Glycerol conversion to 1,3-propanediol by newly isolated clostridia

Summary From pasteurized mud and soil samples glycerol-fermenting clostridia that produced 1,3-propanediol, butyrate and acetate were obtained. The isolates were taxonomically characterized and identified as Clostridium butyricum. The most active strain, SH1 = DSM 5431, was able to convert up to 110 g/l of glycerol to 56 g/l of 1,3-propanediol in 29 h. A few Clostridium strains from culture-collections (3 out of 16 of the C. butyricum group) and some isolates of Kutzner from cheese samples were also able to ferment glycerol, but the final concentration and the productivity of 1,3-propanediol was lower than in strain SH1. Strain SH1 grew well in a pH range between 6.0 and 7.5, with a weak optimum at 6.5, and was stimulated by sparging with N₂. Best overall productivity was obtained in fed-batch culture with a starting concentration of 5% glycerol. In all fermentations the yield of 1,3-propanediol in relation to glycerol was higher than expected from NADH production by acid formation. On the other hand the H₂ production was lower than expected, if per mole of acetyl coenzyme A one mole of H₂ is released. The observations point to a substantial transfer of reducing potential from ferredoxin to NAD, which finally results in increased 1,3-propanediol production.     

Glycerol fermentation of 1,3-propanediol by Clostridium butyricum. Measurement of product inhibition by use of a pH-auxostat

Summary The fermentation of glycerol to 1,3-propanediol, acetate, and butyrate by Clostridium butyricum was studied with respect to growth inhibition by the accumulating products. The clostridia were grown in a pH-auxostat culture at low cell density and product concentration and near maximum growth rate. The products were then added individually to the medium in increasing concentrations and the resulting depression of growth rate was used as a quantitative estimate of product inhibition. Under these conditions growth was totally inhibited at concentrations of 60 g/l for 1,3-propanediol, 27 g/l for acetic acid and 19 g/l for butyric acid at pH 6.5. Appreciable inhibition by glycerol was found only above a concentration of 80 g/l. In a pH-auxostat without added products but with high cell density as well as in batch cultures the product proportions were different. The 1,3-propanediol concentration may approach the value of complete inhibition while the concentrations of acetic and butyric acids remained below these values by at least one order of magnitude. It was therefore concluded that 1,3-propanediol is the first range inhibitor in this fermentation.     

Simultaneous detection of the two most frequent metachromatic leukodystrophy mutations

Metachromatic leukodystrophy (MLD) is an autosomal recessive neurometabolic disorder caused by deficiency of arylsulfatase A (ASA). To detect ASA mutations E2S609 and E8P2382, the two most frequent MLD mutations, a non-radioactive polymerase chain reaction (PCR)-based assay was developed. This assay is a multiple mutated primer-modulated PCR restriction fragment length polymorphism. The primers related to each mutation mismatch to create anXbaI orPstI restriction site in mutation E2S609 or E8P2382, respectively. The assay was designed to give four fragments of 160, 130, 100, and 70 bp, easy to distinguish. An internal control fragment is not necessary since both primer pairs amplify different regions of the ASA gene and fragments will be obtained in all allelic possibilities. This technique produced clear-cut results when genomic DNA, isolated either from leukocytes, cultured human fibroblasts, or paraffin-embedded autopsy material, was used as template. The assay will be of help in comparative studies on the relation between MLD genotype and phenotype, a problem not yet fully understood. Since our method was shown to work also on DNA from paraffin-embedded autopsy material, genotype/phenotype studies would not be restricted to in vivo investigations but could be done also on post mortem material, thus including investigations on a large group of cases and also studies on the relation between genotype and neuropathological features.     

