Reconstruction of the Amazon Basin effective moisture availability over the past 14,000 years

Quantifying the moisture history of the Amazon Basin is essential for understanding the cause of rain forest diversity and its potential as a methane source. We reconstructed the Amazon River outflow history for the past 14,000 years to provide a moisture budget for the river drainage basin. The oxygen isotopic composition of planktonic foraminifera recovered from a marine sediment core in a region of Amazon River discharge shows that the Amazon Basin was extremely dry during the Younger Dryas, with the discharge reduced by at least 40% as compared with that of today. After the Younger Dryas, a meltwater-driven discharge event was followed by a steady increase in the Amazon Basin effective moisture throughout the Holocene.     

Ultrastructural study of ochratoxicosis in quail (Coturnix coturnix japonica)

Ultrathin sections of liver and kidney from 11-week-old quail fed, from day-old, ochratoxin A (OA) (mixed in the diet at levels of 4 and 8 ppm) were examined in the electron microscope. Pathological changes in the kidneys were limited to the proximal convoluted tubules (PCT) and glomeruli. In the PCTs, abnormal mitochondria and excessive numbers of lipid droplets were the principal findings with glomeruli showing thickened basement membranes. Swollen mitochondria and variable glycogen deposition were the chief features present in the livers. It is suggested that OA is more hepatotoxic in quail than in broilers, as well as being nephrotoxic.     

Fermentation of eastern gamagrass (Tripsacum dactyloides [L.] L.) by mixed cultures of ruminal microorganisms with or without supplemental corn

Five dual-flow fermentors (700 mL) were used to determine the effects of eastern gamagrass (Tripsacum dactyloides [L.] L.) diets on microbial metabolism by mixed rumen cultures. Fermentors were incubated with filtered ruminal contents and allowed to adapt for 4 d to diets followed by 3 d of sample collection. Five dietary treatments were tested: 1) gamagrass hay (GH) + no corn (GHNC), 2) gama grass silage (GS) + no corn (GSNC), 3) GS + low corn (GSLC), 4) GS + medium corn (GSMC); and 5) GS + high corn (GSHC). The experiment was conducted as a randomized complete block design with five treatments and three replications. Total VFA concentrations were not affected by diets. Corn addition linearly decreased (P < 0.001) molar proportion of acetate. In contrast, molar proportion of propionate was reduced in GSLC (cubic effect, P < 0.001) but remained similar across other diets. Corn supplementation linearly increased molar proportion of butyrate (P < 0.001). The acetate + butyrate-to-propionate ratio was highest in cultures offered GSLC (cubic effect, P < 0.001) but similar across other diets. Feeding GSNC resulted in a higher ruminal pH compared with GHNC (P < 0.03). Increasing the level of corn supplementation in GS linearly decreased culture pH (P < 0.001). All diets resulted in similar methane production, with the exception of GSMC, which lowered methane output (quadratic effect, P < 0.004). Total substrate fermented to VFA and gas tended to be greater with GHNC than with GSNC (P < 0.06) and linearly increased with the addition of corn (P < 0.004). Neutral detergent fiber digestibility was similar between GH and GS and was not affected by supplemental corn. Microbial N flow increased in cultures offered GSHC (quadratic effect, P < 0.02). Corn supplementation at the medium and high level linearly decreased C 18:0 (P < 0.02) and increased trans-C18:1 (P < 0.004). Including corn at the high level with GS did not have a detrimental effect on fermentation in dual-flow fermentors.     

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

Background

Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation.

Results

In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP).

Conclusion

We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1].

     

Removal of Potassium Alters b-Dimension of Muscovite

By treatment of muscovite with molten lithium nitrate at 300 degrees C we have been able to remove a large portion of the interlayer potassium and observe a decrease in the apparent b-axis length as a function of potassium content over the range of 8.8 to 0.7 percent potassium. The b-axis length of Silversheen mica (a 2M(1) muscovite) decreases from 9.024 to 8.988 A as the potassium content decreases from 8.79 to 3.31 percent. The contraction of the b-dimension results in an effective decrease in the size of the ditrigonal opening in the planar surfaces with a consequent increase in the d(001) upon re-saturation with potassium.     

Specific lipopolysaccharide found in cystic fibrosis airway Pseudomonas aeruginosa

Cystic fibrosis (CF) patients develop chronic airway infections with Pseudomonas aeruginosa (PA). Pseudomonas aeruginosa synthesized lipopolysaccharide (LPS) with a variety of penta- and hexa-acylated lipid A structures under different environmental conditions. CF patient PA synthesized LPS with specific lipid A structures indicating unique recognition of the CF airway environment. CF-specific lipid A forms containing palmitate and aminoarabinose were associated with resistance to cationic antimicrobial peptides and increased inflammatory responses, indicating that they are likely to be involved in airway disease.     

Ecological effects of a major oil spill on panamanian coastal marine communities

In 1986 more than 8 million liters of crude oil spilled into a complex region of mangroves, seagrasses, and coral reefs just east of the Caribbean entrance to the Panama Canal. This was the largest recorded spill into coastal habitats in the tropical Americas. Many population of plants and animals in both oiled and unoiled sites had been studied previously, thereby providing an unprecedented measure of ecological variation before the spill. Documenation of the spread of oil and its biological begun immediately. Intertidal mangroves, algae, and associated invertebrates were covered by oil and died soon after. More surprisingly, there was also extensive mortality of shallow subtidal reef corals and infauna of seagrass beds. After 1.5 years only some organisms in areas exposed to the open sea have recovered.