Coevolution of body size and metabolic rate in vertebrates: a life‐history perspective

Despite many decades of research, the allometric scaling of metabolic rates (MRs) remains poorly understood. Here, we argue that scaling exponents of these allometries do not themselves mirror one universal law of nature but instead statistically approximate the non‐linearity of the relationship between MR and body mass. This ‘statistical’ view must be replaced with the life‐history perspective that ‘allows’ organisms to evolve myriad different life strategies with distinct physiological features. We posit that the hypoallometric allometry of MRs (mass scaling with an exponent smaller than 1) is an indirect outcome of the selective pressure of ecological mortality on allocation ‘decisions’ that divide resources among growth, reproduction, and the basic metabolic costs of repair and maintenance reflected in the standard or basal metabolic rate (SMR or BMR), which are customarily subjected to allometric analyses. Those ‘decisions’ form a wealth of life‐history variation that can be defined based on the axis dictated by ecological mortality and the axis governed by the efficiency of energy use. We link this variation as well as hypoallometric scaling to the mechanistic determinants of MR, such as metabolically inert component proportions, internal organ relative size and activity, cell size and cell membrane composition, and muscle contributions to dramatic metabolic shifts between the resting and active states. The multitude of mechanisms determining MR leads us to conclude that the quest for a single‐cause explanation of the mass scaling of MRs is futile. We argue that an explanation based on the theory of life‐history evolution is the best way forward.     

The Analysis of the Structural Aspects of Cu(II) Binding by Cyclic His/Asp-Analogues of Somatostatin

International Journal of Peptide Research and Therapeutics - Two new somatostatin analogs with a characteristic part of the sequence in their structures, -c(Cys-Phe-Trp-Lys-Thr-Cys)-, were...     

WIS‐neuromath enables versatile high throughput analyses of neuronal processes

Automated analyses of neuronal morphology are important for quantifying connectivity and circuitry in vivo, as well as in high content imaging of primary neuron cultures. The currently available tools for quantification of neuronal morphology either are highly expensive commercial packages or cannot provide automated image quantifications at single cell resolution. Here, we describe a new software package called WIS‐NeuroMath, which fills this gap and provides solutions for automated measurement of neuronal processes in both in vivo and in vitro preparations. Diverse image types can be analyzed without any preprocessing, enabling automated and accurate detection of neurites followed by their quantification in a number of application modules. A cell morphology module detects cell bodies and attached neurites, providing information on neurite length, number of branches, cell body area, and other parameters for each cell. A neurite length module provides a solution for images lacking cell bodies, such as tissue sections. Finally, a ganglion explant module quantifies outgrowth by identifying neurites at different distances from the ganglion. Quantification of a diverse series of preparations with WIS‐NeuroMath provided data that were well matched with parallel analyses of the same preparations in established software packages such as MetaXpress or NeuronJ. The capabilities of WIS‐NeuroMath are demonstrated in a range of applications, including in dissociated and explant cultures and histological analyses on thin and whole‐mount sections. WIS‐NeuroMath is freely available to academic users, providing a versatile and cost‐effective range of solutions for quantifying neurite growth, branching, regeneration, or degeneration under different experimental paradigms. © 2012 Wiley Periodicals, Inc. Develop Neurobiol, 2013     

Human Alveolar Echinococcosis in Poland: 1990–2011

Background

Alveolar echinococcosis (AE) caused by Echinococcus multilocularis infections is a dangerous old disease in the Northern Hemisphere. The aim of the paper was to collect and analyze data on human AE in Poland in the last two decades.

Methodology/Principal Findings

The sources of data were both the cases officially registered and detected by an active field and laboratory surveillance. The cases were verified by clinical, epidemiological, and laboratory criteria. Altogether 121 human cases of AE were detected. Among these 83 (68,6%) cases were classified as confirmed, 16 as probable and 22 as possible. During the two decades a continuous increase in detection rate was noticed. The cases were 6–82 years old at the time of diagnosis (mean - 47.7 years). Sex ratio M/F was 0.86/1.0. The AE was fatal in 23 (19%) patients (mean age at death - 54.1 years). Family agglomeration of AE was found in 4 foci, involving 9 patients. Seventy six of the cases were diagnosed in an advanced stage of disease. In all cases the liver was the primary location of AE. In 30 (24.8%) patients a spread to other organs was observed. Ninety four of the patients were treated with albendazole. In 73 (60%) patients a surgical operation was performed, including 15 liver transplantations.

