Recovery of plant DNA using a reciprocating saw and silica‐based columns

The time needed for hand grinding and the cost of commercially available extraction kits remain to be the major limitations in plant DNA extraction for many researchers. We present inexpensive techniques for (i) simultaneously machine grinding large numbers of plant samples for DNA extraction using a commercially available reciprocating saw; and (ii) DNA recovery using silica column‐based extractions similar to that used in some commercially available kits. Used together, these allow for the rapid recovery of plant DNA at relatively low cost. Furthermore, these methods appear to be widely applicable within plants with good yields recovered in test extractions across major plant groups (ferns, gymnosperms, monocots and eudicots).     

Contamination of the Deep Tissues of Carcasses by Bacteria Present on the Slaughter Instruments or in the Gut

Possible routes by which bacteria might reach the deep tissues of carcasses were tested by placing genetically 'marked'strains of Escherichia coli, Clostridium perfringens or Bacillus thuringiensis on slaughter instruments before use and examining deep tissue samples for their presence post mortem . Bacteria present on the captive bolt pistol were recovered from the spleens of beef cattle and those placed on the pithing rod were found in both spleen and muscle of the flank and neck. Bacteria from the throat cutting ('stick') knife were isolated, on different occasions, from the heart, lung, spleen, liver and kidneys of sheep though rarely from their muscles. Orally administered bacteria were found in the spleen and lung, but not the musculature, of pigs.     

Abscesses of the breast; recurring lesions in the areolar area

Subareolar abscesses beginning either in infected skin glands or in breast ducts have an extraordinary tendency to recur and to be resistant to treatment. About three-fourths of 64 patients observed had from one to many recurrences of abscess after either spontaneous or surgical drainage, and many even after wide excision of scar in an interval of quiescence.The most successful of a number of methods of treatment used was wide removal of scar and underlying chronic abscess cavity combined with removal of the ampulla and mouth of a connecting duct. In a substantial number, after either drainage or unsuccessful excision, the process gradually subsided over a period of months or years. Cancer has not been observed in any of the 64 patients.     

MISCONCEPTIONS ABOUT COERCION AND UNDUE INFLUENCE: REFLECTIONS ON THE VIEWS OF IRB MEMBERS

Payment to recruit research subjects is a common practice but raises ethical concerns relating to the potential for coercion or undue influence. We conducted the first national study of IRB members and human subjects protection professionals to explore attitudes as to whether and why payment of research participants constitutes coercion or undue influence. Upon critical evaluation of the cogency of ethical concerns regarding payment, as reflected in our survey results, we found expansive or inconsistent views about coercion and undue influence that may interfere with valuable research. In particular, respondents appear to believe that coercion and undue influence lie on a continuum; by contrast, we argue that they are wholly distinct: whereas undue influence is a cognitive distortion relating to assessment of risks and benefits, coercion is a threat of harm. Because payment is an offer, rather than a threat, payment is never coercive.     

Inactivation of thioredoxin f1 leads to decreased light activation of ADP‐glucose pyrophosphorylase and altered diurnal starch turnover in leaves of Arabidopsis plants

Chloroplast thioredoxin f (Trx f) is an important regulator of primary metabolic enzymes. However, genetic evidence for its physiological importance is largely lacking. To test the functional significance of Trx f in vivo, Arabidopsis mutants with insertions in the trx f1 gene were studied, showing a drastic decrease in Trx f leaf content. Knockout of Trx f1 led to strong attenuation in reductive light activation of ADP‐glucose pyrophosphorylase (AGPase), the key enzyme of starch synthesis, in leaves during the day and in isolated chloroplasts, while sucrose‐dependent redox activation of AGPase in darkened leaves was not affected. The decrease in light‐activation of AGPase in leaves was accompanied by a decrease in starch accumulation, an increase in sucrose levels and a decrease in starch‐to‐sucrose ratio. Analysis of metabolite levels at the end of day shows that inhibition of starch synthesis was unlikely due to shortage of substrates or changes in allosteric effectors. Metabolite profiling by gas chromatography–mass spectrometry pinpoints only a small number of metabolites affected, including sugars, organic acids and ethanolamine. Interestingly, metabolite data indicate carbon shortage in trx f1 mutant leaves at the end of night. Overall, results provide in planta evidence for the role played by Trx f in the light activation of AGPase and photosynthetic carbon partitioning in plants.     

