DNA extraction from formalin-fixed tissue: new light from the Deep-Sea

DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided

Music notation: a new method for visualizing social interaction in animals and humans

BACKGROUND: Researchers have developed a variety of techniques for the visual presentation of quantitative data. These techniques can help to reveal trends and regularities that would be difficult to see if the data were left in raw form. Such techniques can be of great help in exploratory data analysis, making apparent the organization of data sets, developing new hypotheses, and in selecting effects to be tested by statistical analysis. Researchers studying social interaction in groups of animals and humans, however, have few tools to present their raw data visually, and it can be especially difficult to perceive patterns in these data. In this paper I introduce a new graphical method for the visual display of interaction records in human and animal groups, and I illustrate this method using data taken on chickens forming dominance hierarchies. RESULTS: This new method presents data in a way that can help researchers immediately to see patterns and connections in long, detailed records of interaction. I show a variety of ways in which this new technique can be used: (1) to explore trends in the formation of both group social structures and individual relationships; (2) to compare interaction records across groups of real animals and between real animals and computer-simulated animal interactions; (3) to search for and discover new types of small-scale interaction sequences; and (4) to examine how interaction patterns in larger groups might emerge from those in component subgroups. In addition, I discuss how this method can be modified and extended for visualizing a variety of different kinds of social interaction in both humans and animals. CONCLUSION: This method can help researchers develop new insights into the structure and organization of social interaction. Such insights can make it easier for researchers to explain behavioural processes, to select aspects of data for statistical analysis, to design further studies, and to formulate appropriate mathematical models and computer simulations

‘You don't take things too seriously or un‐seriously’: Beyond recovery to liminal and liminoid possibility in a community arts and mental health project

Recent years have seen a renewed interest in integrating creative activities into statutory mental health practice in high-income countries. In this article, we offer an exploratory analysis of an arts project delivered within UK mental health services, Creativity for Enablement and Wellbeing (CREW). Drawing on data collected for a process evaluation of the project, we suggest that conceptualising CREW as liminal and liminoid provides a helpful way to articulate the processes, atmospheres, relationships, and practices of the project. Through this theoretical lens, we identify CREW as a mode of engagement comprising looseness, possibility and collectivity, all brought together through a unique community event, the showcase. We explore CREW's mode of engagement through three themes: ‘carving out a liminal space’, ‘looseness and experimentation,’ and ‘from liminal to liminoid’. Implications for service delivery are discussed, focussing on how CREW managed to create a transformative space of liminoid possibility rather than a recovery journey delineated by service-defined imperatives

Hospitalization Rates for Coronary Heart Disease in Relation to Residence Near Areas Contaminated with Persistent Organic Pollutants and Other Pollutants

Exposure to environmental pollutants may contribute to the development of coronary heart disease (CHD). We determined the ZIP codes containing or abutting each of the approximately 900 hazardous waste sites in New York and identified the major contaminants in each. Three categories of ZIP codes were then distinguished: those containing or abutting sites contaminated with persistent organic pollutants (POPs), those containing only other types of wastes (“other waste”), and those not containing any identified hazardous waste site (“clean”). Effects of residence in each of these ZIP codes on CHD and acute myocardial infarction (AMI) hospital discharge rates were assessed with a negative binomial model, adjusting for age, sex, race, income, and health insurance coverage. Patients living in ZIP codes contaminated with POPs had a statistically significant 15.0% elevation in CHD hospital discharge rates and a 20.0% elevation in AMI discharge rates compared with clean ZIP codes. In neither of the comparisons were rates in other-waste sites significantly greater than in clean sites. In a subset of POP ZIP codes along the Hudson River, where average income is higher and there is less smoking, better diet, and more exercise, the rate of hospitalization for CHD was 35.8% greater and for AMI 39.1% greater than in clean sites. Although the cross-sectional design of the study prevents definite conclusions on causal inference, the results indirectly support the hypothesis that living near a POP-contaminated site constitutes a risk of exposure and of development of CHD and AMI

Radical “Citizens of the World,” 1790–95: The Early Career of Henry Redhead Yorke

This article takes a new look at British radicalism in the 1790s and explores it within broad geographical and cultural frameworks and through the early career of Henry Redhead Yorke, a West Indian Creole who became a radical in England but frequently recanted his politics. It views radicalism within the Atlantic World and provides a broader interpretation of the excluded majority than as an English working class. It examines the radical “citizens of the world” and sheds new light on the apparent conflict within English radicalism between universalist and constitutionalist ideologies. Politicization and identity are the key themes here examined within micro- and macro-histories

