RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

The rugged nature of the RNA structural free energy landscape allows cellular RNAs to respond to environmental conditions or fluctuating levels of effector molecules by undergoing dynamic conformational changes that switch on or off activities such as catalysis, transcription or translation. Infectious RNAs must also temporally control incompatible activities and rapidly complete their life cycle before being targeted by cellular defenses. Viral genomic RNAs must switch between translation and replication, and untranslated subviral RNAs must control other activities such as RNA editing or self-cleavage. Unlike well characterized riboswitches in cellular RNAs, the control of infectious RNA activities by altering the configuration of functional RNA domains has only recently been recognized. In this review, we will present some of these molecular rearrangements found in RNA viruses, viroids and virus-associated RNAs, relating how these dynamic regions were discovered, the activities that might be regulated, and what factors or conditions might cause a switch between conformations

Analysis of the Two Subgenomic RNA Promoters for Turnip Crinkle Virusin Vivoandin Vitro

AbstractInfection of plants or protoplasts with turnip crinkle virus (TCV), a monopartite RNA virus, results in the synthesis of the genomic RNA and two subgenomic (sg) RNAs. The transcription start site for the 1.45-kb sgRNA was previously mapped to position 2606 (J. C. Carrington, T.J. Morris, P.G. Stockley, and S.C. Harrison, (1987).J. Mol. Biol.194, 265–276) corresponding to position 2607 in the TCVms isolate and the start site for the 1.7-kb sgRNA has now been mapped to position 2333 in TCVms. A 96-base sequence (90 bases upstream and 6 bases downstream) encompassing the transcription start site for the 1.45-kb sgRNA was sufficient for full promoter activity. Similarly, a 94-base sequence (90 bases upstream and 4 bases downstream) encompassing the start site was required for full activity of the 1.7-kb sgRNA promoter. The 1.45-kb sgRNA promoter, but not the 1.7-kb sgRNA promoter, was able to direct synthesis of a nontemplate RNAin vitrousing partially purified TCV RNA-dependent RNA polymerase. Computer generated secondary structures for the two sgRNA promoters revealed an extensive hairpin just upstream from the transcription start site. Comparisons of corresponding sequences from related viruses indicates higher sequence conservation for the 1.45-kb sgRNA promoter compared with the 1.7-kb sgRNA promoter, despite the latter's location within the RNA-dependent RNA polymerase open reading frame

Recruiting Students into the Earth Sciences through Undergraduate Research

This article discusses the challenges of recruiting undergraduate students into STEM disciplines and describes strategies which have been used to stimulate undergraduate interest in Earth sciences research at Stanford University

Na(V)1.5 sodium channel window currents contribute to spontaneous firing in olfactory sensory neurons

Olfactory sensory neurons (OSNs) fire spontaneously as well as in response to odor; both forms of firing are physiologically important. We studied voltage-gated Na+ channels in OSNs to assess their role in spontaneous activity. Whole cell patch-clamp recordings from OSNs demonstrated both tetrodotoxin-sensitive and tetrodotoxin-resistant components of Na+ current. RT-PCR showed mRNAs for five of the nine different Na+ channel α-subunits in olfactory tissue; only one was tetrodotoxin resistant, the so-called cardiac subtype NaV1.5. Immunohistochemical analysis indicated that NaV1.5 is present in the apical knob of OSN dendrites but not in the axon. The NaV1.5 channels in OSNs exhibited two important features: 1) a half-inactivation potential near −100 mV, well below the resting potential, and 2) a window current centered near the resting potential. The negative half-inactivation potential renders most NaV1.5 channels in OSNs inactivated at the resting potential, while the window current indicates that the minor fraction of noninactivated NaV1.5 channels have a small probability of opening spontaneously at the resting potential. When the tetrodotoxin-sensitive Na+ channels were blocked by nanomolar tetrodotoxin at the resting potential, spontaneous firing was suppressed as expected. Furthermore, selectively blocking NaV1.5 channels with Zn2+ in the absence of tetrodotoxin also suppressed spontaneous firing, indicating that NaV1.5 channels are required for spontaneous activity despite resting inactivation. We propose that window currents produced by noninactivated NaV1.5 channels are one source of the generator potentials that trigger spontaneous firing, while the upstroke and propagation of action potentials in OSNs are borne by the tetrodotoxin-sensitive Na+ channel subtypes.This work was aided by support from Boston University, the Rocky Mountain Taste and Smell Center Core for Cellular Visualization and Analysis [National Institute on Deafness and Other Communication Disorders (NIDCD) P30 DC-04657; D. Restrepo, principal investigator], and NIDCD Grants DC-04863 to V. Dionne and DC-006070 to D. Restrepo and T. E. Finger. (Boston University; P30 DC-04657 - Rocky Mountain Taste and Smell Center Core for Cellular Visualization and Analysis [National Institute on Deafness and Other Communication Disorders (NIDCD)]; DC-04863 - Rocky Mountain Taste and Smell Center Core for Cellular Visualization and Analysis [National Institute on Deafness and Other Communication Disorders (NIDCD)]; DC-006070 - Rocky Mountain Taste and Smell Center Core for Cellular Visualization and Analysis [National Institute on Deafness and Other Communication Disorders (NIDCD)])https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122723/Accepted manuscrip

