Minimal Developmental Computation: A Causal Network Approach to Understand Morphogenetic Pattern Formation

What information-processing strategies and general principles are sufficient to enable self-organized morphogenesis in embryogenesis and regeneration? We designed and analyzed a minimal model of self-scaling axial patterning consisting of a cellular network that develops activity patterns within implicitly set bounds. The properties of the cells are determined by internal ‘genetic’ networks with an architecture shared across all cells. We used machine-learning to identify models that enable this virtual mini-embryo to pattern a typical axial gradient while simultaneously sensing the set boundaries within which to develop it from homogeneous conditions—a setting that captures the essence of early embryogenesis. Interestingly, the model revealed several features (such as planar polarity and regenerative re-scaling capacity) for which it was not directly selected, showing how these common biological design principles can emerge as a consequence of simple patterning modes. A novel “causal network” analysis of the best model furthermore revealed that the originally symmetric model dynamically integrates into intercellular causal networks characterized by broken-symmetry, long-range influence and modularity, offering an interpretable macroscale-circuit-based explanation for phenotypic patterning. This work shows how computation could occur in biological development and how machine learning approaches can generate hypotheses and deepen our understanding of how featureless tissues might develop sophisticated patterns—an essential step towards predictive control of morphogenesis in regenerative medicine or synthetic bioengineering contexts. The tools developed here also have the potential to benefit machine learning via new forms of backpropagation and by leveraging the novel distributed self-representation mechanisms to improve robustness and generalization.

Biological Response of Planktic Foraminifera to Decline in Seawater pH

Understanding the way in which a decline in ocean pH can affect calcareous organisms could enhance our ability to predict the impacts of the potential decline in seawater pH on marine ecosystems, and could help to reconstruct the paleoceanographic events over a geological time scale. Planktic foraminifera are among the most important biological proxies for these studies; however, the existing research on planktic foraminifera is almost exclusively based on their geochemical indices, without the inclusion of information on their biological development. Through a series of on-board experiments in the western tropical Pacific (134°33′54″ E, 12°32′47″ N), the present study showed that the symbiont-bearing calcifier Trilobatus sacculifer—a planktic foraminifer—responded rapidly to a decline in seawater pH, including losing symbionts, bleaching, etc. Several indices were established to quantify the relationships between these biological parameters and seawater pH, which could be used to reconstruct the paleoceanographic seawater pH. We further postulated that the loss of symbionts in planktic foraminifera acts as an adaptive response to the stress of low pH. Our results indicate that an ongoing decline in seawater pH may hinder the growth and calcification of planktic foraminifera by altering their biological processes. A reduction in carbonate deposition and predation could have profound effects on the carbon cycle and energy flow in the marine food web.

Notes on the biological development of the darkling beetle Blaps nefrauensis nefrauensis Seidlitz, 1893 (Coleoptera: Tenebrionidae)

Several endemic species of Blaps occur in Tunisia, and the species Blaps nefrauensis nefrauensis has been reported in Moulares (urban zone in west-central Tunisia), where it lives and reproduces in home gardens and old buildings. The aim of this work is to study the life cycle of the darkling beetle, considering both field and laboratory rearing conditions. As a result, the beetle species has different developmental stages (egg, larva, prepupa, pupa, and adult) that last about 15 months. Each year during the same period, adults emerge (early summer) and expire (late autumn), larvae hatch (late summer) and pupate (early summer). There is only one generation per year. Females began laying eggs in late July. The eggs were ovoid, white, and about 2.7 mm in length and 1.5 mm in width. Embryogenesis took an average of nine days. The first instar larvae were at initially only 4.5 mm long and ivory white in color. A brief description of the newly egg hatched larva was provided; thus, the nerve fibers innervating the apical setae in the antennae and ligula were detected. Further light microscopic examination of the embryo before hatching from the egg pointed out that the antennal sensilla are protected during the embryogenesis stage.

Effect of Cry Toxins on Xylotrechus arvicola (Coleoptera: Cerambycidae) Larvae

The beetle Xylotrechus arvicola is a destructive pest in vineyards (Vitis vinifera) in the main wine-producing areas of the Iberian Peninsula. X. arvicola larvae bore into the grapevine wood-making galleries, thus damaging the plant both directly and indirectly; the latter through the proliferation of wood fungi, which can invade the inside of the plant, decreasing the quality and quantity of its production. The susceptibility of X. arvicola larvae to five coleopteran toxic Cry proteins (Cry1B, Cry1I, Cry3A, Cry7A, and Cry23/37) was evaluated under laboratory conditions in order to deepen the knowledge of the effect of these proteins on this insect throughout its biological development.

