A Slow Dynamic RNA Switch Regulates Processing of microRNA-21.

The microRNAs are non-coding RNAs which post-transcriptionally regulate the expression of many eukaryotic genes, and whose dysregulation is a driver of human disease. Here we report the discovery of a very slow (0.1 s-1) conformational rearrangement at the Dicer cleavage site of pre-miR-21, which regulates the relative concentration of readily- and inefficiently-processed RNA structural states. We show that this dynamic switch is affected by single nucleotide mutations and can be biased by small molecule and peptide ligands, which can direct the microRNA to occupy the inefficiently processed state and reduce processing efficiency. This result reveals a new mechanism of RNA regulation and suggests a chemical approach to suppressing or activating pathogenic microRNAs by selective stabilization of their unprocessed or processed states.

Impacts of tracer type, tracer selection, and source dominance on source apportionment with sediment fingerprinting.

Sediment fingerprinting estimates the proportional contribution of fine sediment from distinct catchment sources delivered to downstream receiving environments. Increased attention has focused on assessing the accuracy of source contribution estimates, particularly in relation to tracer selection and statistical un-mixing procedures. However, no studies have systematically tested the impact of source combination or dominance on the accuracy of source estimates. Here, we assess sensitivity to tracer type, selection, and number of sources, and examine how variations in the dominant sediment source affect the accuracy of source apportionments using numerical mixtures. Sources were sampled according to erosion process and land cover from a New Zealand catchment. Topsoil and subsoil (landslide) samples were collected from pasture, harvested pine, kanuka scrub, and native forest, while banks were sampled along the main channel. Samples were analysed for bulk geochemistry, fallout radionuclides, and compound specific stable isotopes (CSSIs). Source apportionment accuracy tended to decrease as source number increased, which reflected decreasing source discrimination. Tracer selection showed variations in accuracy but exhibited no clear pattern overall. Source combination and particularly the dominant source had the largest impact on accuracy, reflecting the level of discrimination for each source. Notably, channel bank was frequently identified as the dominant source when using CSSI tracers. While this partly reflected lower levels of discrimination, the CSSI apportionment was particularly sensitive to the use of post-unmixing corrections routinely applied to derive soil proportional contributions from isotopic proportions. This sensitivity likely related to the low organic carbon content in bank material and the assumption that source apportionments based on isotopic proportions can be corrected using a linear relationship with organic carbon content. These results indicate that the use of CSSI tracers in catchments where erosion sources exhibit large differences in soil organic carbon content may introduce significant unquantified error in source apportionments.

The Use of Big Data to Improve Human Health: How Experience From other Industries Will Shape the Future.

'Data science' represents a set of mathematical and software development related techniques that are applied across a wide range of problems and industries. Practitioners of data science in human health-related domains typically see a world that differs substantially from practitioners in other domains such as advertising, finance, e-commerce, manufacturing, or social networking. This commentary discusses what those differences are (Project vs Product Focus, Independent vs Integrated Efforts, Causality vs Prediction Driven, Statistical vs Machine Learning Centricity) why they exist, and the future convergence that we believe is on the horizon. The concepts discussed can provide a starting point in which health and human performance-focused stakeholders can begin to align well-established data science applications from other domains to further enable innovative health and performance solutions.

Environmental Health Practice Challenges and Research Needs for U.S. Health Departments.

BACKGROUND: Environmental health (EH) professionals, one of the largest segments of the public health workforce, are responsible for delivery of essential environmental public health services. The challenges facing these professionals and research needs to improve EH practice are not fully understood, but 26% of EH professionals working in health departments of the United States plan to retire in 5 y, while only 6% of public health students are currently pursuing EH concentrations. OBJECTIVES: A groundbreaking initiative was recently launched to understand EH practice in health departments of the United States. This commentary article aims to identify priority EH practice challenges and related research needs for health departments. METHODS: A horizon scanning approach was conducted in which challenges facing EH professionals were provided by 1,736 respondents working at health departments who responded to a web-based survey fielded in November 2017. Thematic analyses of the responses and determining the frequency at which respondents reported specific issues and opportunities identified primary EH topic areas. These topic areas and related issues informed focus group discussions at an in-person workshop held in Anaheim, California. The purpose of the in-person workshop was to engage each of the topic areas and issues, through facilitated focus groups, leading to the formation of four to five related problem statements for each EH topic. DISCUSSION: EH professionals are strategically positioned to diagnose, intervene, and prevent public health threats. Focus group engagement resulted in 29 priority problem statements partitioned among 6 EH topic areas: a) drinking water quality, b) wastewater management, c) healthy homes, d) food safety, e) vectors and public health pests, and f) emerging issues. This commentary article identifies priority challenges and related research needs to catalyze effective delivery of essential environmental public health services for common EH program areas in health departments. An unprecedented initiative to revitalize EH practice with timely and strategic recommendations for student and professional training, nontraditional partnerships, and basic and translational research activities is recommended. https://doi.org/10.1289/EHP5161.

