Validation and reproducibility of pressure-corrected aortic distensibility measurements using pulse-wave-velocity Doppler ultrasound

A non-invasive Doppler ultrasound technique is described for the assessment of aortic compliance based on the in vivo measurement of pulse wave velocity along the thoraco-abdominal aortic pathway. A structured protocol, which has been developed to improve the reproducibility of the technique, is validated. A method of correcting for the effect of non-chronic changes in blood pressure on arterial elasticity is considered and applied to compliance measurements performed on 66 normal, healthy volunteers. The results of a study to ascertain the overall reproducibility of the method are provided and problems associated with the technique are discussed. Medical disorders such as atherosclerosis, diabetes mellitus, familial hypercholesterolaemia and growth hormone deficiency have all been shown to affect arterial wall compliance. It is suggested that the in vivo measurement of pressure-corrected aortic distensibility may be a useful, non-invasive tool for assessing such patients' susceptibility to atheromatous arterial disease and for monitoring their response to therapy. Measurements in the aorta may be especially pertinent since the natural history of fatty streaks there tends to parallel that in coronary arteries thereby potentially affording a convenient surrogate estimate of coronary heart disease.     

Effect of disturbance on assemblages: an example using porifera

Extensive sponge assemblages are found in a number of habitats at Lough Hyne Marine Nature Reserve. These habitats are unusual in experiencing a range of environmental conditions, even though they are only separated by small geographic distances (1-500 m), reducing the possibility of confounding effects between study sites (e.g., silica concentrations and temperature). Sponge assemblages were examined on ephemeral (rocks), stable (cliffs), and artificial (slate panels) hard substrata from high- and low-energy environments that were used to represent two measures of disturbance (flow rate and habitat stability). Sponge assemblages varied considerably between habitat types such that only 26% (25 species) of species reported were common to both rock and cliff habitats. Seven species (of a total of 96 species) were found in the least-developed assemblages (slate panels) and were common to all habitats. Sponge assemblages on rocks and panels varied little between high- and low-energy environments, whereas assemblages inhabiting cliffs varied considerably. Assemblage composition was visualized using Bray-Curtis similarity analysis and Multi-Dimensional Scaling, which enabled differences and similarities between sponge assemblages to be visualized. Cliffs from high- and low-energy sites had different assemblage compositions compared to large rocks, small rocks, and panels, all of which had similar assemblages irrespective of environmental conditions. Differences in assemblages were partially attributed to sponge morphology (shape), as certain morphologies (e.g., arborescent species) were excluded from 2-D rock habitats. Other mechanisms were also considered responsible for the sponge assemblages associated with different habitats.     

Evaluating trans-tethys migration: an example using acrodont lizard phylogenetics

A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies eight major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea; Physignathus cocincinus from Southeast Asia is the sister taxon to the Australia-New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through South and East Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All eight clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or Southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia-New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a Southeast Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chameleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia by way of separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between Southeast Asia and Australia-New Guinea, known as Wallace's line: (1) primary vicariance caused by plate separations; (2) secondary contact of Southeast Asian plates with Eurasia, leading to dispersal from Eurasia into Southeast Asia, and (3) dispersal of the Indian fauna (after collision of that subcontinent) to Southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes.     

Quantifying income breeding: using geometrid moths as an example

Although the general concept of capital vs. income breeding has become widely used in insect ecology, finding easy‐to‐measure indices for quantifying the role of larval‐ vs. adult‐derived nutrients in egg production has remained a challenge. When searching for possible candidates for this task, we evaluated the applicability of three morphometric ratios to be measured on freshly eclosed adults: (1) relative size of female abdomen, (2) sexual size dimorphism, and (3) proportion of volume of mature eggs relative to total volume of female abdomen. We report the values of these indices in five species of geometrid moths [Hypomecis punctinalis Scopoli, Ematurga atomaria L., Selenia tetralunaria Hufnagel, Semiothisa clathrata L., and Epirrhoe alternata Müller (all Lepidoptera: Geometridae)] and compare them to the degrees of income breeding measured directly by oviposition experiments. As a comparison, we also recorded the ovigeny index and the effect of income on lifespan. All morphometric indices varied considerably between the species studied, and, as predicted, the values of all three proposed indices were higher in the more capital‐breeding species. The only exception to this pattern was a low proportion of mature eggs in abdomens in one primarily capital‐breeding species, S. tetralunaria. Unlike other capital breeders, this species also proved to be largely synovigenic, indicating that capital breeding and pro‐ovigeny are not strictly linked. The reproductive traits measured concord with ecological niches occupied by the species studied: the oligophagous meadow dwellers were largely income breeding and synovigenic, whereas the polyphagous forest dwellers were capital breeders. The high and predictable among‐species variation in egg‐production strategies suggests that geometrid moths form a promising target group for comparative studies on respective traits. Simple anatomical indices, in turn, appear to be applicable as easy‐to‐record proxies of egg production strategies.     