Conclusions/Significance

The studies confirmed that AE is an emerging disease in Poland, which is the fourth country in Europe with over 120 cases detected. The results also indicate the need of a wider national programme for implementation of screening in the highest AE risk areas (north-eastern Poland) with an effort to increase the public awareness of the possibility of contracting E. multilocularis, and above all, training of the primary care physicians in the recognition of the risk of AE to allow for an early detection of this dangerous disease.     

Development of Methods for Cross-Sectional HIV Incidence Estimation in a Large,Community Randomized Trial

Background

Accurate methods of HIV incidence determination are critically needed to monitor the epidemic and determine the population level impact of prevention trials. One such trial, Project Accept, a Phase III, community-randomized trial, evaluated the impact of enhanced, community-based voluntary counseling and testing on population-level HIV incidence. The primary endpoint of the trial was based on a single, cross-sectional, post-intervention HIV incidence assessment.

Methods and Findings

Test performance of HIV incidence determination was evaluated for 403 multi-assay algorithms [MAAs] that included the BED capture immunoassay [BED-CEIA] alone, an avidity assay alone, and combinations of these assays at different cutoff values with and without CD4 and viral load testing on samples from seven African cohorts (5,325 samples from 3,436 individuals with known duration of HIV infection [1 month to >10 years]). The mean window period (average time individuals appear positive for a given algorithm) and performance in estimating an incidence estimate (in terms of bias and variance) of these MAAs were evaluated in three simulated epidemic scenarios (stable, emerging and waning). The power of different test methods to detect a 35% reduction in incidence in the matched communities of Project Accept was also assessed. A MAA was identified that included BED-CEIA, the avidity assay, CD4 cell count, and viral load that had a window period of 259 days, accurately estimated HIV incidence in all three epidemic settings and provided sufficient power to detect an intervention effect in Project Accept.

Conclusions

In a Southern African setting, HIV incidence estimates and intervention effects can be accurately estimated from cross-sectional surveys using a MAA. The improved accuracy in cross-sectional incidence testing that a MAA provides is a powerful tool for HIV surveillance and program evaluation.     

Discovery of Potential New Gene Variants and Inflammatory Cytokine Associations with Fibromyalgia Syndrome by Whole Exome Sequencing

Fibromyalgia syndrome (FMS) is a chronic musculoskeletal pain disorder affecting 2% to 5% of the general population. Both genetic and environmental factors may be involved. To ascertain in an unbiased manner which genes play a role in the disorder, we performed complete exome sequencing on a subset of FMS patients. Out of 150 nuclear families (trios) DNA from 19 probands was subjected to complete exome sequencing. Since >80,000 SNPs were found per proband, the data were further filtered, including analysis of those with stop codons, a rare frequency (<2.5%) in the 1000 Genomes database, and presence in at least 2/19 probands sequenced. Two nonsense mutations, W32X in C11orf40 and Q100X in ZNF77 among 150 FMS trios had a significantly elevated frequency of transmission to affected probands (p = 0.026 and p = 0.032, respectively) and were present in a subset of 13% and 11% of FMS patients, respectively. Among 9 patients bearing more than one of the variants we have described, 4 had onset of symptoms between the ages of 10 and 18. The subset with the C11orf40 mutation had elevated plasma levels of the inflammatory cytokines, MCP-1 and IP-10, compared with unaffected controls or FMS patients with the wild-type allele. Similarly, patients with the ZNF77 mutation have elevated levels of the inflammatory cytokine, IL-12, compared with controls or patients with the wild type allele. Our results strongly implicate an inflammatory basis for FMS, as well as specific cytokine dysregulation, in at least 35% of our FMS cohort.     

