Simulation studies on bacteriorhodopsin α-helices

Bacteriorhodopsin (BR) is a membrane protein which pumps protons through the plasma membrane. Transmembrane BR helical segments are subjected to simulation studies in order to investigate the effect of bilayer environment in various simulation conditions. A bilayer potential is introduced to the system to mimic the lipid membrane. The structures from the simulations are compared with the experimentally determined structures in terms of geometrical properties. Electrostatic contribution to the helix packing is also investigated. The simulation results show that the packing geometry of the transmembrane helices is highly affected by the bilayer potential. The results obtained from the simulations may be used for further simulation studies and analysis in investigating transmembrane helix packing. Received: 5 July 1999 / Revised version: 5 October 1999 / Accepted: 15 October 1999     

Simulation studies on bacteriorhodopsin bundle of transmembrane α segments

Bacteriorhodopsin (BR) is a membrane protein which pumps protons through the plasma membrane. Seven transmembrane BR helical segments are subjected to simulation studies in order to investigate the packing process of transmembrane helices. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Helix packing is optimized according to a semi-empirical potential mainly composed of six components: a bilayer potential, a crossing angle potential, a helix dipole potential, a helix-helix distance potential, a helix orientation potential and a helix-helix distance restraint potential (a loop potential). Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. The structures from the simulations are compared with the experimentally determined structures in terms of geometry. The structures generated show similar shapes to the experimentally suggested structure even without the helix-helix distance restraint potential. However, the relative locations of individual helices were reproduced only when the helix-helix distance restraint potential was used with restraint conditions. Our results suggest that transmembrane helix bundles resembling those observed experimentally may be generated by simulations using simple potentials. Received: 19 April 1999 / Revised version: 6 September 1999 / Accepted: 17 September 1999     

A simplification of the protein assay method of Ramsay et al. for the quantification of Thiobacillus ferrooxidans in the presence of ferric precipitates

A variation on Ramsay's method for microbial protein determination has been developed in order to quantify Thiobacillus ferrooxidans attached to ferric precipitates or in aqueous suspensions containing such precipitates. Some modifications have been introduced to provide a method that is more sensitive, simple and rapid. A linear standard curve is presented to permit a direct correlation between the protein concentration (mg/l) and the cell concentration (10⁶ cells/ml). An application of this method has been demonstrated in the quantification of biomass immobilized on the surface of polyurethane foam particles in a packed bed reactor, several experiments having been conducted to establish the best conditions for the quantification studies. Received: 12 August 1999 / Received revision: 21 December 1999 / Accepted: 29 December 1999     

DNA hydrolysis by inorganic catalysts

Non-enzymatic reagents that efficiently promote the hydrolytic cleavage of DNA currently receive much attention since they have many potential applications in molecular biology. This review focuses on recent progress in the hydrolysis of the phosphodiester backbone of DNA by metal ions and metal complexes. Pioneering work on the sequence-selective DNA scission by an artificial restriction enzyme, which is prepared by covalent attachment of a cerium(IV) complex to an antisense-deoxyoligonucleotide, is discussed. Received: 22 March 1999 / Received revision: 28 May 1999 / Accepted: 28 May 1999     

Recent developments in the characterization and biotechnological production of sweet-tasting proteins

 The state of the art regarding the six known sweet-tasting proteins (thaumatin, monellin, mabinlin, pentadin, brazzein and curculin) and the taste-modifying protein miraculin is reviewed. Their biochemical properties, molecular genetics and biotechnological production are assessed. All of these proteins have been isolated from plants that grow in tropical rainforests. They share no sequence homology or structural similarities. Nonetheless, one of them, thaumatin, shares extensive homology with certain non-sweet proteins found in other plants. The potential industrial applications of the sweet-tasting proteins are also discussed, placing special emphasis on the barriers that a recombinant product of these characteristics will have to overcome before it reaches the market. Received: 14 June 1999 / Received revision: 30 August 1999 / Accepted: 3 September 1999     

l-Glutamate and l-lysine: traditional products with impetuous developments

 Amino acids have been produced with the aid of microorganisms for nearly 40 years now. The economic importance of these cellular building blocks is enormous. Demand for them is rising continuously and currently more than 10⁶ tonnes/year are required. Continual efforts to increase production performance are directed towards the microorganisms themselves, as well as towards technical improvements of the respective processes. A special position within the amino-acid-producing microorganisms is traditionally occupied by Corynebacterium glutamicum. Molecular research in conjunction with NMR studies of flux has revealed fascinating new properties of this particular organism, including the existence of a new type of exporter and reverse fluxes within the anaplerosis. The knowledge gained will enable the further improvement of production strains and furthermore extend fundamental insights into metabolite flux management within bacteria in general. Received: 8 December 1998 / Received revision: 1 March 1999 / Accepted: 5 March 1999     

