The Haldane malaria hypothesis: facts, artifacts, and a prophecy

Heterozygous thalassemia and sickle cell disease produce mild hematological symptoms but provide protection against malaria mortality and severe malaria symptoms. Two explanations for resistance are considered in the literature - impaired growth of the parasite or enhanced removal by the host immune cells. A critical overview of studies that connect malaria resistance with impaired intra-erythrocytic growth is presented. All studies are fraught with two kinds of bias. The first one resides in the impossibility of reproducing the in vivo situation in the simplified model in vitro. The second stems from the generalized use of RPMI 1640 culture medium. RPMI 1640 has critically low levels of several amino acids; is devoid of hypoxanthine (essential for parasite growth) and adenine; and is low in reduced glutathione. Analysis of representative studies indicates that impaired parasite growth in heterozygous red blood cells (RBCs) may derive from nutrient limitations and, therefore, possibly be of artefactual origin. This conclusion seems plausible because studies were performed with RPMI 1640 medium at relatively high hematocrit and for prolonged periods of time. Mutations considered are particularly sensitive to nutrient deprivation because they have higher metabolic demands due to permanent oxidant stress related to unpaired globin chains, sickle hemoglobin and high levels of membrane-free iron. In addition, non-parasitized AS- and thalassemic-RBCs are dehydrated and microcytic. Thus, the number of metabolically active elements per unit of blood volume is remarkably larger in mutant RBCs compared to normocytes. The latter point may represent a confirmation of Haldane's prophetic statement: 'The corpuscles of the anaemic heterozygotes are smaller than normal, and more resistant to hypotonic solutions. It is at least conceivable that they are also more resistant to attacks by the sporozoa which cause malaria.'     

Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses

Prelude&Fugue are bioinformatics tools aiming at predicting the local 3D structure of a protein from its amino acid sequence in terms of seven backbone torsion angle domains, using database-derived potentials. Prelude(&Fugue) computes all lowest free energy conformations of a protein or protein region, ranked by increasing energy, and possibly satisfying some interresidue distance constraints specified by the user. (Prelude&)Fugue detects sequence regions whose predicted structure is significantly preferred relative to other conformations in the absence of tertiary interactions. These programs can be used for predicting secondary structure, tertiary structure of short peptides, flickering early folding sequences and peptides that adopt a preferred conformation in solution. They can also be used for detecting structural weaknesses, i.e. sequence regions that are not optimal with respect to the tertiary fold. AVAILABILITY: http://babylone.ulb.ac.be/Prelude_and_Fugue.     

Prelude to oral microbes and chronic diseases: past,present and future

Associations between oral and systemic health are ancient. Oral opportunistic bacteria, particularly, Porphyromonas gingivalis and Fusobacterium nucleatum, have recently been deviated from their traditional roles as periodontal pathogens and arguably ascended to central players based on their participations in complex co-dependent mechanisms of diverse systemic chronic diseases risk and pathogenesis, including cancers, rheumatoid-arthritis, and diabetes.     

Microbial oceanography: paradigms, processes and promise

Life on Earth most likely originated as microorganisms in the sea. Over the past approximately 3.5 billion years, microorganisms have shaped and defined Earth's biosphere and have created conditions that have allowed the evolution of macroorganisms and complex biological communities, including human societies. Recent advances in technology have highlighted the vast and previously unknown genetic information that is contained in extant marine microorganisms, from new protein families to novel metabolic processes. Now there is a unique opportunity, using recent advances in molecular ecology, metagenomics, remote sensing of microorganisms and ecological modelling, to achieve a comprehensive understanding of marine microorganisms and their susceptibility to environmental variability and climate change. Contemporary microbial oceanography is truly a sea of opportunity and excitement.     

Tomatoes,lycopene, and prostate cancer: progress and promise

Prostate cancer has emerged as a major public health problem in nations that have an affluent culture with an aging population. The search for etiologic risk factors and an emphasis on the development of chemopreventive agents has gained momentum over the last decade. Among the landmark epidemiologic findings during this period has been the association between the consumption of tomato products and a lower risk of prostate cancer. The traditional reductionist scientific approach has led many investigators to propose that lycopene, a carotenoid consumed largely from tomato products, may be the component responsible for lowering the risk of prostate cancer. Thus, many laboratory and clinical studies are now underway with the goal of assessing the ability of pure lycopene to serve as a chemopreventive agent for prostate and other malignancies. The focus on lycopene should continue, and an improved understanding of lycopene absorption, distribution, role in antioxidant reactions, and metabolism is critical in the quest to elucidate mechanisms whereby this compound could possibly reduce prostate cancer risk. In contrast to the pharmacologic approach with pure lycopene, many nutritional scientists direct their attention upon the diverse array of tomato products as a complex mixture of biologically active phytochemicals that together may have anti-prostate cancer benefits beyond those of any single constituent. These contrasting approaches will continue to be explored in clinical, laboratory and epidemiologic studies in the near future, providing hope that the next generation will benefit from this knowledge and experience a lower risk of prostate cancer.     

