Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models of sequence evolution, which being highly parametrized and computationally-demanding are not appropriate for large-scale analyses. Here we investigate an alternative methodological option based on probabilistic substitution mapping. The idea is to first reconstruct the substitutional history of each site of an alignment under a homogeneous model of sequence evolution, then to characterize variations in the substitution process across lineages based on substitution counts. Using simulated and published datasets, we demonstrate that probabilistic substitution mapping is robust in that it typically provides accurate reconstruction of sequence ancestry even when the true process is heterogeneous, but a homogeneous model is adopted. Consequently, we show that the new approach is essentially as efficient as and extremely faster than (up to 25 000 times) existing methods, thus paving the way for a systematic survey of substitution process heterogeneity across genes and lineages.     

Investigating structural brain changes of dehydration using voxel-based morphometry

Dehydration can affect the volume of brain structures, which might imply a confound in volumetric and morphometric studies of normal or diseased brain. Six young, healthy volunteers were repeatedly investigated using three-dimensional T(1)-weighted magnetic resonance imaging during states of normal hydration, hyperhydration, and dehydration to assess volume changes in gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The datasets were analyzed using voxel-based morphometry (VBM), a widely used voxel-wise statistical analysis tool, FreeSurfer, a fully automated volumetric segmentation measure, and SIENAr a longitudinal brain-change detection algorithm. A significant decrease of GM and WM volume associated with dehydration was found in various brain regions, most prominently, in temporal and sub-gyral parietal areas, in the left inferior orbito-frontal region, and in the extra-nuclear region. Moreover, we found consistent increases in CSF, that is, an expansion of the ventricular system affecting both lateral ventricles, the third, and the fourth ventricle. Similar degrees of shrinkage in WM volume and increase of the ventricular system have been reported in studies of mild cognitive impairment or Alzheime [Formula: see text]s disease during disease progression. Based on these findings, a potential confound in GM and WM or ventricular volume studies due to the subjects' hydration state cannot be excluded and should be appropriately addressed in morphometric studies of the brain.     

Involvement of calmodulin in phagocytotic respiratory burst of leukocytes

The superoxide release of guinea pig exudate leukocytes induced by phagocytosis or by stimulation with cytochalasin D, digitonin or calcium ionophore A23187 was completely inhibited by the inhibitors of calmodulin-stimulated processes such as trifluoperazine at 10 μM. A particulate NADPH-dependent superoxide-forming enzyme from the cytochalasin D-stimulated cells was also inhibited by the inhibitors and by EGTA. The activation of heart phosphodiesterase by a boiled extract of the cells which was dependent on calcium ions and abolished by trifluoperazine was observed. These results suggest the presence of calmodulin in leukocytes and its possible role in the stimulation of the superoxide formation.     

In vivo characterization of the transitional bronchioles by aerosol-derived airway morphometry.

Effective airway dimensions (EADs) were determined in vivo by aerosol-derived airway morphometry as a function of volumetric lung depth (VLD) to identify and characterize, noninvasively, the caliber of the transitional bronchiole region of the human lung and to compare the EADs by age, gender, and disease. By logarithmically plotting EAD vs. VLD, two distinct regions of the lung emerged that were identified by characteristic line slopes. The intersection of proximal and distal segments was defined as VLD(trans) and associated EAD(trans). In our normal subjects (n = 20), VLD(trans) [345 +/- 83 (SD) ml] correlated significantly with anatomic dead space (224 +/- 34 ml) and end of phase II of single-breath nitrogen washout (360 +/- 53 ml). The corresponding EAD(trans) was 0.42 +/- 0. 07 mm, in agreement with other ex vivo measurements of the transitional bronchioles. VLD(trans) was smaller (216 +/- 64 ml) and EAD(trans) was larger (0.83 +/- 0.04 mm) in our patients with chronic obstructive pulmonary disease (n = 13). VLD(trans) increased with age for children (age 8-18 yr; P = 0.006, n = 26) and with total lung capacity for age 8-81 yr (P < 0.001, n = 61). This study extends the usefulness of aerosol-derived airway morphometry to in vivo measurements of the transitional bronchioles.     

Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers

A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy-Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full-sibs, and performs better than a previously developed estimator. When comparing marker-based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co-dominant markers (microsatellites) in studying microgeographic isolation-by-distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.     

