Cloning and characterization of the gene encoding inorganic pyrophosphatase of Escherichia coli K-12.

Escherichia coli K-12 gene ppa encoding inorganic pyrophosphatase (PPase) was cloned and sequenced. The 5' end of the ppa mRNA was identified by primer extension mapping. A typical E. coli sigma 70 promoter was identified immediately upstream of the mRNA 5' end. The structural gene of ppa contains 528 base pairs, from which a 175-amino-acid translation product, Mr 19,572, was deduced. The deduced amino acid composition perfectly fitted with that of PPase as previously determined (P. Burton, D. C. Hall, and J. Josse, J. Biol. Chem. 245:4346-4351, 1970). Furthermore, the partial amino acid sequence (residues 1 to 108) of E. coli PPase determined by S. A. Cohen (Ph.D. thesis, University of Chicago, 1978) was the same as that deduced from the nucleotide sequence. This is the first report of the cloning of a PPase gene.     

Variation in birch bark secondary chemistry between and within clones: implications for herbivory by hares

We studied the variation in bark chemistry between and within 19 European white birch ( Betula pendula ) clones and its implications to resistance to the mountain hare ( Lepus timidus ). We used one-year-old clonal plantlets originating from randomly selected naturally regenerated parental trees. The same clones were used in both chemical analyses and in feeding experiments. The condensed tannins were analysed by an acid butanol assay, other phenolic components by HPLC-DAD, and triterpenoid components by HPLC-MS. The resistance to hare was tested in open-field feeding experiment. The main phenolic compounds in birch bark were catechin derivatives, rhododendrin, platyphylloside, and condensed tannins, and the main triterpenoids were papyriferic acid and pendulic acid. Most of the variation in the concentrations of the studied compounds was found between clones for the studied phenolics and large variation for triterpenoid components were found both between clones and among plantlets within the same clone. Hares clearly selected among the studied clones. Our results suggest that birch bark chemistry play an important role in resistance to herbivory by hare. The total triterpenoids and total flavonoid-aglycones showed significant negative correlation with hare feeding. It seems that a genetic basis for bark chemistry and birch resistance is strong. Such a high variation in secondary chemistry both between clones and within individual clones indicates that European white birch populations have a good resistance towards variable environmental conditions and varying pressures from herbivory.     

Human Saliva-Derived Exosomes: Comparing Methods of Isolation

ExoQuick-TC^TM (EQ), a chemical-based agent designed to precipitate exosomes, was calibrated for use on saliva collected from healthy individuals. The morphological and molecular features of the precipitations were compared with those obtained using the classical, physical-based method of ultracentrifugation (UC). Electron microscopy and immunoelectron microscopy with anti-CD63 showed vesicular nanoparticles surrounded by bi-layered membrane, compatible with exosomes in EQ, similar to that observed with UC. Atomic force microscopy highlighted larger, irregularly shaped/aggregated EQ nanoparticles that contrasted with the single, round-shaped UC nanoparticles. ELISA (performed on 0.5 ml of saliva) revealed a tendency for a higher expression of the specific exosomal markers (CD63, CD9, CD81) in EQ than in UC (p>0.05). ELISA for epithelial growth factor receptor, a non-exosomal-related marker, showed a significantly higher concentration in EQ than in UC (p=0.04). Western blotting of equal total-protein concentrations revealed bands of CD63, CD9 and CD81 in both types of preparations, although they were less pronounced in EQ compared with UC. This may be related to a higher fraction of non-exosomal proteins in EQ. In conclusion, EQ is suitable and efficient for precipitation of salivary exosomes from small volumes of saliva; however, EQ tends to be associated with considerably more biological impurities (non-exosomal-related proteins/microvesicles) as compared with UC.     

Characterization of the 5' flanking region of the Escherichia coli ppa gene encoding inorganic pyrophosphatase: mutations in the ribosome-binding site decrease the level of ppa mRNA.

We have previously cloned and sequenced the ppa gene, encoding inorganic pyrophosphatase (PPase), of Escherichia coli K12 [Lahti, R., Pitk?ranta, T., Valve, E., Ilta, I., Kukko-Kalske, E. & Heinonen, J. (1988) Journal of Bacteriology 170, 5901-5907]. In this work mutations were constructed in the 5' flanking region of E. coli ppa and the effect on expression was determined. The minimum length of the fully active ppa5' flanking region was shown to be 117 bp. Further deletion decreased the activity, and upon deletion to nucleotide -37 the promoter activity was totally lost. A clear point of inflection was observed in the inactivation upon deletion over the nucleotide -50. This is consistent with the fact that by binding to promoters RNA polymerase holoenzyme generally covers the -50 to +20 region in E. coli genes. When the -35 sequence of ppa, AAGACA, was mutated to AAAACA, ppa expression, as measured by PPase production, decreased to 20% of the wild-type, whereas by the change of the -10 sequence, TATAAT, to TTTAAT or TATAAA, the ppa gene was totally inactivated. Furthermore, when the ribosome-binding site (RBS) sequence, AGGAAA, was altered to AAGAAA, PPase production decreased to 19% of the wild-type. Surprisingly, when the RBS sequence was mutated to the consensus RBS sequence, AGGAGG, the intracellular levels of both ppa mRNA and PPase decreased drastically. The implications of these results are discussed.     

