Antigenic variation in babesiosis: is there more than one 'why'?

Many intraerythrocytic hemoparasites survive the host immune system through rapid antigenic variation. Among babesial parasites antigenic variation has been demonstrated convincingly only for Babesia bovis and Babesia rodhaini. The molecular basis for antigenic variation in babesial parasites and its possible connection with cytoadherence and sequestration are discussed.     

Germ-line mosaicism in tuberous sclerosis: how common?

Two-thirds of cases of tuberous sclerosis complex (TSC) are sporadic and usually are attributed to new mutations, but unaffected parents sometimes have more than one affected child. We sought to determine how many of these cases represent germ-line mosaicism, as has been reported for other genetic diseases. In our sample of 120 families with TSC, 7 families had two affected children and clinically unaffected parents. These families were tested for mutations in the TSC1 and TSC2 genes, by Southern blotting and by single-strand conformational analysis. Unique variants were detected in six families. Each variant was present and identical in both affected children of a family but was absent in both parents and the unaffected siblings. Sequencing of the variants yielded two frameshift mutations, one missense mutation, and two nonsense mutations in TSC2 and one nonsense mutation in TSC1. To determine which parent contributed the affected gametes, the families were analyzed for linkage to TSC1 and TSC2, by construction of haplotypes with markers flanking the two genes. Linkage analysis and loss-of-heterozygosity studies indicated maternal origin in three families, paternal origin in one family, and either being possible in two families. To evaluate the possibility of low-level somatic mosaicism for TSC, DNA from lymphocytes of members of the six families were tested by allele-specific PCR. In all the families, the mutant allele was detected only in the known affected individuals. We conclude that germ-line mosaicism was present in five families with mutations in the TSC2 gene and in one family with the causative mutation in the TSC1 gene. The results have implications for genetic counseling of families with seemingly sporadic TSC.     

Detecting decline in a formerly widespread species: how common is the common blue butterfly Polyommatus icarus?

Grid square distribution maps have been used widely to measure rates of decline and target conservation resources. However, common species that may have many populations per grid square can decline substantially from within squares without being lost from entire squares. In order to quantify this process, fine scale population and habitat data have been collected for the common blue butterfly Polyommatus icarus in a 35 km² area of fragmented landscape in north Wales. Present day habitat associations, determined from over 2000 transect walks, combined with data on historical and present day habitat distributions reveal that the species has declined by about 74% since 1901. Similar data concerning the species major host plant Lotus corniculatus indicate a decline of 46%. Based on 1 km² grid maps, neither species have been assessed as declining at all. These results suggest that apparently 'common' species may have declined just as much as many of Britain's rare species: using present methods of assessment these declines are undetected.     

Oxysterol binding proteins: in more than one place at one time?

Oxysterols are potent signalling lipids that directly bind liver X receptors (LXRs) and a subset of oxysterol binding protein (OSBP) related proteins (ORPs). It is relatively well established that the oxysterol-regulated function of LXRs is to control the expression of genes involved in reverse cholesterol transport, catabolism of cholesterol, and lipogenesis. In contrast, the mechanisms by which oxysterols and ORPs affect cellular lipid metabolism have remained poorly understood. In this review, we summarize the information available on function of the ORPs and compare the two families of proteins binding oxysterol to demonstrate the different responses that similar lipids can elicit within cells. The other focus is on the membrane targeting determinants and the protein interaction partners of ORPs, which provide interesting clues to the mode(s) of ORP action. Specifically, we suggest a model in which a general property of ORPs is to function at membrane contact sites, specialized zones of communication between two different organelles.     

Personalizing foods: is genotype necessary?

The inescapable conclusion of a just a decade of nutrigenomics research must now be brought to practice. Humans differ in their responses to diet and many of these differences are being assigned to genetic polymorphisms. However, differences in the varying responses to diet between humans are not solely because of genetic variation. Lifestage, lifestyle, prior nutritional and physiological variables and even your mother's microflora all influence the differences between humans. The question becomes: are all of these inputs to an individual's health measurable as part of a nutritional phenotype assessment? The answer to this question is increasingly, yes. As variations in humans can be both measured and even more importantly understood, the implications of those measures to dietary guidance become actionable. More accurate assessment of the inputs to human health and the consequences of those inputs measured as accurate proteomic and metabolomic analyses would bring personalized health to practice far faster than waiting for a predictive knowledge of genetic variation.     

Plant-endophyte-herbivore interactions: More than just alkaloids?

