Individual mRNA expression profiles reveal the effects of specific microRNAs

BACKGROUND: MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level. We sought, therefore, to determine whether a general lowering of predicted target gene mRNA expression by endogenous miRNAs was detectable within microarray gene expression profiles. RESULTS: The target gene sets predicted for each miRNA were mapped onto known gene expression data from a range of tissues. Whether considering mean absolute target gene expression, rank sum tests or 'ranked ratios', many miRNAs with significantly reduced target gene expression corresponded to those known to be expressed in the cognate tissue. Expression levels of miRNAs with reduced target mRNA levels were higher than those of miRNAs with no detectable effect on mRNA expression. Analysis of microarray data gathered after artificial perturbation of expression of a specific miRNA confirmed the predicted increase or decrease in influence of the altered miRNA upon mRNA levels. Strongest associations were observed with targets predicted by TargetScan. CONCLUSION: We have demonstrated that the effect of a miRNA on its target mRNAs' levels can be measured within a single gene expression profile. This emphasizes the extent of this mode of regulation in vivo and confirms that many of the predicted miRNA-mRNA interactions are correct. The success of this approach has revealed the vast potential for extracting information about miRNA function from gene expression profiles.

Coexistence among native and introduced freshwater amphipods (Crustacea); habitat utilization patterns in littoral habitats

Studies of biological invasions predominantly stress threats to biodiversity through the elimination and replacement of native species. However, we must realise that resident communities may often be capable of integrating invaders, leading to patterns of coexistence. Within the past ninety years, three freshwater amphipod species have invaded Northern Ireland the North American Gammarus tigrinus and Crangonyx pseudogracilis, plus the European G. pulex. These species have come into contact with the ubiquitous native species, G. duebeni celticus. This study examined spatiotemporal patterns of stability of single and mixed species assemblages in an invaded lake. Lough Beg and its associated rivers were surveyed in summer 1994 and winter 1995, and a selection of stations re-sampled in summer one and five years later. All possible combinations of the four amphipod species were found. Although species presence/absence was stable between seasons at the scale of the whole lough, it was extremely fluid at the scale of individual sites, 82% of which changed in species composition between seasons. Overall mean amphipod abundance was similar across 5 distinguishable habitat types, but there were differences in species compositions among these habitats. In addition, although co-occurrences of Gammarus species did not differ from random, there was a strong negative association between Gammarus spp. and C. pseudogracilis. This latter pattern was at least in part generated by the better tolerance of C. pseudogracilis to lower water quality. A review of previous studies indicates that the exclusion of C. pseudogracilis by Gammarus species from high water quality areas is likely to involve biotic interaction. Thus, overall, co-existence of the four species, which is clearly dynamic and scale-dependent, appears promoted by spatial and temporal habitat heterogeneity. However, biotic interactions may also play a role in local exclusions. Since the three introduced species have not eliminated the native species, and each successive invasion has not replaced the previous invader, this study demonstrates that freshwater invaders may integrate with native communities leading to coexistence and increased species diversity.

Cell-specific processing of chromogranin A in endocrine cells of the rat stomach

The rat stomach is rich in endocrine cells. The acid-producing (oxyntic) mucosa contains ECL cells, A-like cells, and somatostatin (D) cells, and the antrum harbours gastrin (G) cells, enterochromaffin (EC) cells and D cells. Although chromogranin A (CgA) occurs in all these cells, its processing appears to differ from one cell type to another. Eleven antisera generated to different regions of rat CgA, two antisera generated to a human (h) CgA sequences, and one to a bovine Ib) CgA sequence, respectively, were employed together with antisera directed towards cell-specific markers such as gastrin (G cells), serotonin (EC cells), histidine decarboxylsae (ECL cells) and somatostatin (D cells) to characterize the expression of CgA and CgA-derived peptides in the various endocrine cell populations of the rat stomach. In the oxyntic mucosa, antisera raised against CgA(291-319) and CGA(316-321) immunostained D cells exclusively, whereas antisera raised against bCgA(82-91) and CgA(121-128) immunostained A-like cells and D cells. Antisera raised against CgA(318-349) and CgA(437-448) immunostained ECL cells and A-like cells, but not D cells. In the antrum, antisera against CgA(291-319) immunostained D cells, and antisera against CgA(351-356) immunostained G cells. Our observations suggest that each individual endocrine cell type in the rat stomach generates a unique mixture of CgA-derived peptides, probably reflecting cell-specific differences in the post-translational processing of CgA and its peptide products. A panel of antisera that recognize specific domains of CgA may help to identify individual endocrine cell populations.

The status of Nathusius' pipistrelle (Pipistrellus nathusii Keyserling & Blasius, 1839) in the British Isles

There are now 91 records of individual Nathusius' pipistrelle Pipistrellus nathusii examined 'in the hand' in the U.K., and bat detector records from a further 36 localities in Britain and Ireland. These records are distributed throughout all months of the year with clear peaks in spring and autumn suggesting migratory movements into and out of the British Isles in autumn and spring, respectively. Three maternity colonies have been located and the species must now also be regarded as a resident breeding species in Britain and Ireland.

