Facies architecture of the Stuttgart Formation (Schilfsandstein, Upper Triassic), central Germany, and its comparison with modern Ganga system, India

The Stuttgart Formation (Schilfsandstein) is approximately 50 m thick in Thuringia, representing deposition during the “Mid-Carnian Wet Intermezzo”. Stratigraphically it occurs between the Grabfeld and Weser formations, which formed under arid conditions. It comprises NNE-SSW-trending elongate, anastomosing channelized sand-rich bodies with erosional bases (channel belts) that are several kilometres wide and pass laterally into predominantly mudstones deposited in interfluve areas. The source area of these clastics was the uplifted Norwegian Caledonides. Muddy interfluve facies is dominant in exposures in Thuringia, Central Germany.The Lower Stuttgart Formation has an unconformable base that is locally overlain by metre-thick “Basal Beds”. These consist of grey mudstones and thin sandstones deposited under humid conditions in predominantly shallow brackish water environments after a marine ingression via the Eastern Carpathian/Upper Silesian Gate. The following 30-40 m-grey, fine-grained sandstones, siltstones and mudstones were deposited in fluvial environments in channel belts and interfluve areas under humid conditions. These are followed by predominantly reddish mudstones and sandstones of mainly fluvial origin, deposited under somewhat drier conditions with seasonal droughts. The Upper Stuttgart Formation may be more than 16 m thick; it comprises reddish and grey sandstones and mudstones that were mostly deposited in lake delta settings by recurring flash floods. During the deposition of this unit climate was weakly humid with less prominent seasonal draughts.The modern Ganga Plain of India is an analogue for the depositional setting of the Stuttgart Formation. Climatic conditions in Ganga Plain are humid monsoonal with seasonal droughts and roughly comparable with those interpreted for Mid-Carnian times in Germany. The sandy deposits of incised channel belts and channels and muddy deposits of interfluve areas in the Ganga Plain are comparable with the sandstone-dominated channelized facies and mudstone dominated interfluve facies of the Stuttgart Formation, respectively.     

A complex rearrangement on chromosome 22 affecting both homologues; haplo-insufficiency of the Cat eye syndrome region may have no clinical relevance

The presence of highly homologous sequences, known as low copy repeats, predisposes for unequal recombination within the 22q11 region. This can lead to genomic imbalances associated with several known genetic disorders. We report here a developmentally delayed patient carrying different rearrangements on both chromosome 22 homologues, including a previously unreported rearrangement within the 22q11 region. One homologue carries a deletion of the proximal part of chromosome band 22q11. To our knowledge, a ‘pure’ deletion of this region has not been described previously. Four copies of this 22q11 region, however, are associated with Cat eye syndrome (CES). While the phenotypic impact of this deletion is unclear, familial investigation revealed five normal relatives carrying this deletion, suggesting that haplo-insufficiency of the CES region has little clinical relevance. The other chromosome 22 homologue carries a duplication of the Velocardiofacial/DiGeorge syndrome (VCFS/DGS) region. In addition, a previously undescribed deletion of 22q12.1, located in a relatively gene-poor region, was identified. As the clinical features of patients suffering from a duplication of the VCFS/DGS region have proven to be extremely variable, it is impossible to postulate as to the contribution of the 22q12.1 deletion to the phenotype of the patient. Additional patients with a deletion within this region are needed to establish the consequences of this copy number alteration. This study highlights the value of using different genomic approaches to unravel chromosomal alterations in order to study their phenotypic impact.     

Characterization of the atypical MAPK ERK4 and its activation of the MAPK-activated protein kinase MK5

The extracellular-regulated kinase (ERK) 4 (MAPK4) and ERK3 (MAPK6) are structurally related atypical MAPKs displaying major differences only in the C-terminal extension. ERK3 is known as an unstable mostly cytoplasmic protein that binds, translocates, and activates the MAPK-activated protein kinase (MK) 5. Here we have investigated the stability and expression of ERK4 and have analyzed its ability to bind, translocate, and activate MK5. We show that, in contrast to ERK3, ERK4 is a stable protein that binds to endogenous MK5. Interaction of ERK4 with MK5 leads to translocation of MK5 to the cytoplasm and to its activation by phosphorylation. In transfected HEK293 cells, where overexpressed catalytically dead ERK3 is able to activate MK5, catalytic activity of ERK4 is necessary for activation of MK5, indicating that ERK4 directly phosphorylates MK5. Interestingly, ERK4 dimerizes and/or oligomerizes with ERK3, suggesting that overexpressed inactive ERK3 recruits active endogenous ERK4 to MK5 for its activation. Hence, ERK3 and ERK4 cooperate in activation of MK5.     

Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7–RILP–p150Glued and late endosome positioning

Late endosomes (LEs) have characteristic intracellular distributions determined by their interactions with various motor proteins. Motor proteins associated to the dynactin subunit p150^Glued bind to LEs via the Rab7 effector Rab7-interacting lysosomal protein (RILP) in association with the oxysterol-binding protein ORP1L. We found that cholesterol levels in LEs are sensed by ORP1L and are lower in peripheral vesicles. Under low cholesterol conditions, ORP1L conformation induces the formation of endoplasmic reticulum (ER)–LE membrane contact sites. At these sites, the ER protein VAP (VAMP [vesicle-associated membrane protein]-associated ER protein) can interact in trans with the Rab7–RILP complex to remove p150^Glued and associated motors. LEs then move to the microtubule plus end. Under high cholesterol conditions, as in Niemann-Pick type C disease, this process is prevented, and LEs accumulate at the microtubule minus end as the result of dynein motor activity. These data explain how the ER and cholesterol control the association of LEs with motor proteins and their positioning in cells.     

Modulation of the oxidative stress and inflammatory cytokine response by thymoquinone in the collagen induced arthritis in Wistar rats

Thymoquinone (TQ) is the major active compound derived from Nigella sativa. Our aim of this work was to evaluate the antioxidant and antiarthritic activity of TQ in Wistar rat by collagen induced arthritis (CIA). TQ was administered at a dose of 5mgkg(-1) body weight once daily for 21days. The effects of treatment in the rats were assessed by biochemical (articular elastase, MPO, LPO, GSH, catalase, SOD and NO), inflammatory mediators (IL-1β, IL-6, TNF-α, IL-10, IFN-γ and PGE(2)) and histological studies in joints. TQ was effective in bringing significant changes on all the parameters (articular elastase, MPO, LPO, GSH, catalase, SOD and NO) studied. Oral administration of TQ resulted in significantly reduced the levels of pro-inflammatory mediators (IL-1β, IL-6, TNF-α, IFN-γ and PGE(2)) and increased level of IL-10. The protective effects of TQ against RA were also evident from the decrease in arthritis scoring and bone histology. In conclusion, the fact that TQ abolished a number of factors known to be involved in RA pathogenesis indicates that the administration of thymoquinone may have potential value in the treatment of inflammatory disease.     

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.     

Copper susceptibility in Acinetobacter junii BB1A is related to the production of extracellular polymeric substances

Acinetobacter junii BB1A cells, grown in different media, were differentially inhibited in the presence of the copper. The minimum inhibitory concentration of Cu²⁺ was influenced by the nutrient status of the media. The production of extracellular polymeric substances (EPS) was stimulated by the copper present in the growth medium. The nature of the EPS was anionic showing non-Newtonian pseudoplastic behaviour. The thermal behaviour of the EPS was studied by differential scanning calorimetry. The EPS was amorphous in nature with a crystalline index of 0.16. Scanning electron micrographs revealed its porous structure. Cells grown in the presence of quorum sensing inhibitor (QSI: 4-Nitropyridine-N-oxide) did not produce EPS and were found to be more sensitive to Cu²⁺ than cells which produced EPS in the absence of QSI. EPS production in different media in the presence and absence of Cu²⁺ was determined. The production of EPS was the highest in brain heart Infusion medium and the lowest in AB minimal medium. The sorption of Cu²⁺ by EPS extracted from cells grown in non-copper-complexing AB medium was demonstrated by energy dispersive X-ray spectroscopy. A pertinent functional aspect of EPS in providing protection to A. junii in copper stress condition has been revealed.     

Herbivory-associated degradation of tomato trichomes and its impact on biological control of Aculops lycopersici

Tomato plants have their leaves, petioles and stems covered with glandular trichomes that protect the plant against two-spotted spider mites and many other herbivorous arthropods, but also hinder searching by phytoseiid mites and other natural enemies of these herbivores. This trichome cover creates competitor-free and enemy-free space for the tomato russet mite (TRM) Aculops lycopersici (Acari: Eriophyidae), being so minute that it can seek refuge and feed inbetween the glandular trichomes on tomato cultivars currently used in practice. Indeed, several species of predatory mites tested for biological control of TRM have been reported to feed and reproduce when offered TRM as prey in laboratory experiments, yet in practice these predator species appeared to be unable to prevent TRM outbreaks. Using the phytoseiid mite, Amblydromalus limonicus, we found exactly the same, but also obtained evidence for successful establishment of a population of this predatory mite on whole plants that had been previously infested with TRM. This successful establishment may be explained by our observation that the defensive barrier of glandular plant trichomes is literally dropped some time after TRM infestation of the tomato plants: the glandular trichome heads first rapidly develop a brownish discoloration after which they dry out and fall over onto the plant surface. Wherever TRM triggered this response, predatory mites were able to successfully establish a population. Nevertheless, biological control was still unsuccessful because trichome deterioration in TRM-infested areas takes a couple of days to take effect and because it is not a systemic response in the plant, thereby enabling TRM to seek temporary refuge from predation in pest-free trichome-dense areas which continue to be formed while the plant grows. We formulate a hypothesis unifying these observations into one framework with an explicit set of assumptions and predictions to be tested in future experiments.