The voice of prophecy: A review article

The Voice of Prophecy and Other Essays. Edvin Ardener. Edited by Malcolm Chapman. Oxford: Basil Blackwell, 1989. xxvii + 288 pp.     

Methods, challenges, and promise of next-generation sequencing in cancer biology

It is generally accepted that cancers result from the aggregation of somatic mutations. The emergence of next-generation sequencing (NGS) technologies during the past half-decade has enabled studies of cancer genomes with high sensitivity and resolution through whole-genome and whole-exome sequencing approaches, among others. This saltatory advance introduces the possibility of assembling multiple cancer genomes for analysis in a cost-effective manner. Analytical approaches are now applied to the detection of a number of somatic genome alterations, including nucleotide substitutions, insertions/deletions, copy number variations, and chromosomal rearrangements. This review provides a thorough introduction to the cancer genomics pipeline as well as a case study of these methods put into practice.     

Pharmacogenetics in drug regulation: promise, potential and pitfalls

Pharmacogenetic factors operate at pharmacokinetic as well as pharmacodynamic levels-the two components of the dose-response curve of a drug. Polymorphisms in drug metabolizing enzymes, transporters and/or pharmacological targets of drugs may profoundly influence the dose-response relationship between individuals. For some drugs, although retrospective data from case studies suggests that these polymorphisms are frequently associated with adverse drug reactions or failure of efficacy, the clinical utility of such data remains unproven. There is, therefore, an urgent need for prospective data to determine whether pre-treatment genotyping can improve therapy. Various regulatory guidelines already recommend exploration of the role of genetic factors when investigating a drug for its pharmacokinetics, pharmacodynamics, dose-response relationship and drug interaction potential. Arising from the global heterogeneity in the frequency of variant alleles, regulatory guidelines also require the sponsors to provide additional information, usually pharmacogenetic bridging data, to determine whether data from one ethnic population can be extrapolated to another. At present, sponsors explore pharmacogenetic influences in early clinical pharmacokinetic studies but rarely do they carry the findings forward when designing dose-response studies or pivotal studies. When appropriate, regulatory authorities include genotype-specific recommendations in the prescribing information. Sometimes, this may include the need to adjust a dose in some genotypes under specific circumstances. Detailed references to pharmacogenetics in prescribing information and pharmacogenetically based prescribing in routine therapeutics will require robust prospective data from well-designed studies. With greater integration of pharmacogenetics in drug development, regulatory authorities expect to receive more detailed genetic data. This is likely to complicate the drug evaluation process as well as result in complex prescribing information. Genotype-specific dosing regimens will have to be more precise and marketing strategies more prudent. However, not all variations in drug responses are related to pharmacogenetic polymorphisms. Drug response can be modulated by a number of non-genetic factors, especially co-medications and presence of concurrent diseases. Inappropriate prescribing frequently compounds the complexity introduced by these two important non-genetic factors. Unless prescribers adhere to the prescribing information, much of the benefits of pharmacogenetics will be squandered. Discovering highly predictive genotype-phenotype associations during drug development and demonstrating their clinical validity and utility in well-designed prospective clinical trials will no doubt better define the role of pharmacogenetics in future clinical practice. In the meantime, prescribing should comply with the information provided while pharmacogenetic research is deservedly supported by all concerned but without unrealistic expectations.     

Voltage-gated sodium channel toxins: poisons,probes, and future promise

Neurotoxins have served as invaluable agents for identification, purification, and functional characterization of voltage-gated ion channels. Multiple classes of these toxins, which target voltage- gated Na+ channels via high-affinity binding to distinct but allosterically coupled sites, have been identified. The toxins are chemically diverse, including guanidinium heterocycles, a variety of structurally unrelated alkaloids, and multiple families of nonhomologous polypeptides having either related or distinct functions. This review describes the biochemistry and pharmacology of these agents, and summarizes the structure-function relationships underlying their interaction with molecular targets. In addition, we explore recent advances in the use of these toxins as molecular scaffolding agents, drugs, and insecticides.