DNA Isolation Method Is a Source of Global DNA Methylation Variability Measured with LUMA. Experimental Analysis and a Systematic Review

In DNA methylation, methyl groups are covalently bound to CpG dinucleotides. However, the assumption that methyl groups are not lost during routine DNA extraction has not been empirically tested. To avoid nonbiological associations in DNA methylation studies, it is essential to account for potential batch effect bias in the assessment of this epigenetic mechanism. Our purpose was to determine if the DNA isolation method is an independent source of variability in methylation status. We quantified Global DNA Methylation (GDM) by luminometric methylation assay (LUMA), comparing the results from 3 different DNA isolation methods. In the controlled analysis (n = 9), GDM differed slightly for the same individual depending on extraction method. In the population analysis (n = 580) there were significant differences in GDM between the 3 DNA isolation methods (medians, 78.1%, 76.5% and 75.1%; p<0.001). A systematic review of published data from LUMA GDM studies that specify DNA extraction methods is concordant with our findings. DNA isolation method is a source of GDM variability measured with LUMA. To avoid possible bias, the method used should be reported and taken into account in future DNA methylation studies.     

Disability Mediates the Impact of Common Conditions on Perceived Health

Background

We examined the extent to which disability mediates the observed associations of common mental and physical conditions with perceived health.

Methods and Findings

WHO World Mental Health (WMH) Surveys carried out in 22 countries worldwide (n = 51,344 respondents, 72.0% response rate). We assessed nine common mental conditions with the WHO Composite International Diagnostic Interview (CIDI), and ten chronic physical with a checklist. A visual analog scale (VAS) score (0, worst to 100, best) measured perceived health in the previous 30 days. Disability was assessed using a modified WHO Disability Assessment Schedule (WHODAS), including: cognition, mobility, self-care, getting along, role functioning (life activities), family burden, stigma, and discrimination. Path analysis was used to estimate total effects of conditions on perceived health VAS and their separate direct and indirect (through the WHODAS dimensions) effects.Twelve-month prevalence was 14.4% for any mental and 51.4% for any physical condition. 31.7% of respondents reported difficulties in role functioning, 11.4% in mobility, 8.3% in stigma, 8.1% in family burden and 6.9% in cognition. Other difficulties were much less common. Mean VAS score was 81.0 (SD = 0.1). Decrements in VAS scores were highest for neurological conditions (9.8), depression (8.2) and bipolar disorder (8.1). Across conditions, 36.8% (IQR: 31.2–51.5%) of the total decrement in perceived health associated with the condition were mediated by WHODAS disabilities (significant for 17 of 19 conditions). Role functioning was the dominant mediator for both mental and physical conditions. Stigma and family burden were also important mediators for mental conditions, and mobility for physical conditions.

Conclusions

More than a third of the decrement in perceived health associated with common conditions is mediated by disability. Although the decrement is similar for physical and mental conditions, the pattern of mediation is different. Research is needed on the benefits for perceived health of targeted interventions aimed at particular disability dimensions.     

Final Disposition and Quality Auditing of the Rehabilitation Process in Wild Raptors Admitted to a Wildlife Rehabilitation Centre in Catalonia,Spain, during a Twelve Year Period (1995–2007)

Background

Variability in reporting and classification methods in previous published data of the final dispositions in the rehabilitation of wild raptors makes use of this data limited in trying to audit the quality of the rehabilitation process. Crude as well as stratified disposition rates are needed if quality auditing of the rehabilitation process is to be adequately performed.

Methodology

Final dispositions of 6221 hospitalized wild raptors admitted at a wildlife rehabilitation centre (WRC) of Catalonia during 1995–2007 were analyzed. These dispositions were calculated as the euthanasia (Er), unassisted mortality (Mr), release (Rr) and captivity rates (Cr)., time to death (Td) for dead and euthanized raptors, and length of stay for released (Tr) raptors was estimated. Stratified analyses by main causes of admission and clinical signs were performed.

