Butanol production from lignocellulosic sugars by Clostridium beijerinckii in microbioreactors

BACKGROUND

Butanol (n-butanol) has been gaining attention as a renewable energy carrier and an alternative biofuel with superior properties to the most widely used ethanol. We performed 48 anaerobic fermentations simultaneously with glucose and xylose as representative lignocellulosic sugars by Clostridium beijerinckii NCIMB 8052 in BioLector® microbioreactors to understand the effect of different sugar mixtures on fermentation and to demonstrate the applicability of the micro-cultivation system for high-throughput anaerobic cultivation studies. We then compared the results to those of similar cultures in serum flasks to provide insight into different setups and measurement methods.

RESULTS

ANOVA results showed that the glucose-to-xylose ratio affects both growth and production due to Carbon Catabolite Repression. The study demonstrated successful use of BioLector® system for the first time for screening several media and sugar compositions under anaerobic conditions by using online monitoring of cell mass and pH in real-time and at unprecedented time-resolution. Fermentation products possibly interfered with dissolved oxygen (DO) measurements, which require a careful interpretation of DO monitoring results.

CONCLUSIONS

The statistical approach to evaluate the microbioreactor setup, and information obtained in this study will support further research in bioreactor and bioprocess design, which are very important aspects of industrial fermentations of lignocellulosic biomass.

Towards a low CO2 emission building material employing bacterial metabolism (1/2): The bacterial system and prototype production

The production of concrete for construction purposes is a major source of anthropogenic CO₂ emissions. One promising avenue towards a more sustainable construction industry is to make use of naturally occurring mineral-microbe interactions, such as microbial-induced carbonate precipitation (MICP), to produce solid materials. In this paper, we present a new process where calcium carbonate in the form of powdered limestone is transformed to a binder material (termed BioZEment) through microbial dissolution and recrystallization. For the dissolution step, a suitable bacterial strain, closely related to Bacillus pumilus, was isolated from soil near a limestone quarry. We show that this strain produces organic acids from glucose, inducing the dissolution of calcium carbonate in an aqueous slurry of powdered limestone. In the second step, the dissolved limestone solution is used as the calcium source for MICP in sand packed syringe moulds. The amounts of acid produced and calcium carbonate dissolved are shown to depend on the amount of available oxygen as well as the degree of mixing. Precipitation is induced through the pH increase caused by the hydrolysis of urea, mediated by the enzyme urease, which is produced in situ by the bacterium Sporosarcina pasteurii DSM33. The degree of successful consolidation of sand by BioZEment was found to depend on both the amount of urea and the amount of glucose available in the dissolution reaction.

High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface

Microorganisms colonize a variety of extreme environments, and based on cultivation studies and analyses of PCR-amplified 16S rDNA sequences, microbial life appears to extend deep into the earth crust. However, none of these studies involved comprehensive characterizations of total DNA. Here we report results of a high-coverage DNA pyrosequencing of an apparently representative and uncontaminated sample from a deep sea oil reservoir located 2.5 km subsurface, attributing a pressure and temperature of 250 bars and 85°C respectively. Bioinformatic analyses of the DNA sequences indicate that the reservoir harbours a rich microbial community dominated by a smaller number of taxa. Comparison of the metagenome with sequences in databases indicated that there may have been contact between the oil reservoir and surface communities late in the sequence of geological events leading to oil reservoir formation. One specific gene, encoding a putative enolase, was synthesized and expressed in Escherichia coli. Enolase activity was confirmed and was found to be much more thermotolerant than for a corresponding E. coli enzyme, consistent with the conditions in the oil reservoir.

