Human encephalization and developmental timing

Human evolution is frequently analyzed in the light of changes in developmental timing. Encephalization in particular has been frequently linked to the slow pace of development in Homo sapiens. The "brain allometry extension" theory postulates that the progressive extension of a conserved primate brain allometry into postnatal life was the basis for brain enlargement in the human lineage. This study shows that published primate and human growth data do not corroborate this model. Instead, the unique encephalization of H. sapiens is alternatively described as the result of evolutionary changes in three aspects of developmental timing. The first is a moderate extension in the duration of brain growth relative to our closest extant relatives, contrary to the view that human brain growth is drastically prolonged into postnatal life. Second, humans evolved a derived brain allometry in comparison with chimpanzees and early hominins. Third, humans (and other anthropoid primates to a lesser degree) display a significant retardation in early postnatal body growth in comparison with other mammals, which directly affects adult encephalization in our species. The rejection of the "brain allometry extension" model may require a reevaluation of the adaptive scenarios proposed to explain how human encephalization evolved.     

A standardized method for quantifying consistent individual differences in schooling behaviour

A method for quantifying consistent individual differences in schooling behaviour is presented. This method, which utilizes a school of models, improves on previous methods by removing the unwanted variation that is introduced by live stimulus fish while still providing the physiological experience of schooling to the focal fish. Three‐spined stickleback Gasterosteus aculeatus observed in the model school assay exhibited consistent individual differences in schooling behaviour.     

A new method for quantifying mitochondrial axonal transport

Axonal transport of mitochondria is critical for neuronal survival and function. Automatically quantifying and analyzing mitochondrial movement in a large quantity remain challenging. Here, we report an efficient method for imaging and quantifying axonal mitochondrial transport using microfluidic-chamber-cultured neurons together with a newly developed analysis package named “MitoQuant”. This tool-kit consists of an automated program for tracking mitochondrial movement inside live neuronal axons and a transient-velocity analysis program for analyzing dynamic movement patterns of mitochondria. Using this method, we examined axonal mitochondrial movement both in cultured mammalian neurons and in motor neuron axons of Drosophila in vivo. In 3 different paradigms (temperature changes, drug treatment and genetic manipulation) that affect mitochondria, we have shown that this new method is highly efficient and sensitive for detecting changes in mitochondrial movement. The method significantly enhanced our ability to quantitatively analyze axonal mitochondrial movement and allowed us to detect dynamic changes in axonal mitochondrial transport that were not detected by traditional kymographic analyses.     

A new method for quantifying iodine in a starch-iodine matrix

A rapid and sensitive method for quantifying iodine in intact starch granules using gas chromatography is described with detection limits as low as 0.2% (w/w) iodine in starch. Sample preparation includes NaBH₄ reduction of the various iodine species associated with starch to the colorless soluble iodide ion, followed by its quantitative derivatization to EtI using in CH₂Cl₂. Identification and quantification of EtI is carried out by extraction and injection of the EtI so generated in CH₂Cl₂ into a gas chromatography-mass spectrometer (GC-MS). Routine quantification of EtI was then performed using GC with a flame ionization detector (GC-FID). Results for different iodine:potassium iodide ratios of the initially bound iodine and for seven different starch matrices showed that in all cases regression coefficients for the standards were high (R² >0.96).     

A new method for quantifying genotyping errors for noninvasive genetic studies

More and more noninvasive genetic data are being produced but a general methodology to quantify genotyping error rates from non-pilot data remains lacking. Here we propose a mathematical approach to estimate genotyping error rates by exploring the relationship between errors and PCR replicates. This method can be used to quantify the error rates for either the multi-tubes approach designed by Taberlet et al. (Nucleic Acids Res 24: 3189–3194, 1996) or the pilot method by Prugh et al. (Mol Ecol 14: 1585–1596, 2005).     

A method for quantifying rotational symmetry

Here, a new approach for quantifying rotational symmetry based on vector analysis was described and compared with information obtained from a geometric morphometric analysis and a technique based on distance alone. A new method was developed that generates a polygon from the length and angle data of a structure and then quantifies the minimum change necessary to convert that polygon into a regular polygon. This technique yielded an asymmetry score (s) that can range from 0 (perfect symmetry) to 1 (complete asymmetry). Using digital images of Geranium robertianum flowers, this new method was compared with a technique based on lengths alone and with established geometric morphometric methods used to quantify shape variation. Asymmetry scores (s) more clearly described variation in symmetry and were more consistent with a visual assessment of the images than either comparative technique. This procedure is the first to quantify the asymmetry of radial structures accurately, uses easily obtainable measures to calculate the asymmetry score and allows comparisons among individuals and species, even when the comparisons involve structures with different patterns of symmetry. This technique enables the rigorous analysis of polysymmetric structures and provides a foundation for a better understanding of symmetry in nature.     

