Teratology on the crossroads: historical aspects and modern approaches

Teratology is the science of congenital developmental disorders (CDDs), overt or latent defects of the organism resulting from the effect of internal and external factors on developmental processes. In this article the significance and position of present-day teratology is discussed in the context of development of this branch of science and related disciplines. The authors present an updated overview of the most important milestones and stages of the development of teratology. Based on the analysis of the historical development of theses and theories that represent a decisive contribution to this field, we present a survey of the fundamental principles of experimental and clinical teratology. The aim of observing these principles is to get insight into developmental relations and to understand mechanisms of action on the level of cell populations (elementary morphogenetic processes), tissues and organs. It is important to realize that any negative intervention into the normal course of these processes, either on genetic or non-genetic basis, inevitably leads to a sequence of subsequent changes resulting in the development of congenital developmental disorders. Despite modern approaches of molecular biology and genetics, along with top diagnostic techniques, we are still not able to identify the actual cause in more than 50% of all congenital defects. One-half of the unidentified cases are referred to as "multifactorial", a term that is rather ambiguous. It either means that some of the basic principles of teratogenesis still escape our attention, or the interpretation of some of the well known principles might be misleading. A third possibility is rather pessimistic. The development of the individual is so sophisticated and dependent on a delicate network of a multitude of factors mutually affecting each other that it is extremely prone to give rise to a plethora of spontaneous errors which are unpredictable and impossible to prevent. Nevertheless, the long and complicated history of scientific endeavour has yielded considerable present-day knowledge on causes and mechanisms of CDDs, a history whose beginnings date back to antiquity.     

A modern tool for classical plant growth analysis

We present an all-inclusive software tool for dealing with the essential core of mathematical and statistical calculations in plant growth analysis. The tool calculates up to six of the most fundamental growth parameters according to a purely 'classical' approach across one harvest-interval. All of the estimates carry standard errors and 95 % confidence limits. The tool is written in Microsoft Excel 2000 and is available free of charge for use in teaching and research from www.aob.oupjournals.org article supplementary data.     

The making of the mitotic chromosome: modern insights into classical questions

The condensation of mitotic chromosomes is essential for the faithful segregation of sister chromatids in anaphase. An emerging view is that chromosome assembly is an active and dynamic process of chromatin reorganization in which two ATP hydrolyzing enzymes, topoisomerase II and the condensin complex, play central roles. In this review, we discuss recent work that sheds new light on the molecular and structural dynamics of mitotic chromosomes.     

Comparing classical pathways and modern networks: towards the development of an edge ontology

Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely, modern high-throughput (HTP) experiments offer standardized networks that facilitate topological calculations. Combining these perspectives, classical pathways can be embedded within large-scale networks and thus demonstrate the crosstalk between them. As more diverse types of HTP data become available, both perspectives can be effectively merged, embedding pathways simultaneously in multiple networks. However, the original problem still remains - the current edge representation is inadequate to accurately convey all the information in pathways. Therefore, we suggest that a standardized and well-defined edge ontology is necessary and propose a prototype as a starting point for reaching this goal.     

A comparison of wood density between classical Cremonese and modern violins

Classical violins created by Cremonese masters, such as Antonio Stradivari and Giuseppe Guarneri Del Gesu, have become the benchmark to which the sound of all violins are compared in terms of their abilities of expressiveness and projection. By general consensus, no luthier since that time has been able to replicate the sound quality of these classical instruments. The vibration and sound radiation characteristics of a violin are determined by an instrument's geometry and the material properties of the wood. New test methods allow the non-destructive examination of one of the key material properties, the wood density, at the growth ring level of detail. The densities of five classical and eight modern violins were compared, using computed tomography and specially developed image-processing software. No significant differences were found between the median densities of the modern and the antique violins, however the density difference between wood grains of early and late growth was significantly smaller in the classical Cremonese violins compared with modern violins, in both the top (Spruce) and back (Maple) plates (p = 0.028 and 0.008, respectively). The mean density differential (SE) of the top plates of the modern and classical violins was 274 (26.6) and 183 (11.7) gram/liter. For the back plates, the values were 128 (2.6) and 115 (2.0) gram/liter. These differences in density differentials may reflect similar changes in stiffness distributions, which could directly impact vibrational efficacy or indirectly modify sound radiation via altered damping characteristics. Either of these mechanisms may help explain the acoustical differences between the classical and modern violins.     

