Proteomic analysis and functional characterization of mouse brain mitochondria during aging reveal alterations in energy metabolism

Mitochondria are the main cellular source of reactive oxygen species and are recognized as key players in several age‐associated disorders and neurodegeneration. Their dysfunction has also been linked to cellular aging. Additionally, mechanisms leading to the preservation of mitochondrial function promote longevity. In this study we investigated the proteomic and functional alterations in brain mitochondria isolated from mature (5 months old), old (12 months old), and aged (24 months old) mice as determinants of normal “healthy” aging. Here the global changes concomitant with aging in the mitochondrial proteome of mouse brain analyzed by quantitative mass‐spectrometry based super‐SILAC identified differentially expressed proteins involved in several metabolic pathways including glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation. Despite these changes, the bioenergetic function of these mitochondria was preserved. Overall, this data indicates that proteomic changes during aging may compensate for functional defects aiding in preservation of mitochondrial function. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001370 ( http://proteomecentral.proteomexchange.org/dataset/PXD001370 ).     

Acceleration of Age-Associated Methylation Patterns in HIV-1-Infected Adults

Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC) of young (20-35) and older (36-56) adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, p<1 x10^-200 and 0.47, p<1x10^-200. Weighted gene correlation network analysis (WGCNA) identified 17 co-methylation modules; module 3 (ME3) was significantly correlated with age (cor=0.70) and HIV-1 status (cor=0.31). Older HIV-1⁺ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015). In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: β_age= 0.007088, p=2.08 x 10^-9; β_HIV= 0.099574, p=0.0011; Data set 2: β_age= 0.008762, p=1.27x 10^-5; β_HIV= 0.128649, p= 0.0001). Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10^-6, odds ratio=1.91). These data demonstrate that HIV-1 infection is associated with methylation patterns that are similar to age-associated patterns and suggest that general aging and HIV-1 related aging work through some common cellular and molecular mechanisms. These results are an important first step for finding potential therapeutic targets and novel clinical approaches to mitigate the detrimental effects of both HIV-1-infection and aging.     

A Survey of UK Healthcare Workers’ Attitudes on Volunteering to Help with the Ebola Outbreak in West Africa

Objective

To understand the barriers and enablers for UK healthcare workers who are considering going to work in the current Ebola outbreak in West Africa, but have not yet volunteered.

Design

After focus group discussions, and a pilot questionnaire, an anonymous survey was conducted using SurveyMonkey to determine whether people had considered going to West Africa, what factors might make them more or less likely to volunteer, and whether any of these were modifiable factors.

Participants

The survey was publicised among doctors, nurses, laboratory staff and allied health professionals. 3109 people answered the survey, of whom 472 (15%) were considering going to work in the epidemic but had not yet volunteered. 1791 (57.6%) had not considered going, 704 (22.6%) had considered going but decided not to, 53 (1.7%) had volunteered to go and 14 (0.45%) had already been and worked in the epidemic.

Results

For those considering going to West Africa, the most important factor preventing them from volunteering was a lack of information to help them decide; fear of getting Ebola and partners’ concerns came next. Uncertainty about their potential role, current work commitments and inability to get agreement from their employer were also important barriers, whereas clarity over training would be an important enabler. In contrast, for those who were not considering going, or who had decided against going, family considerations and partner concerns were the most important factors.

Conclusions

More UK healthcare workers would volunteer to help tackle Ebola in West Africa if there was better information available, including clarity about roles, cover arrangements, and training. This could be achieved with a well-publicised high quality portal of reliable information.     

Demographic Clusters Identified within the Northern Gulf of Mexico Common Bottlenose Dolphin (Tursiops truncates) Unusual Mortality Event: January 2010 - June 2013

