Impact of Natural Genetic Variation on Gene Expression Dynamics

DNA sequence variation causes changes in gene expression, which in turn has profound effects on cellular states. These variations affect tissue development and may ultimately lead to pathological phenotypes. A genetic locus containing a sequence variation that affects gene expression is called an “expression quantitative trait locus” (eQTL). Whereas the impact of cellular context on expression levels in general is well established, a lot less is known about the cell-state specificity of eQTL. Previous studies differed with respect to how “dynamic eQTL” were defined. Here, we propose a unified framework distinguishing static, conditional and dynamic eQTL and suggest strategies for mapping these eQTL classes. Further, we introduce a new approach to simultaneously infer eQTL from different cell types. By using murine mRNA expression data from four stages of hematopoiesis and 14 related cellular traits, we demonstrate that static, conditional and dynamic eQTL, although derived from the same expression data, represent functionally distinct types of eQTL. While static eQTL affect generic cellular processes, non-static eQTL are more often involved in hematopoiesis and immune response. Our analysis revealed substantial effects of individual genetic variation on cell type-specific expression regulation. Among a total number of 3,941 eQTL we detected 2,729 static eQTL, 1,187 eQTL were conditionally active in one or several cell types, and 70 eQTL affected expression changes during cell type transitions. We also found evidence for feedback control mechanisms reverting the effect of an eQTL specifically in certain cell types. Loci correlated with hematological traits were enriched for conditional eQTL, thus, demonstrating the importance of conditional eQTL for understanding molecular mechanisms underlying physiological trait variation. The classification proposed here has the potential to streamline and unify future analysis of conditional and dynamic eQTL as well as many other kinds of QTL data.     

Anhydrobiosis in tardigrades--the last decade

The current state of knowledge about anhydrobiosis in tardigrades is presented. In response to adverse environmental conditions tardigrades arrest their metabolic activity and after complete dehydration enter the so-called “tun” state. In this ametabolic state they are able to tolerate exposure to various chemical and physical extremes. These micrometazoans have evolved various kinds of morphological, physiological and molecular adaptations to reduce the effects of desiccation. In this review we address behavioral adaptation, morphological features and molecules which determine the anhydrobiotic survival. The influence of the time spent in anhydrobiotic state on the lifespan and DNA and the role of the antioxidant defense system are also considered. Finally we summarize recent input from the “omics” sciences.     

Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine

Modified nucleobase analogues can serve as powerful tools for changing physicochemical and biological properties of DNA or RNA. Guanosine derivatives containing bulky substituents at 8 position are known to adopt syn conformation of N-glycoside bond. On the contrary, in RNA the anti conformation is predominant in Watson-Crick base pairing. In this paper two 8-substituted guanosine derivatives, 8-methoxyguanosine and 8-benzyloxyguanosine, were synthesized and incorporated into oligoribonucleotides to investigate their influence on the thermodynamic stability of RNA duplexes. The methoxy and benzyloxy substituents are electron-donating groups, decreasing the rate of depurination in the monomers, as confirmed by N-glycoside bond stability assessments. Thermodynamic stability studies indicated that substitution of guanosine by 8-methoxy- or 8-benzyloxyguanosine significantly decreased the thermodynamic stability of RNA duplexes. Moreover, the presence of 8-substituted guanosine derivatives decreased mismatch discrimination. Circular dichroism spectra of modified RNA duplexes exhibited patterns typical for A-RNA geometry.     

Do all geckos hatch in the same way? Histological and 3D studies of egg tooth morphogenesis in the geckos Eublepharis macularius Blyth 1854 and Lepidodactylus lugubris Duméril & Bibron 1836

The egg tooth of squamates evolved to facilitate hatching from mineralized eggshells. Squamate reptiles can assist their hatching with a single unpaired egg tooth (unidentates) or double egg teeth (geckos and dibamids). Egg tooth ontogeny in two gekkotan species, the leopard gecko Eublepharis macularius and the mourning gecko Lepidodactylus lugubris, was compared using microtomography, scanning electron microscopy, and light microscopy. Investigated species are characterized by different hardnesses of their eggshells. Leopard geckos eggs have a relatively soft and flexible parchment (leathery) shell, while eggshells of mourning geckos are hard and rigid. Embryos of both species, like other Gekkota, have double egg teeth, but the morphology of these structures differs between the investigated species. These differences in shape, localization, and spatial orientation were present from the earliest stages of embryonic development. In mourning gecko, anlagen of differentiating egg teeth change their position on the palate during embryonic development. Initially they are separated by condensed mesenchyme, but later in development, their enamel organs are connected. In leopard geckos, the localization of egg tooth germs does not change, but their spatial orientation does. Egg teeth of this species shift from inward to outward orientation. This is likely related to differences in structure and mechanical properties of eggshells in the studied species. In investigated species, two hatching mechanisms are possible during emergence of young individuals. We speculate that mourning geckos break the eggshell through puncturing action with egg teeth, similar to the pipping phase of chick and turtles embryos. Egg teeth of leopard geckos cut egg membranes similarly to most squamates. Our results also revealed differences in egg tooth implantation between Gekkota and Unidentata: gekkotan egg teeth are subthecodont (in shallow sockets), while those in unidentates are acrodont (attached to the top of the alveolar ridge). © 2020 Wiley Periodicals LLC     

The virulence of Staphylococcus aureus correlates with strain genotype in a chicken embryo model but not a nematode model

Staphylococcus aureus infections are of major importance in human and veterinary medicine. Studies of the virulence of this bacterium are complicated by inconsistent results obtained in different animal models. We searched for an uncomplicated and inexpensive model suitable to study virulence of poultry strains of S. aureus using a genome-wide approach. We determined that a useful model would clearly differentiate strains of high and low virulence, and that this would generally correlate with the genetic relatedness among strains. To this end Gallus gallus (chicken) embryo and Caenorhabditis elegans (nematode) models were selected, and their response to challenge by a set of well-characterized Staphylococcus strains was evaluated. The chicken embryo model allowed to determine variation in virulence among strains of poultry and human origin. The survival of embryos ranged from 0% to almost 100% for the various strains. In contrast, variation in virulence of most strains in the nematode model was comparable, regardless of their origin or genotype, demonstrating limited usefulness of this model. Most importantly, a clear correlation was found between the virulence level in the embryo model and the genotype of the tested poultry strains. Our findings indicate the potential usefulness of embryo model for future identification of host-specific adaptations and virulence factors in S. aureus.     

Light and scanning microscopic studies of integument differentiation in the grass snake Natrix natrix L. (Lepidosauria,Serpentes) during embryogenesis

We analysed the differentiation of body cover in the grass snake (Natrix natrix L.) over the full length of the embryo's body at each developmental stage. Based on investigations using both light and scanning electron microscopes, we divided the embryonic development of the grass snake integument into four phases. The shape of the epidermal cells changes first on the caudal and ventral parts of the embryo, then gradually towards the rostral and dorsal areas. In stage V on the ventral side of the embryo the gastrosteges are formed from single primordia, but on the dorsal side the epidermis forms the scale primordia in stage VII. This indicates that scalation begins on the ventral body surface, and spreads dorsally. The appearance of melanocytes between the cells of the stratum germinativum in stage VII coincides with changes in embryo colouration. The first dermal melanocytes were detected in stage XI so in this stage the definitive skin pattern is formed. In the same stage the epidermis forms the first embryonic shedding complex and the periderm layer begins to detach in small, individual flakes. This process coincides with rapid growth of the embryos.