The evolution of sperm morphometry in pheasants

Post-copulatory sexual selection is thought to be a potent evolutionary force driving the diversification of sperm shape and function across species. In birds, insemination and fertilization are separated in time and sperm storage increases the duration of sperm-female interaction and hence the opportunity for sperm competition and cryptic female choice. We performed a comparative study of 24 pheasant species (Phasianidae, Galliformes) to establish the relative importance of sperm competition and the duration of sperm storage for the evolution of sperm morphometry (i.e. size of different sperm traits). We found that sperm size traits were negatively associated with the duration of sperm storage but were independent of the risk of sperm competition estimated from relative testis mass. Our study emphasizes the importance of female reproductive biology for the evolution of sperm morphometry particularly in sperm-storing taxa.     

Study of nuclear and acrosomal sperm morphometry in ram using a computer-assisted sperm morphometry analysis fluorescence (CASMA-F) method

The aim of this study was to develop a new method that allows morphometric assessment of the sperm nucleus and acrosome in the ram using fluorescence microscopy and free software. The study was divided into three experiments. In the first experiment, semen smears from 20 ejaculates were fixed and labeled with a propidium iodide–pisum sativum agglutinin (PI/PSA) combination. Digital images of the sperm nucleus, acrosome, and whole sperm head were captured and analyzed using the ImageJ program. The computer-assisted sperm morphometry analysis fluorescence (CASMA-F) method used allowed the differentiation, capture, and morphometric analysis of most sperm nuclei, acrosomes, and whole heads with high precision and the assessment of the acrosomal status. In the second experiment, sperm nuclear morphometry by CASMA-F was compared by staining with the PI/PSA combination and staining with Hoechst 33342 as in previous studies. Similar results were obtained using both methods. In the third experiment, CASMA-F with PI/PSA was compared with a more conventional CASMA method (semen smears stained with Hemacolor (HEM) and processed with the ISAS commercial software, HEM). Spermatozoa displayed a bigger size when processed with CASMA-F than with HEM method in all primary sperm head morphometric parameters, but results using both methods were correlated. It was concluded that the CASMA-F method allows the simultaneous assessment of sperm nucleus, acrosome, and head in the ram.     

Discussion of errors and measuring strategies in morphometry using analysis of variance

Statistical techniques known as the analysis of variance make it possible for the morphologist to plan work in such a way as to get quantitative data with the greatest possible economy of effort. This paper explains how to decide how many measurements to make per micrograph, how many micrographs per tissue block or organ, and how many organs or individuals are necessary for getting an exactness of sufficient quality of the results. The examples furnished have been taken from measuring volume densities of mitochondria in heart muscle cells and from cell counting in lymph nodes. Finally we show, how to determine sample sizes, if we are interested in demonstration of significant differences between mean values.     

The vascular morphometry of some brain stem parts

With the view of following the vascular system of the cerebral trunk, there have been simultaneously injected coloured tracers combined with radio-opaque substances and radio-isotopes (32P, 22Ca) by intravital perfusion to 130 animals (dogs, rabbits and rats). The macro- and microscopical vasculature of the human brain stem was studied on 30 specimens of adults and children. The angioarchitecture of the diverse parts and sectors of the brain stem was studied as a whole in tetraline transparentised preparations and on histological section in comparison with the microradiographies and to incorporation of radioisotopes. A particular attention has been given to the irrigation of hypoglossal nuclei, the bulbar oliva, and the pontopeduncular region, all being zones with multiple sources of vascularization. The vascular morphometry has been macro- and microscopically performed, the data being worked out mathematically-statistically by computing some hemodynamical indices in order to estimate the circulation in different zones of the brain stem.     

Improved method for mapping gastric intestinal metaplasia using selective histochemical morphometry

A gastrectomy specimen containing two tubular adenomas from a 67-year-old woman was mapped by an improved method using selective histochemical staining. The specimen was divided into 83 blocks measuring 4.0 cm x 0.5 cm. Sections from the blocks were stained with alcian blue (pH 2.5) to detect mucin. Alcian blue-stained fields were easily identified and measured with the aid of a MOP 30 interactive digital image analyzer. The total area of gastric mucosa analyzed in the 83 sections measured 3,270.9 sq mm while the area occupied by alcian blue-stained goblet cells measured 755.9 sq mm (23.1% of the total area). Intestinal metaplasia was present in 46 of 83 blocks. Both the mean size of alcian blue-positive fields per section as well as the number of alcian blue-positive fields per section were significantly larger in the antral zone I and the intermediate zone II than in the fundal zones III, IV and V. The highest proportion of gastric mucosa with intestinal metaplasia was not found around the two gastric adenomas, but elsewhere. There was no significant difference in the proportion of intestinal metaplasia between the greater and lesser curvatures, further challenging the belief that intestinal metaplasia is always greatest along the lesser curvature. The method described will permit future studies of the possible association between intestinal metaplasia and dysplasias and adenocarcinomas of the stomach.     