A multi-year unusual mortality event (UME) involving primarily common bottlenose dolphins (Tursiops truncates) was declared in the northern Gulf of Mexico (GoM) with an initial start date of February 2010 and remains ongoing as of August 2014. To examine potential changing characteristics of the UME over time, we compared the number and demographics of dolphin strandings from January 2010 through June 2013 across the entire GoM as well as against baseline (1990-2009) GoM stranding patterns. Years 2010 and 2011 had the highest annual number of stranded dolphins since Louisiana’s record began, and 2011 was one of the years with the highest strandings for both Mississippi and Alabama. Statewide, annual numbers of stranded dolphins were not elevated for GoM coasts of Florida or Texas during the UME period. Demographic, spatial, and temporal clusters identified within this UME included increased strandings in northern coastal Louisiana and Mississippi (March-May 2010); Barataria Bay, Louisiana (August 2010-December 2011); Mississippi and Alabama (2011, including a high prevalence and number of stranded perinates); and multiple GoM states during early 2013. While the causes of the GoM UME have not been determined, the location and magnitude of dolphin strandings during and the year following the 2010 Deepwater Horizon oil spill, including the Barataria Bay cluster from August 2010 to December 2011, overlap in time and space with locations that received heavy and prolonged oiling. There are, however, multiple known causes of previous GoM dolphin UMEs, including brevetoxicosis and dolphin morbillivirus. Additionally, increased dolphin strandings occurred in northern Louisiana and Mississippi before the Deepwater Horizon oil spill. Identification of spatial, temporal, and demographic clusters within the UME suggest that this mortality event may involve different contributing factors varying by location, time, and bottlenose dolphin populations that will be better discerned by incorporating diagnostic information, including histopathology.     

The Association between Insomnia and Insomnia Treatment Side Effects on Health Status,Work Productivity,and Healthcare Resource Use

The aims of this study were (1) to compare health outcomes (i.e., health-related quality of life [HRQoL], productivity at work, and healthcare resource use visits) between those with insomnia and non-insomnia controls, (2) to compare health outcomes between those treated for insomnia and non-insomnia controls, and (3) to assess the prevalence of side effects of insomnia medications and their relationship with health outcomes. Data from the 2013 US (N = 75,000) and 5EU (N = 62,000) National Health and Wellness Survey (NHWS) were used. The NHWS is a patient-reported survey administered to a demographically representative sample of adults. Those who met DSM-V criteria for insomnia and, separately, those treated for insomnia were compared with equivalently sized control groups who were identified using a propensity score matching method. Outcomes included HRQoL (Short Form 36v2), productivity at work (Work Productivity and Activity Impairment—General Health questionnaire), and healthcare resource use visits in the past 6 months and were analyzed using one-way ANOVAs. Among those with treated insomnia, those with and without side effects were compared on health outcomes using general linear models controlling for confounding variables. Patients with insomnia (n = 4147) and treated insomnia (n = 2860) in the 5EU reported significantly worse HRQoL than controls (health utilities: 0.60 vs. 0.74; 0.60 vs. 0.74, respectively), greater overall work impairment (38.74% vs. 14.86%; 39.50% vs. 15.66%), and more physician visits in the past 6 months (9.10 vs. 4.08; 9.58 vs. 4.11). Similar findings were observed in the US. Among those treated for insomnia, 13.56% and 24.55% in the US and 5EU, respectively, were non-adherent due to side effects. In the US, non-adherence was associated with significantly worse HRQoL (health utilities: 0.60 vs. 0.64, p <.05) and greater overall work impairment (37.71% vs. 29.08%, p <.05), among other significant differences. These relationships were not significant in the 5EU. A significant burden of insomnia was observed in both the US and 5EU, and the association remained even after treatment. Non-adherence due to side effects was common and, in the case of the US, associated with significantly poorer health outcomes.     

The Scirtothrips dorsalis Species Complex: Endemism and Invasion in a Global Pest

Invasive arthropods pose unique management challenges in various environments, the first of which is correct identification. This apparently mundane task is particularly difficult if multiple species are morphologically indistinguishable but accurate identification can be determined with DNA barcoding provided an adequate reference set is available. Scirtothrips dorsalis is a highly polyphagous plant pest with a rapidly expanding global distribution and this species, as currently recognized, may be comprised of cryptic species. Here we report the development of a comprehensive DNA barcode library for S. dorsalis and seven nuclear markers via next-generation sequencing for identification use within the complex. We also report the delimitation of nine cryptic species and two morphologically distinguishable species comprising the S. dorsalis species complex using histogram analysis of DNA barcodes, Bayesian phylogenetics, and the multi-species coalescent. One member of the complex, here designated the South Asia 1 cryptic species, is highly invasive, polyphagous, and likely the species implicated in tospovirus transmission. Two other species, South Asia 2, and East Asia 1 are also highly polyphagous and appear to be at an earlier stage of global invasion. The remaining members of the complex are regionally endemic, varying in their pest status and degree of polyphagy. In addition to patterns of invasion and endemism, our results provide a framework both for identifying members of the complex based on their DNA barcode, and for future species delimiting efforts.     