Utilization of n-alkanes by a newly isolated strain of Acinetobacter venetianus: the role of two AlkB-type alkane hydroxylases

A bacterial strain capable of utilizing n-alkanes with chain lengths ranging from decane (C10H22) to tetracontane (C40H82) as a sole carbon source was isolated using a system for screening microorganisms able to grow on paraffin (mixed long-chain n-alkanes). The isolate, identified according to its 16S rRNA sequence as Acinetobacter venetianus, was designated A. venetianus 6A2. Two DNA fragments encoding parts of AlkB-type alkane hydroxylase homologues, designated alkMa and alkMb, were polymerase chain reaction-amplified from the genome of A. venetianus 6A2. To study the roles of these two alkM paralogues in n-alkane utilization in A. venetianus 6A2, we constructed alkMa, alkMb, and alkMa/alkMb disruption mutants. Studies on the growth patterns of the disruption mutants using n-alkanes with different chain lengths as sole carbon source demonstrated central roles for the alkMa and alkMb genes in utilization of C10 to C18 n-alkanes. Comparative analysis of these patterns also suggested different substrate preferences for AlkMa and AlkMb in n-alkane utilization. Because both single and double mutants were able to grow on n-alkanes with chain lengths of C20 and longer, we concluded that yet another enzyme(s) for the utilization of these n-alkanes must exist in A. venetianus 6A2.

Interactions of the bacteriocins sakacin P and nisin with food constituents

Bacteriocins are amphiphilic peptides susceptible to adsorption to food macromolecules and proteolytic degradation. These properties may limit their use as preservation agents. The aim of the present work has been to elucidate the fate of the bacteriocin sakacin P in food. Nisin was used in a few experiments for comparison. Recovery of bacteriocins was studied in homogenates of cold-smoked salmon, chicken cold cuts and raw chicken, with verification of the results in the corresponding food products. More than 80% of the added sakacin P and nisin were quickly adsorbed to proteins in the food matrix. In foods that had not been heat-treated, proteolytic activity caused a rapid degradation of the bacteriocins, with less than 1% of the total activity left after 1 week in cold-smoked salmon, and even less in raw chicken. In heat-treated foods, the bacteriocin activity was stable for more than 4 weeks. The high fat content in salmon compared to chicken had no adverse effect on bacteriocin recovery or activity. However, mixing of triglyceride oils and bacteriocin solutions caused a considerable loss of activity. No principal differences were observed between sakacin P and nisin, but less nisin was adsorbed to muscle proteins at low pH, and the negative effect of oils was less pronounced for nisin. Growth of Listeria monocytogenes was completely inhibited for at least 3 weeks in both chicken cold cuts and cold-smoked salmon by addition of sakacin P (3.5 microg/g), despite the proteolytic degradation in the salmon.

Serum hepatocyte growth factor levels in patients with chronic renal disease--effect of GFR and pathogenesis

Hepatocyte growth factor (HGF) is a growth-promoting peptide that appears to act in a renotropic and nephroprotective manner during acute renal damage. Recent studies suggest that HGF is also of importance in chronic renal diseases. The serum HGF level is correlated with serum creatinine, and it has been suggested that glomerular and tubular diseases affect serum HGF differently. In the present study. levels of serum HGF were determined and correlated to glomerular filtration rate (GFR) in 118 patients with various chronic renal diseases. GFR was determined by 99mTc-DTPA clearance, and the GFR values were evenly distributed in the interval 5-155 mL/min/1.73 m2. Serum HGF levels increased slightly with decreasing GFR: the Pearson correlation coefficient being 0.49 (p<0.0001). In 21 additional patients with end-stage renal disease treated with continuous ambulatory peritoneal dialysis, there was a more marked increase in the serum levels of HGF. The effect of glomerular and tubular diseases on serum HGF was examined by comparing the HGF levels in two groups of patients with similar GFR values: 57 patients with mainly glomerular disorders (diabetic nephropathy with micro- or macroalbuminuria or glomerulonephritis) and 14 patients with mainly tubular disorders (polycystic kidney disease). There was no significant difference between the HGF levels of the two groups (p=0.30).

IN CONCLUSION

Serum HGF levels are correlated with GFR (for GFR > or = 5 mL/min/1.73 m2) in patients with chronic renal diseases, and glomerular and tubular disorders seem to affect the HGF level similarly.

