Ralstonia eutropha H16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools

Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied “Knallgas” bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source. It also serves as a model organism to study the metabolism of poly(β-hydroxybutyrate), a polyester which is accumulated within the cells for storage of both carbon and energy. Thermoplastic and biodegradable properties of this polyhydroxyalkanoate (PHA) have attracted much biotechnical interest as a replacement for fossil resource-based plastics. The first applications of R. eutropha aimed at chemolithoautotrophic production of single cell protein (SCP) for food and feed and the synthesis of various PHAs. The complete annotated genome is available allowing systematic biology approaches together with data provided by available omics studies. Besides PHAs, novel biopolymers of 2-hydroxyalkanoates and polythioesters or cyanophycin as well as chemicals such as alcohols, alkanes, alkenes, and further interesting value added chemicals significantly recently extended the range of products synthesized by R. eutropha. High cell density cultivations can be performed without too much effort and the available repertoire of genetic tools is rapidly growing. Altogether, this qualifies R. eutropha strain H16 to become a production platform strain for a large spectrum of products.     

Characterizing of fine particulate matter (PM1) on the platforms and outdoor areas of underground and surface subway stations

A campaign was conducted to assess the PM₁ concentration and elemental composition on the platforms and adjacent outdoor areas of an underground subway station (Imam Khomeini) and a surface subway station (Sadeghiye) in Tehran from June 2014 to November 2014. The respective mean concentrations of PM₁ on the platforms and in the outdoor areas of Imam Khomeini station were 42.04 and 30.92 µg/m³ and for Sadeghiye station 31.42 and 26.02 µg/m³. Statistical analyses demonstrated that the platforms of the Imam Khomeini and Sadeghiye stations were influenced by the adjacent ambient air of these stations (p < 0.05). PM₁ was found to be highly enriched with Fe on the platforms of metro systems, which were more frequently encountered in the Imam Khomeini station than the Sadeghiye station as 41.06% and 37.73% of the total PM₁ mass respectively. Minor elements, particularly Ba, Pb, Cr, Cu, Ni, Mn, Ti, V, and Zn, were elevated for the platform of Imam Khomeini and, to a lesser degree, the platform of Sadeghiye stations, which may be due to abrasion processes between rail tracks, wheels, and brake pads.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

扬子地台中部兰维恩至兰代洛世几丁虫生物地层

本文系统介绍了湖北宜昌普溪河、黔北遵义和四川酉阳丁市兰维恩世至兰代洛世地层中几丁虫的分布发育规律,指出扬子地台中部兰维恩世至兰代洛世的几丁虫自下而上可划分为Ｃｙａｔｈｏｃｈｉｔｉｎａｊｅｎｋｉｎｓｉ,Ｃｏｎｏｃｈｉｔｉｎａｃｏｎｕｌｕｓ,Ｅｉｓｅｎａｃｋｉｔｉｎａｕｔｅｒ和Ｌａｇｅｎｏｃｈｉｔｉｎａｄｅｕｎｆｆｉ等４个生物带,讨论了各几丁虫生物带的时代意义,此外还对几丁虫化石进行了图示和描述。     

The biomechanical analysis of bone strength: A method and its application to platycnemia

Traditional methods of bone analysis (both metric and topographic) are restricted to external characters. Spacial distribution of material is, however, equally critical to an understanding of a bone's function. Dynamic testing to determine whole bone strength can only be performed on fresh specimens. Methods for the calculation of both bending and torsional strength of other specimens (such as preserved or fossil bones) are developed in this paper. In order to illustrate the methods, the functional significance of tibial shaft cross sectional variation is investigated.     

Spatial and temporal variability in early successional patterns of an invertebrate assemblage at an offshore oil platform

The effects of selected physical and biological factors on the early development of a subtidal invertebrate assemblage were examined at an offshore oil platform in the Santa Barbara Channel (California, USA). The effects of date, year, length, and depth of submersion were investigated by replacing sets of ceramic tiles with new tiles at frequencies of 2, 4, 6, 12, and 24 months at three depths (6, 12, and 18 m) over a period of 24 months. The effects of existing colonists and depth were explored in a second experiment by removing selected early colonists from ceramic tiles deployed at the same three depths over a period of 12 months. More than 40 invertebrate taxa from seven phyla colonized the tiles. Colonial tunicates and encrusting bryozoans appeared early in the successional sequence (∼2 months), in cover ranging from <5% to 80% and from <5% to 55%, respectively. Tubiculous amphipods, barnacles, and sponges could also appear early, but in low cover (<20%). Composition of the assemblage changed over time with barnacles, sponges, and mussels becoming the principal space holders on tiles submerged for 24 months. When potential competitors were removed monthly, variation in the cover of dominant taxa (i.e., bryozoans, amphipods, barnacles) was maintained to 12 months, suggesting that other factors, such as larval availability or post-settlement mortality, were responsible for these patterns. Development of this assemblage appeared to fit a pattern of early succession that was largely predictable in terms of the composition and sequence of occurrence of dominant taxa, but variable in rate of development, depending on date of submersion, year, and depth.     

Phosphoproteomics toolbox: computational biology, protein chemistry and mass spectrometry

Protein phosphorylation is important for regulation of most biological functions and up to 50% of all proteins are thought to be modified by protein kinases. Increased knowledge about potential phosphorylation of a protein may increase our understanding of the molecular processes in which it takes part. Despite the importance of protein phosphorylation, identification of phosphoproteins and localization of phosphorylation sites is still a major challenge in proteomics. However, high-throughput methods for identification of phosphoproteins are being developed, in particular within the fields of bioinformatics and mass spectrometry. In this review, we present a toolbox of current technology applied in phosphoproteomics including computational prediction, chemical approaches and mass spectrometry-based analysis, and propose an integrated strategy for experimental phosphoproteomics.     

Extrapolation of depositional geometries of the Menorcan Miocene carbonate ramp with ground-penetrating radar

The Tortonian carbonate ramp of Menorca was previously studied on the basis of outcrops along sea-cliff outcrops. These sea cliffs, in combination with inland water wells, are the basis for a facies model for the reconstruction of the internal architecture and for characterizing the internal heterogeneities of this carbonate platform. However, any such three-dimensional reconstruction is generally limited by the given geometrical arrangement of the two-dimensional outcrops and the uncertainties of correlation with the one-dimensional wells. Here, ground-penetrating radar (GPR) has been employed in order to test and refine the depositional model. Although GPR is well known for being an excellent tool for high-resolution underground studies of sedimentary systems, the application for studying carbonate rocks is still far from routine. The reason for this discrepancy is two-fold: the minor mineralogical contrast between lithologies in carbonate rocks results in subtle reflections, and, even more important, the porosity structure in carbonates is thoroughly and repeatedly changed during diagenesis, commonly across the different facies, leading to problems in predictability of the petrophysical properties. The study of the Menorcan carbonate ramp with large distance–deep penetration GPR sections demonstrates that in spite of these difficulties, GPR is a valuable tool for extrapolating information from outcrops and wells. It is useful for characterizing heterogeneities larger than outcrop scale.