Invasive ecosystem engineers on soft sediment change the habitat preferences of native mayflies and their availability to predators

1. Dreissenid mussels (quagga mussels, Dreissena bugensis, and zebra mussels, D. polymorpha) are invasive species that function as ecosystem engineers in the Laurentian Great Lakes. Dreissena are increasingly abundant on silt, sand and other soft substrates; by altering benthic habitat, these mussels can alter benthic community structure. 2. We used laboratory mesocosm experiments to examine the effects of soft‐sediment Dreissena clusters on the habitat preference of Hexagenia, a native burrowing mayfly that is an important food source to fish. We conducted three experiments to test whether Hexagenia: (1) select for bare sediment, soft sediment covered with live Dreissena (added structure and food resources) or soft sediment with clusters made of empty Dreissena shells (added structure only), (2) prefer a specific density of live Dreissena on soft sediment and (3) select for or avoid sediment with an accumulation of empty Dreissena shells. 3. Contrary to initial expectations, we found that Hexagenia selected for sediment covered with live Dreissena clusters, followed by empty Dreissena shells clusters, and lastly what was previously thought to be the preferred habitat, bare sediment. Not only did Hexagenia prefer Dreissena‐covered sediment, but they also preferred high densities of Dreissena. 4. We also experimentally tested the effects of Dreissena‐covered soft sediment on the availability of Hexagenia to fish. We had three treatment levels representing three distinct habitat types: (1) bare sediment (no Dreissena) treatment in which water was turbid because of mayfly activity, (2) Dreissena‐covered sediment treatment in which water was clear because of Dreissena filtration and (3) Dreissena‐covered sediment with added turbidity. We found that in low light conditions, similar to many locations where both organisms are found to co‐occur, both yellow perch and round goby consumption of Hexagenia significantly decreased when Dreissena covered the bottom sediment. 5. These results suggest that by choosing Dreissena‐covered habitat, Hexagenia receive protection from fish predation in turbid/low light systems. However, protection from predation cannot be the only reason Hexagenia select Dreissena‐covered sediments, as Hexagenia selected for live clusters more often than empty clusters and may be a result of additional food resources.     

Implications of community concordance for assessing stream integrity at three nested spatial scales in Minnesota,U.S.A.

1. Fish and invertebrate assemblage data collected from 670 stream sites in Minnesota (U.S.A.) were used to calculate concordance across three nested spatial scales (statewide, ecoregion and catchment). Predictive taxa richness models, calibrated using the same data, were used to evaluate whether concordant communities exhibited similar trends in human‐induced taxa loss across all three scales. Finally, we evaluated the strength of the relationship between selected environmental variables and the composition of both assemblages at all three spatial scales. 2. Significant concordance between fish and invertebrate communities occurred at the statewide scale as well as in six of seven ecoregions and 17 of the 21 major catchments. However, concordance was not consistently indicative of significant relationships between rates of fish and invertebrate taxa loss at those same scales. 3. Fish and invertebrate communities were largely associated with different environmental variables, although the composition of both communities was strongly correlated with stream size across all three scales. 4. Predictive taxa‐loss models for fish assemblages were less sensitive and precise than models for invertebrate assemblages, likely because of the relatively low number of common fish taxa in our data set. Both models, however, distinguished reference from non‐reference sites. 5. The importance of concordance, geographic context and scale are discussed in relation to the design and interpretation of stream integrity indicators. In particular, our findings suggest that community concordance should not be viewed as a substitute for an evaluation of how assemblages respond to environmental stressors.