Nootkatone—a biotechnological challenge

Due to its pleasant grapefruit-like aroma and various further interesting molecular characteristics, (+)-nootkatone represents a highly sought-after specialty chemical. (+)-Nootkatone is accumulated in its producer plants in trace amounts only, and the demand of the food, cosmetics and pharmaceutical industry is currently predominantly met by chemical syntheses. These typically require environmentally critical reagents, catalysts and solvents, and the final product must not be marketed as a “natural flavour” compound. Both the market pull and the technological push have thus inspired biotechnologists to open up more attractive routes towards natural (+)-nootkatone. The multifaceted approaches for the de novo biosynthesis or the biotransformation of the precursor (+)-valencene to (+)-nootkatone are reviewed. Whole-cell systems of bacteria, filamentous fungi and plants, cell extracts or purified enzymes have been employed. A prominent biocatalytic route is the allylic oxidation of (+)-valencene. It allows the production of natural (+)-nootkatone in high yields under mild reaction conditions. The first sequence data of (+)-valencene-converting activities have just become known.

PLASMANATE?—A New Plasma Substitute for Pediatric Therapy

Plasmanate®, a human-serum protein solution, appears to have all the attributes of an ideal plasma expander. Freedom from infection, immediate availability in a clear, stable solution and the apparent absence of antigenic properties are particularly valuable qualities. The efficacy and safety of Plasmanate was clinically demonstrated in the treatment of 125 infants and children. This solution seems especially effective in the treatment of acute shock states and for the physiologic correction of hypoproteinemia. Comparison with other plasma expanders makes Plasmanate the agent of choice in the initial treatment of shock states in pediatrics.     

Precautionary Defaults—A New Strategy for Chemical Risk Management

In order to give adequate support to risk managers, new risk assessment methods should be developed that are (1) scientifically sound, (2) simplified, and (3) suited for precautionary risk management. In this Perspective we propose that the notion of a precautionary default can be a useful tool in the development of such methods. A precautionary default is a cautious or pessimistic assumption that is used in the absence of adequate information and that should be replaced when such information is obtained. Furthermore, we point out some promising research areas for the development of such indicators, viz. connections between chemical characteristics such as persistence and effect parameters, monitoring of contaminants in polar regions, monitoring of contaminants in breast milk, application of results from (human) toxicology in ecotoxicology and vice versa, (eco)toxicological test systems that are sensitive to effects on reproduction, and the application of bioinformatic methods to complex data, both in genomic research and in ecotoxicology. We conclude that precautionary decision-making does not require less science, but to the contrary it requires more science and improved communication between scientists and risk managers.     

Dispersal-limited species – A challenge for ecological restoration

In recent years, increasing efforts have been directed to the restoration of natural communities affected by human activities. However, restoration success is often reduced because of the lack of dispersal-limited species in the restored site. Numerous rare species are dispersal-limited, having low probabilities to re-colonize restored sites and to establish viable populations. A high species richness enhances the ability of ecosystems to maintain multiple functions. It has been shown that in highly diverse ecosystems such as alpine meadows, tropical forests and coral reefs, the most distinct combinations of functions are supported predominantly by rare species. Thus, more emphasis should be given to support rare species in restoration actions. I suggest that well-known techniques for increasing plant diversity in restoration projects should be complemented with techniques to re-introduce dispersal-limited animals. Re-establishing ecological connectivity might be of benefit for certain species in the long term. However, for the majority of dispersal-limited animal species, translocations of founder individuals might be the only tool to re-establish populations in restored sites.     

Mycobacterial disease—a challenge to biotechnology

Summary The two principal mycobacterial diseases — tuberculosis and leprosy — remain major causes of human suffering in many parts of the world. The struggle against these diseases has been hampered by the inadequacy of methods for their diagnosis, prevention and therapy. Improvements in diagnostic methods, especially for tuberculosis, are required as existing bacteriological techniques are time consuming and insensitive, but immunological tests suffer from a lack of specificity and a failure to distinguish active disease from past sensitization. Tests are required that will either detect the presence of mycobacterial antigens or the occurrence of immune reactions specific to active infection. Prophylaxis by BCG vaccine is never complete and in some regions appears virtually ineffective. In order to determine the reason for this variation, to produce better vaccines, and to use BCG more effectively, a deeper understanding of the immune reactions in mycobacterial disease is required. In particular, the bacterial determinants of virulence and protection and the mode of action of BCG require detailed study. The therapy of tuberculosis and, to a lesser extent, leprosy has undergone an extensive transformation since the introduction of rifampicin. Nevertheless the cost of modern short course regimens for tuberculosis limit their application. Even shorter regimens, made possible by more potent bactericidal drugs or by agents that stimulate the host's defences are thus required. Recent advances in biotechnology could therefore lead to significant advances in the control of these diseases but only if they are integrated into local, self-reliant public health initiatives.

