Raman spectroscopic monitoring of Lactarius latex

Lactarius is a genus of Basidiomycotina with mainly agaricoid representatives, which are characterised by the excretion of a typical milky fluid. In particular, the colour, changes and taste of this latex-like milk are often used as a taxonomically important character. When it is exuded several chemical reactions occur. To date, NMR spectroscopy is generally used for chemical investigation of this latex. However, as a vibrational spectroscopic technique Raman spectroscopy has several advantageous properties for this type of research. The aim of this study is to investigate whether Raman spectroscopy can be used as an alternative analytical technique to monitor the chemical reactions in Lactarius latex. Therefore, this paper presents the first Raman spectra of Lactarius latex and provides an interpretation of the Raman bands that are present. L. lacunarum latex spectra are thoroughly investigated by 2D correlation analysis and are compared with latex spectra of other species (L. chrysorrheus, L. deterrimus, L. fluens, L. glyciosmus and L. salmonicolor).     

Short- and Long-term Tannin Induced Carbon, Nitrogen and Phosphorus Dynamics in Corsican Pine Litter

Pine litter amended with either tannic acid (TA) or condensed tannins (CTs) was studied to assess the effects on C, N and P mineralization in relation to the fate of tannins by incubation experiments during various time intervals. TA induced a rapid short-term effect resulting in high C respiration and net N and P immobilisation. After one week of incubation, TA was decomposed and net C, N and P mineralization and net nitrification resembled that of the control (non-amended litter). CTs exhibited effects on net mineralization on longer terms, i.e. after several weeks of incubation until the end of the experiment (84 days). While net N and P mineralization were greatly reduced, net nitrification was only slightly affected. Most likely CTs formed complexes with organic N of the substrate thereby reducing net N mineralization, while such complexes were not involved in net nitrification processes. The reduction of net P mineralization is due to the lack of need for P by microbes when they cannot get access to N. The fact that decreasing amounts of extractable CTs were accompanied by increasing effects on mineralization processes with incubation time strongly suggests that CTs were incorporated into the litter in such a way that they were inextricable by the common solvents needed to measure tannins, such as for the Folin–Ciocalteu and HCl–butanol assays.     

Strategies of aerobic ammonia-oxidizing bacteria for coping with nutrient and oxygen fluctuations

In most natural environments as well as in engineered environments, such as wastewater treatment plants, ammonia-oxidizing bacteria (AOB) experience fluctuating substrate concentrations. Several physiological traits, such as low maintenance energy demand and decay rate, cell-to-cell communication, cell mobility, stable enzymes and RNAs, could allow AOB to maintain themselves under unfavourable circumstances. This review examines whether AOB possess such traits and how these traits might offer advantages over competing organisms such as heterotrophic bacteria during periods of starvation. In addition, within the AOB groups, differences exist in adaptation to and competitiveness under conditions of high or low ammonia or oxygen concentrations. Because these findings are of importance with regard to the ecology and activity of AOB in natural and engineered environments, concluding remarks are directed towards future research objectives that may clarify unanswered questions, thereby contributing to the general knowledge of the ecology and activity of ammonia oxidizers.     

Modelling genetic regulation of growth and form in a branching sponge

We present a mathematical model of the genetic regulation controlling skeletogenesis and the influence of the physical environment on a branching sponge with accretive growth (e.g. Haliclona oculata or Lubomirskia baikalensis). From previous work, it is known that high concentrations of silicate induce spicule formation and upregulate the silicatein gene. The upregulation of this gene activates locally the production of spicules in the sponge and the deposition of the skeleton. Furthermore, it is known that the expression of the gene Iroquois induces the formation of an aquiferous system, consisting of exhalant and inhalant pores. We propose a model of the regulatory network controlling the separation in time and space of the skeletogenesis and the formation of the aquiferous system. The regulatory network is closely linked with environmental influences. In building a skeleton, silicate is absorbed from the environment. In our model, silicate is transported by diffusion through the environment and absorbed at the surface of a geometric model of the sponge, resulting in silicate gradients emerging in the neighbourhood of the sponge. Our model simulations predict sponge morphology and the positioning of the exhalant pores over the surface of the sponge.     

Base excision repair and its role in maintaining genome stability

For all living organisms, genome stability is important, but is also under constant threat because various environmental and endogenous damaging agents can modify the structural properties of DNA bases. As a defense, organisms have developed different DNA repair pathways. Base excision repair (BER) is the predominant pathway for coping with a broad range of small lesions resulting from oxidation, alkylation, and deamination, which modify individual bases without large effect on the double helix structure. As, in mammalian cells, this damage is estimated to account daily for 10(4) events per cell, the need for BER pathways is unquestionable. The damage-specific removal is carried out by a considerable group of enzymes, designated as DNA glycosylases. Each DNA glycosylase has its unique specificity and many of them are ubiquitous in microorganisms, mammals, and plants. Here, we review the importance of the BER pathway and we focus on the different roles of DNA glycosylases in various organisms.     