The epigenetics of early life adversity and trauma inheritance: an interview with Moshe Szyf

In this interview, Professor Moshe Szyf speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of social epigenetics. Szyf received his PhD from the Hebrew University and did his postdoctoral fellowship in genetics at Harvard Medical School, joined the Department of Pharmacology and Therapeutics at McGill University in Montreal in 1989 and is a fellow of the Royal Society of Canada and the Academy of Health Sciences of Canada. He is the founding codirector of the Sackler Institute for Epigenetics and Psychobiology at McGill and is a Fellow of the Canadian Institute for Advanced Research Experience-Based Brain and Biological Development program. Szyf was the founder of the first pharma to develop epigenetic pharmacology, Methylgene Inc., and the journal Epigenetics. The Szyf lab proposed two decades ago that DNA methylation is a prime therapeutic target in cancer and other diseases and postulated and provided the first set of evidence that the social environment early in life can alter DNA methylation, launching the emerging field of social epigenetics.

Identification of approximate symmetries in biological development

Virtually all forms of life, from single-cell eukaryotes to complex, highly differentiated multicellular organisms, exhibit a property referred to as symmetry. However, precise measures of symmetry are often difficult to formulate and apply in a meaningful way to biological systems, where symmetries and asymmetries can be dynamic and transient, or be visually apparent but not reliably quantifiable using standard measures from mathematics and physics. Here, we present and illustrate a novel measure that draws on concepts from information theory to quantify the degree of symmetry, enabling the identification of approximate symmetries that may be present in a pattern or a biological image. We apply the measure to rotation, reflection and translation symmetries in patterns produced by a Turing model, as well as natural objects (algae, flowers and leaves). This method of symmetry quantification is unbiased and rigorous, and requires minimal manual processing compared to alternative measures. The proposed method is therefore a useful tool for comparison and identification of symmetries in biological systems, with potential future applications to symmetries that arise during development, as observed in vivo or as produced by mathematical models. This article is part of the theme issue ‘Recent progress and open frontiers in Turing’s theory of morphogenesis’.

Facing Phototrophic Microorganisms That Colonize Artistic Fountains and Other Wet Stone Surfaces: Identification Keys

All fountains are inhabited by phototrophic microorganisms, especially if they are functional and located outdoors. This fact, along with the regular presence of water and the intrinsic bioreceptivity of stone material, easily favors the biological development. Many of these organisms are responsible for the biodeterioration phenomena and recognizing them could help to define the best strategies for the conservation and maintenance of monumental fountains. The presence of biological growth involves different activities for the conservation of artistic fountains. This paper is a review of the phototrophic biodiversity reported in 46 fountains and gives a whole vision on coping with biodeteriogens of fountains, being an elementary guide for professionals in the field of stone conservation. It is focused on recognizing the main phototrophs by using simplified dichotomous keys for cyanobacteria, green algae and diatoms. Some basic issues related to the handling of the samples and with the control of these types of microalgae are also briefly described, in order to assist interested professionals when dealing with the biodiversity of monumental fountains.

The First Year Developmental Crisis: Origin of Cultural Action

According to the conception of cultural historical psychology, introduced by L. S. Vigotsky, the first year of a child’s life represents a specific period of development or the first psychological age. Psychological development should be differentiated from biological development and have proper objective indicators. Psychological development starts with the possibility of initial cultural communication between an adult and child, within a unique kind of social situation of development. The goal of the article is to describe the content of the crisis of the first year of life as a psychological phenomenon and to propose psychological and neuropsychological indicators for qualitative assessment of the progress of psychological development at the end of the first year of life. The article opens the discussion about guiding the activity of the first age, new psychological formations of the crisis of the first year, and qualitative changes in the social situation of development. The content of the first psychological age and crisis is presented in the article, according to proposals of cultural historical psychology. Future interdisciplinary research should be continued in order to establish optimal strategies for adult and child interaction during a stable period of development and the crisis of the first year.

A Study on Primigravida Mothers of Rural Karad Taluka, Maharashtra in Acknowledging the Child Developmental Milestones

<strong>Background:</strong> The best moment for any women in this world is to give birth to her child after months of wait and anticipation. She is accompanied with overwhelming feelings of bliss and divinity. The process of growth and development continues throughout the entire life of a human being; however, the duration in which the integral changes take place is from inception to the end of youth. The health workers need to understand this early period as well as the total life cycle of an individual and understand the behavior of parents and other adults who pond care for the child. Thus, it is necessary to educate mothers in the antenatal period about the developmental milestones so that they can impart this knowledge during the care of their children and also this will help them to rule out any developmental delay in their children at the earliest. Objective: To acknowledge child developmental milestones in primigravida mothers of rural Karad taluka, Maharashtra.<strong> Method:</strong> A study was conducted with 98 subjects from in and around Karad. They were selected on the basis of the criteria of inclusion and exclusion and a prior written consent was also taken. Primigravida mothers were included in the study. Then they were assessed with the help of a structured questionnaire on child development milestones. The data was then collected and analysed accordingly. <strong>Result:</strong> After analyzing the data, it was found that primigravida mothers had 53% knowledge about biological development, 34% knowledge about sensory development, 42% knowledge about social development, 28% knowledge about cognitive development, and 36% knowledge about moral development. <strong>Conclusion:</strong> The knowledge about child developmental milestones in primigravida mothers is inadequate. Out of all the developmental domains, they have considerable knowledge about biological development (53%) and the least knowledge about cognitive development (28%).