Robust, tunable biological oscillations from interlinked positive and negative feedback loops

A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant.     

Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes

The malaria parasite, Plasmodium falciparum, exploits multiple ligand-receptor interactions, called invasion pathways, to invade the host erythrocyte. Strains of P. falciparum vary in their dependency on sialated red cell receptors for invasion. We show that switching from sialic acid-dependent to -independent invasion is reversible and depends on parasite ligand use. Expression of P. falciparum reticulocyte-binding like homolog 4 (PfRh4) correlates with sialic acid-independent invasion, and PfRh4 is essential for switching invasion pathways. Differential activation of PfRh4 represents a previously unknown mechanism to switch invasion pathways and provides P. falciparum with exquisite adaptability in the face of erythrocyte receptor polymorphisms and host immune responses.     

Analysis of Piperaceae germplasm by HPLC and LCMS: a method for isolating and identifying unsaturated amides from Piper spp extracts

A method for extraction and high performance liquid chromatography-mass spectrometer (HPLC-MS) analysis of the medicinally important genus Piper (Piperaceae) was developed. This allows for a rapid and accurate measure of unsaturated amides, or piperamides, in black pepper, Piper nigrum L., and in wild species from Central America. Reflux extraction provided the highest recovery of piperine (>80%) from leaf and peppercorn material. HPLC analysis using a binary gradient of acetonitrile and water separated the major amide peaks between 5 and 12 min. Atmospheric pressure chemical ionization (APCI)-MS improved the detection limit to 0.2 ng, 10-fold below the 2 ng limit of the HPLC-diode array detector (DAD) based on linear standard curves between 0.1 and 250 microg/mL (R2 = 0.999). The HPLC-MS method identified pellitorine, piperylin, 4,5-dihydropiperlonguminine, piperlonguminine, 4,5-dihydropiperine, piperine, and pipercide. The biological activity of six Costa Rican Piper species assessed by mosquito larval bioassays correlated well with piperamide content.     

Effect of Geotrichum candidum protein substitution in pelleted fish feed on the growth of rainbow trout (Salmo gairdneri Rich.) and on utilization of the diet

Three experiments were conducted with rainbow trout to determine if Geotrichum candidum GC single cell protein could replace 100, 75 or 50% of fish meal in a pelleted diet. When the fish meal was completely replaced by GC the fish growth was retarded after 3 weeks of the experiment. With the larger fish (individual weight 47–54 g) in the short trial there were significant differences between fish fed the control diet (fish meal) and those fed the 75% substitution of GC diet. The most remarkable differences in fish growth appeared in a 42-day trial with small fish (5 g individual weight) when fish groups fed diets with 0.50 and 75% replacement gave significantly different results (P < 0.05), being 93,9, 46.6 and 34.2% gain, with feed coefficients of 1.49, 2.77 and 3.67, respectively. With large fish fed diets with 0,50 and 75% GC replacement, apparent digestibility of protein was 64.7, 68.2 and 37.5%, but fat digestibility was 79.5, 91.1 and 81.0%, respectively. No significant differences in amounts of free plasma amino acid (PAA) were found between rainbow trout fed diets with 0 or 50% substitution, but there was a marked decrease in PAA in the group fed the diet with 75% GC substitution. Analysis of chosen heavy metals was made on diets, fish and faeces, and Cu in particular was found not to be accumulated in the fish body.     

Estimating illegal and unreported catches from marine ecosystems: a basis for change

To evaluate the impacts of fishing on marine ecosystems, the total extraction of fish must be known. Putting a figure on total extraction entails the difficult task of estimating, in addition to reported landings, discards, illegal and unmandated catches. Unreported catches cast various types of shadow, which may be tracked and estimated quantitatively. Some shadows of unreported catches are reviewed, for example, an innovative, well‐funded NGO publicizes illegal catch in the Southern Ocean. For various reasons, official figures often have the implicit but unacceptable assumption that such categories are null. We present an estimation procedure based on adjustment factors taken from observer reports, correspondents and published information that track changes in a regulatory regime, and hence reflect incentives and disincentives to misreport. Monte Carlo simulations address uncertainty using multiple sources of information to provide upper and lower estimates. Once in place, this method provides preliminary estimates that may be refined without disruption. The method is demonstrated for fisheries in Iceland and Morocco. We use a ‘by‐species’ approach for Icelandic cod and haddock, while the Moroccan catch is divided into demersal and pelagic categories. Results suggest that Icelandic cod catches may have been underestimated by between 1 and 14% at different times, and haddock by between 1 and 28%. Underestimation of Moroccan catches appears to have been as much as by 50%. These case studies show that it is possible to obtain estimates of misreporting, even when direct data are lacking. Our method encourages transparency because sources of information are presented so that uncertain values are easily identified, offering a basis for comment, collaboration and refinement in estimating illegal and unreported fishing.     

Soil carbon dioxide and methane fluxes from long-term tillage systems in continuous corn and corn–soybean rotations

Although the Midwestern United States is one of the world's major agricultural production areas, few studies have assessed the effects of the region's predominant tillage and rotation practices on greenhouse gas emissions from the soil surface. Our objectives were to (a) assess short-term chisel (CP) and moldboard plow (MP) effects on soil CO₂ and CH₄ fluxes relative to no-till (NT) and, (b) determine how tillage and rotation interactions affect seasonal gas emissions in continuous corn and corn–soybean rotations on a poorly drained Chalmers silty clay loam (Typic Endoaquoll) in Indiana. The field experiment itself began in 1975. Short-term gas emissions were measured immediately before, and at increasing hourly intervals following primary tillage in the fall of 2004, and after secondary tillage in the spring of 2005, for up to 168 h. To quantify treatment effects on seasonal emissions, gas fluxes were measured at weekly or biweekly intervals for up to 14 sampling dates in the growing season for corn. Both CO₂ and CH₄ emissions were significantly affected by tillage but not by rotation in the short-term following tillage, and by rotation during the growing season. Soil temperature and moisture conditions in the surface 10 cm were significantly related to CO₂ emissions, although the proportion of variation explained by temperature and moisture was generally very low (never exceeded 27%) and varied with the tillage system being measured. In the short-term, CO₂ emissions were significantly higher for CP than MP and NT. Similarly, mean seasonal CO₂ emissions during the 2-year period were higher for CP (6.2 Mg CO₂-C ha⁻¹ year⁻¹) than for MP (5.9 Mg CO₂-C ha⁻¹ year⁻¹) and NT (5.7 Mg CO₂-C ha⁻¹ year⁻¹). Both CP and MP resulted in low net CH₄ uptake (7.6 and 2.4 kg CH₄-C ha⁻¹ year⁻¹, respectively) while NT resulted in net emissions of 7.7 kg CH₄-C ha⁻¹ year⁻¹. Mean emissions of CO₂ were 16% higher from continuous corn than from rotation corn during the two growing seasons. After 3 decades of consistent tillage and crop rotation management for corn and soybean producing grain yields well above average in the Midwest, continuous NT production in the corn–soybean rotation was identified as the system with the least soil-derived C emissions to the atmosphere from among those evaluated prior to and during corn production.