以胶原蛋白为例浅述古蛋白质组学研究现状与未来*

蛋白质作为参与构建生物体的重要生物大分子,是生物功能与代谢的物质基础,同时蛋白质的序列信息又源自生物的遗传编码信息,因此是认识生物演化本质的重要研究对象。近年来,随着质谱技术的发展,获取生物化石中的古蛋白质序列信息不再遥不可及,这为在形态学与DNA序列信息缺乏的条件下对古生物的认识提供了一条新途径。胶原蛋白(Collagen)在动物骨骼中极为丰富,又因为其特殊的结构,易于在化石中保存,故已成为古蛋白质组学研究的重要对象。本文将以胶原蛋白为例,对古蛋白质组学现有的研究方法与已经取得的研究成果进行总结,并对古蛋白质组学目前面临的挑战与困难及未来研究趋势进行讨论,旨在展示古蛋白质组学的应用潜力,并探讨其在生物演化研究中的意义。     

Quantifying assemblage distinctness with time: an example using temperate epibenthos

Artificial substrata are an often-used tool in assessing community development; here we quantify the changing presence of functional groups of benthos with replicate, depth, site, and time in order to explain differences in the structure of the surrounding mature communities. We placed replicate, machined slate panels (15×15×1 cm) in the intertidal, 6 and 12 m at two sites of differing flow rates at Lough Hyne, SW Ireland. They were placed at the same time of year and removed after 2, 6, 12, and 24 months from 1999 to 2001, to compare with a similar experiment run from 1997 to 1999. Furthermore, to examine trends of local assemblages older than 24 months, we examined boulders from each depth/site combination. Percentage cover of 13 functional groups, selected in relation to their competitive abilities, was measured using point intercept analysis of high-resolution digital images of the panels. These data were then quantified using our derived measure of distinctness. Replicates became more similar, and sites and depths both became more distinct with time from 2 to 24 months, although there was less distinctness at the high flow site throughout all stages of the study. Principal components analysis (PCA) of data suggested that all site/depth panel combinations only became truly distinct at the 24-month stage of the study. From 2 to 24 months, ‘good’ competitors increased in space, ‘intermediate’ competitors peaked after ≈12 months, and ‘poor’ competitors reduced in their space occupation with increasing time. Both in similarity and space occupation of functional groups, the 1997-1999 and 1999-2001 data showed high levels of pattern convergence. That there was little difference between assemblages at 12 and 24 months validated our upper time limit of period of study, but at 24 months, assemblages still differed from natural substrata and we suggest that many years would have been necessary to eliminate this difference.     

The reliability and reproducibility of foot type measurements using a mirrored foot photo box and digital photography compared to caliper measurements

The height of the medial longitudinal arch (MLA) is thought to be a predisposing factor to various lower extremity injuries. Discrepancy exists as to whether MLA height plays a role in injury prevention. The purpose of this study was to determine the intertester and intratester reliability, and the validity of the mirrored foot photo box (MFPB) and caliper measurements to radiographic measurements. METHODS: Thirty subjects with equal numbers of men and women were recruited. Both feet were tested (n=60) in a 90% weight bearing stance. A set of anatomic landmarks were palpated, marked, and measured using a caliper, MFPB, and radiographs. The protocol was completed by two testers on 2 days approximately 1 week apart. Intertester and intratester reliability were determined using the intraclass correlation coefficient (ICC)(2,k) and the ICC(2,1), respectively. Validity of both measurement techniques to radiographic measurements was determined using the ICC(2,k). RESULTS: The intertester reliability ranged from 0.991 to 0.577, while the intratester reliability ranged from 0.994 to 0.527, with first metatarsal angle being the only variable with poor reliability. Most variables demonstrated acceptable validity between the MFPB and the caliper measurements, and acceptable validity between the MFPB and calipers compared to radiographic measurements. The MFPB took 51.3+/-19.6s per foot while the caliper measurements averaged 227.4+/-68.9s to complete the measurements. DISCUSSION: The MFPB is as reliable as the caliper measurements, and offers better intertester reliability. Both the caliper and MFPB measurements demonstrated acceptable validity to radiographic measurements and testing time was reduced when using the MFPB compared to calipers.     