How tumors escape immune destruction and what we can do about it

There is strong circumstantial evidence that tumor progression in cancer patients is controlled by the immune system. As will be detailed below, this conclusion is based on observations that tumor progression is often associated with secretion of immune suppressive factors and/or downregulation of MHC class I antigen presentation functions. The inference is that tumors must have elaborated strategies to circumvent an apparently effective immune response. Importantly, a tumor-specific immune response cannot be detected in most individuals. While this failure is in part technical, it also suggests that the magnitude of the immune responses to which tumors have to respond is low. This raises the concern, which is the underlying theme of this commentary, that a more robust immune response elicited by deliberate vaccination will exacerbate the rate of immune escape and nullify the potential benefits of immune-based therapies. Received: 20 March 1999 / Accepted: 3 May 1999     

Cryoconservation—archiving for the future

Mouse genetics is set to play a pivotal role in the key post-genome challenge—the study of mammalian gene function. Addressing this challenge will involve the development and application of systematic mutagenesis approaches. The expanding mouse mutant resource that will result threatens to overwhelm the currently available animal facility space. Cryopreservation of both mouse embryos and spermatozoa is currently widely employed for the efficient archiving of mouse stocks. Distribution and dissemination of new and existing mouse strains is simplified by the availability of extensive frozen archives. Also, the availability of archives of frozen spermatozoa provides a potential powerful route for the production of backcross progeny for rapid genetic mapping. Moreover, frozen oocytes and ovaries may offer a valuable addition to the current cryopreservation approaches. Comprehensive mouse mutant archives will provide an essential resource for mammalian genetics throughout the 21^st century. Received: 16 December 1999 / Accepted: 17 December 1999     

Pharmaceutically active secondary metabolites of microorganisms

The antibiotics have been useful in our battles against infectious bacteria and fungi for over 50 years. However, many antibiotics are used commercially, or are potentially useful, in medicine for activities other than their antibiotic action. They are used as antitumor agents, immunosuppressive agents, hypocholesterolemic agents, enzyme inhibitors, antimigraine agents, and antiparasitic agents. A number of these products were first discovered as antibiotics which failed in their development as such, or as mycotoxins. In addition to the above alternative applications, new powerful antibiotics have been discovered and commercialized in recent years and others are in clinical testing at the moment. A few successful secondary metabolites appear to have no antibiotic activity. The recently increased development of resistance to older antibacterial and antifungal drugs is being met with the use or clinical testing of older, underutilized or previously nondeveloped narrow-spectrum antibacterial products as well as powerful semisynthetic antifungal agents. Received: 28 December 1998 / Received revision: 26 April 1999 / Accepted: 1 May 1999     

Ice crystallization by Pseudomonas syringae

Several bacterial species can serve as biological ice nuclei. The best characterized of these is Pseudomonas syringae, a widely distributed bacterial epiphyte of plants. These biological ice nuclei find various applications in different fields, but an optimized production method was required in order to obtain the highly active cells which may be exploited as ice nucleators. The results presented here show that P. syringae cells reduce supercooling of liquid or solid media and enhance ice crystal formation at sub-zero temperatures, thus leading to a remarkable control of the crystallization phenomenon and a potential for energy savings. Our discussion focuses on recent and future applications of these ice nucleators in freezing operations, spray-ice technology and biotechnological processes. Received: 21 December 1999 / Received revision: 29 February 2000 / Accepted: 6 March 2000     

Potential commercial applications of microbial surfactants

Surfactants are surface-active compounds capable of reducing surface and interfacial tension at the interfaces between liquids, solids and gases, thereby allowing them to mix or disperse readily as emulsions in water or other liquids. The enormous market demand for surfactants is currently met by numerous synthetic, mainly petroleum-based, chemical surfactants. These compounds are usually toxic to the environment and non-biodegradable. They may bio-accumulate and their production, processes and by-products can be environmentally hazardous. Tightening environmental regulations and increasing awareness for the need to protect the ecosystem have effectively resulted in an increasing interest in biosurfactants as possible alternatives to chemical surfactants. Biosurfactants are amphiphilic compounds of microbial origin with considerable potential in commercial applications within various industries. They have advantages over their chemical counterparts in biodegradability and effectiveness at extreme temperature or pH and in having lower toxicity. Biosurfactants are beginning to acquire a status as potential performance-effective molecules in various fields. At present biosurfactants are mainly used in studies on enhanced oil recovery and hydrocarbon bioremediation. The solubilization and emulsification of toxic chemicals by biosurfactants have also been reported. Biosurfactants also have potential applications in agriculture, cosmetics, pharmaceuticals, detergents, personal care products, food processing, textile manufacturing, laundry supplies, metal treatment and processing, pulp and paper processing and paint industries. Their uses and potential commercial applications in these fields are reviewed. Received: 29 July 1999 / Received revision: 8 November 1999 / Accepted: 9 November 1999     

