Morphometric analysis of the distributing vessels of the kidney

Branching angles and branch diameters of the distributing vessels in the renal networks of rats were measured and the results are compared with data reported previously from the coronary network of the same species. Comparison is also made with what is known to be optimum on theoretical grounds to determine to what extent the branching characteristics of the renal network are governed by considerations of optimality, and to what extent they are affected by other considerations, relating particularly to the role that the network plays in the blood processing function of the kidney.     

Mass and date at departure affect the survival of Ancient Murrelet Synthliboramphus antiquus chicks after leaving the colony

I compared the timing of colony departure and body mass of 53 Ancient Murrelet Synthliboramphus antiquus chicks that were retrapped as adults in Haida Gwaii, British Columbia, with those of 3992 chicks not retrapped. If the probability of recapture is a measure of survival, survival was related to both mass and date. Chicks that left the colony at 26 g or less had a lower chance of survival than heavier chicks, and those that left after the median date of departure survived better in some years than those that left earlier. The effect of date was not related to a seasonal change in departure mass because chick mass declined with departure date. I suggest that, because of heavy adult mortality during breeding, the timing of breeding in the Ancient Murrelet is based on a compromise between the optimum dates for chick and adult survival. This is in contrast to evidence from other, nonprecocial, seabirds.     

Modeling the large-scale geometry of human coronary arteries

Two principles suffice to model the large-scale geometry of normal human coronary arterial networks. The first principle states that artery diameters are set to minimize the power required to distribute blood through the network. The second principle states that arterial tree geometries are set to globally minimize the lumen volume. Given only the coordinates of an arterial tree's source and "leaves", the model predicts the nature of the network connecting the source to the leaves. Measurements were made of the actual geometries of arterial trees from postmortem healthy human coronary arteriograms. The tree geometries predicted by the model look qualitatively similar to the actual tree geometries and have volumes that are within a few percent of those of the actual tree geometries. Human coronary arteries are therefore within a few percent of perfect global volume optimality. A possible mechanism for this near-perfect global volume optimality is suggested. Also, the model performs best under the assumption that the flow is not entirely steady and laminar.     

Departures from the physical optimality in the bronchial tree of rats (Rattus norvegicus)

We studied the departure from the physical optimality of the bronchial tree of rats using both i) the minimum volume and power and ii) the minimum surface and drag criteria, considering the bronchial junction as the unit study based on Zamir's model for vascular trees. Our results show deviations of the junctions of the bronchial tree from the expected optimums in the proximal airway that can be explained by both, the turbulent or transitional flow regime, and the airway's necessity to distribute its terminal branches in the alveolar surface filling the thoracic volume. The departures of the observed values at the optimum for the minimum volume and power were significantly different than the obtained departure values for the minimum surface and drag criteria. The departure from the optimum was directly related to the diameter of the smallest branch. The slopes of the regressions for the two criteria were different. The regression lines intercept at a bronchial diameter d2 = 0.129 mm. This result agreed with the idea that the tube diameter is limited at small values by the increasing flow resistance with decreasing tube diameter while at large values is limited by the increasing tube volume and dead space with increasing tube diameter.     

Construction and Analyses of Human Large-Scale Tissue Specific Networks

Construction and analyses of tissue specific networks is crucial to unveil the function and organizational structure of biological systems. As a direct method to detect protein dynamics, human proteome-wide expression data provide an valuable resource to investigate the tissue specificity of proteins and interactions. By integrating protein expression data with large-scale interaction network, we constructed 30 tissue/cell specific networks in human and analyzed their properties and functions. Rather than the tissue specificity of proteins, we mainly focused on the tissue specificity of interactions to distill tissue specific networks. Through comparing our tissue specific networks with those inferred from gene expression data, we found our networks have larger scales and higher reliability. Furthermore, we investigated the similar extent of multiple tissue specific networks, which proved that tissues with similar functions tend to contain more common interactions. Finally, we found that the tissue specific networks differed from the static network in multiple topological properties. The proteins in tissue specific networks are interacting looser and the hubs play more important roles than those in the static network.     