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Enfermedades producidas por microbacterias. Un desafío a la biotecnologia

Resumen La dos principales enfermedades producidas por micobacterias — tuberculosis y lepra —persisten como las causas más importantes del sufrimiento humano en muchas partes del mundo. La lucha contra estas enfermedades se ha visto dificultada por lo inadecuado de los métodos para su diagnosis, prevención y terapia. Es necesaria una mejora de los métodos de diagnosis, especialmente en el caso de la tuberculosis, ya que las técnicas bacteriológicas existentes son poco sensibles y consumen mucho tiempo y los tests inmunológicos son inespecíficos y no permiten distinguir entre la enfermedad activa y la sensibilidad adquirida. Se necesitan tests capaces de detectar la presencia de antígenos microbacterianos o la existencia de reacciones de inmunización específicas de la infección activa. La profilaxis con la vacuna BCG no es nunca completa y en algunas regiones es virtualmente enefectiva. Con objeto de determinar las razones de esta variación, de producir mejores vacunas y de usar la BCG de forma más eficiente, se necesita entender con más profundidad las reacciones de inmunización en las enfermedades por micobacterias. En particular los determinantes bacterianos de la virulencia y de la protección y la forma de actuar de la BCG precisan de un estudio detallado. La terapia de la tuberculosis y en menor grado la de la lepra, han sufrido una extensa transformación desde la introducción de la rifampicina. Sin embargo, el costo de los modernos tratamientos a corto plazo de la tuberculosis limítan su aplicación. Se requieren tratamientos aún más cortos basados en el desarrollo de drogas bactericidas más potentes o de agentes que estimulen las defensas del enfermo. Los recientes avances en biotecnología podrían por tanto conducir a avances importantes en el control de estas enfermedades pero solamente si se integran en iniciativas médicas públicas consistentes.

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Les maladies à mycobactéries — Un enjeu pour les biotechnologies

Résumé Les deux principales maladies à mycobactéries — la tuberculose et la lèpre — sont toujours des causes majeures de souffrance humaine dans de nombreuses parties du monde. La lutte contre ces maladies est entravée par l'inadéquation des méthodes diagnostiques, préventives et thérapeutiques. Spéciallement en ce qui concerne la tuberculose, l'amélioration des moyens de diagnostic est rendue nécessaire par le fait que les techniques bactériologiques existantes sont longues et peu sensibles, et que les tests immunologiques, n'étant pas spécifiques, ne permettent pas de distinguer entre une maladie en évolution et une sensibilisation ancienne. On a besoin de tests permettant de déceler soit la présence d'antigènes mycobactériens, soit l'apparition de réactions immunitaires spécifiques au cours d'une infection évolutive. La prophylaxie par le BCG n'est jamais complète et parait être pratiquement inefficace dans certaines régions. Pour expliquer cette variation géographique, produire de meilleurs vaccins, et utiliser le BCG efficacement, il convient de mieux connaître les réactions immunitaires au cours des maladies à mycobactéries. En particulier, les déterminants bactériens de la virulence et de la protection, ainsi que le mode d'action du BCG sont à approfondir. La rifampicine a considérablement transformé la thérapeutique de la tuberculose et, à un moindre degré, de la lèpre. Néanmoins, le coût des nouveaux traitements intensifs de la tuberculose limite leur application. Il est nécessaire que des médicaments bactéricides plus puissants ou des agents stimulant les défenses de l'hôte puissent raccourcir encore davantage la durée des traitements. Le progrès biotechnologique peut donc améliorer de façon significative le contrôle des maladies considérées, à la seule condition que ce but soit volontairement intégré dans les initiatives locales en matière de santé publique.

     

Beyond Transcription—New Mechanisms for the Regulation of Molecular Chaperones

Molecular chaperones are an essential part of the universal heat shock response that allows organisms to survive stress conditions that cause intracellular protein unfolding. During the past few years, two new mechanisms have been found to control the activity of several chaperones under stress conditions—the regulation of chaperone activity by the redox state and by the temperature of the environment. Hsp33, for example, is redox-regulated. Hsp33 is specifically activated by disulfide bond formation during oxidative stress, where it becomes a highly efficient chaperone holdase that binds tightly to unfolding proteins. Certain small heat shock proteins, such as Hsp26 and Hsp16.9, on the other hand, are temperature regulated. Exposure to heat shock temperatures causes these oligomeric proteins to disassemble, thereby changing them into highly efficient chaperones. The ATP-dependent chaperone folding system DnaK/DnaJ/GrpE also appears to be temperature regulated, switching from a folding to a holding mode during heat stress. Both of these novel post-translational regulatory strategies appear to have one ultimate goal: to significantly increase the substrate binding affinity of the affected chaperones under exactly those stress conditions that require their highest chaperone activity. This ensures that protein folding intermediates remain bound to the chaperones under stress conditions and are released only after the cells return to non-stress conditions.     

