Anthracotheriid artiodactyl Anthracokeryx and an upper Eocene age for the Youganwo Formation of southern China

Abstract

The two recently collected mammalian dentary fragments from the Eocene Youganwo Formation of Guangdong Province, southern China, are referred to the anthracotheriid species Anthracokeryx naduongensis based on phylogenetic analysis and size comparison. One of these specimens (SYSU-M-1) is the first mammal fossil described from the Youganwo Formation. It was attributed previously to the perissodactyl genus Lunania. Anthracokeryx naduongensis was described originally from the lower upper Eocene Na Duong Formation in Northern Vietnam. The second record of this species supports a basal upper Eocene correlation for the Youganwo Formation, which was estimated previously as middle or late Eocene.     

Accelerated genome engineering of Pseudomonas putida by I-SceI―mediated recombination and CRISPR-Cas9 counterselection

Pseudomonas species have become reliable platforms for bioproduction due to their capability to tolerate harsh conditions imposed by large-scale bioprocesses and their remarkable resistance to diverse physicochemical stresses. The last few years have brought forth a variety of synthetic biology tools for the genetic manipulation of pseudomonads, but most of them are either applicable only to obtain certain types of mutations, lack efficiency, or are not easily accessible to be used in different Pseudomonas species (e.g. natural isolates). In this work, we describe a versatile, robust and user-friendly procedure that facilitates virtually any kind of genomic manipulation in Pseudomonas species in 3–5 days. The protocol presented here is based on DNA recombination forced by double-stranded DNA cuts (through the activity of the I-SceI homing meganuclease from yeast) followed by highly efficient counterselection of mutants (aided by a synthetic CRISPR-Cas9 device). The individual parts of the genome engineering toolbox, tailored for knocking genes in and out, have been standardized to enable portability and easy exchange of functional gene modules as needed. The applicability of the procedure is illustrated both by eliminating selected genomic regions in the platform strain P. putida KT2440 (including difficult-to-delete genes) and by integrating different reporter genes (comprising novel variants of fluorescent proteins) into a defined landing site in the target chromosome.     

The bicentenary of the research on ‘beautiful’ vavilovia (Vavilovia formosa), a legume crop wild relative with taxonomic and agronomic potential

Vavilovia formosa is a relict, endangered species from the highlands of the Caucasus and the Near East. Described in 1812, it has had an uncertain status and was finally recognized as a separate genus of tribe Fabeae (Fabaceae). Our informal international group was established in 2007 to revive the interest in this species as it had been seriously neglected for decades. Here, we provide an overview of the accumulated knowledge on V. formosa and present the results of the most recent multidisciplinary research. Three expeditions were made to two locations in Armenia in 2009, providing the material for anatomical, morphological, chemical and molecular analysis. Unlike previous attempts, ex situ conservation in Yerevan and in vitro propagation, important for potential interspecific hybridization, were successful. Molecular tools were used to clarify the taxonomic position of V. formosa, often considered the closest to the extinct ancestor of the whole tribe. The analysis of four informative regions of plastid and nuclear DNA showed that V. formosa belongs to the same clade as Lathyrus and Pisum, with a distinct status. Preservation and maintenance of V. formosa remains the only basis for further development of all other scientific aspects, especially breeding and uses in agronomy. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 524–531.     

N‐acetylcysteine increases susceptibility of HeLa cells to bacterial invasion

Serratia grimesii are non‐pathogenic bacteria capable, however, to invade eukaryotic cells provided that they synthesize intracellular metalloprotease grimelysin (Bozhokina et al. [2011] Cell. Biol. Int. 35: 111–118). To elucidate how invasion of grimelysin containing bacteria depends on physiological state of host cells, we studied the effect of N‐acetylcysteine (NAC) on susceptibility of HeLa cells to invasion by the wild‐type S. grimesii and recombinant E. coli expressing grimelysin gene. Incubation of HeLa cells with 10 mM NAC resulted in changes of cell morphology and disassembly of actin cytoskeleton that were reversed when NAC was removed from the culture medium. Both in the presence of NAC and upon its removal, the entry of grimelysin producing bacteria increased by a factor of 1.5–2 and 3–3.5 for wild‐type S. grimesii and recombinant E. coli, respectively. This effect does not correlate with cytoskeleton rearrangements but may be due to the NAC‐induced up‐regulation of cell surface receptors playing a role in cell adhesion and cell–cell junctions. A twofold difference in the efficiency of S. grimesii and recombinant E. coli to enter the NAC‐treated cells suggests that the entry of the wild‐type and recombinant bacteria occurs via different receptors which activity is differently affected by NAC. J. Cell. Biochem. 114: 1568–1574, 2013. © 2013 Wiley Periodicals, Inc.     