Exact tests of Hardy-Weinberg equilibrium and homogeneity of disequilibrium across strata

Detecting departures from Hardy-Weinberg equilibrium (HWE) of marker-genotype frequencies is a crucial first step in almost all human genetic analyses. When a sample is stratified by multiple ethnic groups, it is important to allow the marker-allele frequencies to differ over the strata. In this situation, it is common to test for HWE by using an exact test within each stratum and then using the minimum P value as a global test. This approach does not account for multiple testing, and, because it does not combine information over strata, it does not have optimal power. Several approximate methods to combine information over strata have been proposed, but most of them sum over strata a measure of departure from HWE; if the departures are in different directions, then summing can diminish the overall evidence of departure from HWE. An exact stratified test is more appealing because it uses the probability of genotype configurations across the strata as evidence for global departures from HWE. We developed an exact stratified test for HWE for diallelic markers, such as single-nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy-Weinberg disequilibrium. By applying our methods to data from Perlegen and HapMap--a combined total of more than five million SNP genotypes, with three to four strata and strata sizes ranging from 23 to 60 subjects--we illustrate that the exact stratified test provides more-robust and more-powerful results than those obtained by either the minimum of exact test P values over strata or approximate stratified tests that sum measures of departure from HWE. Hence, our new methods should be useful for samples composed of multiple ethnic groups.     

Climb and flight speeds of shorebirds embarking on an intercontinental flight; do they achieve the predicted optimal behaviour?

Most Arctic-breeding waders wintering in West Africa cover the first 4000 km of their northward journey in spring by a single flight to western Europe. We examined the extent to which waders economize their flight behaviour during departure by comparing climb rates and forward flight speeds with predictions based on flight mechanic theory and the relevant morphological measurements made of birds collected on the site. With an optical range finder, we followed 98 wader flocks on their departure from Banc d'Arguin in Mauritania. We also measured wind speed and direction at different altitudes by tracking helium-filled balloons and thus were able to deduce airspeeds from groundspeeds of the departing flocks. Of the nine species examined, six showed the predicted negative relationship between climb rate and airspeed, although only one was statistically significant. By normalizing the data, we found a statistically significant negative correlation across all species. Although 17% of the observed climb rates were greater than the predicted theoretical maximum, the average observed climb rate was lower than the predicted optimum and the average observed airspeed was higher. The absolute deviations of climb rates from theory may have been because of the existence of pockets of rising and sinking air at the boundary of desert and ocean. That the absolute deviations in average climb rate and airspeed followed the predicted negative relationship is in accordance with the current theory of flight mechanics.     

Neurotensin stimulates histamine release from the isolated, spontaneously beating heart of rats

Neurotensin (NT) evoked a transient, dose-dependent histamine release (ED50 170 ng ml-1) from the rat perfused heart. Histamine release by NT occurred within seconds and lasted less than 2 min. The histamine releasing effect of NT was followed by a dose-dependent increase of the perfusion pressure and a slight tachycardia. The histamine releasing effect of NT was completely abolished in hearts derived from rats pretreated for 3 days with high doses of compound 48/80. The coronary vasoconstrictor effect of NT was increased in hearts derived from compound 48/80-pretreated rats. The mast cell inhibitor cromoglycate markedly inhibited NT-induced histamine release without affecting the coronary vasoconstrictor effect of NT. The histamine releasing effect of NT was inhibited, while its coronary vasoconstrictor effect was markedly potentiated, in hearts derived from rats pretreated with the antiallergic and antiinflammatory steroid dexamethasone. The increase of perfusion pressure evoked by NT was not modified by antihistamine drugs. Infusions of exogenous histamine (10(-6)-10(-5) g ml-1) caused a dose-dependent coronary vasodilation in the rat perfused heart. The results suggest that NT stimulates histamine release from cardiac mast cells. These results together with those obtained in previous studies suggest that mast cell mediators (particularly histamine and serotonin) are unlikely to be responsible for the coronary vasoconstrictor effect of NT in the rat perfused heart.     