Effects of pesticides on seagrass beds

In the German Wadden Sea there has been a remarkable decline in seagrass beds. It was the aim of this study to test whether herbicide contamination could be a reason for this. Concentrations of triazine herbicides such as atrazine, simazine and terbutylazine as well as phenylurea herbicides were measured in Wadden Sea sediments within or in the neighbourhood of seagrass meadows. Sediments were thus used as a marker for medium-term contamination of the Wadden Sea. The respective concentrations were examined in relation to the density and status of the seagrass meadows. Preliminary results show that there may be a connection between seagrass decline and herbicide contamination in the parts of the Wadden Sea sampled. A comparison with other contamination is also given. Received: 11 January 1999 / Received in revised form: 1 December 1999 / Accepted: 8 December 1999     

High- and low-molecular-mass microbial surfactants

Microorganisms synthesize a wide variety of high- and low-molecular-mass bioemulsifiers. The low-molecular-mass bioemulsifiers are generally glycolipids, such as trehalose lipids, sophorolipids and rhamnolipids, or lipopeptides, such as surfactin, gramicidin S and polymyxin. The high-molecular-mass bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins or complex mixtures of these biopolymers. The low-molecular-mass bioemulsifiers lower surface and interfacial tensions, whereas the higher-molecular-mass bioemulsifiers are more effective at stabilizing oil-in-water emulsions. Three natural roles for bioemulsifiers have been proposed: (i) increasing the surface area of hydrophobic water-insoluble growth substrates; (ii) increasing the bioavailability of hydrophobic substrates by increasing their apparent solubility or desorbing them from surfaces; (iii) regulating the attachment and detachment of microorganisms to and from surfaces. Bioemulsifiers have several important advantages over chemical surfactants, which should allow them to become prominent in industrial and environmental applications. The potential commercial applications of bioemulsifiers include bioremediation of oil-polluted soil and water, enhanced oil recovery, replacement of chlorinated solvents used in cleaning-up oil-contaminated pipes, vessels and machinery, use in the detergent industry, formulations of herbicides and pesticides and formation of stable oil-in-water emulsions for the food and cosmetic industries. Received: 21 December 1998 / Received revision: 11 March 1999 / Accepted: 14 March 1999     

A bispecific single-chain antibody directed against EpCAM/CD3 in combination with the cytokines interferon α and interleukin-2 efficiently retargets T and CD3+CD56+ natural-killer-like T lymphocytes to EpCAM-expressing tumor cells

 Cytokine-induced killer cells (CIK), generated in vitro from peripheral blood mononuclear cells (PBMC) by addition of interferon γ (IFNγ), interleukin-2 (IL-2), IL-1 and a monoclonal antibody (mAb) against CD3, are highly efficient cytotoxic effector cells with the CD3⁺CD56⁺ phenotype. In this study, we evaluated whether the cytotoxicity of these natural-killer-like T lymphocytes against the colorectal tumor cell line HT29 can be enhanced by the addition of a bispecific single-chain antibody (bsAb) directed against EpCAM/CD3. For determination of bsAb-redirected cellular cytotoxicity we used a new flow-cytometric assay, which directly counts viable tumor cells and can assess long-term cytotoxicity. We found that this bsAb induced distinct cytotoxicity at a concentration above 100 ng/ml with both PBMC and CIK at an effector-to-target cell ratio as low as 1:1. CIK cells revealed higher bsAb-redirected cytotoxicity than PBMC. Cellular cytotoxicity appeared after 24 h whereas PBMC showed the highest bsAb-redirected cytotoxicity after 72 h. The addition of the cytokines IL-2 and IFNα but not granulocyte/macrophage-colony-stimulating factor enhanced bsAb-redirected cytotoxicity of both PBMC and CIK. When the bsAb was combined with the murine mAb BR55-2, which recognizes the Lewis^y antigen, bsAb-redirected cytotoxicity was partly augmented, whereas murine mAb 17-1A, which binds to EpCAM as well, slightly suppressed bsAb-redirected cytotoxicity induced by the bsAb. We conclude that CIK generated in vitro or in vivo combined with this new EpCAM/CD3 bsAb and the cytokine IL-2 should be evaluated for the treatment of EpCAM-expressing tumors. Received: 9 December 1999 / Accepted: 18 May 2000     

