The end of "naive reductionism": rise of systems biology or renaissance of physiology?

Systems biology is an emerging discipline focused on tackling the enormous intellectual and technical challenges associated with translating genome sequence into a comprehensive understanding of how organisms are built and run. Physiology and systems biology share the goal of understanding the integrated function of complex, multicomponent biological systems ranging from interacting proteins that carry out specific tasks to whole organisms. Despite this common ground, physiology as an academic discipline runs the real risk of fading into the background and being superseded organizationally and administratively by systems biology. My goal in this article is to discuss briefly the cornerstones of modern systems biology, specifically functional genomics, nonmammalian model organisms and computational biology, and to emphasize the need to embrace them as essential components of 21st-century physiology departments and research and teaching programs.     

Hallmarks of human "immunosenescence": adaptation or dysregulation?

ABSTRACT: Is immunosenescence an intrinsic ageing process leading to dysregulation of immunity or an adaptive response of the individual to pathogen exposure? Age-associated differences in bone marrow immune cell output and thymic involution suggest the former. Accepted hallmarks of immunosenescence (decreased numbers and percentages of peripheral na?ve T cells, especially CD8?+?cells, and accumulations of memory T cells, especially late-stage differentiated CD8+ cells) suggest the latter, viewed as the result of depletion of the reservoir of na?ve cells over time by contact with pathogens and their conversion to memory cells, the basis of adaptive immunity. Thymic involution beginning early in life limits the generation of naive cells such that the adult is believed to rely to a great extent on the na?ve cell pool produced mostly before puberty. Thus, these hallmarks of immunosenescence would be markedly affected by the history of the individual′s exposure to pathogens. It would be predicted that in modern industrialized populations, the cumulative effects of antigenic "stressors" would be lower than in less hygienic societies, whereas intrinsic processes might be more similar in different populations. Identifying such stressors and taking steps to nullify their impact could therefore result in delayed immunosenescence and contribute significantly to improving public health. Here, I discuss some of the available data bearing on this prediction.     

Decline in sperm counts: an artefact of changed reference range of "normal"?

OBJECTIVE--To investigate a reported fall in sperm counts during 1940-90 in relation to the reduced lower reference value of "normal" during the same period by assuming the null hypothesis that no change had occurred in the probability distribution of the sperm concentration. DESIGN--Analysis by using various mathematical models of the probability distribution of sperm concentration together with experimental data which supported a model employing a logarithmic distribution. SUBJECTS--235 men presenting for stimulated in vitro fertilisation at Midland Fertility Services, Aldridge, in 1992 together with samples of 20 ejaculates from each of five men attending the same centre during 1992-3. RESULTS--The effect of the change in lower reference value for the "normal" sperm concentration (from 60 x 10(9) to 20 x 10(9)/l) depended on the probability distribution of the concentration in the population. If that distribution was normal or uniform, then very little of the reported decline was a consequence of the change in lower reference value. If it was heavily skewed, then most or all of the reported decline may have been a consequence of that change. The limited experimental data available indicate that the distribution was heavily skewed. CONCLUSIONS--Depending on the actual distribution of sperm concentration in the population, the reported decline in concentration may have been accounted for entirely or in part by the change in lower reference value. The original evidence does not support the hypothesis that the sperm count declined significantly between 1940 and 1990.     

"Broad spectrum" antidepressants: is more better for the treatment of depression?

The majority of antidepressants in current use selectively inhibit the reuptake of serotonin and/or norepinephrine. "Broad spectrum" antidepressants are compounds that inhibit the reuptake of norepinephrine, serotonin and dopamine, the three biogenic amines most closely linked to depression. The pharmacological profile of one such compound has recently been described (European Journal of Pharmacology, 461 (2003) 99). DOV 21,947, an azabicyclo[3.1.0]hexane, potently inhibits norepinephrine, serotonin and dopamine reuptake by the corresponding human transporter proteins. DOV 21,947 is orally active in the forced swim and tail suspension tests, preclinical procedures that are highly predictive of antidepressant action in patients. A closely related compound, DOV 216,303 is safe and well-tolerated in Phase I studies. The plasma concentrations of DOV 216,303 following both single and multiple doses appear sufficient to inhibit norepinephrine, serotonin, and dopamine reuptake. Based on the pivotal role proposed for dopamine in depression, it has been hypothesized that a broad spectrum antidepressant will produce a more rapid onset and/or higher efficacy than agents inhibiting the reuptake of serotonin and/or norepinephrine.     