Genetic manipulations in aquaculture: a review of stock improvement by classical and modern technologies

The aim of this review was to highlight the extent to which the genetic technologies are implemented by the aquaculture industry. The review shows that some of the modern genetic technologies are already extensively applied by the diverse aquaculture industries, though not to the same extent for all important aquacultured species (according to FAO 1998 figures). Some species (common carp, Atlantic salmon, rainbow trout, channel catfish, Nile tilapia, and the Pacific oyster) received concentrated breeding efforts, while other major cultured species (Chinese and Indian carps and the giant tiger shrimp) received, so far, relatively limited attention, and a few species (Yesso scallop, blue mussel, white Amur bream, and milkfish) have, apparently, not been genetically improved at all. Most of the genetically improved strains reaching the aquaculture industry were developed through traditional selective breeding (selection, crossbreeding, and hybridization). Emerging, more modern technologies for genetic manipulation seem to take 10-20 years from being established experimentally until applications affect the industry. Thus, chromosome-set and sex manipulations started to affect the industry during the 1980's and 1990's. DNA marker technology and gene manipulations have yet hardly affected the industry. The former have not matured yet, but hold much promise. The latter could have affected the industry already had it not been restricted by public concern.     

Origin and Evolution of Rickettsial Plasmids

Background

Rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. Despite their allopatric lifestyle, almost half of the 26 currently validated Rickettsia species have plasmids. In order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and non-microbial genomes.

Results

Plasmids were differentially present among Rickettsia species. The 11 species had 1 to 4 plasmid (s) with a size ranging from 12 kb to 83 kb. We reconstructed pRICO, the last common ancestor of the current rickettsial plasmids. pRICO was vertically inherited mainly from Rickettsia/Orientia chromosomes and diverged vertically into a single or multiple plasmid(s) in each species. These plasmids also underwent a reductive evolution by progressive gene loss, similar to that observed in rickettsial chromosomes, possibly leading to cryptic plasmids or complete plasmid loss. Moreover, rickettsial plasmids exhibited ORFans, recent gene duplications and evidence of horizontal gene transfer events with rickettsial and non-rickettsial genomes mainly from the α/γ-proteobacteria lineages. Genes related to maintenance and plasticity of plasmids, and to adaptation and resistance to stress mostly evolved under vertical and/or horizontal processes. Those involved in nucleotide/carbohydrate transport and metabolism were under the influence of vertical evolution only, whereas genes involved in cell wall/membrane/envelope biogenesis, cycle control, amino acid/lipid/coenzyme and secondary metabolites biosynthesis, transport and metabolism underwent mainly horizontal transfer events.

Conclusion

Rickettsial plasmids had a complex evolution, starting with a vertical inheritance followed by a reductive evolution associated with increased complexity via horizontal gene transfer as well as gene duplication and genesis. The plasmids are plastic and mosaic structures that may play biological roles similar to or distinct from their co-residing chromosomes in an obligate intracellular lifestyle.     

Homeostatic responses of plants to modern climate change: Spatial and phenological aspects

A series of dates of unfolding of the first leaves and duration of the season of vegetation in the silver birch (Betula pendula Roth. (B. verrucosa Ehrh.)), as well as the duration of flowering of the bird cherry (Padus avium), mountain ash (Sórbus aucupária), and small-leaved lime (Tilia cordata Mill.) for the period 1970–2010 in the central part of European Russia were studied in order to assess the trends. Differences in phenological responses to homogeneous climate changes in the trees of the same species from the northern and southern parts of the range were revealed. If spring events occur 3–7 days earlier in the northern part, no such effect is observed in the south. This fact can be interpreted as a manifestation of the different mechanisms of homeostasis in different populations determined by their biological characteristics (in particular, by the need to pass successfully the periods of organic rest and vegetation).     

Evo-devo aspects of classical and molecular data in a historical perspective

We discuss the interplay between evolution and development as reflected in data and concepts since about 1800. Darwin and his "continental apostle" Haeckel put the striking similarity between early vertebrate embryos in an evolutionary context. Haeckel's partly illicit generalizations discredited evolutionary thinking among early experimental embryologists who moreover noted riddles incompatible with contemporary concepts of homology and evolution. Relevant solutions were suggested by the more recent concept of ontogenetic networks that embody complex regulatory properties and genes with partly overlapping functions. Molecular data on development increasingly reveal evolutionary opportunism, for instance when a widespread signaling chain involved in primitive immune defense was apparently recruited later on for dorso-ventral axis determination in some evolutionarily advanced insect groups. Recently, Rickettsia-related bacteria colonizing many arthropod species were found to "manipulate" the first steps of host development to the advantage of their own propagation, but by ways that could also promote host speciation. Molecular genetics can now document evolutionary steps in ontogenetic networks. In the fruit fly for instance, the novel bicoid gene has superseded a crucial patterning function within a pre-existing network--a case of "molecular caenogenesis." The expression patterns of conserved genes that antagonistically determine dorso-ventral polarity support a literal revolution envisioned almost 200 years ago. This is the dorso-ventral inversion of the body plan in some metazoans--ascribed then to the Articulata, now to the Chordata. The final section posits that the opportunistic character of evolutionary innovations is detrimental to parsimony in development.