Particle Transport through Hydrogels Is Charge Asymmetric

Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks.     

Climatic influences on the mortality of sheep during long-distance sea transport

Research on the causes of sheep death in sea voyages from Australia to the Middle East is limited, in particular little is known about the influence of climatic factors. Mortality data from 417 shipments of sheep exported over an 11-year period (November 2004 to June 2015) were modelled retrospectively to determine associated climatic factors. The statistical analysis were performed for both the full data set with 417 voyages based on actual and estimated departure and arrival dates and a restricted data set with 71 voyages based on actual dates. The results of the full data set demonstrated a seasonal mortality pattern, with more deaths occurring on sea voyages leaving Australia in the southern hemisphere winter or spring than those departing in Australian summer or autumn. Heat stress and inadequate fat mobilisation for energy supply when sheep are inappetant on shipments may explain this seasonality. Based on these two models, the voyage and weather factors associated with sheep mortalities included departure year, autumn departure in the southern hemisphere, voyage duration, single or multiple loading port(s), weekly mean dry bulb temperature and wind speed at departure ports, and humidity at destination ports. Significant correlations were observed between weather variables at the departure ports in the Australian winter and a high sheep mortality rate during voyages. This, together with the anticipated increased heat stress risk as a result of climate change, suggests that there could be review of the trade from Australia in the southern hemisphere winter. The influence of weather at the departure ports should be considered in sheep mortality prediction models, especially Australia’s heat stress risk assessment model.     

Enhancing the Functional Content of Eukaryotic Protein Interaction Networks

Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, these networks face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we apply a robust measure of local network structure called common neighborhood similarity (CNS) to address these challenges. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of human and fly protein interactions, and a set of over GO terms for both, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the measure and other continuous CNS measures perform well this task, especially for large networks. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures to prune out noisy edges and enhance functional coherence in the transformed networks.     

Uncovering network systems within protein structures

Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding.     

Plasminogen-activator of the arterial wall in occluded arteries

The plasminogen activator in 117 specimen of 20 coronary and 29 pulmonary arteries occluded completely by thrombi or emboli within the adventitia and intima was studied using TODD's histochemical method. 39 cadavers were used, 1--18 hours post mortem from subjects aged from 45 to 88 years. In occluded arteries both coronary and pulmonary the plasminogen activator activity was decreased in comparison with normal and atherosclerotic patients. In coronary and pulmonary arterial thrombi a low grade focal activity of plasminogen activator was detected. It is assumed that the decrease of plasminogen activator in the occluded human arterial wall is due to the impaired oxygen supply of the vessel wall and to the consumption of the plasminogen activator for thrombus lysis. These mechanisms are likely to influence the plasminogen activator for a certain and prolonged time, since there were no changes of fibrinolysis within the vessel wall of arteria carotis in rats where an acute thrombosis was elicited by means of an electric current.     

Brief communication: DNA from early Holocene American dog

We present the oldest genetically identified dog in the Americas, directly dated to 9,260 ± 170 Cal. B.P. The DNA was extracted from an occipital condyle imbedded in a human paleofecal sample from Hinds Cave in southwest Texas. A 368 base pair fragment of the mitochondrial genome control region was sequenced. These data were analyzed with comparable data, which included other ancient dogs and extant dogs, wolves and coyotes from around the world. Compiled with published data, our results characterize ancient American dogs within clades rooted by Eurasian wolves. In the Americas, these data provide no evidence of local interbreeding with wolves. This is a departure from the genetic pattern in other areas of the world where interbreeding with local wolf populations is apparent. Our discovery of domestic dog bone in a human paleofecal sample provides the earliest direct evidence for human consumption of dogs in the New World. These data support the hypothesis that dogs were a food source for early Paleoamericans.     

Unequal allelic frequencies at the self‐incompatibility locus within local populations of Prunus avium L.: an effect of population structure?

