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PyroNoise, an algorithm that preclusters the flowgrams generated on a 454 GS FLX with DNA extracted from microbial samples can distinguish between noise and genuine sequence diversity in a metagenomic dataset. We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.

Reproductive failure in mammals due to exposure to polychlorinated biphenyls (PCBs) can occur either through endocrine disrupting effects or via immunosuppression and increased disease risk. To investigate further, full necropsies and determination of summed 25 polychlorinated biphenyls congeners (∑PCBs lipid weight) in blubber were undertaken on 329 UK-stranded female harbour porpoises (1990-2012). In sexually mature females, 25/127 (19.7%) showed direct evidence of reproductive failure (foetal death, aborting, dystocia or stillbirth). A further 21/127 (16.5%) had infections of the reproductive tract or tumours of reproductive tract tissues that could contribute to reproductive failure. Resting mature females (non-lactating or non-pregnant) had significantly higher mean ∑PCBs (18.5 mg/kg) than both lactating (7.5 mg/kg) and pregnant females (6 mg/kg), though not significantly different to sexually immature females (14.0 mg/kg). Using multinomial logistic regression models ΣPCBs was found to be a significant predictor of mature female reproductive status, adjusting for the effects of confounding variables. Resting females were more likely to have a higher PCB burden. Health status (proxied by \"trauma\" or \"infectious disease\" causes of death) was also a significant predictor, with lactating females (i.e. who successfully reproduced) more likely to be in good health status compared to other individuals. Based on contaminant profiles (>11 mg/kg lipid), at least 29/60 (48%) of resting females had not offloaded their pollutant burden via gestation and primarily lactation. Where data were available, these non-offloading females were previously gravid, which suggests foetal or newborn mortality. Furthermore, a lower pregnancy rate of 50% was estimated for \"healthy\" females that died of traumatic causes of death, compared to other populations. Whether or not PCBs are part of an underlying mechanism, we used individual PCB burdens to show further evidence of reproductive failure in the North-east Atlantic harbour porpoise population, results that should inform conservation management.

To understand the biochemistry of methylmercury (MeHg) that leads to the formation of mercury-selenium (Hg-Se) clusters is a long outstanding challenge that promises to deepen our knowledge of MeHg detoxification and the role Se plays in this process. Here, we show that mercury selenide (HgSe) nanoparticles in the liver and brain of long-finned pilot whales are attached to Se-rich structures and possibly act as a nucleation point for the formation of large Se-Hg clusters, which can grow with age to over 5 μm in size. The detoxification mechanism is fully developed from the early age of the animals, with particulate Hg found already in juvenile tissues. As a consequence of MeHg detoxification, Se-methionine, the selenium pool in the system is depleted in the efforts to maintain essential levels of Se-cysteine. This study provides evidence of so far unreported depletion of the bioavailable Se pool, a plausible driving mechanism of demonstrated neurotoxic effects of MeHg in the organism affected by its high dietary intake.

This study aims to assess niche segregation among the five main toothed whales that frequent the NW Iberian Peninsula waters: the common dolphin, the harbour porpoise, the bottlenose dolphin, the striped dolphin and the long-finned pilot whale. We used cadmium (Cd) and stable isotope ratios (delta C-13 and delta N-15) as ecological tracers to assess degree of segregation in diet/trophic level and in foraging habitat, over various time-scales. delta C-13 values highlighted different habitats, while Cd concentrations highlighted feeding differences between oceanic and neritic species. Moreover, delta N-15 values suggest different trophic levels of prey targeted within oceanic and neritic species. Hence, results revealed long-term ecological segregation among five toothed whales that coexist in the NWIP and demonstrated the ability of ecological tracers to discriminate ecological niches among closely related species.