Nanoindentation of 35 Virus Capsids in a Molecular Model: Relating Mechanical Properties to Structure

A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV – satellite panicum mosaic virus) and 135 780 (for NBV – nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic region which extends to a characteristic force . Crossing results in a drop in the force and irreversible damage. Across the 35 capsids studied, both and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number , defined as the mean number of interactions to neighboring amino acids. The Young''s modulus for thin shell capsids rises roughly quadratically with , where 6 is the minimum coordination for elastic stability in three dimensions.     

The role of landscape structure in determining palynological and floristic richness

The associations between floristic and palynological richness and landscape structure were studied based on modern pollen?Cvegetation data from a patchy cultural landscape in southern Estonia (northern temperate vegetation zone). Nine study sites (small lakes and their surrounding vegetation) represent land cover gradient from closed forest to semi-open vegetation. Floristic richness (number of species) and floristic richness of pollen types (number of pollen-equivalent taxa) were used to describe the vegetation within the radius of 250?m from the pollen sampling sites. Palynological richness was calculated to describe the modern pollen samples diversity. Landscape structure was estimated on the basis of landscape openness and three landscape diversity measures: richness of community patches, Simpson evenness of community patches and Simpson diversity of community patches. To study the effect of the spatial scale of landscapes on the vegetation?Clandscape and pollen?Clandscape associations, landscape structure was estimated within eight radii (250?C2,000?m) around each lake. The results showed that landscape openness was the most important determinant of both floristic richness and palynological richness in southern Estonia and that landscape diversity estimated by Simpson diversity index was also significantly associated with the richness estimates. Floristic and palynological richness were significantly positively correlated with landscape structure within the radii greater than 1,000?m from the pollen sampling sites, which is similar to the estimated Relevant Source Area of Pollen in southern Estonia. We conclude that within one floristic or climatic region, palynological richness gives reliable estimates about the variation in floristic richness and landscape structure; however, caution must be taken when comparing pollen-inferred vegetation diversities from different regions or when interpreting fossil pollen records from times with highly different vegetation associations.     

Drivers of plant species composition in alder-dominated forests with contrasting connectivity

The effects of local and regional environmental variables as well as spatial gradients on the plant species composition of two types of alder-dominated forests (riparian forests and alder carrs) with contrasting connectivity were studied across the Western Carpathians from Hungary through Slovakia to Poland. We used large vegetation (240 sampling plots) and environmental (24 variables) datasets, which were accompanied by spatial variables represented by principal coordinates of neighbour matrices. Canonical correspondence analysis (CCA) of the two datasets revealed 13 and 29 variables with significant effects on variation in species composition of alder carrs and riparian alder forests, which jointly explained 41.2% and 36.4% of the variability, respectively. Altitude was the most important factor explaining 7.7% of the variability in the species composition of alder carrs and 8.2% in riparian alder forests. Variation partitioning in CCA revealed that local variables were crucial drivers for species composition patterns in alder carrs, while spatial processes unrelated to the measured environmental variables shaped the vegetation structure of riparian forests.

     

Highly divergent mitogenomes of Geukensia demissa (Bivalvia,Mytilidae) with extreme AT content

Complete sequences of two lineage-specific mitogenomes from mytilid bivalve Geukensia demissa are reported, confirming the existence of doubly uniparental inheritance system in this species. The reported mitogenomes show extreme sequence divergence; at protein level, it is in the range of 12%–55%, exceeding the highest values known from this family to date. Moreover, these mitogenomes are also extraordinarily AT-rich (~72%) making them the most compositionally biased mitogenomes from this family. The compositional bias is even more extreme at neutral sites, reaching 80% AT there. Despite high-sequence divergence, the mitogenomes are both compositionally and structurally similar, with only four trn genes relocated and overall gene order very similar to the phylogenetically close mitogenomes of Perumytilus purpuratus. Lineage-specific differences are limited to the non-coding regions and a short cox2 extension present in the paternally inherited M mitogenome. Phylogenetic analysis shows deeper separation of M and F lineages in Geukensia, than in Perumytilus consistent with higher protein divergence. It can be speculated that stronger mutational pressure in Geukensia is driving faster evolution of its mitogenomes.