Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology.

Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.

How Nanopore Translocation Experiments Can Measure RNA Unfolding.

Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "structure-based" energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores.

Response to Comment on "Enhanced water permeability and tunable ion selectivity in subnanometer carbon nanotube porins".

Horner and Pohl argue that high water transport rates reported for carbon nanotube porins (CNTPs) originate from leakage at the nanotube-bilayer interface. Our results and new experimental evidence are consistent with transport through the nanotube pores and rule out a defect-mediated transport mechanism. Mechanistic origins of the high Arrhenius factor that we reported for narrow CNTPs at pH 8 require further investigation.

Label-Free Single-Molecule Thermoscopy Using a Laser-Heated Nanopore.

When light is used to excite electronic transitions in a material, nonradiative energy during relaxation is often released in the form of heat. In this work, we show that photoexcitation of a silicon nitride nanopore using a focused visible laser results in efficient localized photothermal heating, which reduces the nearby electrolyte viscosity and increases the ionic conductance. In addition, a strong localized thermal gradient in the pore vicinity is produced, evidenced by finite-element simulations and experimental observation of both ion and DNA thermophoresis. After correcting for thermophoresis, the nanopore current can be used as a nanoscale thermometer, enabling rapid force thermoscopy. We utilize this to probe thermal melting transitions in synthetic and native biomolecules that are heated at the nanopore. Our results on single molecules are validated by correspondence to bulk measurements, which paves the way to various biophysical experiments that require rapid temperature and force control on individual molecules.

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing.

Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications. However, reading DNA sequence from sub-nanogram quantities is impractical owing to inefficient delivery of DNA molecules into the confines of zero-mode waveguides-zeptolitre optical cavities in which DNA sequencing proceeds. Here, we show that the efficiency of voltage-induced DNA loading into waveguides equipped with nanopores at their floors is five orders of magnitude greater than existing methods. In addition, we find that DNA loading is nearly length-independent, unlike diffusive loading, which is biased towards shorter fragments. We demonstrate here loading and proof-of-principle four-colour sequence readout of a polymerase-bound 20,000-base-pair-long DNA template within seconds from a sub-nanogram input quantity, a step towards low-input DNA sequencing and mammalian epigenomic mapping of native DNA samples.

Enhanced water permeability and tunable ion selectivity in subnanometer carbon nanotube porins.

Fast water transport through carbon nanotube pores has raised the possibility to use them in the next generation of water treatment technologies. We report that water permeability in 0.8-nanometer-diameter carbon nanotube porins (CNTPs), which confine water down to a single-file chain, exceeds that of biological water transporters and of wider CNT pores by an order of magnitude. Intermolecular hydrogen-bond rearrangement, required for entry into the nanotube, dominates the energy barrier and can be manipulated to enhance water transport rates. CNTPs block anion transport, even at salinities that exceed seawater levels, and their ion selectivity can be tuned to configure them into switchable ionic diodes. These properties make CNTPs a promising material for developing membrane separation technologies.

Studies of RNA Sequence and Structure Using Nanopores.

Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.

Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity.

It has been hypothesized that the ribosome gains additional fidelity during protein translation by probing structural differences in tRNA species. We measure the translocation kinetics of different tRNA species through ∼3 nm diameter synthetic nanopores. Each tRNA species varies in the time scale with which it is deformed from equilibrium, as in the translocation step of protein translation. Using machine-learning algorithms, we can differentiate among five tRNA species, analyze the ratios of tRNA binary mixtures, and distinguish tRNA isoacceptors.

Osmium-Based Pyrimidine Contrast Tags for Enhanced Nanopore-Based DNA Base Discrimination.