A model for improving the precision of paleobathymetric estimates: an example from the northwest Gulf of Mexico

Intraspecific variation in test morphology of ten commonly occurring, benthic foraminiferal species collected from 47 stations and from water depths ranging from 53 to 3230 m in the northwest Gulf of Mexico were subjected to canonical discriminant analysis in order to statistically define an a priori bathymetric zonation. Three species (Bolivina subspinescens, Gavelinopsis translucens, and Uvigerina peregrina) had intraspecific variation capable of statistically dividing the bathyal zone into six contiguous 200 m intervals. Statistical analysis of the remaining seven species (Bolivina albatrossi B. lowmani, Cassidulina subglobosa, Cibicidoides pachyderma C. robertsonianus, Epistominella exigua, and Qridorsalis umbonatus) divided the bathyal zone into five contiguous 250 m intervals. The statistical differences in morphologic variability found in this study appear to be the organism's physiologic response to biogeochemical changes in sea floor habitat as they transcend various water masses. As such, the statistical analyses is a direct measure of the effect of those environmental factors, allowing better resolution and reliability of paleodepth estimates and geodynamic modelling than that commonly attained through faunal association.     

Adaptive intraspecific divergence: an example using the animal cytochrome b gene

The topologies of phylogenetic trees characterized by a high level of intraspecific divergence between the phylogenetic DNA groups (clades) are often explained in terms of the theory of Pleistocene refugia. To elucidate the issue of the adaptive role of intraspecific divergence, the changes in the physicochemical properties of amino acids in the course ofcladogenesis (MM01 model of the TreeSAAP 3.2 package) were analyzed in this work using as an example the nucleotide sequences of the cytochrome b gene in some species of northern animals (lemmings, redbacked voles, chipmunks, flying squirrels, ermines). It was shown that the process of intraspecific divergence was rarely accompanied by radical amino acid substitutions in cytochrome b caused by adaptation (directional selection). In connection with this, the hypothesis is discussed according to which the adaptive variants formed in the species at the peak of cold were lost with climatic warming due to the drift or selection against individuals adapted to cold.     

Potentials for monitoring gene level biodiversity: using Sweden as an example

Programs for monitoring biological diversity over time are needed to detect changes that can constitute threats to biological resources. The convention on biological diversity regards effective monitoring as necessary to halt the ongoing erosion of biological variation, and such programs at the ecosystem and species levels are enforced in several countries. However, at the level of genetic biodiversity, little has been accomplished, and monitoring programs need to be developed. We define “conservation genetic monitoring” to imply the systematic, temporal study of genetic variation within particular species/populations with the aim to detect changes that indicate compromise or loss of such diversity. We also (i) identify basic starting points for conservation genetic monitoring, (ii) review the availability of such information using Sweden as an example, (iii) suggest categories of species for pilot monitoring programs, and (iv) identify some scientific and logistic issues that need to be addressed in the context of conservation genetic monitoring. We suggest that such programs are particularly warranted for species subject to large scale enhancement and harvest—operations that are known to potentially alter the genetic composition and reduce the variability of populations.     

Accurate measurements of dynamics and reproducibility in small genetic networks

Quantification of gene expression has become a central tool for understanding genetic networks. In many systems, the only viable way to measure protein levels is by immunofluorescence, which is notorious for its limited accuracy. Using the early Drosophila embryo as an example, we show that careful identification and control of experimental error allows for highly accurate gene expression measurements. We generated antibodies in different host species, allowing for simultaneous staining of four Drosophila gap genes in individual embryos. Careful error analysis of hundreds of expression profiles reveals that less than ～20% of the observed embryo‐to‐embryo fluctuations stem from experimental error. These measurements make it possible to extract not only very accurate mean gene expression profiles but also their naturally occurring fluctuations of biological origin and corresponding cross‐correlations. We use this analysis to extract gap gene profile dynamics with ～1 min accuracy. The combination of these new measurements and analysis techniques reveals a twofold increase in profile reproducibility owing to a collective network dynamics that relays positional accuracy from the maternal gradients to the pair‐rule genes.