Analysis of the products of mRNA decapping and 3'-to-5' decay by denaturing gel electrophoresis

The majority of mRNA turnover is mediated either by mRNA decapping/5'-to-3' decay or exosome-mediated 3'-to-5' exonucleolytic decay. Current assays to assess mRNA decapping in vitro using cap-labeled RNA substrates rely on one-dimensional thin layer chromatography. This approach does not, however, resolve free phosphate from 7meGDP, the product of Dcp1p-mediated mRNA decapping. This can result in misinterpretation of the levels of mRNA decapping due to the generation of free phosphate following the action of the unrelated scavenger decapping activity on the products of exosome-mediated decay. In this report, we describe a simple denaturing acrylamide gel-based assay that faithfully resolves all of the possible products that can be generated from cap-labeled RNA substrates by turnover enzymes present in cell extracts. This approach allows a one-step assay to quantitatively assess the contributions of the exosome and DCP-1-type decapping on turnover of an RNA substrate in vitro. We have applied this assay to recalculate the effect of competition of cap-binding proteins on decapping in yeast. In addition, we have used the assay to confirm observations made on regulated mRNA decapping in mammalian extracts that contain much higher levels of exosome activity than yeast extracts.     

Does titanium in ionic form display a tissue-specific distribution?

Most studies have focused on the biodistribution of titanium(IV) oxide as nanoparticles or crystals in organism. But several reports suggested that titanium is released from implant in ionic form. Therefore, gaining insight into toxicokinetics of Ti ions will give valuable information, which may be useful when assessing the health risks of long-term exposure to titanium alloy implants in patients. A micro synchrotron radiation-induced X-ray fluorescence (µ-SRXRF) was utilized to investigate the titanium distribution in the liver, spleen and kidneys of rats following single intravenous or 30-days oral administration of metal (6 mg Ti/b.w.) in ionic form. Titanium was mainly retained in kidneys after both intravenous and oral dosing, and also its compartmentalization in this organ was observed. Titanium in the liver was non-uniformly distributed—metal accumulated in single aggregates, and some of them were also enriched in calcium. Correlation analysis showed that metal did not displace essential elements, and in liver titanium strongly correlated with calcium. Two-dimensional maps of Ti distribution show that the location of the element is characteristic for the route of administration and time of exposure. We demonstrated that µ-SRXRF can provide information on the distribution of titanium in internal structures of whole organs, which helps in enhancing our understanding of the mechanism of ionic titanium accumulation in the body. This is significant due to the popularity of titanium implants and the potential release of metal ions from them to the organism.     

Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings

Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next‐generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large‐scale changes in the steppe‐tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south‐western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom‐up effects in the Late Pleistocene steppe‐tundra ecosystem.     

Effects of RuBisCO and CO2 concentration on cyanobacterial growth and carbon isotope fractionation

Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO₂ concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a specific range of genetic and environmental factors that may impact ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacterium Synechococcus elongatus PCC 7942 that overexpresses RuBisCO across varying atmospheric CO₂ concentrations. We hypothesized that changes in RuBisCO expression would impact the net rates of intracellular CO₂ fixation versus CO₂ supply, and thus whole-cell carbon isotope discrimination. In particular, we investigated the impacts of RuBisCO overexpression under changing CO₂ concentrations on both carbon isotope biosignatures and cyanobacterial physiology, including cell growth and oxygen evolution rates. We found that an increased pool of active RuBisCO does not significantly affect the ¹³C/¹²C isotopic discrimination (ε_p) at all tested CO₂ concentrations, yielding ε_p of ≈ 23‰ for both wild-type and mutant strains at elevated CO₂. We therefore suggest that expected variation in cyanobacterial RuBisCO expression patterns should not confound carbon isotope biosignature interpretation. A deeper understanding of environmental, evolutionary, and intracellular factors that impact cyanobacterial physiology and isotope discrimination is crucial for reconciling microbially driven carbon biosignatures with those preserved in the geologic record.     

Do increases in the availability of standing dead trees affect the abundance,nest-site use,and niche partitioning of great spotted and middle spotted woodpeckers in riverine forests?