Acidophiles in bioreactor mineral processing

Mineral processing in bioreactors has become established in several countries during the past decade with industrial application of iron- and sulfur-oxidizing bacteria to release occluded gold from mineral sulfides. Cobalt extraction in bioreactors has also been commercialized, and development of high-temperature biooxidation of copper sulfides has reached pilot-plant scale. A variety of potentially useful mineral sulfide-oxidizing thermophiles have been recognized, but the most active strains have not been fully characterized. Received: July 11, 1999 / Accepted: December 27, 1999     

Large numbers of mice established by in vitro fertilization with cryopreserved spermatozoa: implications and applications for genetic resource banks, mutagenesis screens, and mouse backcrosses

Recent advances in the methodologies for cryopreservation of mouse spermatozoa have opened up a number of opportunities for mouse geneticists. We have investigated various applications for this relatively new technology and have explored the potential of sperm freezing coupled with IVF for archiving, stock building, and the rapid establishment of backcrosses. Firstly, we investigated the use of sperm freezing for the archiving of (C3H/HeH × BALB/c)F₁ progeny from a large-scale mutagenesis program. We have demonstrated that it is possible to establish efficient, comprehensive, and deep archives and that potentially thousands of offspring can be derived from the frozen spermatozoa of a single mutant male mouse. Secondly, we examined the efficacy of sperm freezing for a number of other genotypes. For at least some genotypes, frozen spermatozoa can be utilized to rapidly build stock far more quickly than by conventional methods. Finally, we demonstrated that it is feasible to use frozen spermatozoa from the mouse mutant archive for the rapid generation of mutant backcross progeny. Received: 8 February 1999 / Accepted: 5 May 1999     

A new method for protein domain recognition

A fuzzy cluster method is presented to recognize protein domains. This algorithm can identify domains globally. A protein structure set was used to test the algorithm. Among 219 proteins, 66.7% yielded results that agreed with the reference definitions, 30.6% showed minor differences, and only 2.7% (six proteins) showed major differences with the reference. The new method is more than 20 times fast than previous algorithms. Received: 9 November 1998 / Revised version: 20 December 1999 / Accepted: 20 December 1999     

Aqueous two-phase: the system of choice for extractive fermentation

Extractive fermentation in aqueous two-phase systems is a meaningful approach to overcome low product yield in a conventional fermentation process, and by proper design of the two-phase system it is possible to obtain the product in a cell-free stream. The characteristics of an aqueous two-phase system, various polymers used for forming an aqueous two-phase system, the physicochemical parameters of the aqueous two-phase system, partitioning of biomolecules and cell mass and the effect of individual phase forming polymers on cell growth and product formation are reviewed in this article. The various extractive fermentation processes are also summarised here. At the end, the economic viability and scope of aqueous two-phase fermentation are briefly discussed in relation to the wider application of this topic. Received: 16 June 1999 / Received revision: 29 December 1999 / Accepted: 4 January 2000     

Bacterial magnetosomes: microbiology, biomineralization and biotechnological applications

Magnetotactic bacteria orient and migrate along geomagnetic field lines. This ability is based on intracellular magnetic structures, the magnetosomes, which comprise nanometer-sized, membrane-bound crystals of the magnetic iron minerals magnetite (Fe₃O₄) or greigite (Fe₃S₄). Magnetosome formation is achieved by a mineralization process with biological control over the accumulation of iron and the deposition of the mineral particle with specific size and orientation within a membrane vesicle at specific locations in the cell. This review focuses on the current knowledge about magnetotactic bacteria and will outline aspects of the physiology and molecular biology of the biomineralization process. Potential biotechnological applications of magnetotactic bacteria and their magnetosomes as well as perspectives for further research are discussed. Received: 2 December 1998 / Received revision: 2 March 1999 / Accepted: 5 March 1999     

Short-window spectral analysis of cortical event-related potentials by adaptive multivariate autoregressive modeling: data preprocessing, model validation, and variability assessment

In this article we consider the application of parametric spectral analysis to multichannel event-related potentials (ERPs) during cognitive experiments. We show that with proper data preprocessing, Adaptive MultiVariate AutoRegressive (AMVAR) modeling is an effective technique for dealing with nonstationary ERP time series. We propose a bootstrap procedure to assess the variability in the estimated spectral quantities. Finally, we apply AMVAR spectral analysis to a visuomotor integration task, revealing rapidly changing cortical dynamics during different stages of task processing. Received: 20 August 1999 / Accepted in revised form: 17 December 1999