Complexes assembled from TMV-derived spherical particles and entire virions of heterogeneous nature

Previously, we described some structural features of spherical particles (SPs) generated by thermal remodelling of the tobacco mosaic virus. The SPs represent a universal platform that could bind various proteins. Here, we report that entire isometric virions of heterogeneous nature bind non-specifically to the SPs. Formaldehyde (FA) was used for covalent binding of a virus to the SPs surface for stabilizing the SP—virus complexes. Transmission and high resolution scanning electron microscopy showed that the SPs surface was covered with virus particles. The architecture of SP–virion complexes was examined by immunologic methods. Mean diameters of SPs and SP–human enterovirus C and SP–cauliflower mosaic virus (CaMV) compositions were determined by nanoparticle tracking analysis (NTA) in liquid. Significantly, neither free SPs nor individual virions were detected by NTA in either FA-crosslinked or FA-untreated compositions. Entirely, all virions were bound to the SPs surface and the SP sites within the SP–CaMV complexes were inaccessible for anti-SP antibodies. Likewise, the SPs immunogenicity within the FA-treated SPs–CaMV compositions was negligible. Apparently, the SP antigenic sites were hidden and masked by virions within the compositions. Previously, we reported that the SPs exhibited adjuvant activity when foreign proteins/epitopes were mixed with or crosslinked to SPs. We found that immunogenicity of entire CaMV crosslinked to SP was rather low which could be due to the above-mentioned masking of the SPs booster. Contrastingly, immunogenicity of the FA-untreated compositions increased significantly, presumably, due to partial release of virions and unmasking of some SPs-buster sites after animals immunization.     

Permafrost and fire as regulators of stream chemistry in basins of the Central Siberian Plateau

Stream chemistry in permafrost regions is regulated by a variety of drivers that affect hydrologic flowpaths and watershed carbon and nutrient dynamics. Here we examine the extent to which seasonal dynamics of soil active layer thickness and wildfires regulate solute concentration in streams of the continuous permafrost region of the Central Siberian Plateau. Samples were collected from 2006 to 2012 during the frost-free season (May–September) from sixteen watersheds with fire histories ranging from 3 to 120 years. The influence of permafrost was evident through significantly higher dissolved organic carbon (DOC) concentrations in the spring, when only the organic soil horizon was accessible to runoff. As the active layer deepened through the growing season, water was routed deeper through the underlying mineral horizon where DOC underwent adsorption and concentrations decreased. In contrast, mean concentrations of major cations (Ca²⁺ > Na⁺ > Mg²⁺ > K⁺) were significantly higher in the summer, when contact with mineral horizons in the active zone provided a source of cations. Wildfire caused significantly lower concentrations of DOC in more recently burned watersheds, due to removal of a source of DOC through combustion of the organic layer. An opposite trend was observed for dissolved inorganic carbon and major cations in more recently burned watersheds. There was also indication of talik presence in three of the larger watersheds evidenced by Cl^? concentrations that were ten times higher than those of other watersheds. Because climate change affects both fire recurrence intervals as well as rates of permafrost degradation, delineating their combined effects on solute concentration allows forecasting of the evolution of biogeochemical cycles in this region in the future.     

Globally consistent climate sensitivity of natural disturbances across boreal and temperate forest ecosystems

Disturbance regimes are changing in forests across the world in response to global climate change. Despite the profound impacts of disturbances on ecosystem services and biodiversity, assessments of disturbances at the global scale remain scarce. Here, we analyzed natural disturbances in boreal and temperate forest ecosystems for the period 2001–2014, aiming to 1) quantify their within- and between-biome variation and 2) compare the climate sensitivity of disturbances across biomes. We studied 103 unmanaged forest landscapes with a total land area of 28.2 × 10⁶ ha, distributed across five continents. A consistent and comprehensive quantification of disturbances was derived by combining satellite-based disturbance maps with local expert knowledge of disturbance agents. We used Gaussian finite mixture models to identify clusters of landscapes with similar disturbance activity as indicated by the percent forest area disturbed as well as the size, edge density and perimeter–area-ratio of disturbed patches. The climate sensitivity of disturbances was analyzed using Bayesian generalized linear mixed effect models and a globally consistent climate dataset. Within-biome variation in natural disturbances was high in both boreal and temperate biomes, and disturbance patterns did not vary systematically with latitude or biome. The emergent clusters of disturbance activity in the boreal zone were similar to those in the temperate zone, but boreal landscapes were more likely to experience high disturbance activity than their temperate counterparts. Across both biomes high disturbance activity was particularly associated with wildfire, and was consistently linked to years with warmer and drier than average conditions. Natural disturbances are a key driver of variability in boreal and temperate forest ecosystems, with high similarity in the disturbance patterns between both biomes. The universally high climate sensitivity of disturbances across boreal and temperate ecosystems indicates that future climate change could substantially increase disturbance activity.     

Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids.

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.