Standing dead trees may be a limited resource for woodpeckers in managed forests, especially for species that rely on dead wood for their nest or roost cavity, and as foraging sites. Effective conservation strategies for woodpeckers require a detailed knowledge of species’ responses to dead wood availability. To investigate the importance of standing dead wood (snags) for the abundance and nest-site use of the great spotted woodpecker Dendrocopos major and middle spotted woodpecker Leiopicus medius in mature riverine forests, we compared the responses of birds between two periods—before mass mortality, and during a pulse in standing dead trees. The density of standing dead trees available for cavity excavation by the great spotted woodpecker and the middle spotted woodpecker increased significantly during the study period: 37-fold and 4-fold, respectively. Temporal trends in the abundance of both woodpecker species from 2000 to 2015 were not significant. Great spotted woodpeckers were significantly more likely to use dead trees and places with wounds in species other than oak and ash during the outbreak period than in the pre-outbreak period. Middle spotted woodpeckers were significantly less likely to excavate cavities in tree species other than oak and ash in the outbreak period, but dead trees were more likely selected. An interspecific comparison suggests that the probability of a nest-hole having been excavated by a middle spotted woodpecker increased with a nest-hole sited in ash, in a dead tree, in a limb/branch, and decreased with a nest-hole in a closed forest. These findings suggest that woodpecker species, especially weak excavators, may benefit from an increase in dead wood availability leading to nest niche shifts into more favorable substrates for cavity excavation. However, a strong increase in dead wood availability does not modify the general pattern of niche partitioning between great spotted and middle spotted woodpeckers. Conservation plans for the specialized middle spotted woodpecker must consider the preference for dead and decaying trees. The decreasing number of large ashes and oaks, and the lack of natural regeneration of the latter species, may negatively affect the middle spotted woodpecker in the future.     

An exceptionally preserved Jurassic skink suggests lizard diversification preceded fragmentation of Pangaea

The present distribution of lizards is usually explained as a result of relatively recent global events, i.e. faunal turnovers or exchanges within and between particular continents mostly connected with glaciations and land‐bridges. However, today's disjunct distribution of the North American Xantusiidae and African Cordyliformes (close relatives of skinks) does not fit generally accepted biogeographical patterns. A new, exquisitely preserved specimen of the Late Jurassic lizard Ardeosaurus brevipes from the Solnhofen area, Germany sheds some light on the problem. A posterior projection of its parietal is known only in the Dibamidae, Gekkota and Scincoidea, taxa representing first branches on the molecular tree of lizards. The projection of the parietal is proposed to be an apomorphy of the Squamata that was lost in the common ancestor of Lacertoidea and Toxicofera (snakes, anguimorphs and iguanians). This implies a basalmost position of A. brevipes on the Squamata tree. The location of the supratemporal such as in A. brevipes characterizes all the Scincoidea and some geckos, but most geckos lack osteoderms, which are common in Scincoidea. This makes A. brevipes the oldest known crown‐member of this lineage. Moreover, this indicates that the main groups of modern lizards were already present in the Jurassic. Ancestors of Cordyliformes migrated to Gondwana in the Late Jurassic together with dinosaurs, prior to the Cretaceous separation of this ancient continent.     

The Role of SV Ion Channels Under the Stress of Mycotoxins Induced in Wheat Cells—Protective Action of Selenium Ions

Journal of Plant Growth Regulation - Mycotoxin stress, one of the currently intensively studied, was stimulated in wheat hypocotyl cells through the application of zearalenone, produced by Fusarium...     

Effect of mcl-PHA synthesis in flax on plant mechanical properties and cell wall composition

Transgenic Research - The high demand for new biomaterials makes synthesis of polyhydroxyalkanoates (PHA) in plants an interesting and desirable achievement. Production of polymers in plants is an...     

Behavioural responses to con- and heterospecific alarm cues by an alien and a coexisting native fish

Hydrobiologia - The monkey goby Neogobius fluviatilis is an invasive Ponto-Caspian fish that enters habitats of the native gudgeon Gobio gobio in European freshwaters, likely belonging to the same...