What is a desirable statistical energy functions for proteins and how can it be obtained?

Can one obtain a physical energy function for proteins from statistical analysis of protein structures? A direct answer to this question is likely “no”. A less demanding question is whether one can produce a statistical energy function that has the desirable features of a physical-based energy function. Such a desirable energy function would be founded on a physical basis with few or no adjustable parameters, reproduce the known physical characters of amino acid residues, be mostly database independent and transferable, and, more importantly, reasonably accurate in various applications. In this review, we show how such a desirable energy function can be obtained via introducing a simple physical-based reference state called DRIRE (Distance-scaled, Finite, Ideal-gas Reference state).     

The case for increasing the statistical power of eddy covariance ecosystem studies: why,where and how?

Eddy covariance (EC) continues to provide invaluable insights into the dynamics of Earth's surface processes. However, despite its many strengths, spatial replication of EC at the ecosystem scale is rare. High equipment costs are likely to be partially responsible. This contributes to the low sampling, and even lower replication, of ecoregions in Africa, Oceania (excluding Australia) and South America. The level of replication matters as it directly affects statistical power. While the ergodicity of turbulence and temporal replication allow an EC tower to provide statistically robust flux estimates for its footprint, these principles do not extend to larger ecosystem scales. Despite the challenge of spatially replicating EC, it is clearly of interest to be able to use EC to provide statistically robust flux estimates for larger areas. We ask: How much spatial replication of EC is required for statistical confidence in our flux estimates of an ecosystem? We provide the reader with tools to estimate the number of EC towers needed to achieve a given statistical power. We show that for a typical ecosystem, around four EC towers are needed to have 95% statistical confidence that the annual flux of an ecosystem is nonzero. Furthermore, if the true flux is small relative to instrument noise and spatial variability, the number of towers needed can rise dramatically. We discuss approaches for improving statistical power and describe one solution: an inexpensive EC system that could help by making spatial replication more affordable. However, we note that diverting limited resources from other key measurements in order to allow spatial replication may not be optimal, and a balance needs to be struck. While individual EC towers are well suited to providing fluxes from the flux footprint, we emphasize that spatial replication is essential for statistically robust fluxes if a wider ecosystem is being studied.     

How costly is the honest signaling of need?

ESS models of biological signaling have shown that costly signals can provide honest information. In the context of parent-offspring conflict over the allocation of resources by parents to their young, the theory explains costly offspring solicitation behavior as an accurate signal of offspring need to parents who cannot assess offspring condition directly. In this paper, we provide a simple but general characterization of the honest signaling of need in models of parent-offspring conflict: the offspring's signaling cost is proportional to the parent's fitness loss from satisfying the offspring's resource requirement. The factor of proportionality is given by a measure of the extent of parent-offspring conflict that depends only on coefficients of relatedness. These results hold for interbrood conflict with uniparental investment even if the relationship between offspring condition and resource requirement is not monotonic, and extend to cases of biparental care, uncertainty concerning the parent's condition, and intra-brood conflict. Copyright 1999 Academic Press.     

Maturational profiles and migration in the female adolescent population of Madrid: is there a need for a new perspective?

The aim of this study is to assess anthropometric changes and menstrual cycle characteristics during the maturation process of an adolescent female sample in Madrid, Spain. The new demographic context of Madrid, with a 33.9% of girls coming from Central and South America, makes this study relevant in terms of new epidemiological situations that could possible develop. The sample consists of 284 girls, ages 9 to 16 years, measured and interviewed in four school centres of Madrid. Results show that menarche is slightly earlier in the Spanish girls, but there are no other important differences regarding the characteristics of their menses. However, the Spanish girls have a significantly higher intake of menarcheal pain related drugs. The anthropometric changes accompanying menarche are greater in the immigrants, especially in terms of trunk fatness, leading to an "overweight" characterisation of this sub-sample. These maturational profiles show the need for educational programs, especially focussed on the foreign adolescent population, to cope with health risks related to overweight.     

The need for co-product allocation in the life cycle assessment of agricultural systems—is “biophysical” allocation progress?

Purpose

Several new “biophysical” co-product allocation methodologies have been developed for LCA studies of agricultural systems based on proposed physical or causal relationships between inputs and outputs (i.e. co-products). These methodologies are thus meant to be preferable to established allocation methodologies such as economic allocation under the ISO 14044 standard. The aim here was to examine whether these methodologies really represent underlying physical relationships between the material and energy flows and the co-products in such systems, and hence are of value.

Methods

Two key components of agricultural LCAs which involve co-product allocation were used to provide examples of the methodological challenges which arise from adopting biophysical allocation in agricultural LCA: (1) the crop production chain and (2) the multiple co-products produced by animals. The actual “causal” relationships in these two systems were illustrated, the energy flows within them detailed, and the existing biophysical allocation methods, as found in literature, were critically evaluated in the context of such relationships.