Mating behavior and chemical communication in the order hymenoptera

Insects of the order Hymenoptera are biologically and economically important members of natural and agro ecosystems and exhibit diverse biologies, mating systems, and sex pheromones. We review what is known of their sex pheromone chemistry and function, paying particular emphasis to the Hymenoptera Aculeata (primarily ants, bees, and sphecid and vespid wasps), and provide a framework for the functional classification of their sex pheromones. Sex pheromones often comprise multicomponent blends derived from numerous exocrine tissues, including the cuticle. However, very few sex pheromones have been definitively characterized using bioassays, in part because of the behavioral sophistication of many Aculeata. The relative importance of species isolation versus sexual selection in shaping sex pheromone evolution is still unclear. Many species appear to discriminate among mates at the level of individual or kin/colony, and they use antiaphrodisiacs. Some orchids use hymenopteran sex pheromones to dupe males into performing pseudocopulation, with extreme species specificity.

Individual trade-offs between nutrition and risk of interspecific transmission of disease by grazing: cows, badger latrines and bovine tuberculosis

1. We examine whether various measures of herbivore current physiological state (age, breeding and immune status) and genetic potential can be used as indicators of exposure to and risk from disease. We use dairy cattle and the risks of tuberculosis (TB) transmission posed to them by pasture contaminated with badger excreta (via the fecal-oral route) as a model system to address our aim.

Energetics and litter size variation in domestic dog Canis familiaris breeds of two sizes

We measured resting metabolic rate (RMR), daily energy expenditure (DEE) and metabolisable energy intake (MEI) in two breeds of dog during peak lactation to test whether litter size differences were a likely consequence of allometric variation in energetics. RMR of Labrador retrievers (30 kg, n = 12) and miniature Schnauzers (6 kg, n = 4) averaged 3437 and 1062 kJ/day, respectively. DEE of Labradors (n = 6) and Schnauzers (n = 4) averaged 9808 and 2619 kJ/day, respectively. MEI of Labradors (n = 12) was 22448 kJ/day and of Schnauzers (a = 7) was 5382 kJ/day. DEE of Labrador pups (2.13 kg, n = 19) was 974 kJ/day and Schnauzers (0.89 kg, n = 7) were 490 kJ/day. Although Labradors had higher MEIs than Schnauzers during peak lactation, there was no difference in mass-specific energy expenditure between the two breeds. Hence, it is unlikely that litter size variation is a likely consequence of differences in maternal energy expenditure. Individual offspring were relatively more costly for mothers of the smaller breed to produce. Therefore, litter size variations were consistent with the expectation that smaller offspring should be more costly for mothers, but not that smaller mothers should per se invest more resources in reproduction. (C) 2001 Elsevier Science Inc. All rights reserved.

Algal epiphytes of Zostera marina: Variation in assemblage structure from individual leaves to regional scale

Data from a hierarchical study of four Zostera marina beds in Wales were used to identify the spatial scales of variation in epiphyte assemblages. There were significant within and among bed differences in assemblage structure. The differences in assemblage structure with spatial scale generally persisted when species identifications were aggregated into functional groups. There was also significant within and among bed variability in Zostera density and average length. Local variations in Zostera canopy variables at the quadrat scale (total leaf length, average leaf length and leaf density per quadrat) were not related to epiphyte species richness nor to the structure of the assemblage. In contrast, individual leaf length was significantly related to species richness in two of the beds and the structure of epiphyte assemblages was always related to individual leaf lengths. The absence of links between quadrat scale measurements of canopy variables and assemblage structure may reflect the high turnover of individual Zostera leaves. Experimental work is required to discriminate further between the potential causes of epiphyte assemblage variation within and between beds. No bed represented a refuge where a rare species was abundant. If a species was uncommon at the bed scale, it was also uncommon in beds where it occurred. The heterogeneous assemblages found in this study suggest that a precautionary approach to conservation is advisable.

cpDNA-RFLP in Ceramium (Rhodophyta): Intraspecific polymorphism and species-level phylogeny

Restriction fragment length polymorphism (RFLP) analysis of chloroplast (cp) DNA is a powerful tool for the study of microevolutionary processes in land plants, yet has not previously been applied to seaweed populations. We used cpDNA-RFLP, detected on Southern blots using labeled total plastid DNA, to search for intraspecific and intrapopulational cpDNA RFLP polymorphism in two species of the common red algal genus Ceramium in Ireland and Britain. In C. botryocarpum one polymorphism was detected in one individual among 18 from two populations. Twenty-six individuals of C. virgatum from five populations at three locations exhibited a total of four haplotypes. One was frequent (80.8% of individuals); the others were rare (7.7, 7.7 and 4.2%) and were private to particular populations. Polymorphism was observed in two populations. The corrected mean was 2.26 +/- 0.36 haplotypes per population, which was within the typical range determined for higher plants using similar techniques. The spatial distribution of haplotypes was heterogeneous, with highly significant population differentiation (P = 0.00018; Fisher's exact test). Intraspecific polymorphism in C. virgatum had no impact on species-level phylogenetic reconstruction. This is the first unequivocal report of both intraspecific and intrapopulational cpDNA-RFLP polymorphism in algae.

