Bacterial EPIYA effectors – Where do they come from? What are they? Where are they going?

Recent studies have revealed a distinct class of bacterial effectors defined by the presence of EPIYA or EPIYA‐related motif. These bacterial EPIYA effectors are delivered into host cells via type III or IV secretion, where they undergo tyrosine phosphorylation at the EPIYA motif and thereby manipulate host signalling by promiscuously interacting with multiple SH2 domain‐containing proteins. Up to now, nine EPIYA effectors have been identified from various bacteria. These effectors do not share sequence homology outside the EPIYA motif, arguing against the idea that they have common ancestors. A search of mammalian proteomes revealed the presence of a mammalian EPIYA‐containing protein, Pragmin, which potentiates Src family kinase (SFK) activity by binding and sequestrating the SFK inhibitor Csk upon EPIYA phosphorylation. As several bacterial EPIYA effectors also target Csk, they may have evolved through generation of sequences that mimic the Pragmin EPIYA motif. EPIYA motifs are often diverged through multiple duplications in each bacterial effector. Such a structural plasticity appears to be due to intrinsic disorder of the EPIYA‐containing region, which enables the bacterial effectors to undergo efficient phosphorylation and mediate promiscuous interaction with multiple host proteins. Given the functional versatility of the EPIYA motif, many more bacterial EPIYA effectors will soon be emerging.     

Proteome signatures—how are they obtained and what do they teach us?

The dawn of a new Proteomics era, just over a decade ago, allowed for large-scale protein profiling studies that have been applied in the identification of distinctive molecular cell signatures. Proteomics provides a powerful approach for identifying and studying these multiple molecular markers in a vast array of biological systems, whether focusing on basic biological research, diagnosis, therapeutics, or systems biology. This is a continuously expanding field that relies on the combination of different methodologies and current advances, both technological and analytical, which have led to an explosion of protein signatures and biomarker candidates. But how are these biological markers obtained? And, most importantly, what can we learn from them? Herein, we briefly overview the currently available approaches for obtaining relevant information at the proteome level, while noting the current and future roles of both traditional and modern proteomics. Moreover, we provide some considerations on how the development of powerful and robust bioinformatics tools will greatly benefit high-throughput proteomics. Such strategies are of the utmost importance in the rapidly emerging field of immunoproteomics, which may play a key role in the identification of antigens with diagnostic and/or therapeutic potential and in the development of new vaccines. Finally, we consider the present limitations in the discovery of new signatures and biomarkers and speculate on how such hurdles may be overcome, while also offering a prospect for the next few years in what could be one of the most significant strategies in translational medicine research.     

Mechanosensitive channels: what can they do and how do they do it?

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.     

Bacterial flagella: Do they rotate or do they propagate waves of bending?

Conclusion Whether the flagellum is rigid or nearly so or whether there are moving helical lines of contraction (Astbury et al. 1955,Lowy andSpencer 1968), incompatible sets of bonds at different radii (Klug 1967), subunits which alter their configurational states (Asakura 1966, 1970) or slip between subunits carried by edge dislocations (Harris andScriven 1971, 1973), the prevention of apparent rotation of the flagellum will result in actual rotation of the body. The differences between the two classes of mechanisms have a scale beyond the power of resolution of the light microscope. Because of this it is most unlikely that direct observation of a moving bacterium will provide evidence favouring any one of the mechanisms. The mechanism of movement of bacterial flagella remains unknown.     

WHO fellowships--what do they achieve?

Training health professionals is one of WHO''s major strategies for improving health care in the developing world. The aim, to strengthen a country''s own capacity rather than injecting expertise from outside, is in the best tradition of sustainable development. But how effective is this so called "capacity building in human resources"? Since it accounted for $43m of WHO''s budget in 1992-3 and is considered by WHO to be a major contribution to health in individual countries, it deserves detailed examination.     

Stress management techniques: Are they all equivalent,or do they have specific effects?

This article evaluates the hypothesis that various stress management techniques have specific effects. Studies comparing various techniques are reviewed, as well as previous literature reviews evaluating the effects of individual techniques. There is evidence that cognitively oriented methods have specific cognitive effects, that specific autonomic effects result from autonomically oriented methods, and that specific muscular effects are produced by muscularly oriented methods. Muscle relaxation and/or EMG biofeedback have greater muscular effects and smaller autonomic effects than finger temperature biofeedback and/or autogenic training. EMG biofeedback produces greater effects on particular muscular groups than progressive relaxation, and thermal biofeedback has greater finger temperature effects than autogenic training. Disorders with a predominant muscular component (e.g., tension headaches) are treated more effectively by muscularly oriented methods, while disorders in which autonomic dysfunction predominates (e.g., hypertension, migraine headaches) are more effectively treated by techniques with a strong autonomic component. Anxiety and phobias tend to be most effectively treated by methods with both strong cognitive and behavioral components.This work was supported by grants Nos. HL-34336 and HL-44097 from the Heart, Lung, and Blood Institute of the National Institutes of Health. Material in this article has been condensed and updated from three chapters in Lehrer, P. M., and Woolfolk, R. L. (1993).Principles and practice of stress management, Vol. 2, New York: Guilford Press.     