Glucoamylase P gene of Hormoconis resinae: Molecular cloning, sequencing and introduction into Trichoderma reesei

The glucoamylase P gene of the fungus Hormoconis resinae has been cloned and sequenced from a genomic library. The gene consists of a 2153-bp protein coding region including three introns. The usual number of introns in cloned fungal glucoamylase genes has been four and in some cases five. Two of the glucoamylase P gene introns contain a sequence resembling the consensus sequence found near the 3' splice site in the introns of the fungus Trichoderma reesei cellobiohydrolase 1 (cbh1) gene. The H. resinae glucoamylase P gene, under its own promoter, was introduced into T. reesei, but no expression could be detected.     

Zasp/Cypher internal ZM-motif containing fragments are sufficient to co-localize with alpha-actinin--analysis of patient mutations

Z-band alternatively spliced PDZ-containing protein (ZASP/Cypher) has an important role in maintaining Z-disc stability in striated and cardiac muscle. ZASP/Cypher interacts through its PDZ domain with the major Z-disc actin cross-linker, alpha-actinin. ZASP/Cypher also has a conserved sequence called the ZM-motif, and it is found in two alternatively spliced exons 4 and 6. We have shown earlier that the ZM-motif containing internal regions of two related proteins ALP and CLP36 interact with alpha-actinin rod region, and that the ZM-motif is important in targeting ALP to the alpha-actinin containing structures in cell. Here, we show that the ZASP/Cypher internal fragments containing either ZM exon 4 or 6 co-localized with alpha-actinin in cultured myoblasts and nonmuscle cells. Fragments of 130 residues around the ZM-consensus were sufficient for localization, which is similar to our previous results of ALP. Moreover, ZASP/Cypher protein interacted directly with the alpha-actinin rod and competed with ALP in binding to the rod. During the inhibition of stress fiber assembly ZASP/Cypher and alpha-actinin co-localization could be partially disturbed, suggesting that ZASP/Cypher is bound to alpha-actinin mainly when alpha-actinin is localizing in stress fibers. Many point mutations found in cardiomyopathy patients are located in the internal region of ZASP/Cypher. However, we found no evidence that human patient mutations in the internal domain would affect the ZASP/Cypher co-localization with alpha-actinin, or that the mutations would destabilize the ZASP/Cypher protein.     

Cortinarius sect. Brunnei (Basidiomycota, Agaricales) in North Europe

The section Brunnei was extensively studied based on material from North Europe. To stabilise the nomenclature we studied the relevant types of taxa included in this section. Phylogenetic relationships and species limits were investigated using rDNA ITS sequences and the results were compared with the morphological data. We recognised 11 species: Cortinarius brunneus, C. clarobrunneus comb. nov., C. coleoptera, C. ectypus, C. gentilis, C. glandicolor (neotypified), C. pseudorubricosus, and four species described as new C. caesiobrunneus, C. albogaudis, C. carabus, and C. cicindela. They are described here and their taxonomy, ecology, distribution, and relationships are discussed. In addition, a key to species of the section Brunnei is provided. A total of 77 new sequences of 11 species are published including nine type sequences. Also the taxonomic assignments of sequences in the public databases belonging to the section Brunnei are revised.     

Validating quantitative fatty acid signature analysis to estimate diets of spectacled and Steller’s eiders (Somateria fischeri and Polysticta stelleri)

Fatty acid (FA) signature analysis has been used to study foraging ecology and food webs in marine ecosystems. This powerful method provides information about diets over an extended time period (e.g., 2–4 weeks), rather than just the most recent meal as with most traditional approaches. Using consumer FA signatures, along with a comprehensive database of diet FA signatures, and accounting for consumer FA metabolism, it is possible to estimate the proportions of diet items in the consumer’s diet using quantitative FA signature analysis (QFASA). However, before applying QFASA to free-ranging populations, ideally, controlled feeding studies are performed to determine FA deposition and turnover characteristics. We conducted feeding experiments to validate QFASA in captive spectacled eiders (Somateria fischeri) and Steller’s eiders (Polysticta stelleri) as a minimally invasive method for studying the diets of these threatened species. We determined FA deposition in eider adipose tissue relative to long-term diet, and developed calibration coefficients (CCs) to account for eider lipid metabolism. Using these CCs with subsequent diet trials, QFASA accurately indicated diet and diet switches. QFASA estimates also indicated that turnover of dietary FAs was not complete by 21 or 29 days, and confirmed that diets could be estimated over an extended period of >29 days. Thus, our understanding of diet can be backtracked to more than a month in captive feeding eiders. We conclude that applying QFASA techniques to eiders and other birds in the wild has the potential to provide valuable information about their diets at various life history stages.