Helge Gyllenberg

Stochastic complexity as a taxonomic tool

In this paper we propose a method of constructing a hierarchical classification based on the notion of stochastic complexity. Minimization of stochastic complexity amounts to maximization of the information content of the classification. A dendrogram is obtained by first finding the classification which minimizes stochastic complexity and then by step-wise merging of groups such that at each step there is a minimum loss of information. The method was applied to a database containing 5313 strains of Enterobacteriaceae. The results are in reasonable accordance with present-day views on the taxonomy of Enterobacteriaceae.

A taxonomic treatment of the genus Chlorella by the technique of continuous classification

SummaryForty-one descriptions of members of the genus Chlorella have been analysed by the technique of continuous classification. This preliminary report, though general, indicates the first instance of the application of numerical principles to the algae and furthermore stresses the utility of the Rypka technique in the manual operation of limited materials. By the use of this technique the forty-one isolates have been grouped into 10 clusters.

Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria

In this paper, we compare the performance of two iterative clustering methods when applied to an extensive data set describing strains of the bacterial family Enterobacteriaceae. In both methods, the classification (i.e. the number of classes and the partitioning) is determined by minimizing stochastic complexity. The first method performs the minimization by repeated application of the generalized Lloyd algorithm (GLA). The second method uses an optimization technique known as local search (LS). The method modifies the current solution by making global changes to the class structure and it, then, performs local fine-tuning to find a local optimum. It is observed that if we fix the number of classes, the LS finds a classification with a lower stochastic complexity value than GLA. In addition, the variance of the solutions is much smaller for the LS due to its more systematic method of searching. Overall, the two algorithms produce similar classifications but they merge certain natural classes with microbiological relevance in different ways.

Enterobacteriaceae Taxonomy Approached by Minimization of Stochastic Complexity

We discuss the taxonomy of Enterobacteriaceae in the light of classification by minimization of stochastic complexity (SC). A classification which minimizes SC is optimal from the point of view of information theory. It was found that the SC-minimizing classification of a large database of strains of Enterobacteriaceae resulted in structures which correspond well to the conclusions of experts on the taxonomy of Enterobacteriaceae. The approach based on minimization of SC can therefore be considered as useful in bacterial taxonomy.

An Assessment of Cumulative Classification

We present a method for building systematics when new knowledge is continuously accumulated. The resulting classification is self-correcting and improves itself by sorting new items as they are added to the material and studied. The formulation is based on Bayesian predictive probability distributions. A new item that has not yet been classified is assigned to the class that has maximal posterior probability or is made to form a group of its own. Such a cumulative classification depends on the order in which the items are classified. The introduction of an already classified training set considerably improves the repeatability of the method. As a case study we applied the method to a large data set for the Enterobacteriaceae. The resulting classifications corresponded well to the general structure of the prevailing taxonomy of Enterobacteriaceae.

A Strain of Lactobacillus bifldus which requires Strepogenin

SUMMARY: A strain of Lactobacillus bifidus was isolated from the faeces of a breastfed infant and subcultivated in the minimal medium of Hassinen, Durbin, TomarelliB egg albumin, and blood albumin were the most potent sources. The active material was heat stable, but was completely inactivated by treatment with strong acid. All the properties of this active material studied showed a close resemblance to those of strepogenin.

Effect of the fatty acids of human milk and cow's milk on intestinal lactobacilli.

When cultivated in vitro the main intestinal lactobacillus of infants, Lactobacillus bifidus, and that occurring in the intestines of milk‐fed rats, Lactobacillus acidophilus, are influenced in different ways by free fatty acids. Apart from some short‐chain saturated acids, saturated and unsaturated fatty acids inhibit the growth of L. bifidus. L. acidophilus is inhibited by saturated fatty acids, but requires unsaturated acids as essential nutrients.

Enrichment and Isolation of Methanol-Oxidizing Yeasts and Bacteria with Special Reference to Cell Yields and Amino Acid Content

Summary Yeasts and bacteria, utilizing methanol as carbon source, were isolated from different samples (soil affected by sulphite waste water, waste water purification system, ooze from an eutrofic lake, soil, peat). Cell yields, yield coefficients, and crude protein content of 18 different yeast strains and 9 different bacterial strains isolated were investigated, and the amino acid composition of 5 yeast strains and 2 bacterial strains, supplying high cell yields, was also investigated. Yeasts produced 5–62 mg. of cell mass per 100 ml. of medium. The yield coefficients were good on the average, 6 strains had 30–50%. Bacteria grew better than yeasts in relative terms. 33–144 mg. of cells were produced per 100 ml. of medium. The yield coefficients were relatively low. No strain contained all the essential amino acids in amounts needed by man. The strains investigated did, however, contain most of these to a sufficient extent in relation to the amino acids of the reference protein of FAO (Protein requirements 1965).

Extracellular proteases from soil actinomycetes. II. The hydrolytic features of the extracellular protease of an actinomycete, isolated from peat.

Summary The ammo acids, set free from casein, haemoglobin, and egg albumin by crude fractions of the extracellular protease of a soil actinomycete (labelled AIV17) have been examined and compared with the amino acids liberated by promise, subtilisin, and trypsin under the same conditions. Of the enzymes included in the investigation, pronase showed the widest range of activity in the cleavage of peptide bounds. However, particularly fraction I of AIV17-protease (molecular weight ≥ 30.000) also liberated a wide spectrum of amino acids, especially from casein and haemoglobin. Metal chelating agents like EDTA do not inhibit the caseolytic activity of either un-fractionated AIV17-protease or of fraction I of it. Therefore, neutral metallo-proteinases obviously do not play an important role in the protease complex, produced by the strain AIV17. The activity of AIV17-protease seems to be subjected to the release (a) of alkaline amino acids like lysine, and arginine (b) of hydrophobic amino acids, particularly leucine, and the aromatic acids tyrosine and phenylalanine. The comparatively high amounts of free amino acids released may be due to the simultaneous action of several alkaline serine proteinases in combination with traces of exopeptidases. In the liberation of particularly acid amino acids, glutamic and aspartic acid from haemoglobin, fraction II of AIV17-protease (Mw 10.000–30.000) showed some relationship to subtilisin. The fraction mentioned differed from subtilisin in its pronounced affinity to peptide bounds adjacent to lysine. As a whole, the proteinases of AIV17 seem to possess a higher hydrolytic capacity than the alkaline proteinases of Bacillus subtilis.

Nitrogen metabolism control of the acetate--stimulated carotenoid synthesis in Rhodotorula sanneii.

Summary The addition of sodium acetate to the culture medium stimulated the formation of carotenoids of Rhodotorula sanneii (CBS 333) on a 3% high nitrogen (C/N ahout 11) glycerol medium. Chloramphenicol treatment intensified the favourable effect of sodium acetate on the formation of carotenoids on high nitrogen media. The concentration of chloramphenicol had a strong effect on the intensity of carotenoid synthesis. On low nitrogen medium (C/N 55) acetate did not stimulate the formation of carotenoids neither in the case of the sole addition nor with chloramphenicol. As the sole additive, acetate stimulated the assimilation of ammonium nitrogen both on high and low nitrogen media.