Detection of microRNA Expression in Human Peripheral Blood Microvesicles

Background

MicroRNAs (miRNA) are small non-coding RNAs that regulate translation of mRNA and protein. Loss or enhanced expression of miRNAs is associated with several diseases, including cancer. However, the identification of circulating miRNA in healthy donors is not well characterized. Microvesicles, also known as exosomes or microparticles, circulate in the peripheral blood and can stimulate cellular signaling. In this study, we hypothesized that under normal healthy conditions, microvesicles contain miRNAs, contributing to biological homeostasis.

Methodology/Principal Findings

Microvesicles were isolated from the plasma of normal healthy individuals. RNA was isolated from both the microvesicles and matched mononuclear cells and profiled for 420 known mature miRNAs by real-time PCR. Hierarchical clustering of the data sets indicated significant differences in miRNA expression between peripheral blood mononuclear cells (PBMC) and plasma microvesicles. We observed 71 miRNAs co-expressed between microvesicles and PBMC. Notably, we found 33 and 4 significantly differentially expressed miRNAs in the plasma microvesicles and mononuclear cells, respectively. Prediction of the gene targets and associated biological pathways regulated by the detected miRNAs was performed. The majority of the miRNAs expressed in the microvesicles from the blood were predicted to regulate cellular differentiation of blood cells and metabolic pathways. Interestingly, a select few miRNAs were also predicted to be important modulators of immune function.

Conclusions

This study is the first to identify and define miRNA expression in circulating plasma microvesicles of normal subjects. The data generated from this study provides a basis for future studies to determine the predictive role of peripheral blood miRNA signatures in human disease and will enable the definition of the biological processes regulated by these miRNA.     

DOA1/UFD3 plays a role in sorting ubiquitinated membrane proteins into multivesicular bodies

Ubiquitin (Ub) is a sorting signal that targets integral membrane proteins to the interior of the vacuole/lysosome by directing them into lumenal vesicles of multivesicular bodies (MVBs). The Vps27-Hse1 complex, which is homologous to the Hrs-STAM complex in mammalian cells, serves as a Ub-sorting receptor at the surface of early endosomes. We have found that Hse1 interacts with Doa1/Ufd3. Doa1 is known to interact with Cdc48/p97 and Ub and is required for maintaining Ub levels. We find that the Hse1 Src homology 3 domain binds directly to the central PFU domain of Doa1. Mutations in Doa1 that block Hse1 binding but not Ub binding do not alter Ub levels but do result in the missorting of the MVB cargo GFP-Cps1. Loss of Doa1 also causes a synthetic growth defect when combined with loss of Vps27. Unlike the loss of Doa1 alone, the doa1Delta vps27Delta double mutant phenotype is not suppressed by Ub overexpression, demonstrating that the effect is not due to indirect consequence of lowered Ub levels. Loss of Doa1 results in a defect in the accumulation of GFP-Ub within yeast vacuoles, implying that there is a reduction in the flux of ubiquitinated membrane proteins through the MVB pathway. This defect was also reflected by an inability to properly sort Vph1-GFP-Ub, a modified subunit of the multiprotein vacuolar ATPase complex, which carries an in-frame fusion of Ub as an MVB sorting signal. These results reveal novel roles for Doa1 in helping to process ubiquitinated membrane proteins for sorting into MVBs.     

Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs

Thermodynamic parameters are reported for duplex formation of 40 self-complementary RNA duplexes containing wobble terminal base pairs with all possible 3′ single and double-nucleotide overhangs, mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest neighbor analysis, the addition of a single 3′ dangling nucleotide increases the stability of duplex formation up to 1 kcal/mol in a sequence-dependent manner. The addition of a second dangling nucleotide increases the stability of duplexes closed with wobble base pairs in an idiosyncratic manner. The results allow for the development of a nearest neighbor model, which improves the predication of free energy and melting temperature for duplexes closed by wobble base pairs with 3′ single or double-nucleotide overhangs. Phylogenetic analysis of naturally occurring miRNAs was performed. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent on the orientation of the GU closing base pair rather than the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for the 5′ single terminal overhangs adjacent to wobble closing base pairs are also presented.     