A new NMR method for directly monitoring and quantifying the dissolution kinetics of starch in DMSO

The kinetics of dissolution of starch is needed for (i) understanding digestive processes; (ii) providing data that could correlate with higher levels of starch structure; (iii) improving techniques for starch characterization in solution. A novel method is presented here to directly monitor these dissolution kinetics by time-resolved (1)H solution-state nuclear magnetic resonance (NMR); studies were carried out in deuterated dimethyl sulfoxide (DMSO-d(6)). By assuming pseudo-first-order kinetics with respect to starch concentration, the data for various starch samples yield values of the apparent rate coefficients for the rate of appearance of completely dissolved anhydroglucose units, results which have not been obtained hitherto. The presence of a limited amount of water in DMSO had a drastic effect on dissolution kinetics (slowing it down at high temperatures), indicating multiple pathways for the dissolution mechanism. Dynamic light scattering (DLS) appears to be more limited than the NMR method to monitor the kinetics of dissolution. The newly developed NMR method can be extended to other solvents and polysaccharides.     

A new evaluation method for quantifying PI3K activity by HTRF assay

PIK3CA, coding a catalytic subunit of PI3K p110α, is frequently mutated in cancer. In previous studies, p110α with hotspot mutations such as E545K and H1047R were shown to be gain-of-function mutations. However, quantitative evaluation of these mutants was not well established. Recently, a new method for measuring PI3K activity using homogeneous time-resolved fluorescence (HTRF) has been developed. Using this method, we constructed a quantitative evaluation system for PI3K activity. Serial dilutions of standard PIP3 were subjected to the PI3K-HTRF assay in order to establish a regression line for calibration. The recombinant FLAG-tagged p110α proteins were engineered together with a regulatory subunit p85α in human embryonic kidney 293T cells. Anti-FLAG-Ig immunoprecipitates were then subjected to the assay, which enabled us to quantitatively evaluate the activities of hotspot mutants of p110α. We believe this method will also be applicable to the evaluation of p110α having uncharacterized mutations found in cancer.     

A new mathematical model for combining growth and energy intake in animals: The case of the growing pig

A simultaneous model for analysis of net energy intake and growth curves is presented, viewing the animal's responses as a two dimensional outcome. The model is derived from four assumptions: (1) the intake is a quadratic function of metabolic weight; (2) the rate of body energy accretion represents the difference between intake and maintenance; (3) the relationship between body weight and body energy is allometric and (4) animal intrinsic variability affects the outcomes so the intake and growth trajectories are realizations of a stochastic process. Data on cumulated net energy intake and body weight measurements registered from weaning to maturity were available for 13 pigs. The model was fitted separately to 13 datasets. Furthermore, slaughter data obtained from 170 littermates was available for validation of the model. The parameters of the model were estimated by maximum likelihood within a stochastic state space model framework where a transform-both-sides approach was adopted to obtain constant variance. A suitable autocorrelation structure was generated by the stochastic process formulation. The pigs’ capacity for intake and growth were quantified by eight parameters: body weight at maximum rate of intake (149-281 kg); maximum rate of intake (25.7-35.7 MJ/day); metabolic body size exponent (fixed: 0.75); the daily maintenance requirement per kg metabolic body size (0.232-0.303 MJ/(day×kg^0.75)); reciprocal scaled energy density ; a dimensional exponent, θ₆ (0.730-0.867); coefficient for animal intrinsic variability in intake (0.120-0.248 MJ^0.5) and coefficient for animal intrinsic variability in growth (0.029-0.065 kg^0.5). Model parameter values for maintenance requirements and body energy gains were in good agreement with those obtained from slaughter data. In conclusion, the model provides biologically relevant parameter values, which cannot be derived by traditional analysis of growth and energy intake data.     

A new method for quantifying residue conservation and its applications to the protein folding nucleus

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.     

A method for quantifying aggression in male Drosophila melanogaster

Aggressive behavior is a complex social behavior that is difficult to measure. Here, we describe a simple method for the quantitative analysis of aggression in male Drosophila melanogaster. Traditional measurements of aggressive behavior have relied on a territorial context with a food territory and a female as factors that induce or enhance aggression. The protocol described here is devoid of a food territory or a female, making it simpler than most existing methods used to measure aggressive behavior. Multiple pairs of males are tested simultaneously to obtain an average fighting score. Four parameters are used to quantify the behavior: frequency, index, latency and intensity of fighting based on unambiguous offensive fighting behaviors. The assay takes 15 min, during which time a frequency score is obtained for 20-35 pairs simultaneously. More in-depth analysis, including latency, index and intensity, can be performed on the videotaped record of the experiment. The assay is highly reproducible and requires limited resources in a simple setup.     

