Introns as Gene Regulators: A Brick on the Accelerator

A picture is beginning to emerge from a variety of organisms that for a subset of genes, the most important sequences that regulate expression are situated not in the promoter but rather are located within introns in the first kilobase of transcribed sequences. The actual sequences involved are difficult to identify either by sequence comparisons or by deletion analysis because they are dispersed, additive, and poorly conserved. However, expression-controlling introns can be identified computationally in species with relatively small introns, based on genome-wide differences in oligomer composition between promoter-proximal and distal introns. The genes regulated by introns are often expressed in most tissues and are among the most highly expressed in the genome. The ability of some introns to strongly stimulate mRNA accumulation from several hundred nucleotides downstream of the transcription start site, even when the promoter has been deleted, reveals that our understanding of gene expression remains incomplete. It is unlikely that any diseases are caused by point mutations or small deletions that reduce the expression of an intron-regulated gene unless splicing is also affected. However, introns may be particularly useful in practical applications such as gene therapy because they strongly activate expression but only affect the transcription unit in which they are located

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement

Many introns significantly increase gene expression through a process termed intron-mediated enhancement (IME). Introns exist in the transcribed DNA and the nascent RNA, and could affect expression from either location. To determine which is more relevant to IME, hybrid introns were constructed that contain sequences from stimulating Arabidopsis thaliana introns either in their normal orientation or as the reverse complement. Both ends of each intron are from the non-stimulatory COR15a intron in their normal orientation to allow splicing. The inversions create major alterations to the sequence of the transcribed RNA with relatively minor changes to the DNA structure. Introns containing portions of either the UBQ10 or ATPK1 intron increased expression to a similar degree regardless of orientation. Also, computational predictions of IME improve when both intron strands are considered. These findings are more consistent with models of IME that act at the level of DNA rather than RNA

Biodiversity and Ecosystem Health of the Aldabra Group, Southern Seychelles: Scientific Report to the Government of Seychelles.

National Geographic's Pristine Seas project, in collaboration with the government of the Seychelles, the Island Conservation Society (ICS), the Seychelles Islands Foundation (SIF), and the Waitt Foundation, conducted an expedition to explore the poorly known marine environment around these islands. The goals were to assess the biodiversity of the nearshore marine environment and to survey the largely unknown deep sea realm. The data collected contribute to the marine spatial planning of the Seychelles, in particular the creation of large marine reserves

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

Introns in a wide range of organisms including plants, animals and fungi are able to increase the expression of the gene that they are contained in. This process of intron-mediated enhancement (IME) is most thoroughly studied in Arabidopsis thaliana, where it has been shown that enhancing introns are typically located near the promoter and are compositionally distinct from downstream introns. In this study, we perform a comprehensive comparative analysis of several sequenced plant genomes. We find that enhancing sequences are conserved in the multi-cellular plants but are either absent or unrecognizable in algae. IME signals are preferentially located towards the 5′-end of first introns but also appear to be enriched in 5′-UTRs and coding regions near the transcription start site. Enhancing introns are found most prominently in genes that are highly expressed in a wide range of tissues. Through site-directed mutagenesis in A. thaliana, we show that IME signals can be inserted or removed from introns to increase or decrease gene expression. Although we do not yet know the specific mechanism of IME, the predicted signals appear to be both functional and highly conserved

Development and Reliability of a Measure of Clinician Competence in Providing Illness Management and Recovery

Objective: Illness management and recovery (IMR) is an evidence-based, manualized illness self-management program for people with severe mental illness. This study sought to develop a measure of IMR clinician competence and test its reliability and validity. Methods: Two groups of subject matter experts each independently created a clinician-level IMR competence scale based on the IMR Fidelity Scale and on two unpublished instruments used to evaluate provider competence. The two versions were merged, and investigators used the initial version to independently rate recordings of IMR sessions. Ratings were compared and discussed, discrepancies were resolved, and the scale was revised through 14 iterations. The resulting IMR Treatment Integrity Scale (IT-IS) includes 13 required items and three optional items rated only when the particular skill is attempted. Four independent raters then used the IT-IS to score tapes of 60 IMR sessions and 20 control group sessions. Results: The IT-IS showed excellent interrater reliability (.92). A factor analysis supported a one-factor model that showed good internal consistency. The scale successfully differentiated between IMR and control groups. Reliability and validity of individual items varied widely. Conclusions: The IT-IS is a promising measure of clinician competence in providing IMR. The scale could be used for research and quality assurance and as a supervisory feedback tool. Future research is needed to examine item-level changes, predictive validity of the IT-IS, discriminant validity compared with other more structured interventions, and the reliability and validity of the scale for nongroup IMR

