DNAdigest and Repositive: Connecting the World of Genomic Data

There is no unified place where genomics researchers can search through all available raw genomic data in a way similar to OMIM for genes or Uniprot for proteins. With the recent increase in the amount of genomic data that is being produced and the ever-growing promises of precision medicine, this is becoming more and more of a problem. DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge.     

Detecting Coppice Legacies from Tree Growth

In coppice-with-standards, once a common type of management in Central European lowland forests, selected trees (standards) were left to grow mature among the regularly harvested coppice stools to obtain construction wood. After the underwood was harvested, the forest canopy opened rapidly, giving standard trees an opportunity to benefit from reduced competition. Although this silvicultural system virtually disappeared after WWII, historical management cycles can still be traced in the tree-rings of remaining standards. Our research aims at answering the question whether tree-ring series of standard trees can be used to reconstruct past management practices. The study was carried out on 117 oak standard trees from five sites situated in formerly coppiced calcareous oak-hornbeam and acidophilous oak forests in the Bohemian Karst Protected Landscape Area, Czech Republic. The evaluation was based on the analysis of growth releases representing the response of the standards to coppicing events, and comparison to the archival records of coppice events. Our results showed that coppicing events can be successfully detected by tree-ring analysis, although there are some limitations. Altogether 241 releases were identified (49% of major releases). Large number of releases could be related to historical records, with the major ones giving better results. The overall probability of correct detection (positive predictive power) was 58%, ranging from 50 to 67%, probability for major releases was 78%, ranging from 63 to 100% for different sites. The ability of individual trees to mirror past coppice events was significantly affected by competition from neighboring trees (their number and the sum of distance-weighted basal areas). A dendro-ecological approach to the study of forest management history can serve as an input for current attempts of coppice reintroduction and for conservation purposes.     

Stranding Events of Kogia Whales along the Brazilian Coast

The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.     

Identification of Biomarkers of Mercury Contamination in Brachyplatystoma filamentosum of the Madeira River,Brazil, Using Metalloproteomic Strategies

Biological Trace Element Research - Predator fish can accumulate high levels of mercury, which qualifies them as potential indicators of this toxic metal. The predatory species Brachyplatystoma...     

Immature gannets follow adults in commuting flocks providing a potential mechanism for social learning

Group travel is a familiar phenomenon among birds but the causes of this mode of movement are often unclear. For example, flocking flight may reduce flight costs, enhance predator avoidance or increase foraging efficiency. In addition, naive individuals may also follow older, more experienced conspecifics as a learning strategy. However, younger birds may be slower than adults so biomechanical and social effects on flock structure may be difficult to separate. Gannets are wide‐ranging (100s–1000s km) colonial seabirds that often travel in V or echelon‐shaped flocks. Tracking suggests that breeding gannets use memory to return repeatedly to prey patches 10s–100s km wide but it is unclear how these are initially discovered. Public information gained at the colony or by following conspecifics has been hypothesised to play a role, especially during early life. Here, we address two hypotheses: 1) flocking reduces flight costs and 2) young gannets follow older ones in order to locate prey. To do so, we recorded flocks of northern gannets commuting to and from a large colony and passing locations offshore and used a biomechanical model to test for age differences in flight speeds. Consistent with the aerodynamic hypothesis, returning flocks were significantly larger than departing flocks, while, consistent with the information gathering hypothesis, immatures travelled in flocks more frequently than adults and these flocks were more likely to be led by adults than expected by chance. Immatures did not systematically occupy the last position in flocks and had similar theoretical airspeeds to adults, making it unlikely that they follow, rather than lead, for biomechanical reasons. We therefore conclude that while gannets are likely to travel in flocks in part to reduce flight costs, the positions of immatures in those flocks may result in a flow of information from adults to immatures, potentially leading to social learning.     