A new method for quantifying keratinocyte differentiation using immunofluorescent staining of involucrin and cytofluorography

Involucrin is a precursor protein of detergent-insoluble cornified envelope and a marker of terminal differentiation of epidermal keratinocytes. To quantify differentiation of cultured human keratinocytes, the population of involucrin-positive cells was estimated by immunofluorescent staining using anti-involucrin antibody and flow cytometry. Normal human keratinocytes were cultured under three conditions for induction of differentiation: low Ca2+ concentration (0.1 mM Ca2+), high Ca2+ concentration (1.8 mM Ca2+), and high Ca2+ concentration with 10% fetal bovine serum (FBS). The relationship between fluorescence intensity and involucrin synthesis was confirmed by visual examination of sorted cells. The population of involucrin-positive cells increased from 7.2 to 18.1% by elevating Ca2+ concentration and to 37.0% by adding FBS. The extent of cornified envelope formation under the same culture conditions was consistent with the estimation of involucrin-positive cells. The cytofluorographic analysis of involucrin synthesis made it possible to determine the number of differentiated cells in a large number of samples precisely and reliably. Thus, it is a useful method for quantifying keratinocyte differentiation.     

A photometric method for quantifying the polymorphisms in human acrocentric chromosomes

Summary Photometric measurements on photomicrographs of quinacrine mustard—stained metaphase chromosomes, processed by a reverse developing procedure provide quantitative data on the polymorphisms of human acrocentric chromosomes. The method described is intended for population studies. The method is easily reproducible, allowing comparisons of data obtained by different laboratories.     

A new method for quantifying the probability of segregative plasmid loss inEscherichia coli B/r

Summary A new method for quantifying rates of segregative plasmid loss is described. The probability of plasmid loss is found from the decrease in the fraction of plasmid containing cells, following a synchronous division. Stability inEscherichia coli B/r increased with pH and dilution rate, but decreased with temperature.     

A standardized method for quantifying eggshell spot patterns

Spottiness is an important component of the morphology of bird eggs and a number of methods have been developed for characterizing variation in spottiness. We developed a quantitative method for measuring and comparing eggs to determine if female European Cranes (Grus grus) lay eggs with individually distinct color and spotting patterns. We used photographs taken under standard conditions and developed a computer program (ESPANA) to quantify egg‐spot patterns. The goal of the analysis was to create a “fingerprint” of each eggshell by measuring reflection along virtually drawn lines (transects) on an egg's image. Values measured in the same positions along transects can be compared among eggs by considering them as separate variables defining the pattern. Data were analyzed using cluster analyses and by performing analyses of similarity (ANOSIM). We found that the eggs of female European Cranes (N = 11) had individually distinct color patterns, with eggs laid by a given female more similar to each other than to the eggs of other females. Beyond its potential use for identifying the eggs of specific females, we believe our method could also be useful for investigators quantifying differences in egg‐spot patterns for other reasons, for example, examining possible relationships between egg‐spot patterns and female quality. The program ESPANA is implemented using the Java programming language and is available as supporting information on the Journal of Field Ornithology website.     

A standardized method for quantifying unidirectional genetic introgression

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual‐based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual‐based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample.     

A refined blood collection method for quantifying corticosterone

In many rodent laboratories, blood samples are collected from rats using the tail vein nick procedure and analyzed to quantify blood corticosterone levels as an indicator of stress. The standard method of corticosterone quantification often requires the collection of a relatively large volume of blood, followed by the extraction of the blood plasma. An alternative blood sampling method requires the collection of only a drop of blood on paper (the 'drop' method), minimizing handling of the animals, and does not require plasma extraction. The authors aimed to validate the drop method of blood sampling for use in corticosterone quantification. They induced stress in rats by cerebral ischemia, collected blood samples at various intervals using both the drop method and the plasma extraction method and then quantified corticosterone by radioimmunoassay. Corticosterone levels of the ischemic rats were compared with those of sham-operated rats and those of ischemic rats that had been given metyrapone, a glucocorticoid synthesis inhibitor, prior to vessel occlusion. Blood corticosterone levels in the samples obtained from the same animal using the two different methods were highly correlated for all rats. The authors further provide a regression model that can be used to predict plasma corticosterone values from those obtained from the drop blood samples. Quantification of corticosterone from only a small drop of blood has many practical and ethical advantages and should be considered as an alternative to standard methods.