Nanopores are a promising platform in next generation DNA sequencing. In this platform, an individual DNA strand is threaded into nanopore using an electric field, and enzyme-based ratcheting is used to move the strand through the detector. During this process the residual ion current through the pore is measured, which exhibits unique levels for different base combinations inside the pore. While this approach has shown great promise, accuracy is not optimal because the four bases are chemically comparable to one another, leading to small differences in current obstruction. Nucleobase-specific chemical tagging can be a viable approach to enhancing the contrast between different bases in the sequence. Herein we show that covalent modification of one or both of the pyrimidine bases by an osmium bipyridine complex leads to measureable differences in the blockade amplitudes of DNA molecules. We qualitatively determine the degree of osmylation of a DNA strand by passing it through a solid-state nanopore, and are thus able to gauge T and C base content. In addition, we show that osmium bipyridine reacts with dsDNA, leading to substantially different current blockade levels than exhibited for bare dsDNA. This work serves as a proof of principle for nanopore sequencing and mapping via base-specific DNA osmylation.

Direct and Scalable Deposition of Atomically Thin Low-Noise MoS2 Membranes on Apertures.

Molybdenum disulfide (MoS2) flakes can grow beyond the edge of an underlying substrate into a planar freestanding crystal. When the substrate edge is in the form of an aperture, reagent-limited nucleation followed by edge growth facilitate direct and selective growth of freestanding MoS2 membranes. We have found conditions under which MoS2 grows preferentially across micrometer-scale prefabricated solid-state apertures in silicon nitride membranes, resulting in sealed membranes that are one to a few atomic layers thick. We have investigated the structure and purity of our membranes by a combination of atomic-resolution transmission electron microscopy, elemental analysis, Raman spectroscopy, photoluminescence spectroscopy, and low-noise ion-current recordings through nanopores fabricated in such membranes. Finally, we demonstrate the utility of fabricated ultrathin nanopores in such membranes for single-stranded DNA translocation detection.

Label-free optical detection of biomolecular translocation through nanopore arrays.

In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.

Nanopore-based conformational analysis of a viral RNA drug target.

Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding.

High-bandwidth protein analysis using solid-state nanopores.

High-bandwidth measurements of the ion current through hafnium oxide and silicon nitride nanopores allow the analysis of sub-30 kD protein molecules with unprecedented time resolution and detection efficiency. Measured capture rates suggest that at moderate transmembrane bias values, a substantial fraction of protein translocation events are detected. Our dwell-time resolution of 2.5 µs enables translocation time distributions to be fit to a first-passage time distribution derived from a 1D diffusion-drift model. The fits yield drift velocities that scale linearly with voltage, consistent with an electrophoretic process. Further, protein diffusion constants (D) are lower than the bulk diffusion constants (D0) by a factor of ~50, and are voltage-independent in the regime tested. We reason that deviations of D from D0 are a result of confinement-driven pore/protein interactions, previously observed in porous systems. A straightforward Kramers model for this inhibited diffusion points to 9- to 12-kJ/mol interactions of the proteins with the nanopore. Reduction of µ and D are found to be material-dependent. Comparison of current-blockage levels of each protein yields volumetric information for the two proteins that is in good agreement with dynamic light scattering measurements. Finally, detection of a protein-protein complex is achieved.

Slow DNA transport through nanopores in hafnium oxide membranes.

We present a study of double- and single-stranded DNA transport through nanopores fabricated in ultrathin (2-7 nm thick) freestanding hafnium oxide (HfO2) membranes. The high chemical stability of ultrathin HfO2 enables long-lived experiments with <2 nm diameter pores that last several hours, in which we observe >50 000 DNA translocations with no detectable pore expansion. Mean DNA velocities are slower than velocities through comparable silicon nitride pores, providing evidence that HfO2 nanopores have favorable physicochemical interactions with nucleic acids that can be leveraged to slow down DNA in a nanopore.

Integrating mental health services into humanitarian relief responses to social emergencies, disasters, and conflicts: a case study.

