Methodological considerations on the study of sexual dimorphism in past human populations

The degree of sexual dimorphism in human populations is influenced by stress, social role and by labour division. However, studies on ethnographic populations provided contradictory results. Unfortunately, most of these studies were based on stature only, which, as we could observe in a survey on pre-protohistoric circum-Medirerranean samples, is a poor indicator of functionally related dimorphism. A number of skeletal measurements were examined: skull, stature, transverse trunk diameters, long bones length, circumference and section, in order to assess their usefulness as indicators of functionally related dimorphism. The best indicators were represented by section and circumference of the long bones of the limbs, followed by cross-shoulder breadth (biclavicular length), stature and limb bone length, facial measurements, cranial measurements and sacral breadth. From the methodological point of view, it was found that:

1. It is better to calculate the index of dimorphism for each trait or set of traits within each sample. Then a weighted average of all the available samples is taken. The index derived from pooling a number of samples does not make biological sense. In pooled samples the distinction of between versus within sample differences is obscured;
2. It is better to combine an index which is based on the difference between averages and one which takes variability into account, because variability can also be an aspect of sexual dimorphism;
3. It is better to apply some allometric correction to the measurements used. For instance, the log transformation produces clearer trends of differential dimorphism among the various traits.

     

Species interactions and population density mediate the use of social cues for habitat selection

1. The perspective that populations and communities are structured by antagonistic interactions among individuals has dominated much of ecology. Yet how animals use social information to guide decisions, such as habitat selection, may be influenced by both positive and negative interactions among individuals. Recent theory also suggests that the way animals use social information may be substantially influenced by population density, which alters the potential costs and benefits of such behaviours. 2. I manipulated cues of two competitors, the dominant least flycatcher Empidonax minimus (Baird & Baird) and the subordinate American redstart Setophaga ruticilla (Linnaeus), to assess the use of conspecific and heterospecific cues during habitat selection, and if population density influences these strategies. The experiment consisted of surveying birds during a pre-treatment year, which allows for the control and testing the effect of baseline densities, and a treatment year, in which treatments were applied just prior to settlement. Treatments included broadcasting songs of flycatchers and redstarts, and were compared with controls. 3. When controlling for pre-treatment densities, bird densities, and to a lesser extent arrival dates, during the treatment year suggested that flycatchers were attracted to both conspecific and heterospecific cues during settlement. Furthermore, attraction was strongest for flycatchers in plots with moderate pre-treatment densities. American redstarts were rare in the study area but showed apparent attraction to conspecifics and avoidance of heterospecifics. 4. These results provide experimental evidence for the use of multiple social cues in habitat selection and suggest that heterospecific attraction may operate under broader contexts than originally envisioned. In such instances, nontarget effects can potentially occur when manipulating social cues to elicit settlement in conservation strategies. The impact of population density on the use of social cues shown here can also influence our understanding of metapopulation dynamics by causing complex threshold effects on the likelihood of rescue, which may influence metapopulation stability and the likelihood of local extinction.     

Genomic study of the hereditary pathology and genetic diversity of the Siberian population

The review considers the results of genome research on the Russian program Human Genome carried out in the Institute of Medical Genetics (Tomsk) from 1990. The three major fields were molecular cytogenetics and chromosomal disorders, genomics of Mendelian and high-incidence diseases, and ethnogenomics of the North Asian population. Several human genes were cytogenetically mapped, and numerical and structural abnormalities associated with human diseases studied by fluorescence hybridization. Procedures of DNA diagnostics were developed for 15 hereditary diseases. New data were obtained on genetic heterogeneity of idiopathic hypertrophic cardiomyopathy. The genetic bases of multifactorial (atopic bronchial asthma) and infectious (tuberculosis) diseases were analyzed. The North Eurasian population (41 local populations of 21 ethnic groups) was tested for genetic diversity with numerous genetic markers, including Y-chromosomal haplotypes, autosomal microsatellites, and polymorphic Alu insertions.     

Methodological considerations for assessing autophagy modulators: A study with calcium phosphate precipitates

Autophagy has been implicated in various physiological and disease conditions in recent years. A number of small molecule modulators have been identified, both as tools and as potential therapeutics. Despite extensive characterization of autophagy in yeast, mammalian autophagy pathways are not fully understood. Recently, calcium phosphate precipitates (CPP), which are used to transfect DNA into cells, were reported to induce autophagy, when assayed up to 6 h after treatment. Because of the widespread use of this reagent, we attempted to confirm these findings. Consistent with the previous study, we showed that CPP induces autophagosome synthesis at early time-points, such as 4 h and 6 h. However, at 24 h after treatment, we were surprised to see that autophagy flux was reduced, due to impaired autophagosome-lysosome fusion. At this time point, there was an accumulation of autophagy substrates and the formation of abnormally large autophagosomes. Thus, one may need to consider assaying autophagy modulators at different time-points with a range of assays in order to understand their effects. Finally, the complex consequences of CPP on autophagy suggest that it is best avoided as a transfection reagent in studies aiming to analyse autophagy itself, or processes that are modulated by autophagy, like apoptosis.     