Reconstruction of protein backbones from the BriX collection of canonical protein fragments

As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed from smaller recurrent elements, between 4 and 8 residues long. Finally, we observed that a significant amount of short sequences tend to display strong structural ambiguity between alpha helix and extended conformations. When the sequence length increases, this so-called sequence plasticity is no longer observed, illustrating the context dependency of polypeptide structures.     

Tumor cell killing by in vitro affinity-matured recombinant human monoclonal antibodies

We have developed a method that allows the rapid improvement of the affinity of phage-displayed antibody fragments by selection on intact eukaryotic cells. A single chain Fv fragment, specific for the tumor-associated Ep-Cam molecule, was mutagenized by shuffling of the immunoglobulin light chain variable region and DNA shuffling of both heavy and light chain variable regions. Higher-affinity mutants were selected from small phage display libraries by cell panning under stringent conditions. When converted to an intact fully human antibody, the mutagenized anti-tumor monoclonal antibody displayed an affinity of 0.4 nM, a 15-fold improvement over the affinity of the original antibody. Compared to previously reported affinity maturation schemes, panning on intact cells does not require purified targets for selection and may be particularly useful when the target molecule can not be expressed as a recombinant molecule or easily purified without disrupting its native configuration. In vitro tumor cell killing assays demonstrated an improved performance of the higher-affinity antibody in complement-mediated tumor cell killing. In contrast, the lower-affinity antibody performed somewhat better in antibody-dependent cellular cytotoxicity assays and penetrated better in multicell spheroids of tumor cells, an in vitro model for the tumor penetration capacity of antibodies. Received: 26 February 2000 / Accepted: 26 January 2001     

Buoyancy regulation in Microcystis aeruginosa grown at different temperatures

Abstract The buoyancy regulation in light-limited cultures of the gas vacuolate cyanobacterium Microcystis aeruginosa AK1 was studied at three temperatures, 15, 20 and 28°C. At the two highest temperatures the organism remained buoyant during the entire light period, whereas at the lowest temperature the buoyancy was reduced at the start of the light period. With this temperature the buoyancy was lost during the light period. This reduced buoyancy was caused by an increase in ballast and a decrease in the gas vesicle volume. Buoyancy changes during a transient state with slow changes in temperatures, i.e., 1°C per day, were caused by changes in polysaccharide ballast. The gas vesicle volume showed no significant change during the transient state.
The maximal photosynthetic rate was dependent upon the growth and incubation temperature, whereas the light harvesting efficiency was independent of the temperature. The results are discussed in an ecological context.     

In vitro synthesis of fractofuranosyl-only oligosaccharides from inulin and fructose by purified chicory root fructan:fructan fructosyl transferase

Besides the non-reducing inulin series of gluco-frueto oligosaccharides which are common in Asteraceae, two series of reducing fructofuranosyl-only oligosaccharides occur in overwintering, forced, and sprouting chicory roots. Such inulo-n-oses could be produced by the action of an endo-inulinase on gluco-fructo oligosaccharides. We show here that similar series of inulo-n-oses as found in vivo can be produced by incubating fructose and inulin with a purified fructamfructan tructosyl transferase (FFT; EC 2.4.1.100) from chicory roots ( Cichorium intybus L.). Therefore fructose (but not glucose) can act as an acceptor for FFT. Since the inulo-n-oses only appear in vivo once the endogenous fructose concentration increases, we conclude that they are not the result of a putative endo-inulinase but of FFT activity.     

The paternal sex ratio chromosome in the parasitic wasp Trichogramma kaykai condenses the paternal chromosomes into a dense chromatin mass.

A recently discovered B chromosome in the parasitoid wasp Trichogramma kaykai was found to be transmitted through males only. Shortly after fertilization, this chromosome eliminates the paternal chromosome set leaving the maternal chromosomes and itself intact. Consequently, the sex ratio in these wasps is changed in favour of males by modifying fertilized diploid eggs into male haploid offspring. In this study, we show that in fertilized eggs at the first mitosis the paternal sex ratio (PSR) chromosome condenses the paternal chromosomes into a so-called paternal chromatin mass (PCM). During this process, the PSR chromosome is morphologically unaffected and is incorporated into the nucleus containing the maternal chromosomes. In the first five mitotic divisions, 67% of the PCMs are associated with one of the nuclei in the embryo. Furthermore, in embryos with an unassociated PCM, all nuclei are at the same mitotic stage, whereas 68% of the PCM-associated nuclei are at a different mitotic phase than the other nuclei in the embryo. Our observations reveal an obvious similarity of the mode of action of the PSR chromosome in T. kaykai with that of the PSR-induced paternal genome loss in the unrelated wasp Nasonia vitripennis.