The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lamblia

In the current investigation, we analysed all the known small nucleolar RNAs (snoRNAs) in the deeply branching protozoan parasite Giardia lamblia for potential microRNAs (miRNAs) that might be derived from them. Two putative miRNAs have since been identified by Northern blot, primer extension, 3' RACE and co-immunoprecipitation with Giardia Argonaute (GlAgo), and designated miR6 and miR10. Giardia Dicer (GlDcr) is capable of processing the snoRNAs into the corresponding miRNAs in vitro. Potential miR6 and miR10 binding sites in Giardia genome were predicted bio-informatically. A miR6 binding site was found at the 3' untranslated regions (UTR) of 44 variant surface protein (vsp) genes, whereas a miR10 binding site was identified at the 3' end of 159 vsp open-reading frames. Thirty-three of these vsp genes turned out to contain binding sites for both miR6 and miR10. A reporter mRNA tagged with the 3' end of vsp1267, which contains the target sites for both miRNAs, was translationally repressed by both miRNAs in Giardia. Episomal expression of an N-terminal c-myc tagged VSP1267 was found significantly repressed by introducing either miR6 or miR10 into the cells and the repressive effects were additive. When the 2'-O-methyl antisense oligos (ASOs) of either miR6 or miR10 was introduced, however, there was an enhancement of tagged VSP1267 expression suggesting an inhibition of the repressive effects of endogenous miR6 or miR10 by the ASOs. Of the total 220 vsp genes in Giardia, we have now found 178 of them carrying putative binding sites for all the miRNAs that have been currently identified, suggesting that miRNAsare likely the regulators of VSP expression in Giardia.     

Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching

Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3’-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3’-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple patterns (3’-UTR shortening and lengthening) and two complex patterns. By comparing the results of the two statistical methods, we show that complex patterns account for 1/4 of all observed switching events that happen between normal and cancerous human breast cell lines. Because simple and complex switching patterns may convey different biological meanings, they merit separate study. We therefore propose to combine both the independence test and the linear trend test in practice. First, the independence test should be used to detect APA site switching; second, the linear trend test should be invoked to identify simple switching events; and third, those complex switching events that pass independence testing but fail linear trend testing can be identified.     

Food Recruitment Information can Spatially Redirect Employed Stingless Bee Foragers

Within a rewarding floral patch, eusocial bee foragers frequently switch sites, going from one flower to another. However, site switching between patches tends to occur with low frequency while a given patch is still rewarding, thus reducing pollen dispersal and gene flow between patches. In principle, forager switching and gene flow between patches could be higher when close patches offer similar rewards. We investigated site switching during food recruitment in the stingless bee Scaptotrigona mexicana . Thus, we trained three groups of foragers to three feeders in different locations, one group per location. These groups did not interact each other during the training phase. Next, interaction among trained foragers was allowed. We found that roughly half of the foragers switched sites, the other half remaining faithful to its training feeder. Switching is influenced by the presence of recruitment information. In the absence of recruitment information (bees visiting and recruiting for feeders), employed foragers were site specific. Foragers only switched among feeders that were being visited and recruited to. Switching was not caused by learned aversion to experimental handling. Switching in response to recruitment could provide a fitness benefit to the colony by facilitating rapid switching among exploited patches and provide a benefit of increasing plant gene flow between patches.     

Gene conversions mediating antigenic variation in Trypanosoma brucei can occur in variant surface glycoprotein expression sites lacking 70-base-pair repeat sequences.

African trypanosomes undergo antigenic variation of their variant surface glycoprotein (VSG) coat to avoid immune system-mediated killing by their mammalian host. An important mechanism for switching the expressed VSG gene is the duplicative transposition of a silent VSG gene into one of the telomeric VSG expression sites of the trypanosome, resulting in the replacement of the previously expressed VSG gene. This process appears to be a gene conversion reaction, and it has been postulated that sequences within the expression site may act to initiate and direct the reaction. All bloodstream form expression sites contain huge arrays (many kilobase pairs) of 70-bp repeat sequences that act as the 5' boundary of gene conversion reactions involving most silent VSG genes. For this reason, the 70-bp repeats seemed a likely candidate to be involved in the initiation of switching. Here, we show that deletion of the 70-bp repeats from the active expression site does not affect duplicative transposition of VSG genes from silent expression sites. We conclude that the 70-bp repeats do not appear to function as indispensable initiation sites for duplicative transposition and are unlikely to be the recognition sequence for a sequence-specific enzyme which initiates recombination-based VSG switching.     

The inactivation and reactivation of an expression-linked gene copy for a variant surface glycoprotein in Trypanosoma brucei.

We have previously shown that the gene for variant surface glycoprotein 118 of Trypanosoma brucei (strain 427) is activated by a duplicative transposition to a telomeric expression site. In chronically-infected animals, this expression-linked copy is lost when the 118 gene is replaced at the expression site by another variant surface glycoprotein gene. We show here that expression of the 118 gene can also be switched off without loss of the extra expression-linked copy. In two variants, called 1.8b and 1.8c, we find expression of the variant surface glycoprotein 1.8 gene, notwithstanding the continued presence of the 118 expression-linked copy. The 1.8 gene activated has a telomeric location, like the 118 expression-linked copy. In variant 1.8b, activation is accompanied by duplication of the 1.8 gene, resulting in an extra telomeric gene copy; in variant 1.8c it is not. Variants 1.8b and 1.8c both switch back preferentially to expression of the 118 gene. The 5'-flanking regions of the active, inactive and reactivated versions of the 118 expression-linked copy are indistinguishable by restriction mapping up to 28 kb. We conclude that there are at least two separate telomeric expression sites in our T. brucei strain. How these are switched on and off is unclear. The ability to retain expression-linked copies in inactive form may allow the trypanosome to re-programme the order in which variant surface glycoprotein genes are expressed.     