Methodological considerations for conducting tumor surveys of fishes

The usefulness of tumor surveys in indicating the availability of carcinogenic contaminants in ecosystems hinges largely on decisions made during the planning process. Species used as indicator organisms for monitoring programs are best selected from those known to be susceptible to epizootics of neoplasms. Lesions which can be quickly located and preserved in the field and for which a data base exists to help interpretation include liver neoplasms and external neoplasms. Since tumor frequencies increase with age and may change from season to season, studies should hold these variables constant among locations. During the design of the study investigators should determine the number of fish they need to examine in order to achieve the degree of resolution desired. Finally the field crew must be familiar with fish anatomy and necropsy techniques as well as storage and handling of the chosen preservative.     

Methodological considerations for examining the relationship between sperm morphology and motility

Sperm cells of all taxa share a common goal to reach and fertilize an ovum, yet sperm are one of the most diverse cell types in nature. While the structural diversity of these cells is well recognized, the functional significance of variation in sperm design remains elusive. An important function of spermatozoa is a need to migrate toward the ova, often over long distances in a foreign environment, which may include a complex and hostile female reproductive tract. Several comparative and experimental studies have attempted to address the link between sperm morphology and motility, yet the conclusions drawn from these studies are often inconsistent, even within the same taxa. Much of what we know about the functional significance of sperm design in internally fertilizing species has been gleaned from in vitro studies, for which experimental parameters often vary among studies. We propose that discordant results from these studies are in part due to a lack of consistency of methods, conditions that do not replicate those of the female reproductive tract, and the overuse of simple linear measures of sperm shape. Within this review, we provide a toolkit for imaging, quantifying, and analyzing sperm morphology and movement patterns for in vitro studies and discuss emerging approaches. Results from studies linking morphology to motility enhance our understanding of the evolution of adaptive sperm traits and the mechanisms that regulate fertility, thus offering new insights into methods used in assisted reproductive technologies in animal science, conservation and public health.     

Tyroglyphid mites in stored products Methods for the study of population density

The known methods for detecting the presence of tyroglyphids are described. For coarse materials, such as seeds, sieving is recommended. For flour, it is better to examine exposed surfaces, or to keep samples in glass vessels and examine for the runnels made by mites against the glass. Methods of sampling to provide information about the density and extent of infestations are described. Samples must usually be treated in the laboratory. While methods which do not involve the separation of the mites from the material are referred to, such separation is usually necessary. Mites may be separated from most materials by the modified Berlese funnel method of Chernuishev and Petrova; means of overcoming certain disadvantages are suggested. However, vigorous sieving is recommended for coarse materials, and a flotation method, using dichlorethylene, for fine materials such as flour. It is usually more satisfactory to examine and count the mites than to estimate the numbers volumetrically or gravimetrically. They are counted in a dish containing oil, placed on squared paper under a low-power microscope. A modification of this method, for dealing with large numbers, is described. Methods of expressing population density are briefly discussed.     

Medico-genetic study of the population of Kostroma Province. VII. Approaches to the study of the hereditary pathology load in the population of Kostroma

Complex medical-genetic study was performed in the center of Kostroma Province with the population of about 250 thousands. A method for ascertainment of patients was developed and the information value of different sources of a registration system available is given. The complete algorithm of calculation of both the segregation frequency and the fraction of sporadic cases for autosomal recessive diseases is presented.     

Medico-genetic study of the population of Kostroma Province. I. The population burden of hereditary pathology

Data on the prevalence of hereditary diseases in five regions of the Kostroma province were obtained and analysed. It was shown that the ascertainment was close to the truncate selection for the rural population and to the single selection for the urban population. Segregational analysis proved the rightness of the material subdivision, according to the type of inheritance. The load of hereditary diseases (for the registered forms) in the population was: 0.78 +/- 0.08 X 10(-3) for autosomal dominant, 0.75 +/- 0.08 X 10(-3) for autosomal-recessive and 0.54 +/- 0.1 X 10(-3) for X-linked recessive disorders. The dynamics of the load of hereditary diseases in the populations with different structure is discussed.     

Methodological considerations and factors affecting 8-hydroxy-2-deoxyguanosine analysis

Oxidative stress is related to a number of diseases due to the formation of reactive oxygen species (ROS). There are also several substances found in the occupational environment or as life style related situations that generates ROS. A stable biomarker for oxidative stress on DNA is 8-hydroxy-2'-deoxyguanosine (8-OH-dG).

A potential problem in the work-up and analysis of 8-OH-dG is oxidation of dG with false high levels as a result of analysis. This paper summarizes and discusses some of the critical moments in terms of auto-oxidation. The removal of transition metals, low temperatures, absence of isotopes (or 2'-deoxyguanosine) and incubation times are all important factors. Removal of oxygen is complicated while the problem is reduced if a nitroxide (TEMPO) is added during work-up. Certain reducing agents and enzymes could be critical if added during work-up.

