Effects of polarization in the presence and absence of biocides on biofilms in a simulated paper machine water

The antifouling potential of electric polarization combined and not combined with biocides was studied in nonsaline warm water with high organic content. Deinococcus geothermalis is a bacterium known for forming colored biofilms in paper machines and for its persistence against cleaning and chemical treatments. When D. geothermalis biofilms grown for 24 h in simulated paper machine water were exposed to cathodic or cathodically weighted pulsed polarization at least 60% (P < 0.05) of the biofilms were removed from stainless steel (AISI 316L). Biofilm removal by 25 ppm (effective substances 5-25 ppm) of oxidizing biocides (bromochloro-5,5-dimethylhydantoin, 2,2-dibromo-2-cyanoacetamide, peracetic acid) increased to 70% when combined with cathodically weighted pulsed polarization. Using a novel instrument that allows real-time detection of reactive oxygen species (ROS) we showed that the polarization program effective in antifouling generated ROS in a pulsed manner on the steel surface. We thus suggest that the observed added value of oxidative biocides combined with polarization depended on ROS. This suggestion was supported by the finding that a reductive biocide, methylene bisthiocyanate, counteracted the antifouling effect of polarization.     

Novel polymyxin derivatives are less cytotoxic than polymyxin B to renal proximal tubular cells

The emergence of very multiresistant Gram-negative bacterial strains has reinstated polymyxins (polymyxin B, colistin), pentacationic lipopeptides, in the therapy, in spite of their nephrotoxicity. Extensive tubular reabsorption concentrates polymyxin in proximal tubular cells. The novel polymyxin derivatives NAB739, NAB7061 and NAB741 have their cyclic part identical to that of polymyxin B, but their side chain consists of uncharged octanoyl-threonyl-d-serinyl, octanoyl-threonyl-aminobutyryl, and acetyl-threonyl-D-serinyl respectively. In this study, we compared the toxicities of NAB739, NAB7061 and NAB741 with that of polymyxin B by using the porcine renal proximal tubular cell line LLC-PK1 electroporated or incubated with the selected compound. Both the ability to cause cell necrosis (quantified as the leakage of lactate dehydrogenase) and the ability to cause apoptosis (as quantified by counting apoptotic nuclei) were assessed. In electroporated cells, polymyxin B induced total (>85%) necrosis of the cells at 0.016 mM, whereas an approx. 8-fold concentration of NAB739 and NAB7961 and an approx. 32-fold concentration of NAB741 was required for the same effect. In cells treated without electroporation (incubated), polymyxin B elicited a marked degree (approx. 50%) of necrosis at 0.5mM, whereas the NAB compounds were inert even at 1mM. Neither polymyxin B nor the NAB compounds induced apoptosis.     

Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations

The mechanosensitive channel of large conductance (MscL) has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation.     

Alien Grazing: Indirect Effects of Muskrats on Invertebrates

Effects of alien herbivores on plants are quite well known, especially on oceanic islands. Much less is known about the indirect effects of alien herbivores. Via indirect effects indigenous organisms can become more vulnerable to other ecological factors. We studied the effect of dense muskrat population on aquatic invertebrates in patches, which were in different succession phases after grazing. The succession was divided into three phases:(i) open-water area, (ii) mixed floating and submerged vegetation, and (iii) undisturbed Equisetum stands. Intensive muskrat grazing affected especially the size distribution of invertebrates. The proportion of small invertebrates was greatest in clear-cut areas, whereas that of large invertebrates was greatest in the Equisetum-stands. According to activity traps, the clear-cut areas harboured good populations of small perch, which are known as invertebrate predators. The study showed that the indirect effects of alien herbivore can be considerable. In this case, they seemed to be mediated to invertebrates through the change in vegetative habitat structure. This change rendered invertebrates more vulnerable to fish predation.     

Responses of plankton and fish communities to mass removal of planktivorous fish in a two-basin lake in southern Finland

Hydrobiologia - Responses of plankton and fish communities to mass removal of cyprinid fishes were studied in a two-basin lake, Äimäjärvi, in southern Finland during 1997–2001....     

Identification of "water-soluble" toxins produced by a Stachybotrys atra strain from Finland

Toxins of a Stachybotrys atra strain from Finland proved to be soluble in a simulated gastrointestinal system. They were purified and characterized as satratoxin H, satratoxin G, and an unknown macrocyclic trichothecene with a molecular ion of 528.     