Joint analysis of stressors and ecosystem services to enhance restoration effectiveness

With increasing pressure placed on natural systems by growing human populations, both scientists and resource managers need a better understanding of the relationships between cumulative stress from human activities and valued ecosystem services. Societies often seek to mitigate threats to these services through large-scale, costly restoration projects, such as the over one billion dollar Great Lakes Restoration Initiative currently underway. To help inform these efforts, we merged high-resolution spatial analyses of environmental stressors with mapping of ecosystem services for all five Great Lakes. Cumulative ecosystem stress is highest in near-shore habitats, but also extends offshore in Lakes Erie, Ontario, and Michigan. Variation in cumulative stress is driven largely by spatial concordance among multiple stressors, indicating the importance of considering all stressors when planning restoration activities. In addition, highly stressed areas reflect numerous different combinations of stressors rather than a single suite of problems, suggesting that a detailed understanding of the stressors needing alleviation could improve restoration planning. We also find that many important areas for fisheries and recreation are subject to high stress, indicating that ecosystem degradation could be threatening key services. Current restoration efforts have targeted high-stress sites almost exclusively, but generally without knowledge of the full range of stressors affecting these locations or differences among sites in service provisioning. Our results demonstrate that joint spatial analysis of stressors and ecosystem services can provide a critical foundation for maximizing social and ecological benefits from restoration investments. www.pnas.org/lookup/suppl/doi:10.1073/pnas.1213841110/-/DCSupplementa

Ethylene regulation of fruit softening and cell wall disassembly in Charentais melon

Cell wall disassembly in ripening fruit is highly complex, involving the dismantling of multiple polysaccharide networks by diverse families of wall-modifying proteins. While it has been reported in several species that multiple members of each such family are expressed in the same fruit tissue, it is not clear whether this reflects functional redundancy, with protein isozymes from a single enzyme class performing similar roles and contributing equally to wall degradation, or whether they have discrete functions, with some isoforms playing a predominant role. Experiments reported here sought to distinguish between cell wall-related processes in ripening melon that were softening-associated and softening-independent. Cell wall polysaccharide depolymerization and the expression of wall metabolism-related genes were examined in transgenic melon (Cucumis melo var. cantalupensis Naud.) fruit with suppressed expression of the 1-aminocyclopropane-1-carboxylate oxidase (ACO) gene and fruits treated with ethylene and 1-methylcyclopropene (1-MCP). Softening was completely inhibited in the transgenic fruit but was restored by treatment with exogenous ethylene. Moreover, post-harvest application of 1-MCP after the onset of ripening completely halted subsequent softening, suggesting that melon fruit softening is ethylene-dependent. Size exclusion chromatography of cell wall polysaccharides, from the transgenic fruits, with or without exogenous ethylene, indicated that the depolymerization of both pectins and xyloglucans was also ethylene dependent. However, northern analyses of a diverse range of cell wallrelated genes, including those for polygalacturonases, xyloglucan endotransglucosylase/hydrolases, expansin, and b-galactosidases, identified specific genes within single families that could be categorized as ethylene-dependent, ethylene-independent, or partially ethylene-dependent. These results support the hypothesis that while individual cell wall-modifying proteins from each family contribute to cell wall disassembly that accompanies fruit softening, other closely related family members are regulated in an ethylene-independent manner and apparently do not directly participate in fruit softening

Constraints on Lorentz violation from clock-comparison experiments

Constraints from clock-comparison experiments on violations of Lorentz and CPT symmetry are investigated in the context of a general Lorentz-violating extension of the standard model. The experimental signals are shown to depend on the atomic and ionic species used as clocks. Certain experiments usually regarded as establishing comparable bounds are in this context sensitive to different types of Lorentz violation. Some considerations relevant to possible future measurements are presented. All these experiments are potentially sensitive to Lorentz-violating physics at the Planck scale.Comment: accepted for publication in Physical Review D; scheduled for issue of December 1, 199