Entamoeba histolytica: is conversion of "nonpathogenic" amebae to the "pathogenic" form a real phenomenon?

Entamoeba histolytica isolates have been shown to fall into two groups based on isoenzyme analysis. These groupings ("pathogenic" and "nonpathogenic") correlate well with the clinical course of the infection. A controversy exists over whether isoenzyme patterns are stable or whether under certain circumstances an isolate can convert from one form to the other. Resolution of this uncertainty is of importance since the nonpathogenic pattern has never been observed in amebae isolated from cases of active disease. This implies that, if the patterns are stable, carriers of amebae with this nonpathogenic pattern may never develop invasive disease. Although we set out to study isoenzyme conversion, we have been unable to replicate the two published accounts of this phenomenon. We have examined all of the variables proposed to be involved in the triggering of conversion, both individually and in combination. In none of the experiments was an alteration in the isoenzyme pattern observed. We now believe that isoenzyme patterns are stable and that all available evidence, other than the reported conversions, points to pathogenic and nonpathogenic E. histolytica being distinct species.     

The three leg imaginal discs of Drosophila: "Vive la différence"

The imaginal discs of Drosophila are the larval primordia for the adult cuticular structures of the adult fly. Fate maps of different discs have been generated that show the localization of prospective adult structures. Even though the three legs differ in their morphology, only the fate map for the T1 (prothoracic) leg disc has been generated. Here we present fate maps for the T2 (meso-) and T3 (metathoracic) leg discs. We show that there are many similarities to the map of the T1 leg disc. However, there are also significant differences in the contributions of each disc to the thorax, in the morphology of joints connecting the legs to the thorax, in bristle patterns, and in the positioning of some sensory organs. We also tested the developmental potential of disc fragments and observed that T2 and T3 leg discs have more limited plasticity and are unable to transdetermine. The differences in the cuticle patterns between legs are robust and conserved in many species of dipterans. While most previous analyses of imaginal disc development have not distinguished between the different leg discs, we believe that the underlying differences of the three leg discs demonstrated here cannot be ignored when studying leg disc development.     

Chlamydia pneumoniae in foci of "early" calcification of the tunica media in arteriosclerotic arteries: an incidental presence?

Only a few previous works investigated the involvement of Chlamydia pneumoniae (Chlamydophila pneumoniae) in arterial calcification. The present study investigated a possible association between C. pneumoniae and medial calcification. Carotid artery segments obtained by endarterectomy from 60 patients were examined by PCR and immunohistochemistry to identify the presence of C. pneumoniae. Arterial specimens showing double-positive (n = 17), double-negative (n = 22), and single-positive results (n = 21) were further analyzed by a combination of histology, immunohistochemistry, and electron microscopy. Medial calcification occurred in 10 of 17 (58.8%) C. pneumoniae double-positive arterial specimens, but no medial calcification was observed in any of 22 C. pneumoniae double-negative arterial specimens. Electron microscopy indicated C. pneumoniae in smooth muscle cells (SMCs) in foci of medial calcification. Medial SMCs showing damage to the cytoplasm and basement membrane contained the structures with the appearance of elementary, reticulate, and aberrant bodies of C. pneumoniae. The presence of C. pneumoniae in SMCs was confirmed by electron-microscopic immunocytochemistry. In the extracellular matrix, calcification was observed in C. pneumoniae aberrant bodies that exited the SMCs. The findings offer a new hypothesis of arterial calcification: they suggest that C. pneumoniae infection of medial SMCs may be associated with the pathophysiological events of arteriosclerotic calcification of the tunica media.     