Time-resolved 1H and 13C NMR spectroscopy for detailed analyses of the Azotobacter vinelandii mannuronan C-5 epimerase reaction

AlgE2, AlgE4, and AlgE6 are members of a family of mannuronan C-5 epimerases encoded by Azotobacter vinelandii, and are active in the biosynthesis of alginate, where they catalyze the post-polymerization conversion of beta-D-mannuronic acid residues into alpha-L-guluronic acid residues. To study the kinetics and mode of action of these enzymes, homopolymeric mannuronan and other alginate samples with various composition were epimerized by letting the enzymatic reaction take place in an NMR tube. Series of 1H NMR spectra were recorded to obtain a time-resolved picture of the epimerization progress and the formation of specific monomer sequences. Starting from mannuronan, guluronic acid contents of up to 82% were introduced by the enzymes, and the product specificity, substrate selectivity, and reaction rates have been investigated. To obtain direct information of the GulA-block formation, similar experiments were performed using a 13C-1-enriched mannuronan as substrate. The NMR results were found to be in good agreement with data obtained by a radioisotope assay based on 3H-5-labeled substrates.

Determination of porphobilinogen deaminase activity in human erythrocytes: pertinent factors in obtaining optimal conditions for measurements

Determination of porphobilinogen deaminase (PBGD; EC 4.3.1.8) activity in erythrocytes can contribute to the identification of patients suspected of acute intermittent porphyria. PBGD catalyses the polymerization of four molecules of porphobilinogen (PBG) to the highly unstable 1-hydroxymethylbilane. The 1-hydroxymethylbilane is transformed into uroporphyrinogen III by uroporphyrinogen III synthase. When this enzyme is inactivated, 1-hydroxymethylbilane cyclizes non-enzymatically to uroporphyrinogen I, which can be oxidized to uroporphyrin I. PBGD activity can be measured by quantitation of uroporphyrin I formed from PBG under conditions where this is the only end product. The purpose of the present study was to define the optimal conditions for quantitating PBGD activity in human erythrocytes. The preanalytical factors examined were: anticoagulants and methods for disruption of the erythrocytes. The analytical factors examined were: duration of preincubation, reaction time, reaction temperature, pH, ionic strength and conditions for the oxidation of uroporphyrinogen I to uroporphyrin I. Based on the results, we propose an optimized method for determination of PBGD activity in erythrocytes.

Activity and immunohistochemical localization of porphobilinogen deaminase in rat tissues

Porphobilinogen deaminase (PBGD) is an enzyme involved in the synthesis of heme. Acute intermittent porphyria (AIP) is an inherited disease resulting from a reduced activity of PBGD. The symptoms seem to be due to a neurological dysfunction. Attacks of AIP are often provoked by conditions where the PBGD activity becomes insufficient as a result of an increased synthesis of heme in the liver. How this affects the nervous tissue is still unknown. It may well be that a reduced activity of PBGD in other tissues than the liver is of importance too. The aim of the present study was to examine the activity and the immunohistochemical localization of PBGD in the following tissues of wistar female rats: brain, heart, submandibular gland, liver, kidney, pancreas, ovary, stomach, duodenum, jejunum, ileum, colon and musculature. The PBGD activity varied considerably among the tissues. It was highest in the liver, 14 pkat/g, and lowest in the jejunum, 0.7 pkat/g. The immunohistochemical localization of PBGD was studied by antibodies raised against a 40 amino acid synthetic peptide that corresponds to a segment in the C-terminal part of PBGD. The study demonstrated that the PBGD immunoreactivity was not evenly distributed among the various cell types in a given tissue. Immunohistochemical reactions were pronounced in Kupffer cells in the liver, in smooth muscle cells of arteries and arterioles, in distal and collecting tubules in the kidney, in nerve axons in the brain and in ganglionic cells in the intestine. Especially, the immunohistochemical reaction in nerve cells is notable considering the nervous dysfunction in AIP.

Bovine factor XIIa inhibitor

Bovine factor XIIa inhibitor was purified by an improved method employing affinity for heparin. N-terminal amino acid sequencing revealed a unique sequence without homology to any other known protein sequences. Peptide sequencing, however, showed that a part of the bovine factor XIIa inhibitor was homologous to human C1-inhibitor with a fraction of identical amino acid residues around 70%. Deglycosylation studies and carbohydrate analysis showed the presence of N- and O-linked carbohydrate. Bovine factor XIIa inhibitor did not inhibit plasma kallikrein and trypsin. The reactive site comprised an Arg-Asn bond, and represents the first example of asparagine as a P1' residue in Serpins with well documented inhibitory activity.