Viruses: are they living entities?

The essence (living or nonliving entities) of viruses has today become an aporia, i.e. a difficulty inherent in reasoning because they shared four fundamental characteristics with livings (multiplication, genetic information, mutation and evolution) without having the capacity to have an independent life. For much time, however, they were considered minuscule pathogenetic micro-organisms in observance of Koch and Pasteur's 'germ theory' albeit no microbiologist could show their existence except their filterability and pathogenetic action. Only some voices based on experimental results raised against this dogmatic view, in particular those of Beijerinck, Baur and Mrowka, without dipping effectively into the dominant theory. The discovery relative to their nucleoprotein nature made between 1934 and 1936 (Schlesinger as for the phage, and Bawden and co-operators as for Tobacco mosaic virus; TMV), together with the first demonstrations of their structures thanks to electron microscopy (from 1939 onwards) started on casting a new light on their true identity, which could be more clearly identified when, from 1955 onwards, phage and TMV proved to be decisive factors to understand the strategies of replication of the genetic material. Following the new knowledge, the theoretical view relative to viruses changed rather radically and the current view looks on these pathogenetic agents as nonliving aggregates of macromolecules provided with biological properties. There is, however, a current of thought, made explicitly by Lwoff that places viruses as compromise between living and non living and, perhaps, as primitive forms of life which have had great importance for the evolution of cellular life. At any rate, viruses are peculiar entities whose importance cannot be unacknowledged.     

Pathogenic archaea: do they exist?

Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non-pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future.     

Cytosolic glycosidases: do they exist?

The substrate specificity of the alpha-D-mannosidases of rat liver lysosome and cytosol was examined using oligosaccharides of the oligomannosidic type. The hydrolysis products were characterized by 400 MHz 1H-NMR spectroscopy. Both catabolic pathways occur in ordered ways, but are quite different. In fact, the lysosomal pathway is a two-step process: the first step involves a Zn(2+)-independent alpha-1,2-mannosidase activity, whereas the second involves a Zn(2+)-dependent alpha-1,3- and alpha-1,6-mannosidase activity. The final product is the disaccharide Man(beta 1-4)GlcNAc. In contrast, the cytosolic pathway leads, in one step, to a unique hexasaccharide (Man5GlcNAc) which has the same structure as the polyprenolic intermediate synthesized on the cytosolic face of the rough endoplasmic reticulum during the biosynthesis of N-glycosylprotein glycans: Man(alpha 1-2)-Man(alpha 1-2)Man(alpha 1-3)[Man(alpha 1-6)] Man(beta 1-4)GlcNAc(beta 1-4)-GlcNAc(alpha)P-P-Dol. In addition, the enzymatic parameters of lysosome, endoplasmic reticulum and cytosol alpha-D-mannosidases are quite different. These results lead to the conclusion that the cytosol contains specific alpha-D-mannosidases which do not originate from lysosomes nor from endoplasmic reticulum. The discovery of cytosolic endo-N-acetyl-beta-D-glucosaminidase active on 'immature complex glycans' (glycopeptides of the oligomannosidic type and of the desialylated N-acetyllactosaminic type) as well as on the glycosyl-dolichol pyrophosphate intermediates allows us to hypothesize that these enzymes belong to a control system of N-glycosylprotein biosynthesis, their role being to destroy unfinished glycans. The fate of the formed oligosaccharide structures is discussed: are they destroyed by cytosolic or lysosomal exoglycosidases, or do they carry an 'oligosaccharin-like activity'?     

Density dependence tests,are they?