The importance of time/space in diagnosing the causality of phylogenetic events: towards a "chronobiogeographical" paradigm?

A shift from a traditional biogeographical paradigm in cladistic biogeography to a chronobiogeographical paradigm is proposed. The chronobiogeographical paradigm aims to utilize temporal data in conjunction with spatial data in the detection of discrete historical events, such as vicariance and vicariant speciation, in cladograms. The concepts of primary and secondary congruency are introduced in relation to the distinction between repeated area relationships (primary congruency) and common extrinsic causality (secondary congruency). Simple hypothetical examples demonstrate that area cladograms cannot be safely interpreted purely as representing the sequence of area fragmentation; rather, they reflect recency of biotic interaction. Temporal data are shown to have a direct and potentially profound influence on the results of traditional cladistic biogeographical analyses, indicating the necessity of developing a chronobiogeographical approach. The implementation of the paradigm is considered first from a theoretical viewpoint and then in the context of the type of empirical data usually available. An as yet undevised "time/space algorithm" is deemed necessary for the latter, and guidelines are presented for the development of such an algorithm. Finally, we argue that the most rigorous and philosophically justified approach to the detection of phylogenetic causal events can be found only when temporal and spatial data are considered simultaneously. Consequently, the chronobiogeographical paradigm is seen as a logical elaboration of, not a replacement for, the biogeographical paradigm.     

Molecular genetics of radiation-induced chromosome breaks in a gene area in Drosophila: "position" effect of gene mutation?

On the sample of 43 gamma-ray and neutron-induced inversion or translocation exchanges with the vestigial (vg) phenotype, the molecular cytogenetic analysis of distribution of exchange breakpoints on the molecular map of Drosophila vg region (subsection 49D3-4 on the polytene chromosome 2R) was performed using hybridisation in situ technique. Simultaneously, PCR-assay of DNA alterations in all exons and introns (except for intron 4) of the vg gene for 18 mutants with exchange breakpoints outside of the gene was carried out. The results obtained by these molecular genetic techniques have shown that 1) radiation-induced breaks under chromosome exchanges with the vg phenotype were regularly located inside of the vg gene (19 cases out of 43 studied ones or 44.2%) passing through the large introns; 2) breakpoints were frequently flanked by deletions of the gene as whole (3 exchanges) or of its major part (3 exchanges); 3) many of the breaks (18/43 or 41.8%) are situated outside (distal or proximal) of the gene although such mutants have got the vg phenotype; 4) 2/3 (12/18 or 66.7%) vg mutants with the breakpoint outside of gene show the intragenic DNA lesions (microdeletions, microinversions) occurring obviously independently and simultaneously with the neighbor chromosome breaks; 5) only each third vg mutant with break outside of the gene (6/18 or 33.3%) have the unchanged gene subregions under study and presents obviously the result of "position effect" which appear to manifest itself for a distance of 2-30 kb (more near and farther locations of the proximal and distal breakpoints, respectively, relative to the vg gene). Our findings showing regular induction of the multiple genetic lesions (chromosome breaks and mutations of the adjacent genes) on the both ends of chromosome exchange induced by single track produced by gamma-rays or neutrons were discussed as a scientific basis for the conceptually new approaches to the assessment of both genetic damage numbers in the cell genome with chromosome exchange (the multiple genetic lesions) and radiation genetic risk (our molecular genetic approach showing the need for an increase of risk levels at least on a factor of 3 for the heritable chromosome alterations detected by the ordinary cytogenetic monitoring).     

Heat shock protein 10 and signal transduction: a "capsula eburnea" of carcinogenesis?