A recent paper by Rasmussen et al., (New Phytol 2007; 173:787–97) describes the interactions between Lolium perenne cultivars with contrasting carbohydrate content and the symbiotic fungal endophyte Neotyphodium lolii at different levels of nitrogen supply. In a subsequent study undertaken by Rasmussen et al., (Plant Physiol 2008; 146:1440–53) 66 metabolic variables were analysed in the same material, revealing widespread effects of endophyte infection, N supply and cultivar carbohydrate content on both primary and secondary metabolites. Here, we link insect numerical responses to these metabolic responses using multiple regression analysis.Key words: Neotyphodium lolii, Lolium perenne, high sugar grasses, metabolomics, insect herbivoresPasture grasses are often infected with symbiotic fungal endophytes and benefits for host plants arising out of these associations are generally ascribed to endophyte produced anti-herbivorous alkaloids. We tested the effects of (i) infection with three strains of endophytes differing in their alkaloid profiles, (ii) high vs. low nitrogen (N) supply, and (iii) ryegrass cultivars with high vs. control levels of water soluble carbohydrates (WSCs) on numerical insect responses (aphids, thrips, mites). A difference in WSC content between the cultivars had no significant effect on insect numbers, whereas high N compared to low N supply increased mites, thrips and alate Rhopalosiphum spp., but decreased apterous Rhopalosiphum spp. The effect of endophyte infection was strain dependant and differed for the different insects.A total of 66 metabolic variables of the same plants analysed prior to insect treatment were linked to insect responses using multiple regression analysis. One of the major conclusions to be drawn is that alkaloids are not always the most important factor influencing numerical insect responses which will also be determined by other metabolites, clearly indicating the importance of metabolomics type studies to point the way toward a mechanistic explanation of grass-endophyte-herbivore interactions.Grass species are often hosts of symbiotic clavicipitaceous endophytic fungi¹ residing in the apoplastic spaces of above ground plant parts and usually not causing any visible symptoms of infection.^2–4 These fungal symbionts confer protection from insect herbivory to their host plants through alkaloids,^5–8 some of which (ergovaline, lolitrem B) are also toxic to grazing mammals.^9,10 Natural endophyte strains lacking these mammalian toxins, but still retaining at least some of their insect deterring features, have been commercialized and are now widely used in ryegrass and tall fescue based pastures.^11,12     

Dry matter partitioning in a tomato plant: one common assimilate pool?

The influence of the distance (transport resistance) betweensource and sink on dry matter distribution between fruits andvegetative parts in tomato was studied. In two glasshouse experiments,a control treatment (single-shoot plants, no truss removal)was conducted, together with two double-shoot treatments: double-shootplants with no trusses removed from one shoot and all trussesremoved at anthesis from the other shoot (100–0) and double-shootplants with every second truss removed from both shoots (50–50).Plant growth and dry matter distribution was recorded by periodicaldestructive harvests, during a period of about 100 d after anthesisof the first truss. In experiment 2, plants were probably sink-limited.At the end of both experiments, 58–60% of dry matter wasin the fruits for control plants, whereas for both double-shoottreatments this was 43% (Experiment 1) or 38% (Experiment 2).Until 60–65 d after first flowering, vegetative growthof the individual shoots in both double-shoot treatments wasthe same. Results supported the assumption of one common assimilatepool and showed no significant influence of distance (transportresistance) between source and sink on dry matter partitioning. Key words: Allocation, distance, dry matter distribution, one assimilate pool, partitioning, transport resistance, tomato     

Disease in scleractinian corals: a new problem in the reef at Cayo Sombrero, Morrocoy National Park, Venezuela?

At the beginning of 1996 coral reefs in Morrocoy National Park, Venezuela, suffered an unprecedented mass mortality event. As a consequence, live coral cover dropped to 2-10%. One of the few reefs that kept live coral cover over 35% was Cayo Sombrero; nonetheless, the presence of some coral diseases has been detected within the past 2 years, representing a new source of coral mortality. Due to this situation, this study started a monitoring program on the incidence of coral diseases and syndromes in the reef of Cayo Sombrero. The CARICOMP protocol was used in order to evaluate reef health. Ten parallel band-transects (20 x 2m) where established at two depth intervals: Five between 3-8 m and five between 8-12 m, and the frequency of both, healthy and unhealthy colonies of each coral species was recorded along each band transect. In addition to other sources of coral damage (predation, siltation, etc), significant differences in disease incidence between the two depths intervals were tested with a Kruskall-Wallis test. The main problems observed were coral diseases such as yellow band (4.2%), dark spots (1.61%) and white plague-II (1.4%), mainly affecting Montastraea faveolata, M. annularis and Siderastrea siderea. Siltation, affecting massive colonies, such as Colpophyllia natans and Diploria strigosa; algae overgrowth, predation, anchor damage, and bleaching. Significant differences were found in the incidence of unhealthy (Kruskall-Wallis, p < 0.05) bleached (Kruskall-Wallis, p < 0.05) and colonies affected by siltation (Kruskall-Wallis, p < 0.05). More than 60% of the 585 coral colonies surveyed at both depths were found to be healthy, indicating that the Cayo Sombrero reef is still in good conditions compared to other localities in the Park. This study stresses the need to conduct early monitoring programs that survey coral disease incidence as a source of mortality for this coral reef.     

