A Sequential Binding Mechanism for 5' Splice Site Recognition and Modulation for the Human U1 snRNP.

Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5' splice sites (5'SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5'SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5'SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5'SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5'SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5'SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5'SS recognition.

Strategies for Overcoming the Single-Molecule Concentration Barrier.

Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence techniques at high-concentration, offer applications in both biology and chemistry, and highlight the major milestones that shatter the concentration barrier. We also hope to inspire the widespread use of these techniques so we can begin exploring the new physical phenomena lying beyond this barrier.

Cognitive function in UK adults seropositive for Helicobacter pylori.

Associated with gastritis, peptic-ulcer disease, and gastric carcinoma, Helicobacter pylori (H. pylori) also has been associated with decreased cognitive function and dementia. In this study, we used data from the UK Biobank to further examine associations between H. pylori seropositivity and serointensity and performance on several cognitive tasks in adults 40 to 70 years of age (M = 55.3, SD = 8.1). In these analyses, H. pylori seropositivity (i.e., either positive or negative for H. pylori) and serointensity (concentration of antibodies against H. pylori antigens) in adjusted models were associated with worse function on tasks of Numeric memory, Reasoning, and errors on the Pairs matching test but better function on the Tower rearrangement task. Together, these findings suggest that H. pylori seropositivity and serointensity might be associated with worse cognitive function in this age group.

Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP.

In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used colocalization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5' SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5' SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS and preferentially accumulate at these sequences rather than on close cognates.

cAMP binding to closed pacemaker ion channels is non-cooperative.

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding1. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding2,3, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP5 and provide direct validation of the ligand-induced flip-state model6-9. This approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

Top-down machine learning approach for high-throughput single-molecule analysis.

Single-molecule approaches provide enormous insight into the dynamics of biomolecules, but adequately sampling distributions of states and events often requires extensive sampling. Although emerging experimental techniques can generate such large datasets, existing analysis tools are not suitable to process the large volume of data obtained in high-throughput paradigms. Here, we present a new analysis platform (DISC) that accelerates unsupervised analysis of single-molecule trajectories. By merging model-free statistical learning with the Viterbi algorithm, DISC idealizes single-molecule trajectories up to three orders of magnitude faster with improved accuracy compared to other commonly used algorithms. Further, we demonstrate the utility of DISC algorithm to probe cooperativity between multiple binding events in the cyclic nucleotide binding domains of HCN pacemaker channel. Given the flexible and efficient nature of DISC, we anticipate it will be a powerful tool for unsupervised processing of high-throughput data across a range of single-molecule experiments.

During a chemical or biological process, a molecule may transition through a series of states, many of which are rare or short-lived. Advances in technology have made it easier to detect these states by gathering large amounts of data on individual molecules. However, the increasing size of these datasets has put a strain on the algorithms and software used to identify different molecular states. Now, White et al. have developed a new algorithm called DISC which overcomes this technical limitation. Unlike most other algorithms, DISC requires minimal input from the user and uses a new method to group the data into categories that represent distinct molecular states. Although this new approach produces a similar end-result, it reaches this conclusion much faster than more commonly used algorithms. To test the effectiveness of the algorithm, White et al. studied how individual molecules of a chemical known as cAMP bind to parts of proteins called cyclic nucleotide binding domains (or CNDBs for short). A fluorescent tag was attached to single molecules of cAMP and data were collected on the behavior of each molecule. Previous evidence suggested that when four CNDBs join together to form a so-called tetramer complex, this affects the binding of cAMP. Using the DISC system, White et al. showed that individual cAMP molecules interact with all four domains in a similar way, suggesting that the binding of cAMP is not impacted by the formation of a tetramer complex. Analyzing this data took DISC less than 20 minutes compared to existing algorithms which took anywhere between four hours and two weeks to complete. The enhanced speed of the DISC algorithm could make it easier to analyze much larger datasets from other techniques in addition to fluorescence. This means that a greater number of states can be sampled, providing a deeper insight into the inner workings of biological and chemical processes.