N-glycosylation in Archaea—New roles for an ancient posttranslational modification

Genome analysis points to N-glycosylation as being an almost universal posttranslational modification in Archaea. Although such predictions have been confirmed in only a limited number of species, such studies are making it increasingly clear that the N-linked glycans which decorate archaeal glycoproteins present diversity in terms of both glycan composition and architecture far beyond what is seen in the other two domains of life. In addition to continuing to decipher pathways of N-glycosylation, recent efforts have revealed how Archaea exploit this variability in novel roles. As well as encouraging glycoprotein synthesis, folding and assembly into properly functioning higher ordered complexes, N-glycosylation also provides Archaea with a strategy to cope with changing environments. Archaea can, moreover, exploit the apparent species-specific nature of N-glycosylation for selectivity in mating, and hence, to maintain species boundaries, and in other events where cell-selective interactions are required. At the same time, addressing components of N-glycosylation pathways across archaeal phylogeny offers support for the concept of an archaeal origin for eukaryotes. In this MicroReview, these and other recent discoveries related to N-glycosylation in Archaea are considered.     

Hishot Display—A New Combinatorial Display for Obtaining Target-Recognizing Peptides

Display technologies are procedures used for isolating target-recognizing peptides without using immunized animals. In this study, we describe a new display method, named Hishot display, that uses Escherichia coli and an expression plasmid to isolate target-recognizing peptides. This display method is based on the formation, in bacteria, of complexes between a polyhistidine (His)-tagged peptide including random sequences and the peptide-encoding mRNA including an RNA aptamer against the His-tag. When this system was tested using a sequence encoding His-tagged green fluorescent protein that included an RNA aptamer against the His-tag, the collection of mRNA encoding the protein was dependent on the RNA aptamer. Using this display method and a synthetic library of surrogate single-chain variable fragments consisting of VpreB and Ig heavy-chain variable domains, it was possible to isolate clones that could specifically recognize a particular target (intelectin-1 or tumor necrosis factor-α). These clones were obtained as soluble proteins produced by E. coli, and the purified peptide clones recognizing intelectin-1 could be used as detectors for sandwich enzyme-linked immunosorbent assays. The Hishot display will be a useful method to add to the repertoire of display technologies.     

The Latex Serologic Test for Syphilis—A New Screening Procedure

A new macroscopic screening test for syphilis, the Latex-sts test, is extraordinarily simple. After inactivation of the patient''s serum for 30 minutes at 56°C the test is performed by mixing the patient''s serum with latex particles coated with cardiolipin and a protein fraction obtained from the non-pathogenic Reiter strain of Treponema pallidum. Two to three minutes after mixing, the result of the test is observed on a ringed serologic plate. The sensitivity, specificity and reproducibility of the new test are equivalent to those of the qualitative Venereal Disease Research Laboratory tube test. The advantages of the Latex-sts are that it can be done in a short time, it is simple and it requires a minimum of laboratory equipment. The coated latex particles are stable for 12 months.     

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Since 2010, the European Molecular Biology Laboratory''s (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students.In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.     

New hepatocytes for toxicology?

In a recent article M.G. Sacco and co-workers described the establishment of immortalized untransformed transgenic hepatocyte (MMH-GH) cell lines, obtained from a cross between the AT/cytoMet and Hsp70/hGH transgenic mice. This strategy proved to be successful because the MMH-GH showed stability in culture and sensitivity to chemical exposure. Based on these results, the MMH-GH cell lines could prove to be a valid alternative cell-based assay for use in toxicological studies.     

Cumacean Lamprops pumilio—A New Species for the Sea of Japan

The treatment of materials collected in Srednyaya Bight (Peter the Great Bay) revealed in a sample taken on December 3, 1986, a female Lamprops pumilioZimmer with oostegites (3.5 mm long). The sample was obtained using an Okean bottom sampler (with the mouth area of 0.25 m²), at a depth of 10 m, from fine sand, at a temperature of –1.5°C.