Propappidae and aquatic Enchytraeidae (Oligochaeta) from the farthest southeast of Russia

Two mountain streams north and northeast of Vladivostok were studied in 1983–1984. In the Komarovka Stream, a great variety of Mesenchytraeus occurred in the spring zone, among them M. crenobius sp. n. with giant setae in the ventral bundles of VI–VIII and M. vshivkovae sp. n. with numerous spermathecal diverticula. In the stream zone of the Frolovka Stream Cernosvitoviella pensau sp. n., characterized by a complicated penial bulb and a very long spermathecal ampulla, was the dominant oligochaete. Propappus arhynchotus Sokolskaya was the second most abundant oligochaete in this stream. It proved to be a true member of this genus and not synonymous with any other species. These are the first records of aquatic enchytraeids for the Primorski Region of Russia.     

Molecular dynamics simulations of EMI-BF₄ in nanoporous carbon actuators

An artificial muscle composite material consisting of carbide derived carbon (CDC) and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF₄) ionic liquid was modeled using molecular dynamics (MD) simulations, in order to determine the molecular structural rearrangements causing actuation. CDC was represented as separate curved graphene-like flakes with charges of +2, 0 or −2 on each flake, with 24–27 aromatic rings each. The charge distribution in the flakes was determined by PM6 semi-empirical optimization. The pore size distribution of CDC and the density of the material were comparable to experimental data. Molecular structure analysis revealed a preferential parallel orientation for the cations over the negatively charged CDC surfaces, while cationic rotations and reorientations could be observed for positively charged CDC. Changes in the pore occupancy for each ionic type were observed for pore sizes between 4 and 7 ?, which, together with the replacement of large cations with smaller anions, could explain the volume decrease in the anodes (and, vice versa, the volume increase in the cathodes) in this type of actuator.     

Intensive aquaculture selects for increased virulence and interference competition in bacteria

Although increased disease severity driven by intensive farming practices is problematic in food production, the role of evolutionary change in disease is not well understood in these environments. Experiments on parasite evolution are traditionally conducted using laboratory models, often unrelated to economically important systems. We compared how the virulence, growth and competitive ability of a globally important fish pathogen, Flavobacterium columnare, change under intensive aquaculture. We characterized bacterial isolates from disease outbreaks at fish farms during 2003–2010, and compared F. columnare populations in inlet water and outlet water of a fish farm during the 2010 outbreak. Our data suggest that the farming environment may select for bacterial strains that have high virulence at both long and short time scales, and it seems that these strains have also evolved increased ability for interference competition. Our results are consistent with the suggestion that selection pressures at fish farms can cause rapid changes in pathogen populations, which are likely to have long-lasting evolutionary effects on pathogen virulence. A better understanding of these evolutionary effects will be vital in prevention and control of disease outbreaks to secure food production.     

Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens

Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133‐day‐long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human‐impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).     

Active Site Conformational Dynamics in Human Uridine Phosphorylase 1

Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil (5-FU) and capecitabine. Additionally, specific molecular inhibitors of this enzyme have been found to raise endogenous uridine concentrations, which can produce a cytoprotective effect on normal tissues exposed to these drugs. Here we report the structure of hUPP1 bound to 5-FU at 2.3 Å resolution. Analysis of this structure reveals new insights as to the conformational motions the enzyme undergoes in the course of substrate binding and catalysis. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. Further, a loop toward the back end of the uracil binding pocket is shown to flexibly adjust to the varying chemistry of different compounds through an “induced-fit” association mechanism that was not observed in earlier hUPP1 structures. The details surrounding these dynamic aspects of hUPP1 structure and function provide unexplored avenues to develop novel inhibitors of this protein with improved specificity and increased affinity. Given the recent emergence of new roles for uridine as a neuron protective compound in ischemia and degenerative diseases, such as Alzheimer''s and Parkinson''s, inhibitors of hUPP1 with greater efficacy, which are able to boost cellular uridine levels without adverse side-effects, may have a wide range of therapeutic applications.     

Macrozoobenthos of Lake Peipsi-Pihkva: taxonomical composition, abundance, biomass, and their relations to some ecological parameters

The large but shallow (3,558 km², up to 15.3 m deep) lake is eutrophic, with Chironomus plumosus and Potamothrix hammoniensis as dominating macroinvertebrates in the profundal. The extensive well-aerated sublittoral with sandy bottom sediments has a mesotrophic appearance and supports a diverse fauna with several oxyphilous species, including a very abundant population of Dreissena polymorpha. The phytophilous fauna is limited to small sheltered areas only. The average abundance of the small animals of macrozoobenthos (without big molluscs) was 2,617 ind. m^–2, their biomass 12.34 g m^–2 (corresponding to 52.2 kJ m^–2) in 1964–1994. The same figures for big molluscs (mostly Dreissena) were 304 ind. m^–2 and 238 g m^–2 in 1964–1994, and even 864 ind. m^–2 and 687 g m^–2 in 1985–1988, at the time of their special mapping. The sublittoral zone revealed the lowest biomass of small animals but the highest biomass of big molluscs. The southern, shallower lake regions, more enriched with nutrients and better protected from wind, revealed a significantly higher biomass of small macrozoobenthos in the near-shore zone than the cleaner and open northern part, while no positive effect of enrichment was observed neither in the biomass of profundal zoobenthos nor in that of big molluscs. The production of the small macrozoobenthos was calculated as 111 and 53 kJ m^–2 during two annual cycles in Lake Peipsi s. s., the most productive period being the autumn overturn. Lake Peipsi-Pihkva has the highest abundance and biomass of macrozoobenthos among the large lakes of North Europe.