In this paper, we investigated the genetic structure and distribution of allelic frequencies at the gametophytic self-incompatibility locus in three populations of Prunus avium L. In line with theoretical predictions under balancing selection, genetic structure at the self-incompatibility locus was almost three times lower than at seven unlinked microsatellites. Furthermore, we found that S-allele frequencies in wild cherry populations departed significantly from the expected isoplethic distribution towards which balancing selection is expected to drive allelic frequencies (i.e. identical frequency equal to the inverse of the number of alleles in the population). To assess whether this departure could be caused either by drift alone or by population structure, we used numerical simulations to compare our observations with allelic frequency distributions expected : (1) within a single deme from a subdivided population with various levels of differentiation; and (2) within a finite panmictic population with identical allelic diversity. We also investigated the effects of sample size and degree of population structure on tests of departure from isoplethic equilibrium. Overall, our results showed that the observed allele frequency distributions were consistent with a model of subdivided population with demes linked by moderate migration rate.     

Characterising neurological time series data using biologically motivated networks of coupled discrete maps

Artificial biochemical networks (ABNs) are a class of computational dynamical system whose architectures are motivated by the organisation of genetic and metabolic networks in biological cells. Using evolutionary algorithms to search for networks with diagnostic potential, we demonstrate how ABNs can be used to carry out classification when stimulated with time series data collected from human subjects with and without Parkinson's disease. Artificial metabolic networks, composed of coupled discrete maps, offer the best recognition of Parkinsonian behaviour, achieving accuracies in the region of 90%. This is comparable to the diagnostic accuracies found in clinical diagnosis, and is significantly higher than those found in primary and non-expert secondary care. We also illustrate how an evolved classifier is able to recognise diverse features of Parkinsonian behaviour and, using perturbation analysis, show that the evolved classifiers have interesting computational behaviours.     

Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks

Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting signals within the data, including those caused by long-branch attraction. We illustrate this approach using a set of taxa from three unambiguously monophyletic families within the Pelecaniformes: the darters, the cormorants and shags, and the gannets and boobies. These three families are universally acknowledged as forming a monophyletic group, but the relationship between the families remains contentious. Using sequence data from three mitochondrial genes (12S, ATPase 6, and ATPase 8) we demonstrate that the relationship between these three families is difficult to resolve because they are separated by a short internal branch and there are conflicting signals due to long-branch attraction, which are confounded with nonhomogeneous sequence evolution across the different genes. Spectral analysis, Neighbor-Net, and consensus networks reveal conflicting signals regarding the placement of one of the darters, with support found for darter monophyly, but also support for a conflicting grouping with the outgroup, pelicans. Furthermore, parsimony and maximum-likelihood analyses produced different trees, with one of the two most parsimonious trees not supporting the monophyly of the darters. Monte Carlo simulations, however, were not sensitive enough to reveal long-branch attraction unless the branches are longer than those actually observed. These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data.     

Factors affecting social behavior and reproductive success of male rhesus monkeys

This paper reviews aspects of life history that influence the reproductive success of male rhesus monkeys. Recent theories propose that there is some optimum level of inbreeding for each population and that behaviors related to group transfer by males are the result of selection pressure toward such an optimum. Group changing by males is clearly linked to the effects of testosterone at sexual maturation. A male’s maternal genealogical rank is not consistently related to the age at which it leaves the natal group, but social interactions within the natal group may influence the age of departure. Choice of the new group is influenced by the operational sex ratio and the presence of maternal relatives. Rank in the new group is positively correlated with seniority. Seniority, in turn, is influenced by the rank of the male’s natal group, his mother’s genealogical rank, and the presence of male siblings in the new group. Much of this effect is due to the high mortality of males born to females and/or groups of low rank. Most studies show a positive association between male reproductive success and rank. Males from high-ranking groups and/or maternal genealogies that join groups containing brothers tend to remain in those groups longer, attain a higher rank, and probably achieve higher levels of reproduction than other males.