TargetRNA2: identifying targets of small regulatory RNAs in bacteria

Many small, noncoding RNAs (sRNAs) in bacteria act as posttranscriptional regulators of messenger RNAs. TargetRNA2 is a web server that identifies mRNA targets of sRNA regulatory action in bacteria. As input, TargetRNA2 takes the sequence of an sRNA and the name of a sequenced bacterial replicon. When searching for targets of RNA regulation, TargetRNA2 uses a variety of features, including conservation of the sRNA in other bacteria, the secondary structure of the sRNA, the secondary structure of each candidate mRNA target and the hybridization energy between the sRNA and each candidate mRNA target. TargetRNA2 outputs a ranked list of likely regulatory targets for the input sRNA. When evaluated on a comprehensive set of sRNA-target interactions, TargetRNA2 was found to be both accurate and efficient in identifying targets of sRNA regulatory action. Furthermore, TargetRNA2 has the ability to integrate RNA-seq data, if available. If an sRNA is differentially expressed in two or more RNA-seq experiments, TargetRNA2 considers co-differential gene expression when searching for regulatory targets, significantly improving the accuracy of target identifications. The TargetRNA2 web server is freely available for use at http://cs.wellesley.edu/∼btjaden/TargetRNA2

Challenges and Opportunities of International Cooperation for Safety & Mission Assurance (SMA) on the European Service Module (ESM) of the Orion Program

ESA is providing the ESM to NASA for the Orion Program in accordance with the Implementing Arrangement (IA) established between the two Agencies in 2012. This IA is a barter agreement, in which ESA provides Service Module vehicles for the first two flights of Orion in exchange for two servicing missions to the ISS. This arrangement has provided opportunities and challenges to both communities. It represents an important opportunity for ESA to build on its experience in the development and operations of ATV and play an active role in the development and flight of a manned space vehicle. This paper will explore some of the unique aspects of this arrangement as it affects Safety & Mission Assurance (SMA).The assessment of ESM compliance with applicable safety requirements is the responsibility of the Joint Safety and Engineering Review Panel (JSERP). The JSERP has two features that are relatively unique amongst NASA safety panels. First, NASA Engineering and SMA organizations co-chair this Panel. Previously, Safety has chaired, with Engineering as a member of the Panel. Inclusion of Engineering as a co-chair has offered greater leverage within the technical community. Second, the JSERP includes a second set of co-chairs from ESA Engineering and ESA Product Assurance and Safety (PA/S) organizations. This recognizes the international arrangement as one of partnership.Another source of both opportunity and challenge is the differing experience base of ESA and NASA. NASA has decades of experience in manned spaceflight, dating back to the Mercury program and following through Gemini, Apollo, Apollo-Soyuz, Skylab, Shuttle and the International Space Station. The risk posture for manned missions is much more rigorous than for unmanned missions. ESA brings a wealth of knowledge as well, with their flights of Ariane and Automated Transfer Vehicle (ATV), development and operation of the Columbus module on ISS, and satellite programs. The result is that both parties have developed paradigms related to risk and failure that contribute to ESM discussions.Orion represents humanity's first venture beyond Low-Earth Orbit (LEO) in over fifty years. Much of that experience is captured in program documents, but first-hand knowledge is limited to a few spaceflight veterans. Missions to LEO have offered the opportunity of direct, near-instantaneous communications and assistance, and the ability to return to Earth within a matter of hours in case of emergency. Outward-bound missions do not have these features and will require a more autonomous spacecraft with attendant safety-related issues.This paper will explore these and other challenges as we approach the flight of the first Orion vehicle

Target prediction for small, noncoding RNAs in bacteria

Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs

Tracking the evolution of a single composite particle during redox cycling for application in H-2 production

Composite materials consisting of metal and metal oxide phases are being researched intensively for various energy conversion applications where they are often expected to operate under redox conditions at elevated temperature. Understanding of the dynamics of composite evolution during redox cycling is still very limited, yet critical to maximising performance and increasing durability. Here we track the microstructural evolution of a single composite particle over 200 redox cycles for hydrogen production by chemical looping, using multi-length scale X-ray computed tomography. We show that redox cycling triggers a centrifugal redispersion of the metal phase and a centripetal clustering of porosity, both seemingly driven by the asymmetric nature of oxygen exchange in composites. Initially, the particle develops a large amount of internal porosity which boosts activity, but on the long term this facilitates structural and compositional reorganisation and eventually degradation. These results provide valuable insight into redox-driven microstructural changes and also for the design of new composite materials with enhanced durability

Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women

Neisseria gonorrhoeae is a bacterial pathogen responsible for the sexually transmitted infection gonorrhea. Emergence of antimicrobial resistance (AMR) of N. gonorrhoeae worldwide has resulted in limited therapeutic choices for this infection. Men who seek treatment often have symptomatic urethritis; in contrast, gonococcal cervicitis in women is usually minimally symptomatic, but may progress to pelvic inflammatory disease. Previously, we reported the first analysis of gonococcal transcriptome expression determined in secretions from women with cervical infection. Here, we defined gonococcal global transcriptional responses in urethral specimens from men with symptomatic urethritis and compared these with transcriptional responses in specimens obtained from women with cervical infections and in vitro-grown N. gonorrhoeae isolates. This is the first comprehensive comparison of gonococcal gene expression in infected men and women. RNA sequencing analysis revealed that 9.4% of gonococcal genes showed increased expression exclusively in men and included genes involved in host immune cell interactions, while 4.3% showed increased expression exclusively in women and included phage-associated genes. Infected men and women displayed comparable antibiotic-resistant genotypes and in vitro phenotypes, but a 4-fold higher expression of the Mtr efflux pump-related genes was observed in men. These results suggest that expression of AMR genes is programed genotypically and also driven by sex-specific environments. Collectively, our results indicate that distinct N. gonorrhoeae gene expression signatures are detected during genital infection in men and women. We propose that therapeutic strategies could target sex-specific differences in expression of antibiotic resistance genes. IMPORTANCE Recent emergence of antimicrobial resistance of Neisseria gonorrhoeae worldwide has resulted in limited therapeutic choices for treatment of infections caused by this organism. We performed global transcriptomic analysis of N. gonorrhoeae in subjects with gonorrhea who attended a Nanjing, China, sexually transmitted infection (STI) clinic, where antimicrobial resistance of N. gonorrhoeae is high and increasing. We found that N. gonorrhoeae transcriptional responses to infection differed in genital specimens taken from men and women, particularly antibiotic resistance gene expression, which was increased in men. These sex-specific findings may provide a new approach to guide therapeutic interventions and preventive measures that are also sex specific while providing additional insight to address antimicrobial resistance of N. gonorrhoeae

Small non-coding RNAs in Streptomyces coelicolor

In bacteria, small RNAs (sRNAs) make important regulatory contributions to an ever increasing number of cellular processes. To expand the repertoire of known sRNAs, we sought to identify novel sRNAs in the differentiating, multicellular bacterium Streptomyces coelicolor. We describe a combined bioinformatic and experimental approach that enabled the identification and characterization of nine novel sRNAs in S. coelicolor, including a cis-encoded antisense sRNA. We examined sRNA expression throughout the S. coelicolor developmental cycle, which progresses from vegetative mycelium formation, to aerial mycelium formation and finally sporulation. We further determined the effects of growth medium composition (rich versus minimal medium) on sRNA gene expression, and compared wild-type sRNA expression profiles with those of four developmental mutants. All but two of the sRNAs exhibited some degree of medium dependence, with three sRNAs being expressed exclusively during growth on one medium type. Unlike most sRNAs characterized thus far, several sRNA genes in S. coelicolor were expressed constitutively (apart from during late sporulation), suggesting a possible housekeeping role for these transcripts. Others were expressed at specific developmental stages, and their expression profiles were altered in response to developmental mutations. Expression of one sRNA in particular was dependent upon the sporulation-specific sigma factor σWhiG

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points

The Future of Comparative and International Education in a Globalised World

Abstract – This article examines the history and future prospects of comparative and international education with particular reference to the impact of globalisation and Information and Communications Technologies (ICTs). Connections and interactions between comparative educationists and the technologies of printing and electronic communications are examined in a historical context. The global nature of commu-nications in comparative and international education is demonstrated both spatially and historically, using information from all regions of the world. The changing nature of technologies is noted to have broadened the audience for comparative insights. The development of textbooks, journals, conferences, international agencies, the Internet, web-based communications, and professional comparative education soci-eties is related to the themes of communications and globalisation. Zusammenfassung – In diesem Artikel werden die Geschichte und die künftigen Aussichten der vergleichenden und internationalen Bildung untersucht mit besonderem Augenmerk auf den Einfluss von Globalisierung und Informations- und Kom-munikationstechnologien. Verbindungen und Interaktionen zwischen vergleichende

MLpronto: A tool for democratizing machine learning.

The democratization of machine learning is a popular and growing movement. In a world with a wealth of publicly available data, it is important that algorithms for analysis of data are accessible and usable by everyone. We present MLpronto, a system for machine learning analysis that is designed to be easy to use so as to facilitate engagement with machine learning algorithms. With its web interface, MLpronto requires no computer programming or machine learning background, and it normally returns results in a matter of seconds. As input, MLpronto takes a file of data to be analyzed. MLpronto then executes some of the more commonly used supervised machine learning algorithms on the data and reports the results of the analyses. As part of its execution, MLpronto generates computer programming code corresponding to its machine learning analysis, which it also supplies as output. Thus, MLpronto can be used as a no-code solution for citizen data scientists with no machine learning or programming background, as an educational tool for those learning about machine learning, and as a first step for those who prefer to engage with programming code in order to facilitate rapid development of machine learning projects. MLpronto is freely available for use at https://mlpronto.org/