The discovery of novel noncoding RNAs in 50 bacterial genomes.

Structured noncoding RNAs (ncRNAs) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. Few ncRNA classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. We previously developed a computational pipeline that enables the near-comprehensive identification of structured ncRNAs expressed from individual bacterial genomes. The regions between protein coding genes are first sorted based on length and the fraction of guanosine and cytidine nucleotides. Long, GC-rich intergenic regions are then examined for sequence and structural similarity to other bacterial genomes. Herein, we describe the implementation of this pipeline on 50 bacterial genomes from varied phyla. More than 4700 candidate intergenic regions with the desired characteristics were identified, which yielded 44 novel riboswitch candidates and numerous other putative ncRNA motifs. Although experimental validation studies have yet to be conducted, this rate of riboswitch candidate discovery is consistent with predictions that many hundreds of novel riboswitch classes remain to be discovered among the bacterial species whose genomes have already been sequenced. Thus, many thousands of additional novel ncRNA classes likely remain to be discovered in the bacterial domain of life.

Architectures and complex functions of tandem riboswitches.

Riboswitch architectures that involve the binding of a single ligand to a single RNA aptamer domain result in ordinary dose-response curves that require approximately a 100-fold change in ligand concentration to cover nearly the full dynamic range for gene regulation. However, by using multiple riboswitches or aptamer domains in tandem, these ligand-sensing structures can produce additional, complex gene control outcomes. In the current study, we have computationally searched for tandem riboswitch architectures in bacteria to provide a more complete understanding of the diverse biological and biochemical functions of gene control elements that are made exclusively of RNA. Numerous different arrangements of tandem homologous riboswitch architectures are exploited by bacteria to create more 'digital' gene control devices, which operate over a narrower ligand concentration range. Also, two heterologous riboswitch aptamers are sometimes employed to create two-input Boolean logic gates with various types of genetic outputs. These findings illustrate the sophisticated genetic decisions that can be made by using molecular sensors and switches based only on RNA.

Coping styles as predictors of negative affective conditions in Asian Indians: does being optimistic still make a difference?

The present study examined the role of optimism, as measured by the Life Orientation Test-Revised, and coping styles, as measured by the COPE scale, in predicting negative affective conditions (viz., depressive symptoms, stress, and negative affect) among 386 Asian Indian young adults (197 females and 189 males). Results from our hierarchical regression analyses indicated that coping styles accounted for a medium-large amount of variance in negative affective conditions, after controlling for demographic factors (i.e. age, gender, parent's education, and monthly income). Five coping styles were significant in predicting negative affective conditions across all three indices; mental disengagement, denial, and venting emotions were found to be maladaptive, while positive reinterpretation and humor were found to be adaptive among Asian Indian young adults. Furthermore, when optimism was included in the prediction model, optimism consistently accounted for additional variance in negative affective conditions, beyond coping styles. Due to the additional variance among negative affective conditions accounted for by optimism when compared to coping, we advise that mental health professionals consider prioritizing the reinforcement of positive expectancy in addition to enhancing adaptive coping styles and reducing the use of maladaptive coping among Asian Indians.

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.

Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.

Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria.

An intriguing consequence of ongoing riboswitch discovery efforts is the occasional identification of metabolic or toxicity response pathways for unusual ligands. Recently, we reported the experimental validation of three distinct bacterial riboswitch classes that regulate gene expression in response to the selective binding of a guanidinium ion. These riboswitch classes, called guanidine-I, -II, and -III, regulate numerous genes whose protein products include previously misannotated guanidine exporters and enzymes that degrade guanidine via an initial carboxylation reaction. Guanidine is now recognized as the primal substrate of many multidrug efflux pumps that are important for bacterial resistance to certain antibiotics. Guanidine carboxylase enzymes had long been annotated as urea carboxylase enzymes but are now understood to participate in guanidine degradation. Herein, we report the existence of a fourth riboswitch class for this ligand, called guanidine-IV. Members of this class use a novel aptamer to selectively bind guanidine and use an unusual expression platform arrangement that is predicted to activate gene expression when ligand is present. The wide distribution of this abundant riboswitch class, coupled with the striking diversity of other guanidine-sensing RNAs, demonstrates that many bacterial species maintain sophisticated sensory and genetic mechanisms to avoid guanidine toxicity. This finding further highlights the mystery regarding the natural source of this nitrogen-rich chemical moiety.

A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation.

Dozens of candidate orphan riboswitch classes have been discovered previously by using comparative sequence analysis algorithms to search bacterial genomic sequence databases. Each orphan is classified by the presence of distinct conserved nucleotide sequences and secondary structure features, and by its association with particular types of genes. One previously reported orphan riboswitch candidate is the "NMT1 motif," which forms a hairpin structure with an internal bulge that includes numerous highly conserved nucleotides. This motif associates with genes annotated to encode various dioxygenase enzymes, transporters, or proteins that have roles associated with thiamin or histidine metabolism. Biochemical evaluation of numerous ligand candidates revealed that NMT1 motif RNA constructs most tightly bind 8-azaxanthine, xanthine, and uric acid, whereas most other closely related compounds are strongly rejected. Genetic assays revealed that NMT1 motif RNAs function to turn off gene expression upon ligand binding, likely by regulating translation initiation. These results suggest that NMT1 motif RNAs function as aptamer domains for a riboswitch class that specifically responds to high concentrations of oxidized purines. Members of this "xanthine riboswitch" class appear to regulate genes predominantly related to purine transport and oxidation, thus avoiding the effects of overproduction of these common purine derivatives.

The past, present, and future of National Aeronautics and Space Administration spaceflight diet in support of microgravity rodent experiments.

Rodents have been the most frequently flown animal model used to study physiological responses to the space environment. In support of future of space exploration, the National Aeronautics and Space Administration (NASA) envisions an animal research program focused on rodents. Therefore, the development of a rodent diet that is suitable for the spaceflight environment including long duration spaceflight is a high priority. Recognizing the importance of nutrition in affecting spaceflight physiological responses and ensuring reliable biomedical and biological science return, NASA developed the nutrient-upgraded rodent food bar (NuRFB) as a standard diet for rodent spaceflight. Depending on future animal habitat hardware and planned spaceflight experiments, modification of the NuRFB or development of a new diet formulation may be needed, particularly for long term spaceflights. Research in this area consists primarily of internal technical reports that are not readily accessible. Therefore, the aims of this contribution are to provide a brief history of the development of rodent spaceflight diets, to review the present diet used in rodent spaceflight studies, and to discuss some of the challenges and potential solutions for diets to be used in future long-term rodent spaceflight studies.