Model of burrow selection predicts pattern of burrow switching by Leach's Storm‐Petrels

Patterns of nest site selection exhibited at the scale of a population should result from initial preferences of individuals occupying nest sites as well as preferences exhibited by individuals moving between nest sites. We tested whether nest‐site preferences measured at the population scale were predictive of patterns of burrow switching by Leach's Storm‐Petrels (Oceanodroma leucorhoa), a long‐lived seabird that nests in underground burrows. Breeding pairs generally choose from the pool of available existing burrows rather than constructing new burrows, and a portion of the burrows in a colony remains unused in any breeding season. We quantified burrow preference at a colony on Kent Island, New Brunswick, over four breeding seasons. We used a classification and regression tree analysis to build a predictive model of nest‐site selection. Preferentially occupied burrows were drier, longer, had larger nest chambers, and were in areas of higher burrow density. To measure preferences during burrow switching, we tracked individuals that switched burrows, comparing characteristics of the burrows in which these birds were originally found to those they inhabited at the end of the study period. Characteristics preferred by switching individuals were a subset of those observed at the scale of the population; individuals moved to burrows that were drier, longer, and had larger nest chambers. Our results show how preferences of individuals that move between nest sites contribute to nest site preferences exhibited at the population scales commonly tested.     

Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water‐use efficiency and abiotic stress tolerance in plants

We have generated 3900 enhancer‐based activation‐tagged plants, in addition to 1030 stable Dissociator‐enhancer plants in a widely cultivated indica rice variety, BPT‐5204. Of them, 3000 were screened for water‐use efficiency (WUE) by analysing photosynthetic quantum efficiency and yield‐related attributes under water‐limiting conditions that identified 200 activation‐tagged mutants, which were analysed for flanking sequences at the site of enhancer integration in the genome. We have further selected five plants with low Δ¹³C, high quantum efficiency and increased plant yield compared with wild type for a detailed investigation. Expression studies of 18 genes in these mutants revealed that in four plants one of the three to four tagged genes became activated, while two genes were concurrently up‐regulated in the fifth plant. Two genes coding for proteins involved in 60S ribosomal assembly, RPL6 and RPL23A, were among those that became activated by enhancers. Quantitative expression analysis of these two genes also corroborated the results on activating–tagging. The high up‐regulation of RPL6 and RPL23A in various stress treatments and the presence of significant cis‐regulatory elements in their promoter regions along with the high up‐regulation of several of RPL genes in various stress treatments indicate that they are potential targets for manipulating WUE/abiotic stress tolerance.     

An African trypanosome variant surface glycoprotein gene whose expression is not activated by duplication

A variant surface glycoprotein (VSG) of Trypanosoma brucei is encoded by a gene whose expression is not governed by duplication-transposition. There are two copies of this gene. The 5' flanking regions of the two genes are indistinguishable by restriction mapping, although each possesses approximately 5-10 Kbp of DNA which is devoid of restriction sites. All restriction enzymes tested appeared to cut genomic DNA at a uniform distance 3' of the gene. This, coupled with the observed sensitivity of both genes to BAL 31, indicates that they lie near chromosomal termini. Length variation occurs 3' of these genes in bloodstream clones and their procyclic derivatives, although the number of length variants is conserved. This suggests that length variation alone does not control VSG switching or gene expression and that constraints exist on the extent to which 3' flanking regions can vary in length.     

Role of the maleyl-albumin receptor in activation of murine peritoneal macrophages in vitro

It has been previously demonstrated that maley-lated-BSA (maleyl-albumin) induces functional activation in murine peritoneal macrophages. Furthermore, maleyl-albumin has been shown to interact with two distinct sites on human monocytes; one site is the scavenger receptor, a 260-kDa oligomeric protein which recognizes modified forms of low density lipoprotein (LDL), and the second is a lower affinity site which has yet to be structurally characterized. In the present study, we wished to quantitatively assess the number and character of maleyl-albumin-binding sites on murine peritoneal macrophages and to determine which site or sites are involved in signaling the macrophage to undergo extensive functional development. Binding studies. demonstrate at least two distinct receptors for maleyl-albumin on murine peritoneal macrophages. Scatchard analyses of the binding isotherms reveal two sites characterized by dissociation constants (Kd) of 17.6 nM and 4.9 microM and maximal binding of 1.2 x 10(5) and 1 x 10(6) sites/cell, respectively. The contribution of the scavenger receptor, determined by binding analyses of malondialdehyde-LDL, is described by two sites with Kd of 39.4 pM and 9.6 nM, and maximal binding of 2.7 x 10(3) and 1.9 x 10(4) sites/cell, respectively. Maleyl-albumin blocks binding of malondialdehyde-LDL, whereas modified LDL fails to inhibit binding of maleyl-albumin. Maleyl-albumin, at concentrations producing lower affinity binding, stimulates tumor cytolysis, expression of mRNA encoding TNF, and suppression of INF-gamma-induced expression of Ia Ag. Malondialdehyde-LDL fails to elicit these responses. We conclude that macrophage activation produced by maleyl-albumin is mediated by interaction with the low affinity, high capacity binding site for maleyl-albumin rather than the scavenger receptor.