Effect of pH and acetic acid on growth and 2,3-butanediol production of Enterobacter aerogenes in continuous culture

Summary The effect of pH and acetic acid on growth and 2,3-butanediol production of Enterobacter aerogenes from glucose was investigated in a microaerobic continuous culture. At a dilution rate of 0.20 h^–1 and a fixed oxygen uptake rate (OUR) of 31.5 mmol l^–1 h^–1 the biomass concentration increased with pH ranging from 5.0 to 7.0, while the specific ATP requirement of the cells decreased. In the pH range 5.5–6.5 the product concentration (butanediol + acetoin) was maximal and nearly constant. However, the specific production continuously declined with increasing pH. Experiments with addition of acetic acid showed that the various effects of pH are due to inhibition of the by-product acetic acid on cell growth. The strength of the acetic and inhibition depended only on the concentration of its undissociated form [HAc]. The biomass concentration and the specific OUR were also only functions of [HAc], irrespective of the pH. Although the specific ATP requirement (q ATP) strongly depended on the pH, [HAc] at constant pH. Offprint requests to: W.-D. Deckwer     

Tree thinking cannot taken for granted: challenges for teaching phylogenetics

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data

We present a software algorithm that combines ion trap and orbitrap product ion spectra acquired in parallel. The hybrid product ion spectra identify more peptides than when using two separate searches for the orbitrap and LTQ data. The program extracts the high-accuracy mass data from the Orbitrap mass analyzer and combines it with the high-sensitivity data analyzed in the LTQ linear ion trap; the m/z values of the high-confidence fragment ions are corrected to orbitrap mass accuracies and the fragment ion intensities are amplified. This approach utilizes the parallel spectrum measurement capabilities of the LTQ-Orbitrap. We present our approach to handling this type of hybrid data, explain our alignment program, and discuss the advantages of the chosen methodology.     

Wood diameter indicates diurnal and long-term patterns of xylem water potential in Norway spruce

The stem diameter of adult Norway spruce trees was measured to see whether changes in xylem water potential lead to detectable radial deformation of the wood. The dendrometers used in these experiments measured only the dimensional changes of the woody cylinder (sap- and heartwood). Wood diameter was measured close to the ground and just below the living crown. After correction for thermal expansion of dendrometers and wood, diurnal variation of wood diameter ranged between 50 and 180 µm. Psychrometric measurements showed that xylem water potential varied in parallel to wood diameter. Diameter changes were always more pronounced at the higher stem position and exhibited a clear diurnal pattern. During the day, wood diameter decreased with increasing vapor pressure deficit and transpiration rate and with decreasing twig water potential. At night, the wood re-expanded but did not always reach the dimension of the previous day. Pre-dawn wood diameter decreased during periods of soil drought, a process which rapidly stopped and reversed after rain events. On several days, oscillation in wood diameter was observed during the mid-day hours. The oscillation had a period of approximately 50 min and showed a phase shift between different stem heights. All observed patterns of wood shrinkage and expansion were consistent with the hypothesis that xylem water tension leads to an elastic contraction of xylem conduits. The results demonstrate that xylem diameter is more suitable than whole-stem diameter for monitoring changes in xylem water potential.     

Seabird life histories and climatic fluctuations: a phylogenetic-comparative time series analysis of North Atlantic seabirds

In the light of the predicted changes in climate as a consequence of global warming, it is a major concern how animal species will respond to altered meteorological and oceanographic conditions. Seabirds constitute a diverse group of marine top predators which have relatively low fecundity and high annual survival rates. In order to predict effects of climate change, it is a necessary precondition to first understand responses to naturally occurring climatic fluctuations. While the ecological effects of different large-scale climatic phenomena have received much attention in the recent past, the factors determining the responses of seabirds are still little understood. We analyze more than a hundred previously published time series of seabird offspring production and adult survival rates in the North Atlantic in order to detect climatic signals in this data base. As our analyses are phylogenetic-comparative, we are able to search for patterns across species. Using the correlation of these parameters with the North Atlantic Oscillation (NAO) as a measure of responsiveness to climatic variability, we find that effects of climate on either parameters considered are not more common than expected by chance. The magnitudes of the responsivenesses were entirely randomly distributed throughout the seabird phylogeny, but were not strongly related to the explanatory variables considered. However, some tendencies indicate that both life-history traits and feeding ecology may influence how seabirds respond to climatic variability. An explanation of those patterns based on life-history theory is given.