Flow Phase Diagram for the Helium Superfluids

The flow phase diagram for He II and $^3$He-B is established and discussed based on available experimental data and the theory of Volovik [JETP Letters {\bf{78}} (2003) 553]. The effective temperature - dependent but scale - independent Reynolds number $Re_{eff}=1/q=(1+\alpha')/\alpha$, where $\alpha$ and $\alpha'$ are the mutual friction parameters and the superfluid Reynolds number characterizing the circulation of the superfluid component in units of the circulation quantum are used as the dynamic parameters. In particular, the flow diagram allows identification of experimentally observed turbulent states I and II in counterflowing He II with the turbulent regimes suggested by Volovik.Comment: 2 figure

Colored Motifs Reveal Computational Building Blocks in the C. elegans Brain

Background: Complex networks can often be decomposed into less complex sub-networks whose structures can give hints about the functional organization of the network as a whole. However, these structural motifs can only tell one part of the functional story because in this analysis each node and edge is treated on an equal footing. In real networks, two motifs that are topologically identical but whose nodes perform very different functions will play very different roles in the network. Methodology/Principal Findings: Here, we combine structural information derived from the topology of the neuronal network of the nematode C. elegans with information about the biological function of these nodes, thus coloring nodes by function. We discover that particular colorations of motifs are significantly more abundant in the worm brain than expected by chance, and have particular computational functions that emphasize the feed-forward structure of information processing in the network, while evading feedback loops. Interneurons are strongly over-represented among the common motifs, supporting the notion that these motifs process and transduce the information from the sensor neurons towards the muscles. Some of the most common motifs identified in the search for significant colored motifs play a crucial role in the system of neurons controlling the worm's locomotion. Conclusions/Significance: The analysis of complex networks in terms of colored motifs combines two independent data sets to generate insight about these networks that cannot be obtained with either data set alone. The method is general and should allow a decomposition of any complex networks into its functional (rather than topological) motifs as long as both wiring and functional information is available

Did North Atlantic overturning halt 17,000 years ago?

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 23 (2008): PA1101, doi:10.1029/2007PA001500.Models indicate that a complete shutdown of deep and intermediate water production is a possible consequence of extreme climate conditions in the northern North Atlantic, and the high ratio of 231Pa to 230Th on Bermuda Rise is evidence that this might have happened ∼17 ka during Heinrich event 1 (H1). However, new radiocarbon data from bivalves that lived at ∼4.6 km on the Bermuda Rise during H1 lead to a different conclusion. The bivalve data do indeed indicate ventilation of the deep western North Atlantic was suppressed during H1 but not as much as it was during the last glacial maximum. We propose that high diatom flux to the Bermuda Rise during H1 is at least in part responsible for increased 231Pa/230Th at that time. Although we cannot say for sure why opal production was so high in a gyre center location at that time, increased leakage of silica rich waters from the Southern Ocean to the North Atlantic is one possibility.This work was funded by a grant from the Comer Foundation to WHOI’s Ocean and Climate Change Institute

Exosome-mediated Delivery of Hydrophobically Modified siRNA for Huntingtin mRNA Silencing

Delivery represents a significant barrier to the clinical advancement of oligonucleotide therapeutics for the treatment of neurological disorders, such as Huntington\u27s disease. Small, endogenous vesicles known as exosomes have the potential to act as oligonucleotide delivery vehicles, but robust and scalable methods for loading RNA therapeutic cargo into exosomes are lacking. Here, we show that hydrophobically modified small interfering RNAs (hsiRNAs) efficiently load into exosomes upon co-incubation, without altering vesicle size distribution or integrity. Exosomes loaded with hsiRNAs targeting Huntingtin mRNA were efficiently internalized by mouse primary cortical neurons and promoted dose-dependent silencing of Huntingtin mRNA and protein. Unilateral infusion of hsiRNA-loaded exosomes, but not hsiRNAs alone, into mouse striatum resulted in bilateral oligonucleotide distribution and statistically significant bilateral silencing of up to 35% of Huntingtin mRNA. The broad distribution and efficacy of hsiRNA-loaded exosomes delivered to brain is expected to advance the development of therapies for the treatment of Huntington\u27s disease and other neurodegenerative disorders