Non-indigenous fish in the northern branch of the central European invasion corridor

The assessment of risks associated with non-indigenous species implies a detailed knowledge of their taxonomical composition and distribution within a certain region. The northern branch of the central European ‘invasion corridor’—a series of canals connecting different watersheds—has formed an important migratory route for Ponto-Caspian fish (i.e. fish from the Black Sea, the Sea of Azov and the Caspian Sea). However, the current status of non-indigenous fish species in this region is very scarce. This article presents a comprehensive overview of recent distribution data of non-indigenous fish species in the northern branch of the central European invasion corridor. Here, extensive data are integrated based on studies performed during 2003–2014 comprising reliable published and unpublished records from the last 12 years. Altogether, ten non-indigenous fish species were currently found in the northern branch of the central European invasion corridor, constituting 19 % of its freshwater fish diversity. Three species, including the Prussian carp (Carassius gibelio), the round goby (Neogobius melanostomus), and the Chinese sleeper (Perccottus glenii), are considered invasive species. Eight species may potentially invade this region in the near future. A comparison of the history of non-indigenous fish species introduction in the inland waters of the northern branch and other countries of the central European invasion corridor revealed similar introduction trends. Potential expansion of non-indigenous fish species across the central European invasion corridor has international implications that require awareness, cooperation, and government support from each individual country. Disclosure of recently operating vectors for non-indigenous fish introductions within the central European invasion corridor will help predict and prevent their further spread and establishment in this region.     

Carbohydrates and Activity of Natural and Recombinant Tissue Factor

The effect of glycosylation on tissue factor (TF) activity was evaluated, and site-specific glycosylation of full-length recombinant TF (rTF) and that of natural TF from human placenta (pTF) were studied by liquid chromatography-tandem mass spectrometry. The amidolytic activity of the TF·factor VIIa (FVIIa) complex toward a fluorogenic substrate showed that the catalytic efficiency (V_max) of the complex increased in the order rTF_1–243 (Escherichia coli) < rTF_1–263 (Sf9 insect cells) < pTF for the glycosylated and deglycosylated forms. Substrate hydrolysis was unaltered by deglycosylation. In FXase, the K_m of FX for rTF_1–263-FVIIa remained unchanged after deglycosylation, whereas the k_cat decreased slightly. A pronounced decrease, 4-fold, in k_cat was observed for pTF·FVIIa upon deglycosylation, whereas the K_m was minimally altered. The parameters of FX activation by both rTF_1–263D-FVIIa and pTF_D-FVIIa were identical and similar to those for rTF_1–243-FVIIa. In conclusion, carbohydrates significantly influence the activity of TF proteins. Carbohydrate analysis revealed glycosylation on asparagines 11, 124, and 137 in both rTF_1–263 and pTF. The carbohydrates of rTF_1–263 contain high mannose, hybrid, and fucosylated glycans. Natural pTF contains no high mannose glycans but is modified with hybrid, highly fucosylated, and sialylated sugars.     

Chemical mapping of cytosines enzymatically flipped out of the DNA helix

Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in protein-DNA complexes. The generality of this method was verified with two other DNA cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein-DNA complexes.     

Cell wall structure and function in lactic acid bacteria

The cell wall of Gram-positive bacteria is a complex assemblage of glycopolymers and proteins. It consists of a thick peptidoglycan sacculus that surrounds the cytoplasmic membrane and that is decorated with teichoic acids, polysaccharides, and proteins. It plays a major role in bacterial physiology since it maintains cell shape and integrity during growth and division; in addition, it acts as the interface between the bacterium and its environment. Lactic acid bacteria (LAB) are traditionally and widely used to ferment food, and they are also the subject of more and more research because of their potential health-related benefits. It is now recognized that understanding the composition, structure, and properties of LAB cell walls is a crucial part of developing technological and health applications using these bacteria. In this review, we examine the different components of the Gram-positive cell wall: peptidoglycan, teichoic acids, polysaccharides, and proteins. We present recent findings regarding the structure and function of these complex compounds, results that have emerged thanks to the tandem development of structural analysis and whole genome sequencing. Although general structures and biosynthesis pathways are conserved among Gram-positive bacteria, studies have revealed that LAB cell walls demonstrate unique properties; these studies have yielded some notable, fundamental, and novel findings. Given the potential of this research to contribute to future applied strategies, in our discussion of the role played by cell wall components in LAB physiology, we pay special attention to the mechanisms controlling bacterial autolysis, bacterial sensitivity to bacteriophages and the mechanisms underlying interactions between probiotic bacteria and their hosts.     