Production of Cyanotoxins by Microcystis aeruginosa Mediates Interactions with the Mixotrophic Flagellate Cryptomonas.

Eutrophication of inland waters is expected to increase the frequency and severity of harmful algal blooms (HABs). Toxin-production associated with HABs has negative effects on human health and aquatic ecosystem functioning. Despite evidence that flagellates can ingest toxin-producing cyanobacteria, interactions between members of the microbial loop are underestimated in our understanding of the food web and algal bloom dynamics. Physical and allelopathic interactions between a mixotrophic flagellate (Cryptomonas sp.) and two strains of a cyanobacteria (Microcystis aeruginosa) were investigated in a full-factorial experiment in culture. The maximum population growth rate of the mixotroph (0.25 day-1) occurred during incubation with filtrate from toxic M. aeruginosa. Cryptomonas was able to ingest toxic and non-toxic M. aeruginosa at maximal rates of 0.5 and 0.3 cells day-1, respectively. The results establish that although Cryptomonas does not derive benefits from co-incubation with M. aeruginosa, it may obtain nutritional supplement from filtrate. We also provide evidence of a reduction in cyanotoxin concentration (microcystin-LR) when toxic M. aeruginosa is incubated with the mixotroph. Our work has implications for "trophic upgrading" within the microbial food web, where cyanobacterivory by nanoflagellates may improve food quality for higher trophic levels and detoxify secondary compounds.

Mapping Forbidden Emission to Structure in Self-Assembled Organic Nanoparticles.

The interplay between micromorphology and electronic properties is an important theme in organic electronic materials. Here, we show that a spirofluorene-functionalized boron-dipyrromethene (BODIPY) with an alkyl norbornyl tail self-assembles into nanoparticles with qualitatively different properties as compared to the polymerized species. Further, the nanoparticles exhibit a host of unique emissive properties, including photobrightening, a blue satellite peak, and spectral diffusion. Extensive photophysical characterization, including single-particle imaging and spectroscopy, and time-resolved fluorescence, coupled with electronic structure calculations based on an experimentally determined crystal structure, allow a mechanism to be developed. Specifically, BODIPY chromophores are observed to form quasi-two-dimensional layers, where stacking of unit cells adds either J-aggregate character or H-aggregate character depending on the direction of the stacking. Particularly strongly H-coupled domains show the rare process of emission from an upper exciton state, in violation of Kasha's rule, and result in the blue satellite peak. The spatial heterogeneity of structure thus maps onto a gradient of photophysical behavior as seen in single-particle imaging, and the temporal evolution of structure maps onto fluctuating emissive behavior, as seen in single-particle spectroscopy. Taken together, this system provides a striking example of how physical structure and electronic properties are intertwined, and a rare opportunity to use one to chart the other.

Local and systemic effects of a silver nitrate coated indwelling pleural catheter in an animal model of pleurodesis.

Purpose/Aim of the study: This study assessed the safety and potential toxicity of a silver nitrate coated indwelling pleural catheter (SNCIPC) designed to create pleurodesis in a large animal model. MATERIALS AND METHODS: Sixteen animals underwent insertion of either a SNCIPC or an uncoated silicone catheter. Half of the animals were sacrificed at day 7 and the others at day 30. Animal weight and assessment of well-being, pleural fluid and blood collection were performed at regular intervals. Pleurodesis was assessed at necropsy and histopathological examination of organs performed. RESULTS: No mortality or significant clinical findings were observed throughout the experiment. SNCIPC treated animals had increased pleural fluid drainage overall (p < 0.001) and specifically on days 1-4. No differences in hemoglobin, white blood cell count or neutrophil counts were detected between groups. No treatment related histological findings were observed in any of the evaluated tissues outside of the treated area. Serum silver levels in SNCIPC catheter treated animals peaked on Day 4 (0.185 µg/mL, 30 day group) then gradually decreased for the remainder of the study period. The highest tissue silver concentrations were noted in the SNCIPC groups in tissues close to the treatment site in addition to the liver (59.8ug/g +/- 8.6 and 73.3ug/g +/- 25). Pleurodesis scores were significantly higher in SNCIPC treated animals for both the 7 day (median 6.5 vs. 1.0, p = 0.029) and 30 day cohorts (median 7.0 vs. 1.5, p = 0.029). CONCLUSIONS: SNCIPC are well tolerated and not associated with any significant signs of toxicity. Silver levels were elevated in local tissues, serum and liver but without evidence of pathological impact. Effective pleurodesis was present by day 7 and more established by day 30. Clinical studies to investigate the safety and efficacy of this device in patients with malignant pleural effusions appear warranted.