Two strategies exist for seeding low-temperature anaerobic reactors: the use of specialist psychrophilic biomass or mesophilic bioreactor sludge acclimated to low temperature. We sought to determine the low-temperature limitation of anaerobic sludge from a bioreactor acclimated to UK temperatures (<15 °C). Anaerobic incubation tests using low-strength real domestic wastewater (DWW) and various alternative soluble COD sources were conducted at 4, 8 and 15 °C; methanogenesis and acidogenesis were monitored separately. Production of methane and acetate was observed; decreasing temperature resulted in decreased yields and increased ‘start-up’ times. At 4 °C methanogenesis not hydrolysis/acidogenesis was rate-limiting. The final methane yields at 4 °C were less than 35% of the theoretical potential whilst at 8 and 15 °C more than 75 and 100% of the theoretical yield was achieved respectively. We propose that the lower temperature limit for DWW treatment with anaerobic bioreactor sludge lies between 8 and 4 °C and that 8 °C is the threshold for reliable operation.

Understanding the effects of changes in prey abundance on predators is essential to predict responses of marine ecosystems to perturbation and ensure sustainable fishing. As abundant top predators feeding largely on commercially exploited fish, common dolphins Delphinus delphis are expected to be affected by fluctuations in fish abundance. Previous studies variously suggest that common dolphins show a preference for energy-rich species or that they are opportunistic predators. In the latter case, the intensity of predation on all prey species would be expected to vary in proportion to their abundances. If such relationships are seen for only a few prey species, and the importance of other species varies inversely with the abundance of these ‘preferred’ prey, this would indicate selective feeding. We suggest that studies on diet at the population level can provide insights into such individual-level foraging decisions. We analysed stomach contents from 514 stranded and by-caught common dolphins in Galicia (NW Spain), collected over 2 decades. The most important prey were sardine, blue whiting and hake. Using zero-inflated generalised additive models to deal with non-linear relationships and the high number of zeros in prey count data, we tested for evidence of ‘preference’ for the main prey species, as well as confirming the existence of ontogenetic, spatial and seasonal variation in diet. Relationships between diet and annual prey abundance do not conclusively confirm either opportunistic or selective predation, but there is more evidence for the former. Lack of evidence for selective predation on energy-rich sardine could be due to current low stock levels.

Short-beaked common dolphins Delphinus delphis in the eastern North Atlantic (ENA) are subject to mortality due to entanglement in various types of fishing gear. However, for this region, there is no population-level information available on trends in abundance, (incidental) mortality rates or even the actual distributional range. Working under the assumption that only 1 population exists in ENA waters, the current study presents basic life history data and investigates whether biological information obtained from postmortem data is, in itself, useful for managing this population. Life history parameters were estimated by analysing postmortem data obtained over a 16 yr period by UK, Irish, French, Galician (northwest Spain) and Portuguese stranding and bycatch observer programmes. An annual pregnancy rate of 26%, a calving interval of 3.79 yr, an average age attained at sexual maturity of 8.22 yr and an average length at sexual maturity of 188 cm were determined. With respect to the findings based solely on mortality data, significance testing failed to detect differences that could be construed as evidence of the population exhibiting what might be density-dependent compensatory responses. The low annual pregnancy rate reported throughout the sampling period may suggest either that the level of anthropogenic mortality did not cause a substantial population level decline, or a prey base declining at approximately the same rate as the dolphin population. However, this approach alone does not facilitate an assessment of the current state of the D. delphis population in the ENA. Population abundance estimates, trends in abundance and knowledge of factors that affect the dynamics of the population, such as annual mortality rates in fisheries, temporal variations in prey abundance and effects of contaminants on reproductive activity, are required not only to set management objectives, but also to give context to cross-sectional life history information.

The present study is the first record of twinning in Lagenorhynchus acutus and indeed any Lagenorhynchus sp. Both foetuses were male and located in the left uterine horn, had distinct grossly normal placentas and amniotic sacs, and were therefore likely dizygotic twins. The twins were an incidental finding in an animal that died of a systemic Brucella ceti infection.