Libraries and the University Research Enterprise: An International Perspective

Research Information Management (RIM) is the aggregation, curation, and utilization of information about research. It is emerging as a part of scholarly communications practice in many university libraries and is a service that is typically provided in collaboration with a university’s research enterprise. RIM may interoperate with and support research repositories, researcher profiles, awards management workflows, internal reports, and external assessment. Universities have diverse goals for implementing RIM, and case studies from the US and Australia will be demonstrated in this talk.Research university libraries are increasingly involved in RIM activities because of the expertise and value that library professionals provide to manage information relating to publications, data, persistent identifiers and so forth. Library expertise adds value in terms of connecting research information across a wide range of library-managed information sources and systems which can assist and enhance assessment activities, grant management, strategic collaborations, teaching and research planning, commercialisation and other activities.Librarians provide knowledge and expertise which are essential for connecting up relevant applications, information and metadata within RIM systems. They provide knowledge and expertise to visualise, interpret, collect and highlight relationships between data elements in order to demonstrate and define impact and reach of institutional research collaborations and outputs. In this presentation we will share how the libraries at La Trobe and Syracuse Universities are partnering with other campus stakeholders to achieve these outcomes.This presentation is an outcome of collaborative research by librarians practicing on three continents through the OCLC Research Library Partnership, and is part of a growing body of RIM research to support libraries, researchers, and institutions

Requirement of a 5′-Proximal Linear Sequence on Minus Strands for Plus-Strand Synthesis of a Satellite RNA Associated with Turnip Crinkle Virus

AbstractViral RNA replication begins with specific recognition of cis-acting RNA elements by the viral RNA-dependent RNA polymerase (RdRp) and/or associated host factors. A short RNA element (3′-AACCCCUGGGAGGC) located 41 bases from the 5′ end of minus strands of satellite RNA C (satC), a 356-base subviral RNA naturally associated with turnip crinkle virus (TCV), was previously identified as important for plus-strand synthesis using an in vitro RdRp assay (H. Guan, C. Song, A. E. Simon, 1997, RNA 3, 1401–1412). To examine the functional significance of this element in RNA replication, mutations were introduced into the consecutive C residues in the element. A single mutation of the 3′-most C residue resulted in undetectable levels of satC plus strands when transcripts were assayed in protoplasts and suppressed transcription directed by the element in vitro. However, satC minus strands were detectable at 6 h postinoculation (hpi) of protoplasts, accumulating to about 10% of wild-type levels at 24 hpi. This mutation, when in the plus-sense orientation, had little or no effect on minus-strand synthesis from full-length satC plus strands in vitro, suggesting that the 5′-proximal RNA element is required for satC plus-strand synthesis. In addition, in vivo genetic selection revealed a strict requirement for 10 of the 14 nucleotides of the element, indicating that the primary sequence is essential for RNA accumulation

Effect of case management on neonatal mortality due to sepsis and pneumonia.

