Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein.     

Cork-oak woodlands as key-habitats for biodiversity conservation in Mediterranean landscapes: a case study using rove and ground beetles (Coleoptera: Staphylinidae, Carabidae)

Land-use intensification in Mediterranean agro-forest systems became a pressure on biodiversity, concerning particularly the woodland sensitive species. In 2001, the effects of a land-use gradient from old-growth cork-oak forest to a homogeneous agricultural area were assessed using rove beetles as indicators in a Mediterranean landscape. The aim was to find which species were negatively affected by land-use intensification at the landscape level and whether they benefited from cork-oak patches occurring along the land-use gradient. A total of 3,196 rove beetles from 88 taxa were sampled from all landscape types. Agricultural area recorded significantly higher numbers of abundance and species richness in relation to the cork-oak mosaics, i.e. the old-growth forest and the managed agro-forest landscapes (montados). Moreover, 70% of rove beetle indicator species common enough to be tested by IndVal displayed their highest indicator value for agriculture, showing a lower number of woodland indicators in comparison to ground beetles. Nevertheless, one rove beetle taxon was considered a specialist of closed woodland mosaics while no specialist ground beetle was found for that landscape typology. Some rare rove beetle species were also important in typifying diversity patterns of old-growth cork-oak forests. Hence, future management in Mediterranean landscapes should take into account not only indicator species common enough to be tested by IndVal, but also rare and endemic species. Considering the added value of cork-oak woodland cover for sensitive rove and ground beetle diversity, the strengthening of cork-oak woodland connectivity seems to be a crucial management that is required in agricultural Mediterranean landscapes.     

Genetic Modification of Carbon Catabolite Repression in Trichoderma reesei for Improved Protein Production

The cellulase and hemicellulase genes of the filamentous fungus Trichoderma reesei have been shown to be under carbon catabolite repression mediated by the regulatory gene cre1. In this study, strains were constructed in which the cre1 gene was either completely removed or replaced by a truncated mutant variant, cre1-1, found previously in the Rut-C30 mutant strain with enhanced enzyme production capability. The T. reesei transformants with either deletion or truncation of cre1 had clearly altered colony morphology compared with the parental strains, forming smaller colonies and fewer aerial hyphae and spores. Liquid cultures in a medium with glucose as a carbon source showed that the transformants were derepressed in cellulase and hemicellulase production. Interestingly, they also produced significantly elevated levels of these hydrolytic enzymes in fermentations carried out in a medium inducing the hydrolase genes. This suggests that cre1 acts as a modulator of cellulase and hemicellulase gene expression under both noninducing and inducing conditions. There was no phenotypic difference between the Δcre1 and cre1-1 mutant strains in any of the experiments done, indicating that the cre1-1 gene is practically a null allele. The results of this work indicate that cre1 is a valid target gene in strain engineering for improved enzyme production in T. reesei.The filamentous fungus Trichoderma reesei (Hypocrea jecorina) produces large amounts of extracellular enzymes. The majority of the secreted proteins are various plant polymer-degrading enzymes; the most abundant of these enzymes are the cellobiohydrolases and endoglucanases that act synergistically to break down cellulose. This fungus has been used as a production host for various industrial enzymes, including products tailored for textile, feed, food, and pulp and paper applications (6, 10). It has been reported that protein production levels in the industrial T. reesei process exceed 100 g/liter (7).The major cellulase and hemicellulase genes are regulated in a coordinate manner by the carbon source available (2, 9, 14). Cellulose and other plant materials and other substances (for example, lactose) induce the expression of cellulase and hemicellulase genes, while glucose acts as a repressing carbon source. Several genes coding for regulators of cellulase and hemicellulase expression have been isolated. These include CREI mediating carbon catabolite repression, the repressor ACEI, the activator ACEII, the CCAAT binding complex Hap2/3/5 (reviewed in references 2, 17, and 27) and the activator XYRI (29). The CREI protein has sequence similarity with other fungal proteins mediating glucose repression, such as Aspergillus nidulans CREA (8) and Saccharomyces cerevisiae MIG1 and RGR1 (22). In T. reesei, glucose repression has been shown to occur upon binding of CREI to specific sequences in the cbh1 promoter (13). A mutant cre1 gene (cre1-1) encoding a truncated form of CREI has been isolated from the hypercellulolytic T. reesei strain Rut-C30, which is capable of cellulase and hemicellulase production on glucose-containing media. Further evidence for the function of CREI in glucose repression was obtained by complementation of the cre1-1 mutation of Rut-C30 by the wild-type cre1 gene, which restored the glucose-repressed phenotype of the strain (15).In this paper, we wanted to address three questions. (i) What is the effect of cre1 mutations in the wild-type background? (ii) Is cre1-1 a null mutation? (iii) Can enzyme production be further improved by cre1 deletion in an industrial production strain improved greatly by mutagenesis and screening programs? Therefore, we introduced cre1-1 allele and cre1 deletion to the wild-type strain QM6a and the cre1 deletion into the industrial strain VTT-D-80133 and studied the effects of these mutations on enzyme production.     