To date, little is known either about the physical interactions of heat shock protein 10 (Hsp10) with other proteins within the cell or its involvement in signal transduction pathways. Hsp10 has been considered mainly as a partner of Hsp60 in the Hsp60/10 protein folding machine. Only recently, Hsp10 was reported to interact with proteins involved in deoxyribonucleic acid checkpoint inactivation, termination of M-phase, messenger ribonucleic acid export, import of nuclear proteins, nucleocytoplasmic transport, and pheromone signaling pathways. At the same time, Hsp10 expression can be up-regulated in cancer cells, because it accumulates as the cell transformation progresses. Recent data suggest that Hsp10 may be not only a component of the folding machine but also an active player of the cell signaling network, influencing cell cycle, nucleocytoplasmic transport, and metabolism, with putative roles in the lack of cell differentiation and in the inhibition of apoptosis. In this review, we revise the involvement of Hsp10 in signal transduction pathways and its possible role in cancer etiology.     

Using SINEs to probe ancient explosive speciation: "hidden" radiation of African cichlids?

Cichlid fishes of the east African Great Lakes represent a paradigm of adaptive radiation. We conducted a phylogenetic analysis of cichlids including pan-African and west African species by using insertion patterns of short interspersed elements (SINEs) at orthologous loci. The monophyly of the east African cichlids was consistently supported by seven independent insertions of SINE sequences that are uniquely shared by these species. In addition, data from four other loci indicated that the genera Tilapia (pan-African) and Steatocranus (west African) are the closest relatives to east African cichlids. However, relationships among Tilapia, Steatocranus, and the east African clade were ambiguous because of incongruencies among topologies suggested by insertion patterns of SINEs at six other loci. One plausible explanation for this phenomenon is incomplete lineage sorting of alleles containing or missing a SINE insertion at these loci during ancestral speciation. Such incomplete sorting may have taken place earlier than 14 MYA, followed by random and stochastic fixation of the alleles in subsequent lineages. These observations prompted us to consider the possibility that cichlid speciation occurred at an accelerated rate during this period when the African Great Lakes did not exist. The SINE method could be useful for detecting ancient exclusive speciation events that tend to remain hidden during conventional sequence analyses because of accumulated point mutations.     

The Cambrian "explosion" of metazoans and molecular biology: would Darwin be satisfied?

The origins of metazoan bodyplans and the extent to which they are coincident with the Cambrian "explosion" are both areas of continuing debate. The fossil record has a unique advantage in terms of historical perspective, but remains highly contentious on account of the often controversial interpretations of particular groups (e.g. halkieriids, vetulicolians) and the heavy reliance on "windows" of exceptional preservation (e.g. Chengjiang, Burgess Shale). Molecular and developmental biology offer other unique insights, but may be problematic in terms of conflicting phylogenetic signals and questions revolving around gene co-option, evolution of developmental systems and even convergence. Such topics, far from frustrating the enterprise, actually widen our understanding of the nature of the evolutionary process with the exciting promise of the discovery of more general principles.     

Caspase-8 in apoptosis: the beginning of "the end"?

Caspase-8 is a member of the cysteine proteases, which are implicated in apoptosis and cytokine processing. Like all caspases, caspase-8 is synthesized as an inactive single polypeptide chain zymogen procaspase and is activated by proteolytic cleavage, through either autoactivation after recruitment into a multimeric complex or trans-cleavage by other caspases. Thus, ligand binding-induced trimerization of death receptors results in recruitment of the receptor-specific adapter protein Fas-associated death domain (FADD), which then recruits caspase-8. Activated caspase-8 is known to propagate the apoptotic signal either by directly cleaving and activating downstream caspases or by cleaving the BH3 Bcl2-interacting protein, which leads to the release of cytochrome c from mitochondria, triggering activation of caspase-9 in a complex with dATP and Apaf-1. Activated caspase-9 then activates further "downstream caspases," including caspase-8. Knockout data indicate that caspase-8 is required for killing induced by the death receptors Fas, tumor necrosis factor receptor 1, and death receptor 3. Moreover, caspase-8-/- mice die in utero as a result of defective development of heart muscle and display fewer hematopoietic progenitor cells, suggesting that the FADD/caspase-8 pathway is absolutely required for growth and development of specific cell types.