Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.     

Active selection for large guppies, Poecilia reticulata, by the pike cichlid, Crenicichla saxatilis

Size-selective predation has been proposed to be one important evolutionary force shaping life-history traits in guppies ( Poecilia reticulata ). Populations living in the presence of the ring-tailed pike cichlid ( Crenicichla saxatilis ) are smaller, mature earlier, allocate more energy to offspring and get more and smaller young than guppies in localities without Crenicichla . We investigated if Crenicichla saxatilis is a size-selective predator, if the selectivity is a result of active choice and if the optimal prey size can be explained according to an optimal foraging model. In single-prey experiments we quantified the predators' pre-capture costs (time), capture success, and post-capture costs (time) for four different prey sizes spanning from 10 to 40 mm total length. To see which of the components of the prey cycle the predator takes into account for its choice, we then predicted prey values and optimal prey size with 6 different models that included one or more of the prey cycle components.
In two multiple prey experiments, the cichlids were given the choice of the two and four different prey sizes simultaneously. Crenicichla saxatilis actively selected the largest guppies in both cases. The three prey-value functions that included handling time (post-capture cost) did not accurately predict the prey choice. Instead the prey-value functions that took into account pre-capture cost (approach and attack time) were able to correctly predict the choice of the largest guppy size, suggesting that pre-capture costs may be more important than post-capture costs for prey choice in Crenicichla saxatilis . The study confirms that Crenicichla saxatilis is a size-selective predator selecting large guppies, while earlier evidence for selectivity for large prey in Crenicichla cichlids has been weak and equivocal. Our result strengthen the possibility that size-selective predation is a mechanism in life-history evolution in guppies.     

Membrane destabilizing properties of cell-penetrating peptides

Although cell-penetrating peptides (CPPs), also denoted protein transduction domains (PTDs), have been widely used for intracellular delivery of large and hydrophilic molecules, the mechanism of uptake is still poorly understood. In a recent live cell study of the uptake of penetratin and tryptophan-containing analogues of Tat(48-60) and oligoarginine, denoted TatP59W, TatLysP59W and R(7)W, respectively, it was found that both endocytotic and non-endocytotic uptake pathways are involved [Thoren et al., Biochem. Biophys. Res. Commun. 307 (2003) 100-107]. Non-endocytotic uptake was only observed for the arginine-rich peptides TatP59W and R(7)W. In this paper, the interactions of penetratin, R(7)W, TatP59W and TatLysP59W with phospholipid vesicles are compared in the search for an understanding of the mechanisms for cellular uptake. While R(7)W, TatP59W and TatLysP59W are found to promote vesicle fusion, indicated by mixing of membrane components, penetratin merely induces vesicle aggregation. Studies of the leakage from dye-loaded vesicles indicate that none of the peptides forms membrane pores and that vesicle fusion is not accompanied by leakage of the aqueous contents of the vesicles. These observations are important for a proper interpretation of future experiments on the interactions of these peptides with model membranes. We suggest that the discovered variations in propensity to destabilize phospholipid bilayers between the peptides investigated, in some cases sufficient to induce fusion, may be related to their different cellular uptake properties.     

Inhibition of shivering in hypothermic seals during diving

The mammalian response to hypothermia is increased metabolic heat production, usually by way of muscular activity, such as shivering. Seals, however, have been reported to respond to diving with hypothermia, which in other mammals under other circumstances would have elicited vigorous shivering. In the diving situation, shivering could be counterproductive, because it obviously would increase oxygen consumption and therefore reduce diving capacity. We have measured the electromyographic (EMG) activity of three different muscles and the rectal and brain temperature of hooded seals (Cystophora cristata) while they were exposed to low ambient temperatures in a climatic chamber and while they performed a series of experimental dives in cold water. In air, the seals had a normal mammalian shivering response to cold. Muscles were recruited in a sequential manner until body temperature stopped dropping. Shivering was initiated when rectal temperature fell below 35.3 +/- 0.6 degrees C (n = 6). In the hypothermic diving seal, however, the EMG activity in all of the muscles that had been shivering vigorously before submergence was much reduced, or stopped altogether, whereas it increased again upon emergence but was again reduced if diving was repeated. We conclude that shivering is inhibited during diving to allow a decrease in body temperature whereby oxygen consumption is decreased and diving capacity is extended.     

Chlorosome Proteins Studied by MALDI-TOF-MS: Topology of CsmA in Chlorobium tepidum

Chlorosomes, the light-harvesting apparatus of green bacteria, are a unique antenna system, in which pigments are organized in aggregates rather than associated with proteins. Isolated chlorosomes from the green sulphur bacterium Chlorobium tepidum contain 10 surface-exposed proteins. Treatment of chlorosomes from Chlorobium tepidum with protease caused changes in the spectral properties of bacteriochlorophyll c and digestion of chlorosome proteins. Using SDS-PAGE analysis, immunoblotting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) we have investigated the topology of the 59-residue CsmA protein. Our results show that at the N-terminus, the only amino acid available for protease degradation is the methionine. At the C-terminus, amino acids can be removed by protease treatment to produce a residual protein containing at least the sequence between residues 2 and 38. These results indicate that the N-terminal portion of the CsmA protein, which is predicted to be mainly hydrophobic, is buried in the chlorosome envelope.     

Synthesis of alkyne derivatives of a novel triazolopyrazine as A(2A) adenosine receptor antagonists

A novel [1,2,4]triazolo[1,5-a]pyrazine core was synthesized and coupled with terminal acetylenes. The structure-activity relationship of the alkynes from this novel template was studied for their in vitro and in vivo adenosine A(2A) receptor antagonism. Selected compounds from this series were shown to have potent in vitro and in vivo activities against adenosine A(2A) receptor. Compound 12, in particular, was found to be orally active at 3mg/kg in both a mouse catalepsy model and a 6-hydroxydopamine-lesioned rat model.     

Design of improved membrane protein production experiments: quantitation of the host response

Eukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial-and-error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high-performance bioreactors under tightly-defined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly-controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels of FPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology.     

On the effect of misclassification on bias of perfectly measured covariates in regression

This note clarifies under what conditions a naive analysis using a misclassified predictor will induce bias for the regression coefficients of other perfectly measured predictors in the model. An apparent discrepancy between some previous results and a result for measurement error of a continuous variable in linear regression is resolved. We show that similar to the linear setting, misclassification (even when not related to the other predictors) induces bias in the coefficients of the perfectly measured predictors, unless the misclassified variable and the perfectly measured predictors are independent. Conditional and asymptotic biases are discussed in the case of linear regression, and explored numerically for an example relating birth weight to the weight and smoking status of the mother.