Results

The disposition for the total population were: Er  = 30.6%, Mr = 19.1%, Rr  = 47.2%, and Cr  = 3%. By main causes of admission, Er was higher in the trauma category (34.2%), whereas Mr was found similar between trauma (37.4%) and non-trauma categories (34.8%). The highest Rr was observed for the orphaned group (77.9%). Furthermore, Cr was low in all the categories (<4%). By clinical signs, the highest Er was found in animals suffering musculoskeletal (37.9%) or skin (32.3%) lesions; Mr was high in infectious/parasitic diseases (66.7%) and in case of neurological symptoms (64.5%). The euthanized birds had a median Td  = 1 day (P₁₀ = 0-P₉₀ = 59) for both trauma and non-trauma categories, and Td  = 36 days for the orphaned young group (P₁₀ = 0; P₉₀ = 596). The median Td in the unassisted dead birds was 2 days for all the categories (P₁₀ = 0-P₉₀ = 31). Finally, the median Tr in the centre was variable among categories.

Conclusions/Significance

Reporting of final dispositions in wildlife rehabilitation should include the crude and stratified rates (Er, Mr, Rr, and Cr), by causes and clinical presentation, as well as Td and Tr, to allow meaningful auditing of the rehabilitation process quality.     

Realigning Thunder and Lightning: Temporal Adaptation to Spatiotemporally Distant Events

The brain is able to realign asynchronous signals that approximately coincide in both space and time. Given that many experience-based links between visual and auditory stimuli are established in the absence of spatiotemporal proximity, we investigated whether or not temporal realignment arises in these conditions. Participants received a 3-min exposure to visual and auditory stimuli that were separated by 706 ms and appeared either from the same (Experiment 1) or from different spatial positions (Experiment 2). A simultaneity judgment task (SJ) was administered right afterwards. Temporal realignment between vision and audition was observed, in both Experiment 1 and 2, when comparing the participants’ SJs after this exposure phase with those obtained after a baseline exposure to audiovisual synchrony. However, this effect was present only when the visual stimuli preceded the auditory stimuli during the exposure to asynchrony. A similar pattern of results (temporal realignment after exposure to visual-leading asynchrony but not after exposure to auditory-leading asynchrony) was obtained using temporal order judgments (TOJs) instead of SJs (Experiment 3). Taken together, these results suggest that temporal recalibration still occurs for visual and auditory stimuli that fall clearly outside the so-called temporal window for multisensory integration and appear from different spatial positions. This temporal realignment may be modulated by long-term experience with the kind of asynchrony (vision-leading) that we most frequently encounter in the outside world (e.g., while perceiving distant events).     

Habitat selection by Southern water vole (Arvicola sapidus) in riparian environments of Mediterranean mountain areas: a conservation tool for the species

The Southern water vole, Arvicola sapidus, is endemic to the Iberian Peninsula and France. Despite being catalogued as vulnerable, our current knowledge of this species is not sufficient to establish measures for its conservation and recovery, particularly in riparian zones of Mediterranean mountain areas. The aim of this study was to identify factors related to habitat configuration that determine the presence or absence of the species in the Montsant River. Specifically, we associated the presence/absence of this arvicolid rodent with composition of vegetation, river bank morphology, and watercourse characteristics. The results suggest that, in this area, the most favorable places for the species are those with a high degree of cover of herbaceous plants (mainly helophytes) and moderate to low levels of tree and shrub cover; gently sloping banks and a soft substrate; and the presence of water, with moderate to high stream widths and depths. In addition, we developed a classification method which allowed us to classify and characterize habitat conditions: the optimal scenario (preferential for arvicoline establishment), the suboptimal scenario (whose use is related to opportunities to find best scenarios), and the hostile scenario (not acceptable for use). In such riparian areas, the results revealed that the Southern water vole is a specialist in terms of habitat selection, but behaves as a generalist in terms of occupancy. Its ability to adapt to suboptimal conditions widens the options for managing Southern water vole populations, and indicates that the maintenance and rehabilitation of habitat along continuous stretches of river is the most effective approach to achieving self-sustaining populations.     

