Methylation analyses on promoters of mPer1, mPer2, and mCry1 during perinatal development

Recent studies revealed dramatic changes in circadian clock genes’ expression during the perinatal period. In this study, we characterized DNA methylation for three clock genes mPer1, mPer2, and mCry1 at their selected promoter regions during development. Results for the suprachiasmatic nucleus (SCN) and liver (at embryonic day 19, postnatal day 1 and postnatal day 7) were compared to those of sperm. Few methylations were detected for the mPer2 and mCry1 promoters. The 3rd E-box region of the mPer1 promoter exhibited methylation only in sperm. Significant demethylation was observed in the 4th E-box region of the mPer1 promoter between E19 and P1 in the SCN but not in liver tissue. This demethylation state was maintained at P7 for the SCN. Luciferase reporter assays using in vitro methylated promoters revealed an inhibitory effect of promoter methylation on mPer1 expression. The results suggested that epigenetic mechanisms such as DNA methylation might contribute to the developmental expression of clock genes.     

DDS: Dynamics of Developmental Systems

Abstract. The acronym Developmental systems theory (DST) has been introduced into the literature on development in at least three different contexts in recent years – twice for DST, and before that, for Dynamical Systems Theory – and in all cases, to designate a new perspective for understanding development. Subtle but significant differences in argument and aims distinguish these uses, and confound the difficulty of saying just what DST is. My aim in this paper is to disambiguate these different terms – both to call attention to the difference of perspectives, and to carve out a conceptual space for the concrete issues at stake.     

DNA methylation profiling of pseudogene-parental gene pairs and two gene families

A substantial proportion of human genes contain tissue-specifically DNA-methylated regions (TDMRs). However, little is known about the evolutionary conservation of differentially methylated loci, how they evolve, and the signals that regulate them. We have studied TDMR conservation in the PLG and TBX gene families and in 32 pseudogene–parental gene pairs. Among the members of the recently evolved PLG gene family, 5′-UTR methylation is conserved and inversely correlated with the cognate gene expression, indicating as well a conserved regulatory role of DNA methylation. Conversely, many genes of the much older TBX family display complementary tissue-specific methylation, suggesting an epigenetic complementation in the evolution of this gene family. Similar to gene families, unprocessed pseudogenes arose from gene duplications and we found TDMR conservation in some pseudogene–parental gene pairs displaying short evolutionary distances. However, for the majority of unprocessed pseudogenes and for all processed pseudogenes examined, we found that tissue-specific methylation arose de novo after gene duplication.     

Kant on epigenesis, monogenesis and human nature: the biological premises of anthropology

The aim of this paper is to show that for Kant, a combination of epigenesis and monogenesis is the condition of possibility of anthropology as he conceives of it and that moreover, this has crucial implications for the biological dimension of his account of human nature. More precisely, I begin by arguing that Kant's conception of mankind as a natural species is based on two premises: firstly the biological unity of the human species (monogenesis of the human races); and secondly the existence of 'seeds' which may or may not develop depending on the environment (epigenesis of human natural predispositions). I then turn to Kant's account of man's natural predispositions and show that far from being limited to the issue of races, it encompasses unexpected human features such as gender, temperaments and nations. These predispositions, I argue, are means to the realisation of Nature's overall purpose for the human species. This allows me to conclude that man's biological determinism leads to the species' preservation, cultivation and civilisation.     

Identifying the morphological signatures of hybridization in primate and human evolution

Recent studies point to contact and possible admixture among contemporaneous hominin species during the Plio-Pleistocene. However, detection of hybridization in fossils-and especially fossil hominins-is contentious, and it is hindered in large part by our lack of understanding about how morphological hybridity is manifested in the primate skeleton. Here, we report on a study of known-pedigree, purebred yellow and olive baboons (n = 112) and their hybrids (n = 57), derived from the baboon colony of the Southwest Foundation for Biomedical Research. The hybrids were analyzed in two different groups: (1) F1 = olive x yellow first-generation hybrids; (2) B1 = olive x F1 backcross hybrids. Thirty-nine metric variables were tested for heterosis and dysgenesis. Nonmetric data were also collected from the crania. Results show that these primate hybrids are somewhat heterotic relative to their parental populations, are highly variable, and display novel phenotypes. These effects are most evident in the dentition and probably indicate the mixing of two separately coadapted genomes and the breakdown in the coordination of early development, despite the fact that these populations diverged fairly recently. Similar variation is also observed in museum samples drawn from natural hybrid zones. The results offer a strategy for detecting hybrid zones in the fossil record; implications for interpreting the hominin fossil record are discussed.     

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics.     

The Developmental Basis of Identity

We are each the product of our development. The nature of the developmental process by which each of us was formed is described from gametogenesis to neonatality. The varied influences upon that process and their relative balance and patterns of interaction are then considered. In particular, the relative importance of epigenetic and genetic factors is discussed. It is concluded that development is a continuous process involving epigenetic/genetic interactions throughout. The contemporary emphasis on the genetic basis for human individuality is reviewed critically.     

How dams on the River Danube might have caused hybridization and influenced the appearance of a new cyprinid taxon

Synopsis When a new species is found, or a known one collected outside its recognized distribution, most people either assume that the species has been overlooked in the past or that it has recently invaded the area in question from elsewhere. While other, more evolutionary explanations are possible, these are nearly always ignored, in spite of the common perception that animals are constantly in states of change. Recent findings in the Danube River are used as examples for such alternative interpretations. The case of two forms of Vimba — short and long snouted — which live in sympatry in the upper Danube is dispelled, as one of them is identified as a hybrid between female V. vimba and male Blicca bjoerkna. Frequent occurrences of this hybrid (and a few of its backcrosses) in recent times are explained by man-induced alteration of reproductive isolation between their parent species, caused by the impoundment of the river by dams built as part of the Rhein-Main-Donau Kanal. These impoundments, however, might be responsible not only for the creation of hybrids but also for direct speciation, as the case of Gobio albipinnatus may represent. The ability for epigenetic creation of two alternative life-history states (as part of the theory of alprehost) and the survival of an alternative state when environmental conditions change might be ultimately responsible for the appearance of a new taxon.