On The Potential of Dynamic Nuclear Polarization Enhanced Diamonds in Solid-State and Dissolution (13) C†NMR Spectroscopy.

Dynamic nuclear polarization (DNP) is a versatile option to improve the sensitivity of NMR and MRI. This versatility has elicited interest for overcoming potential limitations of these techniques, including the achievement of solid-state polarization enhancement at ambient conditions, and the maximization of (13) C signal lifetimes for performing in vivo MRI scans. This study explores whether diamond's (13) C behavior in nano- and micro-particles could be used to achieve these ends. The characteristics of diamond's DNP enhancement were analyzed for different magnetic fields, grain sizes, and sample environments ranging from cryogenic to ambient temperatures, in both solution and solid-state experiments. It was found that (13) C NMR signals could be boosted by orders of magnitude in either low- or room-temperature solid-state DNP experiments by utilizing naturally occurring paramagnetic P1 substitutional nitrogen defects. We attribute this behavior to the unusually long electronic/nuclear spin-lattice relaxation times characteristic of diamond, coupled with a time-independent cross-effect-like polarization transfer mechanism facilitated by a matching of the nitrogen-related hyperfine coupling and the (13) C Zeeman splitting. The efficiency of this solid-state polarization process, however, is harder to exploit in dissolution DNP-enhanced MRI contexts. The prospects for utilizing polarized diamond approaching nanoscale dimensions for both solid and solution applications are briefly discussed.

Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR.

A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5mm NMR tubes. All these ingredients--particularly the ⩾ 3000× (1)H polarization enhancements over 11.7T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

Human health risks of geothermally derived metals and other contaminants in wild-caught food.

Arsenic (As) and mercury (Hg) associated with geothermally influenced lakes and rivers represent a potential health risk to communities where wild-caught food is consumed. The Rotorua Lakes region of New Zealand has extensive natural geothermal activity and a large proportion (35%) of indigenous Maori population, for whom wild food gathering is an important cultural activity. The aim of this study was to measure selected heavy metal and organochlorine (OC) concentrations in important local fish and shellfish species and assess the potential health risk to the local population of consuming these species. Following U.S. Environmental Protection Agency (EPA) protocols, consumption limits were calculated based on both excess lifetime cancer risk and noncancer risk. These were compared with local consumption rates, which were determined by questionnaire (n = 19). Median and 95th percentile contaminant concentrations were calculated to approximate random and most extreme contaminant consumption scenarios. Only Hg concentrations exceeded established Food Standards Australia New Zealand (FSANZ) guideline values of 0.5 mg/kg, namely, for rainbow trout (Oncorhynchus mykiss; 62% of the study sites) and koura (freshwater crayfish; Paranephrops planifrons; 25% of sites). The major risk was from consumption of trout, where the local consumption rate (1.5 meals/mo) exceeded the consumption limit of 0.9 meals/mo (median data) and 0.4 meals/mo (95th percentile data). Shellfish--pipi (Paphies australis) and mussel (Perna canaliculus)--collected from the only estuarine site also had local consumption rates (3.5 meals/mo) above calculated consumption limits (2.6 and 2.9 meals/mo, respectively). Our results, while based on a limited sample size and therefore exploratory in nature, nevertheless provide the basis for developing consumption guidelines. This study makes a significant contribution to broadening our understanding of the complexities of managing customary fisheries.

A survey of emerging contaminants in the estuarine receiving environment around Auckland, New Zealand.