Results and discussion

The premise of many biophysical allocation methodologies has been to define relationships which describe how the energy input to agricultural systems is partitioned between co-products. However, we described why none of the functional outputs from animal or crop production can be considered independently from the rest on the basis of the inputs to the system. Using the example of manure in livestock systems, we also showed why biophysical allocation methodologies are still sensitive to whether a system output has economic value or not. This sensitivity is a longstanding criticism of economic allocation which is not resolved by adopting a biophysical approach.

Conclusions

The biophysical allocation methodologies for various aspects of agricultural systems proposed to date have not adequately explained how the physical parameters chosen in each case represent causal physical mechanisms in these systems. Allocation methodologies which are based on shared (but not causal) physical properties between co-products are not preferable to allocation based on non-physical properties within the ISO hierarchy on allocation methodologies and should not be presented as such.

     

How important is the statistical approach for analyzing categorical data? A critique using artificial nests

Ecologists rely heavily upon statistics to make inferences concerning ecological phenomena and to make management recommendations. It is therefore important to use statistical tests that are most appropriate for a given data-set. However, inappropriate statistical tests are often used in the analysis of studies with categorical data (i.e. count data or binary data). Since many types of statistical tests have been used in artificial nests studies, a review and comparison of these tests provides an opportunity to demonstrate the importance of choosing the most appropriate statistical approach for conceptual reasons as well as type I and type II errors.
Artificial nests have routinely been used to study the influences of habitat fragmentation, and habitat edges on nest predation. I review the variety of statistical tests used to analyze artificial nest data within the framework of the generalized linear model and argue that logistic regression is the most appropriate and flexible statistical test for analyzing binary data-sets. Using artificial nest data from my own studies and an independent data set from the medical literature as examples, I tested equivalent data using a variety of statistical methods. I then compared the p-values and the statistical power of these tests. Results vary greatly among statistical methods. Methods inappropriate for analyzing binary data often fail to yield significant results even when differences between study groups appear large, while logistic regression finds these differences statistically significant. Statistical power is is 2–3 times higher for logistic regression than for other tests. I recommend that logistic regression be used to analyze artificial nest data and other data-sets with binary data.     

What is the best reference state for designing statistical atomic potentials in protein structure prediction?

Many statistical potentials were developed in last two decades for protein folding and protein structure recognition. The major difference of these potentials is on the selection of reference states to offset sampling bias. However, since these potentials used different databases and parameter cutoffs, it is difficult to judge what the best reference states are by examining the original programs. In this study, we aim to address this issue and evaluate the reference states by a unified database and programming environment. We constructed distance-specific atomic potentials using six widely-used reference states based on 1022 high-resolution protein structures, which are applied to rank modeling in six sets of structure decoys. The reference state on random-walk chain outperforms others in three decoy sets while those using ideal-gas, quasi-chemical approximation and averaging sample stand out in one set separately. Nevertheless, the performance of the potentials relies on the origin of decoy generations and no reference state can clearly outperform others in all decoy sets. Further analysis reveals that the statistical potentials have a contradiction between the universality and pertinence, and optimal reference states should be extracted based on specific application environments and decoy spaces.     

Neuropeptide signaling near and far: how localized and timed is the action of neuropeptides in brain circuits?

Neuropeptide signaling is functionally very diverse and one and the same neuropeptide may act as a circulating neurohormone, as a locally released neuromodulator or even as a cotransmitter of classical fast-acting neurotransmitters. Thus, neuropeptides are produced by a huge variety of neuron types in different parts of the nervous system. Within the central nervous system (CNS) there are numerous types of peptidergic interneurons, some with strictly localized and patterned branching morphologies, others with widespread and diffuse arborizations. From morphology alone it is often difficult to predict the sphere of influence of a peptidergic interneuron, especially since it has been shown that neuropeptides can diffuse over tens of micrometers within neuropils, and that peptides probably are released exclusively in perisynaptic (or non-synaptic) regions. This review addresses some questions related to peptidergic signaling in the insect CNS. How diverse are the spatial relations between peptidergic neurons and their target neurons and what determines the sphere of functional influence? At one extreme there is volume transmission and at the other targeted cotransmission at synapses. Also temporal aspects of peptidergic signaling are of interest: how transient are peptidergic messages? Factors important for these spatial and temporal aspects of peptidergic signaling are proximity between release sites and cognate receptors, distribution of peptidase activity that can terminate peptide action and colocalization of other neuroactive compounds in the presynaptic peptidergic neuron (and corresponding receptors in target neurons). Other factors such as expression of different channel types, receptor inactivation mechanisms and second messenger systems probably also contribute to the diversity in temporal properties of peptide signaling.     

Elevated glucose levels in the elderly: is there a need for intensive treatment?