A particular case and a general pattern: hyperaggressive behaviour by one species may mediate avifaunal decreases in fragmented Australian forests

We quantitatively assessed edge effects associated with elevated abundance of a hyper aggressive bird species, the noisy miner Manorina melanocephala, in fragmented eucalypt forest adjoining developed land. Long‐term data from Toohey Forest, subtropical Australia, show that noisy miner colonies intensively occupy a zone of 20 m from the forest edge, with frequent use occurring up to 100 m from the edge, but little beyond 200 m. Within noisy miner colonies, the abundance and species richness of other birds were both about half those recorded at nearby transects which were outside the colonies' main activity area. Bird species smaller than noisy miners, which are also those with similar diets, were collectively 20–25 times more abundant, and their species richness tenfold greater, outside miner colonies than within them, whereas larger species, which have less dietary overlap, did not differ. Exclusion of small insectivorous birds has been hypothesised to cause elevated insect herbivore density, but we found no difference between tree crown defoliation or dieback rates within versus outside miner colonies. Aggression by noisy miners can be viewed as a mechanism of interspecific competition, since miners have a relatively large body size for their diet and are hence able to exclude virtually all potential competitors at relatively little cost. We examine evidence indicating that reduced bird diversity in eucalypt forest fragments of eastern Australia is often simply the effect of noisy miner occupancy of edges, acting directly on the densities of other species through their aggressive behaviour. With an edge effect 200 m deep, a remnant 10 ha in size is likely to become entirely occupied by noisy miners, and this is a size threshold that has been commonly reported in association with area‐standardised avian diversity reductions. Convergent patterns of species loss from small forest fragments in different continents are the result of different underlying ecological processes.     

Carotenoid status signaling in captive and wild red-collared widowbirds: independent effects of badge size and color

Carotenoid-based plumage ornaments are typically consideredto be sexually selected traits, functioning as honest condition-dependentsignals of phenotypic quality, but few studies have addressedthe function of carotenoid color variation in male contestcompetition. Using two experiments, we investigated the statussignaling function of the variable (ranging from yellow tored) carotenoid throat patch (collar) in the polygynous, sexually dimorphic red-collared widowbird (Euplectes ardens). First,we tested if the red collar functions as a dominance signalby painting spectrometrically controlled collar patches ontothe brown plumage of nonbreeding males and staging dyadic malecontests over food resources. Red-collared males dominatedorange males, which in turn dominated the control brown andnovel blue collars. Red dominance persisted when the collar manipulations were reversed within dyads and also when testedagainst testosterone implanted males. In the second experimentthe collar size and color of breeding males were manipulatedin the field before and after territories were established.All males with enlarged red and most with enlarged orange orreduced red collars obtained territories, whereas most maleswith reduced orange and all with blackened (removed) collarsfailed to establish or retain territories. In addition, amongthe territorial males, those with reduced signals defendedsmaller territories, received more intrusions, and spent moretime in aggressive interactions. Redness and, to a lesser extent,size of the carotenoid ornament both seem to independently indicate male dominance status or fighting ability in male contest competition.     

The ZbYME2 gene from the food spoilage yeast Zygosaccharomyces bailii confers not only YME2 functions in Saccharomyces cerevisiae, but also the capacity for catabolism of sorbate and benzoate, two major weak organic acid preservatives

A factor influencing resistances of food spoilage microbes to sorbate and benzoate is whether these organisms are able to catalyse the degradation of these preservative compounds. Several fungi metabolize benzoic acid by the beta-ketoadipate pathway, involving the hydroxylation of benzoate to 4-hydroxybenzoate. Saccharomyces cerevisiae is unable to use benzoate as a sole carbon source, apparently through the lack of benzoate-4-hydroxylase activity. However a single gene from the food spoilage yeast Zygosaccharomyces bailii, heterologously expressed in S. cerevisiae cells, can enable growth of the latter on benzoate, sorbate and phenylalanine. Although this ZbYME2 gene is essential for benzoate utilization by Z. bailii, its ZbYme2p product has little homology to other fungal benzoate-4-hydroxylases studied to date, all of which appear to be microsomal cytochrome P450s. Instead, ZbYme2p has strong similarity to the matrix domain of the S. cerevisiae mitochondrial protein Yme2p/Rna12p/Prp12p and, when expressed as a functional fusion to green fluorescent protein in S. cerevisiae growing on benzoate, is largely localized to mitochondria. The phenotypes associated with loss of the native Yme2p from S. cerevisiae, mostly apparent in yme1,yme2 cells, may relate to increased detrimental effects of endogenous oxidative stress. Heterologous expression of ZbYME2 complements these phenotypes, yet it also confers a potential for weak acid preservative catabolism that the native S. cerevisiae Yme2p is unable to provide. Benzoate utilization by S. cerevisiae expressing ZbYME2 requires a functional mitochondrial respiratory chain, but not the native Yme1p and Yme2p of the mitochondrion.