Application of methyl jasmonate reduces growth but increases chemical defence and resistance against Hylobius abietis in Scots pine seedlings

Scots pine (Pinus sylvestris L., Pinaceae) produces a terpenoid resin which consists of monoterpenes and resin acids that offer protection against herbivores and pathogen attacks. Methyl jasmonate (MJ) is a potential plant elicitor which induces a wide range of chemical and anatomical defence reactions in conifers and might be used to increase resistance against biotic damage. Different amounts of MJ (control, 10 mm , and 100 mm ) were applied to Scots pine to examine the vigour, physiology, herbivory performance, and induction of secondary compound production in needles, bark, and xylem of 2‐year‐old Scots pine seedlings. Growth decreased significantly in both MJ treated plants, and photosynthesis decreased in the 100 mm MJ treated plants, when compared to 10 mm MJ or control plants. The large pine weevil (Hylobius abietis L.) (Coleoptera: Curculionidae) gnawed a significantly smaller area of stem bark in the 100 mm treated plants than in the control or 10 mm treated plants. The 100 mm MJ treatment increased the resin acid concentration in the needles and xylem but not in the bark. Furthermore, both MJ treatments increased the number of resin ducts in newly developing xylem. The changes in plant growth and chemical parameters after the MJ treatments indicate shifts in carbon allocation, but MJ also affects plant physiology and xylem development. Terpenoid resin production was tissue‐specific, but generally increased after MJ treatments, which means that this compound may offer potential protection of conifers against herbivores.     

Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs

An increasingly important problem in genome sequencing is the failure of the commonly used shotgun assembly programs to correctly assemble repetitive sequences. The assembly of non-repetitive regions or regions containing repeats considerably shorter than the average read length is in practice easy to solve, while longer repeats have been a difficult problem. We here present a statistical method to separate arbitrarily long, almost identical repeats, which makes it possible to correctly assemble complex repetitive sequence regions. The differences between repeat units may be as low as 1% and the sequencing error may be up to ten times higher. The method is based on the realization that a comparison of only a part of all overlapping sequences at a time in a data set does not generate enough information for a conclusive analysis. Our method uses optimal multi-alignments consisting of all the overlaps of each read. This makes it possible to determine defined nucleotide positions, DNPs, which constitute the differences between the repeat units. Differences between repeats are distinguished from sequencing errors using statistical methods, where the probabilities of obtaining certain combinations of candidate DNPs are calculated using the information from the multi-alignments. The use of DNPs and combinations of DNPs will allow for optimal and rapid assemblies of repeated regions. This method can solve repeats that differ in only two positions in a read length, which is the theoretical limit for repeat separation. We predict that this method will be highly useful in shotgun sequencing in the future.     

Development of the stages of the cycle in mouse seminiferous epithelium after transplantation of green fluorescent protein-labeled spermatogonial stem cells

To study the mechanism of male germ cell differentiation, testicular germ cells carrying green fluorescent protein (GFP) as a transgene marker were transplanted into infertile mouse testis. Fluorescence-positive seminiferous tubule segments colonized with GFP-labeled donor germ cells were isolated and measured, and differentiated germ cells were analyzed in living squashed preparations. Cell associations in normal stages of the seminiferous epithelial cycle were also studied and used as a reference. Two months after transplantation, the average length of the colonies was 1.3 mm. The cell associations of transplanted colonies were consistent with those of normal stages of the cycle. However, stages of the cycle were not necessarily identical in different colonies. Three months after transplantation, the average length of transplanted colonies was 3.4 mm, and the cell association in every portion of a colony was similar to that of the corresponding stage of the cycle. Even in long fused colonies made by transplantation of a higher concentration of male germ cells, the cell association patterns in various regions of a single colony were similar and consistent with those of some of the normal stages of the cycle. Development of different stages inside the colony was observed by 6 mo after transplantation. These results indicate that the commencement of spermatogonial stem cell differentiation occurs randomly to develop different stages of the cycle in different colonies. Then, each colony shows one single stage of the cycle for a long time, even if it becomes a very large colony or fuses with other colonies. These observations indicate the existence of some kind of synchronization mechanism. By 6 mo, however, normal development of the stages of the cycle appeared in seminiferous tubules.