Is genetic variability so important? Non-native salmonids in South America

Three salmonid species introduced in Patagonian national parks in Argentine have experienced different degrees of expansion. Atlantic salmon Salmo salar is restricted to a few river-lake systems and its populations have been declining over recent years. Both rainbow Oncorhynchus mykiss and brown trout Salmo trutta populations have expanded from their introduction sites and now occupy a wide range of freshwater ecosystems. Genetic variation at the same neutral markers (microsatellite loci) was examined for different populations of the three species acclimatized to the same areas, and compared with that of native populations. Founder effects denoted as reduced variability and great differentiation with respect to the native populations were detected. Significant reduction in variability has not been an obstacle for successful adaptation of rainbow and brown trout, indicating that genetic variability per se cannot be claimed as the reason for their different outcomes in the new habitats.     

Evolution of competitive fitness in experimental populations of E. coli: What makes one genotype a better competitor than another?

An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10000 generations, the average fitness of the derived genotypes had increased by 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.     

Evaluation of genetic tests for susceptibility to common complex diseases: why, when and how?

Recent research into the human genome has generated a wealth of scientific knowledge and increased both public and professional interest in the concept of personalised medicine. Somewhat unexpectedly, in addition to increasing our understanding about the genetic basis for numerous diseases, these new discoveries have also spawned a burgeoning new industry of ‘consumer genetic testing’. In this paper, we present the principles learnt though the evaluation of tests for single gene disorders and suggest a comparable framework for the evaluation of genetic tests for susceptibility to common complex diseases. Both physicians and the general public will need to be able to assess the claims made by providers of genetic testing services, and ultimately policy-makers will need to decide if and when such tests should be offered through state funded healthcare systems.     

Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants?

Background

The presence of chloroplast-related DNA sequences in the nuclear genome is generally regarded as a relic of the process by which genes have been transferred from the chloroplast to the nucleus. The remaining chloroplast encoded genes are not identical across the plant kingdom indicating an ongoing transfer of genes from the organelle to the nucleus.

Scope

This review focuses on the active processes by which the nuclear genome might be acquiring or removing DNA sequences from the chloroplast genome. Present knowledge of the contribution to the nuclear genome of DNA originating from the chloroplast will be reviewed. In particular, the possible effects of stressful environments on the transfer of genetic material between the chloroplast and nucleus will be considered. The significance of this research and suggestions for the future research directions to identify drivers, such as stress, of the nuclear incorporation of plastid sequences are discussed.

Conclusions

The transfer to the nuclear genome of most of the protein-encoding functions for chloroplast-located proteins facilitates the control of gene expression. The continual transfer of fragments, including complete functional genes, from the chloroplast to the nucleus has been observed. However, the mechanisms by which the loss of functions and physical DNA elimination from the chloroplast genome following the transfer of those functions to the nucleus remains obscure. The frequency of polymorphism across chloroplast-related DNA fragments within a species will indicate the rate at which these DNA fragments are incorporated and removed from the chromosomes.Key words: Stress, DNA transfer, organelles and nucleus, genome integration     

Neuroscience: how is three-dimensional space encoded in the brain?

A recent study in the rat has shown that hippocampal place cells and entorhinal grid cells exhibit vertically-elongated firing fields, indicating that the rat's brain may encode the animal's elevation less accurately than its horizontal position.     

The Mastodon in the room: how Darwinian is neo-Darwinism?

Failing to acknowledge substantial differences between Darwinism and neo-Darwinism impedes evolutionary biology. Darwin described evolution as the outcome of interactions between the nature of the organism and the nature of the conditions, each relatively autonomous but both historically and spatially intertwined. Furthermore, he postulated that the nature of the organism was more important than the nature of the conditions, leading to natural selection as an inevitable emergent product of biological systems. The neo-Darwinian tradition assumed a creative rather than selective view of natural selection, with the nature of the organism determined by the nature of the conditions, rendering the nature of the organism and temporal contingency unnecessary. Contemporary advances in biology, specifically the phylogenetics revolution and evo-devo, underscore the significance of history and the nature of the organism in biology. Darwinism explains more biology better, and better resolves apparent anomalies between living systems and more general natural laws, than does neo-Darwinism. The "extended" or "expanded" synthesis currently called for by neo-Darwinians is Darwinism.     

Grades in neural complexity: how large is the span?

The span of complexity in brains, between the simplest flatworms and the most advanced mammals is exceedingly great, measured by the number of different anatomical parts, physiological processes, sensory discriminations, and behavioral alternatives in the repertoire. Most evolution of brains has been adaptive radiation within the same grade of complexity. Distinct grades of complexity have appeared a dozen or more times and quite often in the retrograde direction. Advancement has not been inevitable or obviously advantageous in survival value but has happened-long before primates or mammals or vertebrates. Compare cuttlefish and the most advanced gastropods, bees and the best brine shrimp, primates and the most advanced reptiles known-all twigs with common branches. This repeated achievement of evolution has had all too little study in respect of the detailed listing of differences between major taxa of distinct grades of complexity. Connectivity at the level now known for the mammalian cortex is much needed in other classes, with estimates of reciprocity, intrinsic differentiation, dendritic parcellation and afferent and efferent connections, both locally and projecting to other centers, each done quantitatively to permit comparison. Physiological system organization, personality properties of neurons and circuits, proclivities and emergent phenomena at several integrative levels are sketchily known only for parts of a few systems. Examples are given of opportunities for new research that can more adequately characterize grades of brains.