Crystal structure of wild-type chaperonin GroEL

The 2.9A resolution crystal structure of apo wild-type GroEL was determined for the first time and represents the reference structure, facilitating the study of structural and functional differences observed in GroEL variants. Until now the crystal structure of the mutant Arg13Gly, Ala126Val GroEL was used for this purpose. We show that, due to the mutations as well as to the presence of a crystallographic symmetry, the ring-ring interface was inaccurately described. Analysis of the present structure allowed the definition of structural elements at this interface, essential for understanding the inter-ring allosteric signal transmission. We also show unambiguously that there is no ATP-induced 102 degrees rotation of the apical domain helix I around its helical axis, as previously assumed in the crystal structure of the (GroEL-KMgATP)(14) complex, and analyze the apical domain movements. These results enabled us to compare our structure with other GroEL crystal structures already published, allowing us to suggest a new route through which the allosteric signal for negative cooperativity propagates within the molecule. The proposed mechanism, supported by known mutagenesis data, underlines the importance of the switching of salt bridges.     

Hydraulic regime-based zonation scheme of the Curonian Lagoon

The aim of this study was to delineate the spatial zonation of the Curonian Lagoon based on the hydraulic regime and the sediment characteristics. A finite element hydrodynamic model has been applied to the Curonian Lagoon to simulate the circulation patterns for three years. With the help of a transport diffusion model the salinity distribution and the residence times of the Curonian Lagoon have been investigated when forced by river runoff and by wind. The finite element method permitted to follow the details of bathymetry and morphology of the lagoon, describing the areas of special interest with higher resolution. The hydrodynamic model has been validated using in situ water level and salinity measurements. A statistical GIS analysis of the bottom sediment characteristics and the modeled residence times and salinity distribution led to a synthetic hydraulic regime-based zonation scheme. The derived classification scheme is of crucial value for understanding the renewal capacity and biota distribution patterns in the lagoon. Guest editors: A. Razinkovas, Z. R. Gasiūnaitė, J. M. Zaldivar & P. Viaroli European Lagoons and their Watersheds: Function and Biodiversity     

4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII

A series of 4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides were designed and synthesised. Their binding potencies as inhibitors of selected recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII were measured using isothermal titration calorimetry and the thermal shift assay. To determine the structural features of inhibitor binding, the crystal structures of several compounds in complex with hCA II were determined. Several compounds exhibited selectivity towards isozymes I, II, and XIII, and some were potent inhibitors of hCA VII.     

Spectroscopic study of ALA-induced endogenous porphyrins in arthritic knee tissues: targeting rheumatoid arthritis PDT.

The inflamed synovium of rheumatoid arthritis exhibits many features typical for neoplastic tissue implying that the photodynamic therapy might be an efficient modality for chronic poliarthritis. The accumulation of endogenously produced porphyrins after administration of exogenous 5-aminolevulinic acid (ALA) in a rabbit model of rheumatoid arthritis was evaluated by fluorescence spectroscopy. Independent of the way, intravenously or intra-articularly, in which ALA was administered to the experimental animals, the highest fluorescence intensity of endogenously produced porphyrins was detected in the tissues of the inflamed joints. Besides, the application of ALA had a systemic sensitising effect on the whole organism of rabbits. The highest amount of endogenously produced porphyrins in the inflamed joints measured from the surface of the skin above the synovium tissues was detected 1-3 h after the administration of ALA. Fluorescence measurements performed on the tissue specimens ex vivo showed the predominant accumulation of porphyrins in the synovium of the inflamed joints. The fluorescence of porphyrins was also observed in the cartilage tissues taken from knee joints. However, the fluorescence spectra features indicated that the composition of porphyrins detected in the cartilage tissues was different than that in the synovial tissues. The selective accumulation of porphyrins in the inflamed synovial tissues stands up for the application of photodynamic therapy in the treatment of rheumatoid arthritis and implies the possibility to use optical non-invasive methods based on fluorescence detection of endogenously produced porphyrins for diagnostics of inflamed tissues.