Comparative Study of Sugar Fermentation and Protein Expression Patterns of Two Lactobacillus plantarum Strains Grown in Three Different Media

A comparative study of two strains of Lactobacillus plantarum (REB1 and MLBPL1) grown in commercial medium (MRS broth), cucumber juice, and liquid pig feed was performed to explore changes to the metabolic pathways of these bacteria, using a proteomics approach (two-dimensional electrophoresis and liquid chromatography-tandem mass spectrometry) combined with analyses of fermentable sugars and fermentation end products. The protein expression showed that even with an excess of glucose in all media, both strains could metabolize different carbohydrates simultaneously and that hexoses could also be used via a phosphoketolase pathway with preferential expression in liquid feed. Sugar analyses showed that the fermentation of sugars was homolactic for all media, with some heterolactic activity in liquid feed, as shown by the production of acetate. Cucumber juice (the medium with the highest glucose content) showed the lowest hexose consumption (10%), followed by liquid feed (33%) and MRS broth (50%). However, bacterial growth was significantly higher in cucumber juice and liquid feed than in MRS broth. This discrepancy was due to the growth benefit obtained from the utilization of the malate present in cucumber juice and liquid feed. Despite different growth conditions, the synthesis of essential cellular components and the stress response of the bacteria were unaffected. This study has improved our understanding of the mechanisms involved in the growth performance of an appropriate lactic acid bacterium strain to be used for food and feed fermentation, information that is of crucial importance to obtain a high-quality fermented product.     

Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization

This study describes novel algorithms for searching for most parsimonious trees. These algorithms are implemented as a parsimony computer program, PARSIGAL, which performs well even with difficult data sets. For high level search, PARSIGAL uses an evolutionary optimization algorithm, which feeds good tree candidates to a branch-swapping local search procedure. This study also describes an extremely fast method of recomputing state sets for binary characters (additive or nonadditive characters with two states), based on packing 32 characters into a single memory word and recomputing the tree simultaneously for all 32 characters using fast bitwise logical operations. The operational principles of PARSIGAL are quite different from those previously published for other parsimony computer programs. Hence it is conceivable that PARSIGAL may be able to locate islands of trees that are different from those that are easily located with existing parsimony computer programs.     

Reidentification of chromosomal CUP1 translocations in the wine yeasts Saccharomyces cerevisiae

Reciprocal translocations between chromosomes XVI and VIII were revealed in eight Saccharomyces cerevisiae strains (mostly wine ones) using pulse-field electrophoresis of native chromosomal DNAs and their hybridizations with the CUP1 and GAL4 probes. New and reciprocal translocations of at least the gene CUP1 occur at the expense of crossing-over in the hybrids of such strains with the genetic lines of normal karyotype during meiosis. Relationship between these reciprocal translocations and the sulfite (Na₂SO₃) resistance gene SSU1-R is discussed.     

Quantifying patterns and controls of mire vegetation succession in a southern boreal bog in Finland using partial ordinations

Question: How do we distinguish between concurrent allogenic and autogenic forcings behind changing patterns in plant community structures during mire development? Location: Lakkasuo raised bog, southern Finland. Methods: Two radiometrically dated peat profiles were studied using high resolution plant macrofossil analysis. A combination of partial direct and indirect gradient analyses (CCA and DCA) was applied to quantify the role of different drivers of vegetation changes. Results: Autogenic hydroseral succession explained 16% of the compositional variation in the vegetation. Disturbance successions initiated by fire explained 15% of the variation in the hummock, but only 9% in the wetter lawn. The early post‐disturbance successional stages were characterized by Eriophorum vaginatum. After partialling out the effects of peat depth and time since fire, a moisture gradient explained 29% of variation in the hummock core and 26% in the lawn. The analyses also indicated alternation between species with a similar niche. This interaction gradient explained 26% and 31% of the compositional variation in the hummock and lawn, respectively. The similar order of species replacement from both cores supported the existence of general directional succession in mire vegetation, both during the mire development and after fire events. The autogenic succession was slow and gradual while the disturbance successions were episodic and fast. Conclusion: Our results support the paradigm of the complex nature of mire vegetation dynamics where several interlinked agents have simultaneous effects. The approach of combining partial ordinations developed here appeared to be a useful tool to assess the role of different environmental factors in controlling the vegetation succession.     

Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

The human gastrointestinal (GI) tract harbors a complex community of bacterial cells in the mucosa, lumen, and feces. Since most attention has been focused on bacteria present in feces, knowledge about the mucosa-associated bacterial communities in different parts of the colon is limited. In this study, the bacterial communities in feces and biopsy samples from the ascending, transverse, and descending colons of 10 individuals were analyzed by using a 16S rRNA approach. Flow cytometric analysis indicated that 10(5) to 10(6) bacteria were present in the biopsy samples. To visualize the diversity of the predominant and the Lactobacillus group community, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was performed. DGGE analysis and similarity index comparisons demonstrated that the predominant mucosa-associated bacterial community was host specific and uniformly distributed along the colon but significantly different from the fecal community (P < 0.01). The Lactobacillus group-specific profiles were less complex than the profiles reflecting the predominant community. For 6 of the 10 individuals the community of Lactobacillus-like bacteria in the biopsy samples was similar to that in the feces. Amplicons having 99% sequence similarity to the 16S ribosomal DNA of Lactobacillus gasseri were detected in the biopsy samples of nine individuals. No significant differences were observed between healthy and diseased individuals. The observed host-specific DGGE profiles of the mucosa-associated bacterial community in the colon support the hypothesis that host-related factors are involved in the determination of the GI tract microbial community.     

Stability of the recombinant plasmid carrying theBacillus amyloliquefaciens α-amylase gene inB. subtilis

Summary Theα-amylase gene ofBacillus amyloliquefaciens has previously been cloned into pUB110 to give the recombinant plasmid, pKTH10 (Palva 1982. Gene 19:81–87). Strains transformed by this plasmid are promising candidates for industrialα-amylase production. The stability of pKTH10 was determined in variousB. subtilis strains possessing specific alleles which affect the level ofα-amylase secretion.B. subtilis strains carrying pKTH10 were cultivated in starch-containing medium for up to 50 generations without antibiotic selection and then screened for the presence of pKTH10. The plasmid proved stable enough (< 1.0% cured after 50 generations) for industrial batchwise enzyme production in two strains, but in asacU9 strain (thesacU9 mutation increases concominantly the production ofα-amylase levansucrase and proteases) 99.9% of cells had lost pKTH10 after 50 generations, although the parental plasmid (pUB110) was stable in this strain (0.09% cured after 50 generations). The instability of pKTH10 in thesacU9 strain seems somehow to be related to high expression of the clonedα-amylase gene: when grown in a medium restrictingα-amylase production, only 0.53% ofsacU9 cells had lost pKTH10 after 50 generations.     

Superfamily of α-galactosidase MEL genes of the Saccharomyces sensu stricto species complex

In order to study the molecular evolution of the yeasts grouped in the Saccharomyces sensu stricto species complex by analysis of the MEL gene family, we have cloned and sequenced two new species-specific MEL genes from Saccharomyces yeasts: S. paradoxus (MELp) and a Japanese Saccharomyces sp. (MELj). The clones were identified by sequence homology to the S. cerevisiae MEL1 gene. Both clones revealed an ORF of 1413 bp coding for a protein of 471 amino acids. The deduced molecular weights of the α-galactosidase enzymes were 52 767 for MELp and 52 378 for MELj. The nucleotide sequences of the MELp (EMBL accession no. X95505) and the MELj (EMBL accession no. X95506) genes showed 74.7% identity. The degree of identity of MELp to the MEL1 gene was 76.8% and to the S. pastorianus MELx gene, 75.7%. The MELj coding sequence was 75.1% identical to the MEL1 gene and 80.7% to the MELx gene. The data suggest that MEL1, MELj, MELp, and MELx genes are species-specific MEL genes. The strains studied each have only one MEL locus. The MELp gene is located on the S. paradoxus equivalent of S. cerevisiae chromosome X; the MELj gene was on the chromosome that comigrates with the S. cerevisiae chromosome VII/XV doublet and hybridizes to the S. cerevisiae chromosome XV marker HIS3.