Ultrastructural characteristics, secretory and phagocytotic activity of Paneth cells

Paneth cells in the depth of Lieberkühn's crypts were studied ultrastructurally in three human jejunal biopsy material. Fine structural elements were observed indicative of phagocytosis. It is also assumed that the cells had regulatory function of normal intestinal flora. The importance of ultrastructural examinations of Lieberkühn's crypts under pathological conditions is emphasized.     

Sperm quality and morphometry characterization of cryopreserved canine sperm in ACP-106c or TRIS

Morphological sperm evaluation supported by the morphometry can be used in the determination of the seminal quality and in the investigation of potential extenders. Although there are studies comparing TRIS and ACP extenders, there are no comparative studies between them for the computerized assisted semen analysis (CASA), sperm viability, membrane functionality and sperm morphometry parameters of cryopreserved canine semen. Hence, we aimed to evaluate the effects of ACP-106c and TRIS on post-freezing canine sperm quality. Five dogs were submitted to semen collection twice with one-week interval. The semen was evaluated within the parameters: total motility, vigor, concentration, viability, plasma membrane functionality, morphology and morphometry. In the morphometric evaluation, the morphologically normal sperm was measured as: length, width, area and perimeter of the head and the midpiece, tail length and total length. The parameters of ellipticity, elongation, regularity and roughness were determined. Then, the semen was divided into two aliquots that were diluted in TRIS or ACP-106c, with the addition of egg yolk and glycerol. The diluted semen was refrigerated and frozen. The thawed samples were evaluated. Total motility, viability, sperm membrane functionality and normal morphology reduced after thawing in both extenders (morphology reduced from 89.60 ± 1.3% to 84.40 ± 1.8 and 84.60 ± 1.1% in TRIS and ACP-106c, respectively). However, it did not differ between TRIS and ACP-106c. In the ACP-106c the sperm head defects in cryopreserved semen were higher compared to fresh semen (P < 0.05). For all the morphometric parameters evaluated, there were no differences between fresh and cryopreserved samples (3.70 ± 0.4% vs. 2.30 ± 0.5%). In kinetics, with an interval of one week statistical differences between the extenders were found only in the parameters ALH and LIN (P < 0.05). Regardless of the extender, there were no changes in the morphometric parameters of sperm after thawing.     

Semi-automated mitral valve morphometry and computational stress analysis using 3D ultrasound

In vivo human mitral valves (MV) were imaged using real-time 3D transesophageal echocardiography (rt-3DTEE), and volumetric images of the MV at mid-systole were analyzed by user-initialized segmentation and 3D deformable modeling with continuous medial representation, a compact representation of shape. The resulting MV models were loaded with physiologic pressures using finite element analysis (FEA). We present the regional leaflet stress distributions predicted in normal and diseased (regurgitant) MVs. Rt-3DTEE, semi-automated leaflet segmentation, 3D deformable modeling, and FEA modeling of the in vivo human MV is tenable and useful for evaluation of MV pathology.     

Ultrastructural morphometry of blastogenesis

Summary As a companion to an earlier study, the morphometric attributes of stimulated (blast-derived) lymphocytes in mouse axillary lymph nodes have been established using stereological and autoradiographic methods. Blast transformation was induced in vivo with dinitrochlorobenzene (DNCB) and stimulated cells were labelled with tritiated thymidine. Random samples of cells were taken for light and electron microscopic morphometry.In comparison to the unstimulated lymphocyte, the stimulated cell increased in size and possessed a greater plasma membrane surface area. Increase in cell size was the result of increases in the volumes of all measured subcellular compartments both in the nucleus and the cytoplasm. Heterogeneity of the stimulated cell population precludes firm conclusions regarding the significance of all these ultrastructural changes, though alterations in cell surface are discussed in the context of known biochemical differences accompanying blastogenesis.M.M. Al-Hamdani was supported by a grant from the Ministry of Higher Education and Scientific Research, Republic of Iraq