Utilizing lessons learned from development and implementation of "Project Liberty" in New York City, created in response to the attacks of September 11, 2001, this paper explores the importance of integrating structured mental health services with community-based social service programs offered in large-scale humanitarian relief responses. Relevant international research studies illustrating similar integrated programs are also reviewed. The primary approach is community-based and resilience-enhancement focused, offering structure, stability, support, and community cohesion, with an added integrated screening component to identify persons with severe treatable mental health conditions. Because there is thus far little evidence that resilience-enhancing programs are effective for severe mental health conditions, a secondary program initiated in parallel would be staffed with more specialized providers offering services for those referred from the primary program. The key implication supports the establishment of more effective links between programs and professionals from different disciplines, who then can more effectively implement integrated program responses to large-scale disasters.

Does school attendance reduce the risk of youth homelessness in Tanzania?

BACKGROUND: This paper is based on data gathered from a 2006 survey of 1,098 "street children" in Northern Tanzania. It examines the role that school may play in preventing the migration of vulnerable youth to become homeless "street children". Specific focus is placed on the correlations found between children's attendance in school, their reports of abuse or support in their family, and their status of living "on the street" full-time or part-time. METHODS: This study is from quantitative interview data gathered from 1,098 children and youth between 5 and 24 years old on the streets of Moshi and Arusha, Tanzania, over a 48-hour period during the school year on October 26th and 27th, 2006. Respondents were given survey questions about their home, school and street life experiences, in order to measure the impact of outreach work being performed by a Tanzanian NGO. Interviewers used purposive sampling, approaching all young people who appeared to be under the age of 25 years within a number of precincts in each town known to be where 'street children' were known to congregate. RESULTS: Results suggest that regular attendance in school may be a significant protective factor for children in preventing migration to the street life. Statistical analysis revealed that those young people who dropped out of school had nearly 8 times higher chances for ending up on the streets permanently than those who attended school daily. CONCLUSIONS: This study supports the new concept of "multi-layered social resilience", providing evidence from research completed by one NGO on how community-based organizations can help enhance resilience in a broader social context, spanning individuals, households and community structures.

Social cohesion through football: a quasi-experimental mixed methods design to evaluate a complex health promotion program.

UNLABELLED: Social isolation and disengagement fragments local communities. Evidence indicates that refugee families are highly vulnerable to social isolation in their countries of resettlement. Research to identify approaches to best address this is needed. Football United is a program that aims to foster social inclusion and cohesion in areas with high refugee settlement in New South Wales, Australia, through skills and leadership development, mentoring, and the creation of links with local community and corporate leaders and organisations. The Social Cohesion through Football study's broad goal is to examine the implementation of a complex health promotion program, and to analyse the processes involved in program implementation. The study will consider program impact on individual health and wellbeing, social inclusion and cohesion, as well as analyse how the program by necessity interacts and adapts to context during implementation, a concept we refer to as plasticity. The proposed study will be the first prospective cohort impact study to our knowledge to assess the impact of a comprehensive integrated program using football as a vehicle for fostering social inclusion and cohesion in communities with high refugee settlement. METHODS/DESIGN: A quasi-experimental cohort study design with treatment partitioning involving four study sites. The study employs a 'dose response' model, comparing those with no involvement in the Football United program with those with lower or higher levels of participation. A range of qualitative and quantitative measures will be used in the study. Study participants' emotional well being, resilience, ethnic identity and other group orientation, feelings of social inclusion and belonging will be measured using a survey instrument complemented by relevant data drawn from in-depth interviews, self reporting measures and participant observation. The views of key informants from the program and the wider community will also be solicited. DISCUSSION: The complexity of the Football United program poses challenges for measurement, and requires the study design to be responsive to the dynamic nature of the program and context. Assessment of change is needed at multiple levels, drawing on mixed methods and multidisciplinary approaches in implementation and evaluation. Attention to these challenges has underpinned the design and methods in the Social Cohesion through Football study, which will use a unique and innovative combination of measures that have not been applied together previously in social inclusion/cohesion and sport and social inclusion/cohesion program research.