Observing Single-Molecule Dynamics at Millimolar Concentrations.

Single-molecule fluorescence microscopy is a powerful tool for revealing chemical dynamics and molecular association mechanisms, but has been limited to low concentrations of fluorescent species and is only suitable for studying high affinity reactions. Here, we combine nanophotonic zero-mode waveguides (ZMWs) with fluorescence resonance energy transfer (FRET) to resolve single-molecule association dynamics at up to millimolar concentrations of fluorescent species. This approach extends the resolution of molecular dynamics to >100-fold higher concentrations, enabling observations at concentrations relevant to biological and chemical processes, and thus making single-molecule techniques applicable to a tremendous range of previously inaccessible molecular targets. We deploy this approach to show that the binding of cGMP to pacemaking ion channels is weakened by a slower internal conformational change.

Structure and dynamics underlying elementary ligand binding events in human pacemaking channels.

Although molecular recognition is crucial for cellular signaling, mechanistic studies have relied primarily on ensemble measures that average over and thereby obscure underlying steps. Single-molecule observations that resolve these steps are lacking due to diffraction-limited resolution of single fluorophores at relevant concentrations. Here, we combined zero-mode waveguides with fluorescence resonance energy transfer (FRET) to directly observe binding at individual cyclic nucleotide-binding domains (CNBDs) from human pacemaker ion channels critical for heart and brain function. Our observations resolve the dynamics of multiple distinct steps underlying cyclic nucleotide regulation: a slow initial binding step that must select a 'receptive' conformation followed by a ligand-induced isomerization of the CNBD. X-ray structure of the apo CNBD and atomistic simulations reveal that the isomerization involves both local and global transitions. Our approach reveals fundamental mechanisms underpinning ligand regulation of pacemaker channels, and is generally applicable to weak-binding interactions governing a broad spectrum of signaling processes.

Trends in adult suicides in New Mexico: utilizing data from the New Mexico violent death reporting system.

Although many suicide prevention programs focus on youth suicides, data indicate the vast majority of suicides occur among adults (18-64 years). In 2005 New Mexico joined the Centers for Disease Control and Prevention's National Violent Death Reporting System, collecting data on suicides, homicides, and unintentional firearm fatalities to better inform state and national prevention programs. We utilized data collected by the New Mexico Violent Death Reporting System in its first 2 years of operation (2005 and 2006) in order to define the demographic patterns of adult suicides in the state and characterize risk factors. A total of 526 suicides occurred among adults during this time, with the majority being male (78.5%) and White non-Hispanic (56.7%). The highest incidence was in adults between 45 and 54 years (28.1%). Firearms were the most commonly used mechanism, and "current depressed mood" the most commonly identified risk factor. High rates of adult suicide indicate the need for targeted prevention programs.

Physicians answer more clinical questions and change clinical decisions more often with synthesized evidence: a randomized trial in primary care.