Factors affecting the activation of pulps with laccase

Activation of fibres by radical formation is the first step when aiming at oxidative coupling of new functional groups on the fibre bound lignin. In this work, factors affecting the amount of phenoxy radicals created to unbleached TMP, CTMP, softwood kraft and hardwood kraft pulp fibres in the laccase catalysed oxidation were determined by EPR. Laccase was able to catalyse the oxidation of all the pulps studied. The reactivity of the pulp was found to be affected by both the physical accessibility of lignin in the fibres and the chemistry of the surface lignin accessible to laccase. Laccase dosage, use of extra oxygen in the laccase catalysed radicalization reaction, treatment time and also the amount and type of low-molecular weight compounds (LMWC) present in the pulp were all found to contribute to the radical content of pulp fibres measured after the enzymatic reaction. It could not been excluded that two types of reactions take place during the radical formation in fibres. Within the fibre matrix there may be both fibre material bound and soluble lignin fragments differing with respect to accessibility, molecular weight or chemical structure which can be radicalized at various rates, and the formed radicals may also undergo cross-coupling reactions reducing the amount of the total radicals.     

Multiple whole bacterial antigens in polyvalent vaccine may result in inhibition of specific responses in rainbow trout (Oncorhynchus mykiss)

The goal of fish vaccination today is to protect fish against multiple bacterial fish pathogens simultaneously using polyvalent vaccines. However, many immunological processes such as antigenic cross-reaction, antigenic competition, affinity maturation and antigen-induced suppression may affect the specificity, avidity and level of antibodies. Consequently, the biological function of antibodies may be markedly different from that predicted by conventional serologic tests. Here, we investigated the effects of vaccination and composition of vaccine on the plasma antibody levels, biological function of antibodies in opsonophagocytosis as well as the effects of vaccination on the blood leucocyte counts. Rainbow trout were vaccinated with saline or with two different polyvalent, mineral oil-adjuvanted vaccines. Vaccine 1 contained Aeromonas salmonicida, Listonella anguillarum and both Th and Fd serotypes of Flavobacterium psychrophilum antigens and vaccine 2 contained A. salmonicida, L. anguillarum and only Fd serotype of Fl. psychrophilum. The antibody-mediated opsonophagocytosis was determined as the respiratory burst (RB) activity of blood monocytes and granulocytes against the tested bacterial antigens. Three weeks after vaccination both vaccine groups and the control group showed increased RB activity against all bacterial strains. However, the increase in RB activities was non-specific and originated from the increased number of circulating granulocytes and monocytes. On the other hand, at 6 weeks post-vaccination both specific antibodies and antibody-dependent opsonophagocytosis appeared in both vaccine groups. However, the composition of the vaccine had a marked effect on the magnitude of specific responses. The Fd+Th vaccine enhanced the target specific opsonophagocytosis, to a lesser extent than the Fd vaccine. Both polyvalent vaccines appeared to mainly affect the numbers of circulating monocytes and our results suggest that the monocytes play a more significant role than the granulocytes in antibody-dependent opsonophagocytosis. Our results also suggest that the presented opsonophagocytic assay is an advantageous method to predict vaccine efficiency and that the number, and properties, of bacterial antigens in polyvalent vaccines should be carefully selected in order to avoid inhibitory effects of antigens on the specific response of fish.     

Freezing and chemical preservatives alter the stable isotope values of carbon and nitrogen of the Asiatic clam (Corbicula fluminea)

We tested the impacts of most common sample preservation methods used for aquatic sample materials on the stable isotope ratios of carbon and nitrogen in clams, a typical baseline indicator organism for many aquatic food web studies utilising stable isotope analysis (SIA). In addition to common chemical preservatives ethanol and formalin, we also assessed the potential impacts of freezing on δ¹³C and δ¹⁵N values and compared the preserved samples against freshly dried and analysed samples. All preservation methods, including freezing, had significant impacts on δ¹³C and δ¹⁵N values and the effects in general were greater on the carbon isotope values (1.3–2.2‰ difference) than on the nitrogen isotope values (0.9–1.0‰ difference). However, the impacts produced by the preservation were rather consistent within each method during the whole 1 year experiment allowing these to be accounted for, if clams are intended for use in retrospective stable isotope studies.     

Boreal carabid-beetle (Coleoptera, Carabidae) assemblages along the clear-cut originated succession gradient

We examined the occurrence of carabid beetles along a forest successiongradient in central Finland (forest age classes: 5, 10, 20, 30 and 60years since clear-cutting). Species richness of carabids was higherin the two youngest age classes, while no clear differences were detected incarabid abundance. The high species richness in the young, open sites was due toinvasion of open-habitat species. Many forest species were absent from or scarcein the young sites and became gradually more abundant towards the older forestage classes. The catches indicated a drastic decrease and assemblage-levelchange in concert with canopy closure, i.e. 20–30 years afterclear-cutting. Some forest specialists with poor dispersal ability may facelocal extinction, if the proportion of mature forest decreases further and theremaining mature stands become more isolated. We recommend that, whileharvesting timber, connectivity between mature stands is ensured, mature standsare maintained close (a few tens of metres) to each other and the matrix qualityis improved for forest species by green tree retention.     

Plant strategies along mountain vegetation gradients: a test of two theories

Abstract. We test the predictions of two theories on plant strategies along vegetation gradients of a North Scandinavian mountain area, from herb-rich birch forests at 250 m. a.s.l. to the summit at 1530 m. a.s.l. According to Grime's theory, stressful physical conditions select for an adaptational syndrome called S-strategy. The theory predicts that the prevalence of S-strategic features increases monotonically from forests to high-alpine boulder fields. Alternatively, the traits that Grime regards as S-strategic can be interpreted as adaptations to high natural-grazing pressure which culminates in moderately stressful habitats: productive enough to sustain grazers but yet so barren that moderate grazer densities suffice to deplete the vegetation. The observed vegetation patterns support this alternative view. We thus suggest that Grime's triangle should be revised as to make the role of grazing as the central causal factor behind the third strategy explicit.