How will bioinformatics influence metabolic engineering?

Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development.     

Where will new antibiotics come from?

There is a constant need for new antibacterial drugs owing to the inevitable development of resistance that follows the introduction of antibiotics to the clinic. When a new class of antibiotic is introduced, it is effective at first, but will eventually select for survival of the small fraction of bacterial populations that have an intrinsic or acquired resistance mechanism. Pathogens that are resistant to multiple drugs emerge around the globe, so how robust are antibiotic discovery processes?     

How long will long-term potentiation last?

The paramount feature of long-term potentiation (LTP) as a memory mechanism is its characteristic persistence over time. Although the basic phenomenology of LTP persistence was established 30 years ago, new insights have emerged recently about the extent of LTP persistence and its regulation by activity and experience. Thus, it is now evident that LTP, at least in the dentate gyrus, can either be decremental, lasting from hours to weeks, or stable, lasting months or longer. Although mechanisms engaged during the induction of LTP regulate its subsequent persistence, the maintenance of LTP is also governed by activity patterns post-induction, whether induced experimentally or generated by experience. These new findings establish dentate gyrus LTP as a useful model system for studying the mechanisms governing the induction, maintenance and interference with long-term memory, including very long-term memory lasting months or longer. The challenge is to study LTP persistence in other brain areas, and to relate, if possible, the properties and regulation of LTP maintenance to these same properties of the information that is actually stored in those regions.     

Who will develop new antibacterial agents?

The golden age of antimicrobial drug development is a distant memory, and the likelihood of there being another seems slim. In part, this is because the pharmaceutical industry, which has now adopted an unsustainable business model, abandoned the anti-infective sector, and the pipeline is almost empty. The contribution to this crisis of national governments, health agencies and funders also merits discussion. Much of the basis for drug discovery is funded by the public sector, thereby generating intellectual property and leads for drug development that are often not pursued owing to funding gaps. In particular, the cost of testing drug efficacy in clinical trials is beyond the means of most companies and organizations. Lack of a concerted international effort to develop new antimicrobials is particularly alarming at a time when multidrug-resistant bacteria threaten all areas of human medicine globally. Here, the steps that led to this situation are retraced, and some possible solutions to the dilemma are proposed.     

Pharmacogenomics: will the promise be fulfilled?

Tools such as genome resequencing and genome-wide association studies have recently been used to uncover a number of variants that affect drug toxicity and efficacy, as well as potential drug targets. But how much closer are we to incorporating pharmacogenomics into routine clinical practice? Five experts discuss how far we have come, and highlight the technological, informatics, educational and practical obstacles that stand in the way of realizing genome-driven medicine.     

How will oil palm expansion affect biodiversity?

Oil palm is one of the world's most rapidly increasing crops. We assess its contribution to tropical deforestation and review its biodiversity value. Oil palm has replaced large areas of forest in Southeast Asia, but land-cover change statistics alone do not allow an assessment of where it has driven forest clearance and where it has simply followed it. Oil palm plantations support much fewer species than do forests and often also fewer than other tree crops. Further negative impacts include habitat fragmentation and pollution, including greenhouse gas emissions. With rising demand for vegetable oils and biofuels, and strong overlap between areas suitable for oil palm and those of most importance for biodiversity, substantial biodiversity losses will only be averted if future oil palm expansion is managed to avoid deforestation.     

Achalasia: will genetic studies provide insights?

Despite increasing understanding of the pathophysiology of achalasia, the etiology of this esophageal motility disorder remains largely unknown. However, the occurrence of familial achalasia and its association with well-defined genetic syndromes suggest the involvement of genetic factors. Mutant mouse models display gastrointestinal disturbances that are similar to those observed in achalasia patients. The candidate gene approach has revealed some promising results; however, it has not established conclusive links to specific genes so far. The aim of this review was to summarize current knowledge of the genetics of achalasia. We also discuss the extent to which our understanding of achalasia is likely to be enhanced through future molecular genetic research.     