BACKGROUND: Each year almost one million newborns die from infections, mostly in low-income countries. Timely case management would save many lives but the relative mortality effect of varying strategies is unknown. We have estimated the effect of providing oral, or injectable antibiotics at home or in first-level facilities, and of in-patient hospital care on neonatal mortality from pneumonia and sepsis for use in the Lives Saved Tool (LiST). METHODS: We conducted systematic searches of multiple databases to identify relevant studies with mortality data. Standardized abstraction tables were used and study quality assessed by adapted GRADE criteria. Meta-analyses were undertaken where appropriate. For interventions with biological plausibility but low quality evidence, a Delphi process was undertaken to estimate effectiveness. RESULTS: Searches of 2876 titles identified 7 studies. Among these, 4 evaluated oral antibiotics for neonatal pneumonia in non-randomised, concurrently controlled designs. Meta-analysis suggested reductions in all-cause neonatal mortality (RR 0.75 95% CI 0.64- 0.89; 4 studies) and neonatal pneumonia-specific mortality (RR 0.58 95% CI 0.41- 0.82; 3 studies). Two studies (1 RCT, 1 observational study), evaluated community-based neonatal care packages including injectable antibiotics and reported mortality reductions of 44% (RR = 0.56, 95% CI 0.41-0.77) and 34% (RR = 0.66, 95% CI 0.47-0.93), but the interpretation of these results is complicated by co-interventions. A third, clinic-based, study reported a case-fatality ratio of 3.3% among neonates treated with injectable antibiotics as outpatients. No studies were identified evaluating injectable antibiotics alone for neonatal pneumonia. Delphi consensus (median from 20 respondents) effects on sepsis-specific mortality were 30% reduction for oral antibiotics, 65% for injectable antibiotics and 75% for injectable antibiotics on pneumonia-specific mortality. No trials were identified assessing effect of hospital management for neonatal infections and Delphi consensus suggested 80%, and 90% reductions for sepsis and pneumonia-specific mortality respectively. CONCLUSION: Oral antibiotics administered in the community are effective for neonatal pneumonia mortality reduction based on a meta-analysis, but expert opinion suggests much higher impact from injectable antibiotics in the community or primary care level and even higher for facility-based care. Despite feasibility and low cost, these interventions are not widely available in many low income countries. FUNDING: This work was supported by the Bill & Melinda Gates Foundation through a grant to the US Fund for UNICEF, and to Saving Newborn Lives Save the Children, through Save the Children US

The Role of Citizen Science and Volunteer Data Collection in Zoological Research

In many ways, science has never been as popular as it is now. With an ever-increasing number of popular science books on everything from astronomy to climate change and evolution and entire TV channels devoted to science output, the public seems spoilt for choice. However, paradoxically, there is also an increasing disconnect between science—and scientists—and society, and this is certainly evident in the life sciences. This disconnect comes in two forms: interest and level of knowledge. Indeed, one has only to look at the 2012 US presidential election campaign to see the lack of scientific knowledge possessed by many of the political elite about topics such as climate change. If high profile scientific topics are still so widely misunderstood by those in the public eye, it is unsurprising that there is such a lack of understanding of, and interest in, scientific topics in the general public. It should, in theory, be the easiest to address this discontent in subjects like zoology, where the evidence is all around us and can be easily seen, appreciated, and studied by the world’s citizens

Bristol girls dance project feasibility study: Using a pilot economic evaluation to inform design of a full trial

Background: There is currently little guidance for pilot trial economic evaluation where health outcomes and costs are influenced by a range of wider determinants and factors. Objectives: This article presents the findings of a pilot economic evaluation study running alongside the Bristol Girls Dance Project (BGDP) feasibility study. Design: 3-arm, cluster randomised, controlled pilot trial and economic evaluation. 7 schools (n=210) from the Bristol and greater Bristol area, UK were randomly allocated to the intervention arm 3 schools (n=90) and the control arm 4 schools (n=120). Intervention: Girls aged 11-12 years with parental consent were provided with two, 90 min dance sessions per week for 9 weeks at school facilities. Economic outcome measures: Programme costs and girls' preferences for attributes of dance and preferences for competing leisure time activities were measured. Results: The mainstream average cost of the BGDP programme (not including research, control and dance teacher training costs) per school was $2126.40, £1329 and €1555 and per participant was$70.90, £44.31 and €51.84 in 2010-2011 prices. Discrete choice experiment (DCE) methods are acceptable to girls of this age indicating time available for other leisure activities on dance class days is the attribute girls valued most and 2 h leisure time remaining preferred to 3 h. Conclusions: This pilot study indicates that providing full cost data for a future trial of the BGDP programme is feasible and practical. There is no evidence from preference data to support adjustment to intervention design. A future economic evaluation is likely to be successful utilising the resource use checklist developed. The importance of categorising separately resources used to develop, prepare, deliver and maintain the programme to estimate mainstream costs accurately is demonstrated