Impact of resilience enhancing programs on youth surviving the Beslan school siege.

The objective of this study was to evaluate a resilience-enhancing program for youth (mean age = 13.32 years) from Beslan, North Ossetia, in the Russian Federation. The program, offered in the summer of 2006, combined recreation, sport, and psychosocial rehabilitation activities for 94 participants, 46 of who were taken hostage in the 2004 school tragedy and experienced those events first hand. Self-reported resilience, as measured by the CD-RISC, was compared within subjects at the study baseline and at two follow-up assessments: immediately after the program and 6 months later. We also compared changes in resilience levels across groups that differed in their traumatic experiences. The results indicate a significant intra-participant mean increase in resilience at both follow-up assessments, and greater self-reported improvements in resilience processes for participants who experienced more trauma events.

Sports and games for post-traumatic stress disorder (PTSD).

BACKGROUND: Traumatic experiences evoke emotions such as fear, anxiety and distress and may encourage avoidance of similar situations in the future. For a proportion of those exposed to a traumatic event, this emotional reaction becomes uncontrollable and can develop into Post Traumatic Stress Disorder (PTSD) (Breslau 2001). Most of those diagnosed with PTSD fully recover while a small proportion develop a chronic PTSD a year after the event (First 2004). Sports and games may be able to alleviate symptoms of PTSD. PRIMARY OBJECTIVE: 1. To assess the effectiveness of sports, and games in alleviating and/or diminishing the symptoms of PTSD when compared to usual care or other interventions. SECONDARY OBJECTIVE: 2. To assess the effectiveness of different types of sports and games in alleviating and/or diminishing symptoms of PTSD. SEARCH STRATEGY: The Cochrane Collaboration Depression, Anxiety and Neurosis Controlled Trials Registers (CCDAN-CTR) were searched up to June 2008.The following databases were searched up to June 2008: the Cochrane Central registry of Controlled Trials; MEDLINE; EMBASE; CINAHL; PsycINFO. Reference lists of relevant papers were searched and experts in the field were contacted to determine if other studies were available. SELECTION CRITERIA: To be included, participants had to be diagnosed with PTSD using criteria outlined in the Diagnostic and Statistical Manual for Mental Disorders (DSM IV) and/or ICD criteria. Randomised controlled trials (RCTs) that considered one or more well-specified sports or games for alleviating and/or diminishing symptoms of PTSD were included.Sports, and games were defined as any organized physical activity done alone or with a group and non-physical activities such as computer games and card games done alone or with a group. Psychological interventions such as music therapy, art therapy and play therapy and behavioural therapy were excluded. DATA COLLECTION AND ANALYSIS: Two reviewers (SL and MD) separately checked the titles and abstracts of the search results to determine which studies met the pre-determined inclusion criteria. A flow chart was used to guide the selection process. No studies met the inclusion criteria. MAIN RESULTS: The search strategy identified five papers but none of the studies met inclusion criteria. AUTHORS' CONCLUSIONS: No studies met the inclusion criteria. More research is therefore required before a fair assessment can be made of the effectiveness of sports and games in alleviating symptoms of PTSD.

A survey of street children in northern Tanzania: how abuse or support factors may influence migration to the street.

In October 2006, a survey was undertaken of youth "on the streets" in the Arusha and Kilimanjaro regions of Tanzania (n = 1,923). The question of interest was if street children who live on streets full-time differ concerning reports of abuse and support, compared to reports of children who are only part-time on the streets, and to children who don't self-identify as "street children" at all. Results show full-time street children reporting significantly more abuse than part-time counterparts, or children who were not street children (mean difference = -1.44, P < .001). Concerning support scores, non-street children and part-time street children reported significantly more support from their family than full-time street children (mean difference = 1.70, P < .001). This information identifies possible reasons why vulnerable children migrate to live on the streets in the urban areas, and contributes to the limited literature and data on this subject.