Diabetes mellitus is a frequently occurring disease which is often found in combination with other diseases in older people. An interval of more than ten years is often seen between the first signs of diabetes and the diagnosis. The causes and consequences of insufficient production of insulin and the available diagnostic and therapeutic possibilities, with attention for hypoglycemia in older people, are discussed. In the early phase of diabetes glucose levels are only incidentally elevated and patients have no complaints. Elevated blood glucose values aggravate other diseases and decrease the effectivity of treatment for these diseases. Treatment can prevent or postpone secondary complications leading to improved quality of life. A plea is made for (regular) testing of blood glucose and adequate action when elevated values are found in older people.     

Crystal structure of the disulfide bond-deficient azurin mutant C3A/C26A: how important is the S-S bond for folding and stability?

Azurin has a beta-barrel fold comprising eight beta-strands and one alpha helix. A disulfide bond between residues 3 and 26 connects the N-termini of beta strands beta1 and beta3. Three mutant proteins lacking the disulfide bond were constructed, C3A/C26A, C3A/C26I and a putative salt bridge (SB) in the C3A/S25R/C26A/K27R mutant. All three mutants exhibit spectroscopic properties similar to the wild-type protein. Furthermore, the crystal structure of the C3A/C26A mutant was determined at 2.0 A resolution and, in comparison to the wild-type protein, the only differences are found in the immediate proximity of the mutation. The mutants lose the 628 nm charge-transfer band at a temperature 10-22 degrees C lower than the wild-type protein. The folding of the zinc loaded C3A/C26A mutant was studied by guanidine hydrochloride (GdnHCl) induced denaturation monitored both by fluorescence and CD spectroscopy. The midpoint in the folding equilibrium, at 1.3 M GdnHCl, was observed using both CD and fluorescence spectroscopy. The free energy of folding determined from CD is -24.9 kJ.mol-1, a destabilization of approximately 20 kJ.mol-1 compared to the wild-type Zn2+-protein carrying an intact disulfide bond, indicating that the disulfide bond is important for giving azurin its stable structure. The C3A/C26I mutant is more stable and the SB mutant is less stable than C3A/C26A, both in terms of folding energy and thermal denaturation. The folding intermediate of the wild-type Zn2+-azurin is not observed for the disulfide-deficient C3A/C26A mutant. The rate of unfolding for the C3A/C26A mutant is similar to that of the wild-type protein, suggesting that the site of the mutation is not involved in an early unfolding reaction.     

Hunting Bambi—evaluating the basis for selective harvesting of juveniles

Human harvesting is often a major mortality factor and, hence, an important proximate factor driving the population dynamics of large mammals. Several selective harvesting regimes focus on removing animals with low reproductive value, such as “antlered” harvests in North America and juvenile harvesting in many European countries. Despite its widespread use and assumed impact, the scientific basis of juvenile harvesting is scattered in the literature and not empirically well-documented. We give the first overview of demographic, evolutionary and practical management arguments for selective harvesting of juveniles. Furthermore, we empirically test two demographic arguments based on harvest statistics of Red Deer (Cervus elaphus) in seven European countries. P₁: Harvesting juveniles has little influence on harvest growth compared with harvesting adult females due to the lower reproductive value of juveniles than adult females; P₂: Harvesting of juveniles dampens variance in harvest due to lower and more variable natural survival rates of juveniles compared with adults. We found that harvesting juveniles has little effect on harvest growth rate, while harvesting adult females has a significant negative effect (consistent with P₁), but that increasing the proportion of juveniles in the harvest did not decrease the variability in harvest between years (P₂ not supported). Based on our empirical findings and overview of arguments, we discuss how the merits of juvenile harvesting may vary over time as populations move from a low density to a very high density state.     

Is the Mbita trap a reliable tool for evaluating the density of anopheline vectors in the highlands of Madagascar?

BACKGROUND: One method of collecting mosquitoes is to use human beings as bait. This is called human landing collection and is a reference method for evaluating mosquito density per person. The Mbita trap, described by Mathenge et al in the literature, consists of an entry-no return device whereby humans are used as bait but cannot be bitten. We compared the Mbita trap and human landing collection in field conditions to estimate mosquito density and malaria transmission. METHODS: Our study was carried out in the highlands of Madagascar in three traditional villages, for 28 nights distributed over six months, with a final comparison between 448 men-nights for human landing and 84 men-nights for Mbita trap, resulting in 6,881 and 85 collected mosquitoes, respectively. RESULTS: The number of mosquitoes collected was 15.4 per human-night and 1.0 per trap-night, i.e. an efficiency of 0.066 for Mbita trap vs. human landing. The number of anophelines was 10.30 per human-night and 0.55 per trap-night, i.e. an efficiency of 0.053. This efficiency was 0.10 for indoor Anopheles funestus, 0.24 for outdoor An. funestus, and 0.03 for Anopheles arabiensis. Large and unexplained variations in efficiency were observed between villages and months. CONCLUSION: In the highlands of Madagascar with its unique, highly zoophilic malaria vectors, Mbita trap collection was poor and unreliable compared to human landing collections, which remains the reference method for evaluating mosquito density and malaria transmission. This conclusion, however, should not be extrapolated directly to other areas such as tropical Africa, where malaria vectors are consistently endophilic.