indicating the initiation of protein synthesis or a decline in yolk protein degradation. These concentrations increased to near initial values in the blastula and were nearly doubled in the yolk plus fry at hatching.