A large number of time series of abundances of insects and birds from a variety of data sets were submitted to a new density dependence test. The results varied enormously between data sets, but the relation between the frequency of statistically significant density dependence (SSDD) and the length of the series was similar to that of the power curve of the test, making the results consistent with the hypothesis of the density-dependent model being universally applicable throughout the data used. Pest and non-pest species did not differ in the incidence of SSDD. The more sampling error present in the data, the higher the percentages of SSDD. This was expected given that the power of the test increases with increasing sampling error in the data. Many of the data used here, as well as in the literature, clearly violate the basic assumption of the test that the organism concerned should be univoltine and semelparous. Yet the incidence of SSDD was the same in univoltine as in bi/polyvoltine species and the same in semelparous organisms as in birds that are reproductively active in more than one year. The seasonal migrant Autographa gamma in Britain and Czechoslovakia and even rainfall data were found to have SSDD. Statistical significance, however, does not automatically lead to the conclusion of density-dependent regulation. Any series of random variables which are in a stochastic equilibrium, such as a series of independent, identically distributed, random variables, is typically described better by the alternative (density-dependent) model than by the null (density-independent) model. Significant test results were often obtained with sloppy data, with data that clearly violate the basic assumptions of the test and with other data where an interpretation of the results in terms of densitydependent regulation was absurd. Given the fact that other explanations have to be found for significant test results for all these cases, mechanisms other than regulation may very well be applicable too where the data are entirely appropriate for the test. The test is simply a data-based choice between a model without and one with a stochastic equilibrium. A time series as such does not contain any information about the causes of the fluctuation pattern, so that one cannot expect statistics to produce such information from that time series. A significant test result using suitable data is entirely consistent with the hypothesis of density-dependent regulation, but also with any other suitable hypotheses. Because the test results were generally consistent with the hypothesis of a universal applicability of the density-dependence model, a negative test result may only mean that the time series was not long enough for the density dependence that was present to become statistically significant. Positive results are difficult to interpret, but so are negative results. A final decision needs to be based not so much on the test result as on much detailed information about the population concerned. Because the density-dependence test does not test for the presence of the mechanism of density-dependent regulation and because of the loaded, multiple meanings of the term density-dependence, calling the test a test of statistical density dependence may be preferable.     

Whose turtles are they,anyway?

The hawksbill turtle (Eretmochelys imbricata), listed since 1996 by the IUCN as Critically Endangered and by the Convention on International Trade in Endangered Species (CITES) as an Appendix I species, has been the subject of attention and controversy during the past 10 years due to the efforts of some nations to re-open banned international trade. The most recent debate has centred on whether it is appropriate for Cuba to harvest hawksbills from shared foraging aggregations within her national waters. In this issue of Molecular Ecology, Bowen et al. have used molecular genetic data to show that such harvests are likely to have deleterious effects on the health of hawksbill populations throughout the Caribbean.     

Late-onset porphyrias: what are they?

Porphyrias are inherited disorders of heme biosynthesis. ALA dehydratase porphyria (ADP) and congenital erythropoietic porphyria (CEP) are autosomal recessive porphyrias, and are typically expressed at birth or in childhood. However, a few cases of late-onset recessive porphyrias have been reported. Recently we encountered a late-onset ADP patient who developed symptoms of acute porphyria when he was 63 years old. This was accompanied by polycythemia vera. It was concluded that he developed the porphyria because an abnormal ALAD allele was clonally expanded by polycythemia vera. Upon reviewing the literature, a few cases of late-onset CEP were found to be also associated with hematologic abnormalities suggestive of myelodysplastic syndrome (MDS), another clonal disorder. These findings suggest that these late-onset porphyrias may be heterozygous for their gene defects, but clinical expression may be elicited if there is a loss of heterozygosity, either by a clonal expansion of the porphyric allele or by a loss of function mutation in the other allele.     

The timing of hibernation in Tasmanian echidnas: why do they do it when they do?

We investigated the patterns of hibernation and arousals in seven free-ranging echidnas Tachyglossus aculeatus setosus (two male, five female) in Tasmania using implanted temperature data loggers. All echidnas showed a ‘classical’ pattern of mammalian hibernation, with bouts of deep torpor interrupted by periodic arousals to euthermia (mean duration 1.04±0.05 (n=146). Torpor bout length increased as body temperature fell during the hibernation season, and became more variable as temperature rose again. Hibernation started in late summer (February 28±5 days, n=6) and males aroused just before the winter solstice (June 15±3 days, n=3), females that subsequently produced young aroused 40 days later (July 25±3, n=4) while females that did not produce young hibernated for a further two months (arousal Sept 27±5, n=7). We suggest that hibernation in Tasmanian echidnas can be divided into two phases, the first phase, marked by declining minimum body temperatures as ambient temperature falls, appears to be obligatory for all animals, while the second phase is ‘optional’ and is utilised to varying amounts by females. We suggest that early arousal and breeding is the favoured option for females in good condition, and that the ability to completely omit breeding in some years, and hibernate through to spring is an adaptation to an uncertain climate.