PURPOSE: Clinicians need evidence in a format that rapidly answers their questions. DynaMed is a database of synthesized evidence. We investigated whether primary care clinicians would answer more clinical questions, change clinical decision making, and alter search time using DynaMed in addition to their usual information sources. METHODS: Fifty-two primary care clinicians naïve to DynaMed searched for answers to 698 of their own clinical questions using the Internet. On a per-question basis, participants were randomized to have access to DynaMed (A) or not (N) in addition to their usual information sources. Outcomes included proportions of questions answered, proportions of questions with answers that changed clinical decision making, and median search times. The statistical approach of per-participant analyses of clinicians who asked questions in both A and N states was decided before data collection. RESULTS: Among 46 clinicians in per-participant analyses, 23 (50%) answered a greater proportion of questions during A than N, and 13 (28.3%) answered more questions during N than A (P = .05). Finding answers that changed clinical decision making occurred more often during A (25 clinicians, 54.3%) than during N (13 clinicians, 28.3%) (P = .01). Search times did not differ significantly. Overall, participants found answers for 263 (75.8%) of 347 A questions and 250 (71.2%) of 351 N questions. Answers changed clinical decision making for 224 (64.6%) of the A questions and 209 (59.5%) of the N questions. CONCLUSIONS: Using DynaMed, primary care clinicians answered more questions and changed clinical decisions more often, without increasing overall search time. Synthesizing results of systematic evidence surveillance is a feasible method for meeting clinical information needs in primary care.

Resolving disputes about toxicological risks during military conflict : the US Gulf War experience.

In the last 15 years, the US and UK have fought two major wars in the Persian Gulf region. Controversy has arisen over the nature and causes of health problems among military veterans of these two wars. Toxic exposures have been hypothesised to cause the majority of the long-term health problems experienced by veterans of the 1991 Gulf War. The assessment of these toxic exposures and the resolution of controversy about their health effects provide a unique case study for understanding how toxicological disputes are settled in the US. Neither clinical examination of ill war veterans nor scientific research studies have been sufficient to answer contentious questions about toxic exposures. Numerous expert review panels have also been unable to resolve these controversies except for the US National Academy of Sciences Institute of Medicine (IOM). The IOM has conducted exhaustive and independent investigations based on peer-reviewed scientific literature related to potential health risks during the two Gulf Wars. In four recent studies, IOM committees identified a wide range of previously documented illnesses associated with common occupational and environmental exposures after considering thousands of relevant publications; however, they did not identify a new medical syndrome or a specific toxic exposure that caused widespread health problems among Gulf War veterans. These IOM studies have, therefore, added little to our basic knowledge of environmental hazards because most of the health effects were well known. Nevertheless, this expert review process, which is on-going, has been generally acceptable to a wide range of competing interests because the findings of the IOM have been perceived as scientifically credible and independent, and because none of the postulated toxicological risks have been completely ruled-out as possible causes of ill health among veterans.

Particulates, not plants, dominate nitrogen processing in a septage-treating aerated pond system.

In pond and wetland systems for wastewater treatment, plants are often thought to enhance the removal of ammonium and nitrogen through the activities of root-associated bacteria. In this study, we examined the role of plant roots in an aerated pond system with floating plants designed to treat high-strength septage wastewater. We performed both laboratory and full-scale experiments to test the effect of different plant root to septage ratios on nitrification and denitrification, and measured the abundances of nitrifying bacteria associated with roots and septage particulates. Root-associated nitrifying bacteria did not play a significant role in ammonium and total nitrogen removal. Investigations of nitrifier populations showed that only 10% were associated with water hyacinth [Eichhornia crassipes (Mart.) Solms] roots (at standard facility plant densities equivalent to 2.2 wet g roots L(-1) septage); instead, nitrifiers were found almost entirely (90%) associated with suspended septage particulates. The role of root-associated nitrifiers in nitrification was examined in laboratory batch experiments where high plant root concentrations (7.4 wet g L(-1), representing a 38% net increase in total nitrifier populations over plant-free controls) yielded a corresponding increase (55%) in the non-substrate-limited nitrification rate (V(max)). However, within the full-scale septage-treating pond system, nitrification and denitrification rates remained unchanged when plant root concentrations were increased to 7.1 g roots L(-1) (achieved by increasing the surface area available for plants while maintaining the same tank volume). Under normal facility operating conditions, nitrification was limited by ammonium concentration, not nitrifier availability. Maximizing plant root concentrations was found to be an inefficient mechanism for increasing nitrification in organic particulate-rich wastewaters such as septage.