Noninvasive molecular sexing: An evaluation and validation of the SRY‐ and amelogenin‐based method in three new lemur species

Many lemur species are arboreal, elusive, and/or nocturnal and are consequently difficult to approach, observe and catch. In addition, most of them are endangered. For these reasons, non‐invasive sampling is especially useful in primates including lemurs. A key issue in conservation and ecological studies is to identify the sex of the sampled individuals to investigate sex‐biased dispersal, parentage, social organization and population sex ratio. Several molecular tests of sex are available in apes and monkeys, but only a handful of them work in the lemuriform clade. Among these tests, the coamplification of the SRY gene with the amelogenin X gene using strepsirhine‐specific X primers seems particularly promising, but the reliability and validity of this sexing test have not been properly assessed yet. In this study, we (i) show that this molecular sexing test works on three additional lemur species (Microcebus tavaratra, Propithecus coronatus and P. verreauxi) from two previously untested genera and one previously untested family, suggesting that these markers are likely to be universal among lemurs and other strepsirrhines; (ii) provide the first evidence that this PCR‐based sexing test works on degraded DNA obtained from noninvasive samples; (iii) validate the approach using a large number of known‐sex individuals and a multiple‐tubes approach, and show that mismatches between the field sex and the final molecular consensus sex occur in less than 10% of all the samples and that most of these mismatches were likely linked to incorrect sex determinations in the field rather than genotyping errors. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Absence of soil frost affects plant-soil interactions in temperate grasslands

Background and aims

Intermittently frozen ground in winter is expected to disappear over large areas in the temperate zone due to ongoing climate warming. The lack of soil frost influences plant soil interactions and needs to be studied in more detail.

Methods

Winter soil frost was avoided by belowground heating wires in a field experiment over two subsequent winters in a temperate grassland. Soil respiration, soil nitrogen availability and plant performance (aboveground biomass, root length at two depth levels, greenness, nutrient content) were compared between “no-frost” and reference plots which underwent repeated freeze-thaw cycles in both winters.

Results

Soil respiration increased in the “no-frost” treatment during the warming phase (+291 %). N-availability in the upper 10 cm of the soil profile was not affected, possibly due to increased plant N accumulation during winter (+163 %), increased plant N concentration (+18 %) and increased biomass production (+31.5 %) in the growing season. Translocation of roots into deeper soil layers without changes in total root length in response to the “no-frost” treatment, however, may be a sign of nutrient leaching.

Conclusions

The cumulative effect on carbon cycling due to warmer soils therefore depends on the balance between increased winter carbon loss due to higher soil biotic activity and enhanced plant productivity with higher nutrient accumulation in the growing season.     

Adapting light trap to catch household insects in central Cameroon: a pilot study

Various trapping methods and techniques developed for entomological studies are inefficient in attracting all arthropod groups. A new simple light trap, the basin light trap (BLT), to collect arthropod fauna around household in central Cameroon was thus designed. Its performance is evaluated by comparing collected data with those obtained by the Centre for Disease Control light trap (CDC) commonly used in mosquito studies. BLT were activated between 6 and 10 pm and CDC between 5 pm and 8 am. A total of 36,804 arthropods specimens were collected and sorted into 115 families within 20 orders and three phyla (Myriapoda, Arachnida and Hexapoda). BLT attracted more individuals (22,250 vs 14,554), families (106 vs 65) and significantly more families per night (33.0 ± 15.9 vs 21.0 ± 8.5) than CDC. Some families were collected by only one specific trap type while others overlapped between the two traps. Prosopistomatidae (Ephemeroptera) was the most abundant family collected by BLT. In contrast, Cecidomyiidae (Diptera) was the most abundant taxon trapped by CDC. These results indicate that collecting methods such as BLT complement available trapping methods in evaluating arthropod fauna in and around households.     

Ultrastructure of the spermatozoon of Anomotaenia quelea (Mettrick, 1961) (Cestoda,Cyclophyllidea, Dilepididae), an intestinal parasite of Quelea quelea (Aves,Ploceidae) in Senegal

The mature spermatozoon of Anomotaenia quelea exhibits an apical cone of electron-dense material and two helicoidal crest-like bodies. The apical cone near its base is surrounded by a lucent cytoplasm and a spiraled layer of cortical microtubules. The crest-like bodies are of different lengths, spiraled and make an angle of 30–40° to the hypothetical spermatozoon axis. The axoneme is of the 9 + ‘1’ trepaxonematan pattern and is surrounded by a periaxonemal sheath of electron-dense material. The cytoplasm contains in regions III and IV numerous electron-dense granules situated between the periaxonemal sheath and the cortical microtubules. The posterior extremity of the spermatozoon of A. quelea exhibits a nucleus and a disorganized axoneme and cortical microtubules. This type of posterior extremity of the mature spermatozoon has never been described previously in a Dilepididae. Similarly, two crest-like bodies have not been observed before in a dilepidid cestode.