Coupling scanning electron microscopy with DNA bar coding: a novel approach for thrips identification

The small size and cryptic nature of thrips pests often make their monitoring and the identification process difficult. With the aim to obtain accurate identification of various pest species in the order Thysanoptera, a pilot study was conducted on an invasive thrips species Scirtothrips dorsalis Hood in Florida. The specific objective of this pilot study was to assess if the thrips specimens processed to be observed under scanning electron microscopy (SEM) can be further utilized for DNA based assays. Larvae and adults of S. dorsalis were subjected to traditional morphological identification using high resolution SEM prior to their DNA extraction. Sequence results of both mtCO1 and ITS rDNA of individual larva and adult S. dorsalis were found to be in agreement with the taxonomic identification conducted using SEM and each result confirmed the other technique. Our results suggest that steps involved during specimen preparation and observation under SEM does not impact DNA analysis of the sample. The two techniques together could be used for the correct identification of various thrips species using the same specimen. The proof of concept was further tested on three other important thrips species Frankliniella occidentalis (Pergande), F. schultzei (Trybom) and Thrips palmi Karny, which confirmed the robustness of the technique. The technique has broader significance for different areas under entomological sciences especially medical, forensic and taxonomic studies where the samples put under a high beam of ions for investigation are often required for DNA analysis.     

Phenomenological partial-specific volumes for G-quadruplex DNAs

Accurate partial-specific volume ([`(v)] \overline{v} ) values are required for sedimentation velocity and sedimentation equilibrium analyses. For nucleic acids, the estimation of these values is complicated by the fact that [`(v)] \overline{v} depends on base composition, secondary structure, solvation and the concentrations and identities of ions in the surrounding buffer. Here we describe sedimentation equilibrium measurements of the apparent isopotential partial-specific volume ϕ′ for two G-quadruplex DNAs and a single-stranded DNA of similar molecular weight and base composition. The G-quadruplex DNAs are a 22 nucleotide fragment of the human telomere consensus sequence and a 27 nucleotide fragment from the human c-myc promoter. The single-stranded DNA is 26 nucleotides long and is designed to have low propensity to form secondary structures. Parallel measurements were made in buffers containing NaCl and in buffers containing KCl, spanning the range 0.09 M ≤ [salt] ≤ 2.3 M. Limiting values of ϕ′, extrapolated to [salt] = 0 M, were: 22-mer (NaCl-form), 0.525 ± 0.004 mL/g; 22-mer (KCl-form), 0.531 ± 0.006 mL/g; 27-mer (NaCl-form), 0.548 ± 0.005 mL/g; 27-mer (KCl-form), 0.557 ± 0.006 mL/g; 26-mer (NaCl-form), 0.555 ± 0.004 mL/g; 26-mer (KCl-form), 0.564 ± 0.006 mL/g. Small changes in ϕ′ with [salt] suggest that large changes in counterion association or hydration are unlikely to take place over these concentration ranges.     

Developing Native Multispecies Sod: An Alternative Rehabilitation Method for Disturbed Lands

Natural and anthropogenic disturbance provides a mechanism for resetting the species assemblage within natural communities. Following anthropogenic disturbance particularly, there are generally more weedy species. Restoration of ecosystem structure and function in disturbed areas could aid in the control of these undesirable species. Attempts to re‐establish vegetation via direct sowing, hydroseeding, drill seeding, imprinting or plugging of either native or non‐native species can be effective, but can result in increased erosion and weed proliferation prior to desirable cover of the intended species. The use of native species for rehabilitation can be preferable because non‐native species are often less suited to the local environment and can pose a threat to the integrity of adjacent ecosystems. Native multispecies sod could become a useful rehabilitation tool, but research is needed to determine which species to use and the appropriate number of species to include. Mixtures of 4–7 native species were grown for 7 months, and clipped dry biomass, species percent abundance, and total ground cover were assessed over time in order to determine the suitability of 20 native species for sod production. Despite differences between mixtures at some harvests, all mixtures established and produced similar biomass by the end of the study. Final percent cover varied widely among species; 16 of the 20 species increased significantly over the course of production. Differences in total ground cover between mixtures were explained by the growth of the particular species rather than any synergistic effect of species diversity.