Increasing urbanisation in the future will put mounting stresses on the receiving environments around those urban centres due to increased sedimentation and contaminant runoff. Emerging contaminants (ECs) are an extensive array of chemicals and many are not under regulatory action. Within New Zealand likely future pressures from ECs will be in both urban centres and rural areas due to intensive agriculture, although at present there is a lack of information on the state of the environment in both sectors. This study was initiated to gauge the distribution of ECs in the urban environment by measuring concentrations of flame retardants, plasticisers, alkylphenols, herbicides and pesticides, steroid oestrogens, pharmaceuticals and heavy metals in sediment from 13 estuarine sites around Auckland, New Zealand's biggest city. Total polybrominated diphenyl ether (PBDE) flame retardant concentrations ((7)ΣPBDE) ranged from 0.55 to 573 ng/g (dw). The phthalate plasticiser di(2-ethylhexyl)phthalate (DEHP) was measured at up to 11,500 ng/g from one site. Nonylphenol (NP) was found at up to 32,000 ng/g at one site adjacent to the city's major wastewater treatment plant (WWTP). However, median concentrations of NP were 153 ng/g, suggesting this site was not representative of the region. Nonylphenol mono- and di-ethoxylates (NPEO1,2) had highest concentrations (1600 ng/g) at a marina. Highest glyphosate concentrations (up to 950 ng/g) were observed at residential sites. Steroid oestrogens were detected at extremely low concentrations (maximum 2.2 ng/g), while all other pesticides or herbicides were not detected at any sites. Multi-residue analysis of 46 pharmaceuticals showed presence of 21 compounds at one or more sites, with average concentrations ranging from 0.16 to 7.66 ng/g. Generally, environmental concentrations of ECs were similar to those reported world-wide. However, comparisons for pharmaceuticals were problematic, due to very few studies on pharmaceutical concentrations in estuarine sediments, with most focussed on sewage and stream water phases.

Adverse events in clinical islet transplantation: one institutional experience.

Islet transplantation is one of the most promising treatments for an unstable form of type 1 diabetes. However, islet transplantation still has some obstacles, such as low success rate of islet isolation, difficulty to obtain long-term insulin freedom, and adverse events related to transplant protocol. We describe the adverse events of current clinical islet transplantation at our institute in this report. Nine type 1 diabetic patients received 17 islet infusions from March 2005 to October 2008. The islet infusion procedure and immunosuppression regimen were based on a modified Edmonton protocol. Severe adverse events (SAEs) were defined as events that were more than grade 3 according to the Terminology Criteria for Adverse Events in Trials of Adult Pancreatic Islet Transplantation, version 4.1 (Collaborative Islet Transplant Registry, CITR). Sixteen events were reported as SAEs and among them 12 events were probably or definitely related to transplant protocols; all occurred within 1 year after infusion except for one. Five adverse events (31%) occurred within 10 days after transplantation and were related to infusion procedures. Seven events (44%) occurred after 50 days and were related to immunosuppressive therapy. SAEs related to the protocol included three events of elevated liver enzymes, two of hemorrhage into gall bladder or peritoneal cavity, two of neutropenia, two of infection, one of vomiting, one of diarrhea, and one of renal dysfunction. All events were grade 3, except for one case that was grade 4 of neutropenia. All SAEs resolved with no sequelae. Neoplasms and deaths were not observed in our study. The present study suggests need to improve both infusion procedure and immunosuppressive strategy from the view of preventing SAEs.

Organochlorines and heavy metals in wild caught food as a potential human health risk to the indigenous Maori population of South Canterbury, New Zealand.

Increasing concentrations of anthropogenic contaminants in wild kai (food) of cultural, recreational and economic importance to the indigenous Maori of New Zealand is a potential human health risk. Contaminants that are known to bioaccumulate through the food chain (e.g., organochlorine pesticides (OCPs), PCBs and selected heavy metals) were analysed in important kai species including eel (Anguilla sp.), brown trout (Salmo trutta), black flounder (Rhombosolea retiaria) and watercress (Nasturtium officinale) from important harvesting sites in the region of South Canterbury. Eels contained relatively high wet weight concentrations of p,p'-DDE (8.6-287ng/g), PCBs ((32)Σ(PCB); 0.53-58.3ng/g), dieldrin (<0.05-16.3ng/g) and Σchlordanes (0.03-10.6ng/g). Trout and flounder contained lower concentrations of organochlorines than eels, with p,p'-DDE wet weight concentrations ranging from 2.2 to 18.5ng/g for trout and 6.4 to 27.8ng/g for flounder. Total arsenic wet weight concentrations were below detection limits for eels but ranged from 0.27 to 0.89µg/g for trout and 0.12 to 0.56µg/g for flounder. Mercury concentrations ranged from 0.02 to 0.56µg/g, 0.11 to 0.50µg/g and 0.04 to 0.10µg/g (ww) for eel, trout and flounder respectively. Lifetime excess cancer risk was calculated through established risk assessment procedures, highlighting dieldrin, ΣPCBs and p,p'-DDE in eels and arsenic in trout and flounder as primary contaminants of concern. A second non-cancer chronic health risk assessment indicated that mercury and PCBs were a potential concern in eels and mercury in trout. A cumulative lifetime cancer risk assessment showed potential health risk for consumption of some species, even at low consumption rates and provided the basis for establishing recommended dietary consumption limits for harvest sites within the study region.

Body mass index reflects islet isolation outcome in islet autotransplantation for patients with chronic pancreatitis.