Immunocontraception for population control: will resistance evolve?

The prospect for successful biocontrol using immunocontraception is threatened if there is adaptation to the vaccine through natural selection of individuals that are genetically resistant to the contraceptive agent. To assess this possibility we examined the literature and found that little relevant data are available for any species on the appropriate trait, fertility variation among immunized individuals, or about appropriate population and genetic parameters influencing the likelihood of a selection response. Some data are available on variation in antibody response to immunocontraceptives, but the relationship between antibody response and fertility levels is poorly documented. The antibody response data indicate low heritability for this trait suggesting that fertility levels of contraceptive-resistant individuals will also have a low heritability. Slow evolution of contraception resistance might therefore be anticipated. The absence of information about relevant parameters makes the construction of quantitative models premature. We discuss factors in particular need of investigation if predictions about resistance evolution are to be made. These include: 1. the genetic basis of fertility retention, 2. the proportion of the population resistant to the contraceptive agent and how this is affected by gene flow from refuge populations, 3. the genetically-based fitness tradeoffs of resistant individuals that often accompany selection, 4. cross-generation effects that can thwart the effects of selection, and 5. the efficiency of delivery of the contraceptive agent. An understanding of the above for particular species, and the development of appropriate divergently acting multiple vaccines that can be used in temporal rotation or in mixtures, should facilitate the development of management options to minimize resistance evolution.     

Dual-specificity protein kinases: will any hydroxyl do?

Protein kinases are classified by the target amino acid in their substrates. Those protein kinases that phosphorylate hydroxyamino acids comprise two groups, the protein-tyrosine and protein-serine/threonine kinases, which, until recently, had been thought to be mutually exclusive. However, several new protein kinases have been discovered that, by the criterion of primary structure, would be classified as protein-serine/threonine kinases but which, surprisingly, are able to phosphorylate tyrosine residues. Even more surprising, there are reports of protein kinases that are capable of phosphorylating both tyrosine and serine/threonine residues. We review and discuss recent developments concerning these 'dal-specificity' protein kinases.     

Lateral gene transfer: when will adolescence end?

The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.     

How far will you go to sense voltage?

Despite tremendous progress in the study of voltage-gated channels, the molecular mechanism underlying voltage sensing has remained a matter of debate. We review five new studies that make major progress in the field. The studies employ a battery of distinct approaches that have the common aim of measuring the motion of the voltage sensor. We interpret the results in light of the recent crystal structure of the mammalian potassium channel Kv1.2. We focus on the transmembrane movement of the voltage sensor as a key element to the detection of membrane potential and to the control of channel gating.     

Harmonia axyridis: What will stop the invader?

In recent years Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) has become a very popular insect among biological control practitioners and scientists, not only for its potential to be an efficient biological control agent but also because it is considered invasive. Individuals of this species were deliberately introduced into several countries for biological control of different arthropods pests. However the predator itself became an invasive species, affecting the dynamics and composition of several guilds through direct or indirect interactions with established species, including intraguild predation. In this paper we discuss the reasons why the species has a high invasiveness and what are the limits to invasion by this species. It is not clear if the invasiveness of the beetle is linked to its biological, ecological and behavioural abilities, or to other factors such as invasibility and interactions between the invaders, the noninvaders, and the habitat, which may in part explain the reasons of its success and help us to answer the question “what will stop the invader?” We also discuss the reason for the absence of the predator in the Azores islands. Despite the intentional introduction of H. axyridis in the Azores and the high number of individuals released, there are no records of this species in the wild, despite recent extensive sampling effort. In this paper we discuss the reasons for the apparent failure or the delay in establishment of the predator. One factor which may hamper the establishment of H. axyridis in some of the Azores islands is the absence of winter environmental conditions, mainly the temperature which is seldom lower than 12°C, essential for the induction of diapause. The lack of success in the establishment could be also related to functional diversity saturation, that is species saturation and competitive exclusion of H. axyridis by other previously established species may be operating.