Effect of pH, temperature, and moisture on the formation of volatile compounds in glycine/glucose model systems

Mixtures of glycine, glucose, and starch were extrusion cooked using sodium hydroxide at 0, 3, and 6 g/L of extruder water feed, 18% moisture, and 120, 150, and 180 degreesC target die temperatures, giving extrudates with pH values of 5.6, 6.8, and 7.4. Freeze-dried equimolar solutions of glucose and glycine were heated either dry or after equilibration to similar to 13% moisture at 180 degreesC in a reaction-tube system designed to mimic the heating profile in an extruder. Volatile compounds were isolated onto Tenax and analyzed by gas chromatography-mass spectrometry. For the extrudates, total yields of volatiles increased with decreasing pH at 180 degreesC, reached a maximum at pH 6.S at 150 degreesC, and increased with increasing pH at 120 degreesC. Amounts increased with temperature at all pH values. Pyrazines were the most abundant class for all sets of conditions (54-79% of total volatiles). Pyrroles, ketones, furans, oxazoles, and pyridines were also identified. Yields of volatiles from the reaction-tube samples increased by > 60% in the moist system. Levels of individual classes also increased in the presence of moisture, except pyrazines, which decreased similar to3.5-fold. Twenty-one of the compounds were common to the reaction-tube samples and the extrudates.

Formation of Strecker aldehydes and pyrazines in a fried potato model system

Sugars and amino acids were removed from potato slices by soaking in water and ethanol. They were then infused with various combinations of sugars (glucose and/or fructose) and amino acids (asparagine, glutamine, leucine, isoleucine, phenylalanine, and/or methionine) and fried. Volatile compounds were trapped onto Tenax prior to gas chromatography-mass spectrometry. Relative amounts of compounds (relative to the internal standard) and relative yields (per mole of amino acid infused into the slices) were determined. Amounts of 10 pyrazines, 4 Strecker aldehydes, and 4 other compounds were monitored. Relative amounts and relative yields of compounds varied according to the composition of the system. For the single amino acid-glucose systems, leucine gave the highest relative amount and relative yield of its Strecker aldehyde. Asparagine and phenylalanine gave the highest total relative amount and total relative Yield, respectively, of pyrazines. In the system containing all of the amino acids and glucose, the relative amount of 3-methylbutanal was higher, whereas the amounts of the other monitored Strecker aldehydes were lower. Most of the relative amounts of individual pyrazines were lower compared to the glucose-asparagine system, whereas the total relative yield of pyrazines was lower, compared to all of the single amino acid-glucose mixtures. Addition of fructose to the mixed amino acid-glucose model system generated Strecker aldehydes and pyrazines in ratios that were more similar to those of untreated potato chips than to those from the same system but without fructose. Both the sugars and the amino acids present in potato are crucial to the development of flavor compounds in fried potato slices.

The preparation of reach to grasp movements in adults with Down syndrome

The aim of this study was to determine the extent to which adults with Down syndrome (DS) are able to utilise advance information to prepare reach to grasp movements. The study comprised ten adults with DS; ten children matched to an individual in the group with DS on the basis of their intellectual ability, and twelve adult controls. The participants used their right hand to reach out and grasp illuminated perspex blocks. Four target blocks were positioned on a table surface, two to each side of the midsagittal plane. In the complete precue condition, participants were provided with information specifying the location of the target. In the partial precue condition, participants were given advance information indicating the location of the object relative to the midsagittal plane (left or right). In the null condition, advance information concerning the position of the target object was entirely ambiguous. It was found that both reaction times and movement times were greater for the participants with DS than for the adults without DS. The reaction times exhibited by individuals with DS in the complete precue condition were lower than those observed in the null condition, indicating that they had utilised advance information to prepare their movements. In the group with DS, when advance information specified only the location of the target object relative to the midline, reaction times were equivalent to those obtained when ambiguous information was given. In contrast, the adults without DS exhibited reaction times that were lower in both the complete and partial precue conditions when compared to the null condition. The pattern of results exhibited by the children was similar to that of the adults without DS. The movement times exhibited by all groups were not influenced by the precue condition. In summary, our findings indicate that individuals with DS are able to use advance information if it specifies precisely the location of the target object in order to prepare a reach to grasp movement. The group with DS were unable, however, to obtain the normal advantage of advance information specifying only one dimension of the movement goal (i.e., the position of an object relative to the body midline). (C) 2001 Elsevier Science B.V. All rights reserved.

The application of a Trous wave filtering and Monte Carlo analysis on secis 2001 solar eclipse observations

Eight thousand images of the solar corona were captured during the June 2001 total solar eclipse. New software for the alignment of the images and an automated technique for detecting intensity oscillations using multi-scale wavelet analysis were developed. Large areas of the images covered by the Moon and the upper corona were scanned for oscillations and the statistical properties of the atmospheric effects were determined. The a Trous wavelet transform was used for noise reduction and Monte Carlo analysis as a significance test of the detections. The effectiveness of those techniques is discussed in detail.