Pro-apoptotic protein kinase C delta is associated with intranuclear inclusions in a transgenic model of Huntington's disease

In order to investigate any effect of truncated mutant huntingtin (tNhtt) aggregation on protein kinase C (PKC) signaling in Huntington's disease (HD), we studied a possible association of PKC isoforms with the aggregates using cellular and transgenic models of HD. In this report we describe an association of mutant tNhtt with at least three PKC isoforms (alpha, delta, zeta), as revealed by co-immunoprecipitation assays and immunocytochemistry in a cellular model of HD (Neuro2a cells expressing tNhtt-150Q-EGFP), as well as a specific association of PKC delta with intranuclear aggregates in a transgenic model (R6/2 mice). Immunoblot analysis of isolated nuclear fractions shows an elevation of nuclear PKC delta in transgenic brain tissue. The observed elevation has a strong similarity with the apoptotic translocation of PKC delta detected in experiments with the mouse neuroblastoma Neuro2a cells. Using a Neuro2a cell line expressing tNhtt with the nuclear localization signal, we demonstrate the association of PKC delta with intranuclear aggregates and present evidence that accumulation of PKC delta in cell nuclei does not depend on mutant htt nuclear translocation. Our results suggest that the association of PKC delta with intranuclear htt-aggregates may affect its apoptotic function in a transgenic model of HD.     

Fate and effects of phosphorus additions in soils under N2-fixing red alder

Soil phosphorus (P) dynamics are controlled by the interaction of geochemical, biochemical and biological processes. Changes in species composition or management could alter the relative importance of these processes. We examined soil P dynamics in two plantations of N₂-fixing red alder (Alnus rubra) by determining the fate and effects of added fertilizer P. History of the plantations varied such that sites were previously occupied by 60-yr-old stands of alder or non-fixing Douglas-fir (Pseudotsuga menziesii). Without fertilization, the soil with a longer period of alder influence had more organic P (P_o) and less sorbed inorganic P (Hydroxide- and Bicarb-extractable P_i). Fertilization increased soil total P, and 88% of the fertilizer was accounted for in the surface mineral soil (0–15 cm). Sorbed P_i was the major sink for fertilizer P (55–60%), independent of site history. Although P_o was 35–70% of soil P in unfertilized plots, added P did not accumulate as P_o. Neither site history nor P addition influenced phosphatase activity. Fertilization increased decomposition during incubation of the organic horizon, suggesting that late-stage decomposition is P-limited in these N-rich soils. On the time-scale of a few years, geochemical sorption and desorption of inorganic P were the most important processes controlling the distribution of added P. Organic P accumulation is expected to occur over a longer time frame, linked to the production and turnover of organic matter.     

Interleukin-12 P40 induces the expression of TNF-α in microglia and macrophages

Recently, it has been found that overproduction of IL-12 can be dangerous to the host as it is involved in the pathogenesis of a number of autoimmune inflammatory diseases such as multiple sclerosis. It is composed of two different subunits – p40 and p35. Expression of p40 mRNA but not that of p35 mRNA in excessive amount in the CNS of patients with Multiple Sclerosis (MS) suggests that IL-12 p40 may have a role in the pathogenesis of the disease. The present study was undertaken to explore the role of p40 in the expression of TNF-α in microglia. Interestingly, we have found that IL-12 p70, p402 (the p40 homodimer) and p40 (the p40 monomer) dose-dependently induced the production of TNF-α in BV-2 microglial cells. This induction of TNF-α production was accompanied by an induction of TNF-α mRNA. In addition to BV-2 glial cells, p70, p402 and p40 also induced the production of TNF-α in mouse primary microglia and peritoneal macrophages. Since the activation of both NF-κB and C/EBPb is important for the expression of TNF-α in microglial cells, we investigated the effect of p40 on the activation of NF-κB as well as C/EBPb. Activation of NF-κB as well as C/EBPb by p40 and inhibition of p40-induced expression of TNF-α by Dp65, a dominant-negative mutant of p65, and DC/EBPb, a dominant-negative mutant of C/EBPb, suggests that p40 induces the expression of TNF-α through the activation of NF-κB and C/EBPb. This study delineates a novel role of IL-12 p40 in inducing the expression of TNF-α in microglial cells which may participate in the pathogenesis of neuroinflammatory diseases.
Acknowledgements:   This study was supported by NIH grants (NS39940 and AG19487).