Total pancreatectomy with autologous islet cell transplantation (TP with AIT) is an effective treatment for chronic pancreatitis patients with severe abdominal pain. Body mass index (BMI) of the pancreatic donor is proven to be a useful predictor for islet isolation and transplantation outcomes in allogenic islet transplantation. However, the association between BMI and islet isolation outcome and/or metabolism after AIT was previously unclear. Twelve patients who received TP with AIT at our hospital were included in this study. All pancreata were preserved with both pancreatic ductal injection and oxygen-charged static two-layer method using ET-Kyoto solution. The cohort was divided into two groups: low BMI group (BMI <23 kg/m(2), n=5) and high BMI group (BMI ≥23, n=7). The high BMI group had a significantly higher islet yield per gram than the low BMI group both in pancreas postdigestion and in final product (postdigestion: 7330 ± 539 vs. 3509 ± 563 IE/g; p<0.001; final product: 6555 ± 585 vs. 3476 ± 546 IE/g; p=0.004). For islet yield in final product per patient body weight, the high BMI group also had significantly higher islet yield than the low BMI group (7997 ± 779 vs. 4175 ± 750 IE/kg, p=0.007). Insulin independence rate in the high BMI group (71%) was also higher than that low BMI group (40%), but it did not reach statistical significance. Pancreata from patients with higher BMI could obtain higher islet yield in the setting of autologous islet cell transplantation for chronic pancreatitis.

Intermediate rate atomic trajectories of RNA by solid-state NMR spectroscopy.

Many RNAs undergo large conformational changes in response to the binding of proteins and small molecules. However, when RNA functional dynamics occur in the nanosecond-microsecond time scale, they become invisible to traditional solution NMR relaxation methods. Residual dipolar coupling methods have revealed the presence of extensive nanosecond-microsecond domain motions in HIV-1 TAR RNA, but this technique lacks information on the rates of motions. We have used solid-state deuterium NMR to quantitatively describe trajectories of key residues in TAR by exploiting the sensitivity of this technique to motions that occur in the nanosecond-microsecond regime. Deuterium line shape and relaxation data were used to model motions of residues within the TAR binding interface. The resulting motional models indicate two functionally essential bases within the single-stranded bulge sample both the free and Tat-bound conformations on the microsecond time scale in the complete absence of the protein. Thus, our results strongly support a conformational capture mechanism for recognition: the protein does not induce a new RNA structure, but instead captures an already-populated conformation.

Hydration dependent dynamics in RNA.

The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms-ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in (2)H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state (13)C relaxation measurements, we establish that ns-micros motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration.

Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR.

Complexes of the HIV transactivation response element (TAR) RNA with the viral regulatory protein tat are of special interest due in particular to the plasticity of the RNA at this binding site and to the potential for therapeutic targeting of the interaction. We performed REDOR solid-state NMR experiments on lyophilized samples of a 29 nt HIV-1 TAR construct to measure conformational changes in the tat-binding site concomitant with binding of a short peptide comprising the residues of the tat basic binding domain. Peptide binding was observed to produce a nearly 4 A decrease in the separation between phosphorothioate and 2'F labels incorporated at A27 in the upper helix and U23 in the bulge, respectively, consistent with distance changes observed in previous solution NMR studies, and with models showing significant rearrangement in position of bulge residue U23 in the bound-form RNA. In addition to providing long-range constraints on free TAR and the TAR-tat complex, these results suggest that in RNAs known to undergo large deformations upon ligand binding, 31P-19F REDOR measurements can also serve as an assay for complex formation in solid-state samples. To our knowledge, these experiments provide the first example of a solid-state NMR distance measurement in an RNA-peptide complex.

Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR.

We have performed solid-state 31P-19F REDOR nuclear magnetic resonance (NMR) experiments to monitor changes in minor groove width of the oligonucleotide d(CGCAAA2'FUTGGC)*d(GCCAAT(pS)TT GCG) (A3T2) upon binding of the drug distamycin A at different stoichiometries. In the hydrated solid-state sample, the minor groove width for the unbound DNA, measured as the 2'FU7-pS19 inter-label distance, was 9.4 +/- 0.7 A, comparable to that found for similar A:T-rich DNAs. Binding of a single drug molecule is observed to cause a 2.4 A decrease in groove width. Subsequent addition of a second drug molecule results in a larger conformational change, expanding this minor groove width to 13.6 A, consistent with the results of a previous solution NMR study of the 2:1 complex. These 31P-19F REDOR results demonstrate the ability of solid-state NMR to measure distances of 7-14 A in DNA-drug complexes and provide the first example of a direct spectroscopic measurement of minor groove width in nucleic acids.