ALS is increasingly recognized as a biologically heterogeneous disease in which several molecular and pathological mechanisms converge on a similar clinical phenotype. One of these molecular markers is ferritin accumulation which is observed in a subset of ALS cases and has been shown to directly correlate with TDP-43 pathology in some brain regions. Additionally, TDP-43 proteinopathy is observed outside of ALS which may complicate the interpretation of case vs control approaches to target discovery. Here, we propose a pathology-stratified approach to empower targeted theranostics. We hypothesised that biologically distinct ALS subtypes may be defined by specific metabolic dysfunction linked to brain-accumulated ferritin and TDP-43 pathology. Post-mortem primary motor cortex tissue from 15 ALS cases and 20 age- and sex-matched controls was stratified, using immunohistochemistry, by single- or co-occurrence of ferritin accumulation, and pathological TDP-43. Untargeted metabolomics (>1,000 metabolites) was performed, and samples were stratified into dual positive (ferritin and TDP-43), single positive (either), or negative. Group-discriminating metabolites were identified using partial least squares discriminant analysis. Dual ferritin and TDP-43 pathology reflected a distinct metabolomic profile, separable from single-pathology states. This dual positive metabolic signature was characterised by disruption of lysophospholipid, lysoplasmalogen, and fatty acid metabolism, consistent with impaired membrane and energy homeostasis. In contrast, pathological TDP-43 presence without ferritin, was characterised metabolically by significant depletion of secondary bile acids and increase in glycosylation markers, whilst ferritin accumulation alone reflected significant increase in oxidative stress and depletion of lipid peroxidation inhibition markers. The dual positive state suggests failure of compensatory metabolic responses present in single-pathology conditions. Ferritin accumulation and TDP-43 pathology define biologically distinct subtypes associated with ALS with divergent metabolic vulnerabilities. The metabolic signature associated with dual pathology provides a mechanistic correlate to MRI-visible ferritin accumulated iron, supporting paired non-invasive biomarker and target discovery for pathology-dependent patient stratification. These findings argue for pathway-targeted, subtype-specific therapeutic strategies and highlight the necessity of precision medicine approaches in ALS.

The recognition that disease-associated proteinopathies can manifest in peripheral organs outside the central nervous system preceding the onset of neurological symptoms, has transformed our understanding of Parkinson's disease, in wide terms of pathogenesis, detection and diagnosis. For amyotrophic lateral sclerosis, non-motor symptoms, and non-central nervous system pathologies are gaining increased recognition but remain incompletely understood. Here, using a TDP-43 RNA aptamer and a cryptic exon transcript BaseScope™ ISH probe, we identify widespread peripheral organ TDP-43 pathology prior to motor symptom onset in a discovery cohort of ante-mortem tissues from people who went on to develop ALS. Peripheral organs exhibiting both TDP-43 toxic gain- and loss-of function include muscle, lymph node, gallbladder, colon and with notably high incidence, skin. Given the accessibility of skin as a readily biopsiable tissue, representing a promising substrate for the detection of disease-associated proteinopathies and the development of minimally invasive biomarkers, we established an extended cohort of ante-mortem skin samples for TDP-43 pathology validation and further investigation. In skin biopsies taken during life from 17 individuals who went on to develop ALS we identify TDP-43 pathology from all 17 individuals in a wide distribution of anatomical sites, up to 26.5 years before ALS diagnosis - a presymptomatic period comparable to that observed for skin α-synucleinopathy in Parkinson's disease. TDP-43 pathology was most abundant in skin biopsies from the back and shoulder, with sweat and sebaceous glands showing the highest involvement. TDP-43 pathology was also associated with structural changes. As skin α-synucleinopathy has been established as a biomarker for both the detection of Parkinson's disease and the differentiation of Parkinson's disease from multiple system atrophy, we propose that skin TDP-43 likewise holds diagnostic and discrimination potential for diseases characterised by TDP-43 proteinopathy.