The application of the ³²P-HPLC method to analyze 8-OH-dG is discussed. The ³²P-HPLC method is suitable for 8-OH-dG analysis and avoids several factors that oxidizes dG by removal of dG before addition of isotopes. Factors of crucial importance (columns, eluents, gradients and detection of ³²P) for the analysis of 8-OH-dG are commented upon and certain recommendations are made to make it possible to apply the ³²P-HPLC methodology for this type of analysis.     

Toxicology and pathology considerations for the design of juvenile animal studies

Although exposure to drugs or toxicants can affect children and adults very differently, many compounds lack specific safety information for children. Studies in juvenile animals can help researchers assess pediatric patients' potential response to certain chemicals. Juvenile studies are highly sensitive to animal age, sex and species and must be planned with care to prevent misinterpretation of experimental data. The author reviews considerations for the design of these studies, focusing on toxicological and pathological aspects.     

Measurement of organic-35S and organic-S in lake sediments: Methodological considerations

Three protocols for the determination of inorganic and organic sulfur fractions were tested for their suitability to estimate total indigenous organic sulfur (S_org) and³⁵S_org formed from added³⁵SO₄ ^2– in sediments of chemically dilute lakes in the ELA. The protocols tested have all been reported in the literature. It was found that two protocols involving sequential analyses for S fractions following acid treatment gave estimates of both S_org and³⁵S_org up to 87% lower than a non-sequential protocol. The low estimates were largely due to hydrolysis and solubilization of solid phase S which was then removed in a rinsing step. The non-sequential protocol, in which total reduced inorganic sulfur and total sulfur were determined on separate aliquots, is recommended as the most reliable of the three. Individual analyses in this protocol were verified for these lake sediments using a variety of S standards.     

Comparing measures of travel distances in primates: Methodological considerations and socioecological implications

Travel costs can influence numerous aspects of the lives of primates, including net energy balance (and therefore reproductive success of females) and maximum group size. Despite their potential impact, there has been no systematic comparison of different measures of travel distance. We compared three measures of travel distance in 30 min (actual distance of individuals, straight‐line distance of individuals, and straight‐line distance of groups) and their ratios in a small group and a large group of vervet monkeys (Cercopithecus aethiops) and between the large group of vervets and a group of patas monkeys (Erythrocebus patas) of roughly similar size. The large group of vervets traveled farther than the small group regardless of the measure used, but the ratios of the different measures were not significantly different between those groups. Patas monkeys traveled significantly farther than the large group of vervets regardless of the measure used. In both vervets and patas, straight‐line distances of individuals (ISLD) and groups (GSLD) underestimated actual distances traveled by individuals (IAD), but the degree to which they did so differed between species. IAD is more accurate than the other two measures and is preferred for studies of energetics and individual reproductive success, although ISLD or GSLD may be substituted when the ratios of IAD/ISLD or IAD/GSLD do not differ between groups or species. The ratio of IAD/ISLD was larger in vervets than in patas, suggesting that individual vervets meander more over short periods of time than patas. The ratio of ISLD/GSLD was larger in patas than in vervets, suggesting that patas move at angles or across the group's center‐of‐mass whereas vervets move more consistently along with others in their group. This has implications for the formation of spatial subgroups and alliances within groups. Am. J. Primatol. 48:87–98, 1999. © 1999 Wiley‐Liss, Inc.     

Cause and effect considerations in diagnostic pathology and pathology phenotyping of genetically engineered mice (GEM)

Over the next several decades, biology is embarking on its most ambitious project yet: to annotate the human genome functionally, prioritizing and focusing on those genes relevant to development and disease. Model systems are fundamental prerequisites for this task, and genetically engineered mice (GEM) are by far the most accessible mammalian system because of their anatomical, physiological, and genetic similarity to humans. The scientific utility of GEM has become commonplace since the technology to produce them was established in the early 1980s. Conceptually, however, an efficiently coordinated high-throughput approach that permits correlation between newly discovered genes, functional properties of their protein products, and biological relevance of these products as drug targets has yet to be established. The discipline of veterinary anatomical pathology (hereafter referred to as pathology) is not immune to this requirement for evolution and adaptation, and to address relationships and tissue consequences between tens of thousands of genes and their cognate proteins, novel interdisciplinary technologies and approaches must emerge. Although many of the techniques of pathology are well established, in the context of pathology's contribution to functional annotation of the genome, several conceptually important and unresolved issues remain to be addressed. While an ever-increasing arsenal of genetic and molecular tool-sets are available to evaluate and understand the function of genes and their pathophysiological mechanisms, pathology will continue to play an essential role in confirming cause and effect relationships of gene function in development and disease. This role will continue to be dependent on keen observation, a systematic but disciplined approach, expert knowledge of strain-dependent anatomical differences and incidental lesions, and relevant tissue-based evidence. Miniaturization and high-throughput adaptation of these methods must also continue so that they can complement parallel phenotyping efforts, provide pathology-based data in pace with concurrent phenotyping efforts, and continue to find new utility in the collective effort of functional annotation.