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Biological Variation (biological + variation)
Selected AbstractsBiomarker discovery in breast cancer serum using 2-D differential gel electrophoresis/ MALDI-TOF/TOF and data validation by routine clinical assaysELECTROPHORESIS, Issue 8 2006Hong-Lei Huang Abstract In the present study, we used 2-D differential gel electrophoresis (2-D DIGE) and MS to screen biomarker candidates in serum samples obtained from 39,patients with breast cancer and 35,controls. First, we pooled the serum samples matched with age and menopausal status. Then, we depleted the two most abundant proteins albumin and IgG by immunoaffinity chromatography under partly denaturing conditions in order to enrich low-abundance proteins and proteins with low molecular weight. Concentrated and desalted samples were labeled with three different CyDyes including one internal standard, pooled from all the samples, and separated with 2-D DIGE in triplicate experiments. Biological variations of the protein expression level were analyzed with DeCyder software and evaluated for reproducibility and statistical significance. The profile of differentially expressed protein spots between patients and controls revealed proapolipoprotein A-I, transferrin, and hemoglobin as up-regulated and three spots, apolipoprotein,A-I, apolipoprotein,C-III, and haptoglobin,,2 as down-regulated in patients. Finally, routine clinical immunochemical reactions were used to validate selected candidate biomarkers by quantitative determination of specific proteins in all individual serum samples. The serum level of transferrin correlated well with the 2-D-DIGE results. However, the serum levels of apolipoprotein A-I and haptoglobin could not be detected with the clinical routine diagnostic tests. This demonstrated an advantage 2-D DIGE still has over other techniques. 2-D DIGE can distinguish between isoforms of proteins, where the overall immunochemical quantification does fail due to a lack of isoform-special antibodies. [source] Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversityECOLOGY LETTERS, Issue 1 2010James P. O'Dwyer Abstract Predicting the variation of biodiversity across the surface of the Earth is a fundamental issue in ecology, and in this article we focus on one of the most widely studied spatial biodiversity patterns: the species,area relationship (SAR). The SAR is a central tool in conservation, being used to predict species loss following global climate change, and is striking in its universality throughout different geographical regions and across the tree of life. In this article we draw upon the methods of quantum field theory and the foundation of neutral community ecology to derive the first spatially explicit neutral prediction for the SAR. We find that the SAR has three phases, with a power law increase at intermediate scales, consistent with decades of documented empirical patterns. Our model also provides a building block for incorporating non-neutral biological variation, with the potential to bridge the gap between neutral and niche-based approaches to community assembly. Ecology Letters (2010) 13: 87,95 [source] A TEST OF THE NEUTRAL MODEL OF EXPRESSION CHANGE IN NATURAL POPULATIONS OF HOUSE MOUSE SUBSPECIESEVOLUTION, Issue 2 2010Fabian Staubach Changes in expression of genes are thought to contribute significantly to evolutionary divergence. To study the relative role of selection and neutrality in shaping expression changes, we analyzed 24 genes in three different tissues of the house mouse (Mus musculus). Samples from two natural populations of the subspecies M. m. domesticus and M. m. musculus were investigated using quantitative PCR assays and sequencing of the upstream region. We have developed an approach to quantify expression polymorphism within such populations and to disentangle technical from biological variation in the data. We found a correlation between expression polymorphism within populations and divergence between populations. Furthermore, we found a correlation between expression polymorphism and sequence polymorphism of the respective genes. These data are most easily interpreted within a framework of a predominantly neutral model of gene expression change, where only a fraction of the changes may have been driven by positive selection. Although most genes investigated were expressed in all three tissues analyzed, significant changes of expression levels occurred predominantly in a single tissue only. This adds to the notion that enhancer-specific effects or transregulatory effects can modulate the evolution of gene expression in a tissue-specific way. [source] Do endogenous seasonal cycles of food intake influence foraging behaviour and intake by grazing sheep?FUNCTIONAL ECOLOGY, Issue 5 2000G. R. Iason Abstract 1.,Large herbivores living in temperate regions show different degrees of seasonal biological variation, including voluntary food intake (VFI). The decline of VFI in winter has been hypothesized to be an evolved response to lower food availability or quality, which can act as an internal constraint on food intake. 2.,The hypotheses were tested that (i) animals that have a greater inherent seasonal variation of VFI, measured indoors under ad libitum conditions, would also have a greater seasonal variation in intake and grazing behaviour under field conditions, and (ii) greater seasonal variation in intake and grazing behaviour under field conditions would be expressed at a higher level of food availability. 3.,The intake and grazing behaviour in summer and winter, of three breeds of sheep, were compared at two levels of food availability (at pasture heights of 3·7 and 5·4 cm). The breeds were known to have contrasting degrees of seasonal variation in food intake when fed ad libitum; the VFI of the Shetland (SH) and Scottish Blackface (BF) sheep varies greatly between seasons whereas that of the Dorset Horn (DH) is less seasonally variable. 4.,All three breeds consistently increased their rates of biting and duration of grazing activity in the winter, taking many more smaller bites each day than in the summer, and both digestibility and intake were lower in winter than in summer. 5.,Contrary to expectation, the DH ewes had the highest seasonal difference of dry matter intake at pasture, whereas the SH breed had the lowest variation of intake between seasons. 6.,This experiment provides no evidence that differences between seasons in intake and foraging behaviour in the field vary with the animals' degree of endogenous seasonal variation in VFI. Variation between seasons was consistent at both levels of resource availability, suggesting that it resulted from seasonal changes in food quality (digestibility) rather than biomass availability. It is not easy to extrapolate from laboratory feeding studies, where animals' own physiological constraints apply, to foraging ecology in the field, where constraints imposed by the environment may be more important. [source] Mitotic counting in surgical pathology: sampling bias, heterogeneity and statistical uncertaintyHISTOPATHOLOGY, Issue 1 2001F B J M Thunnissen Mitotic counting in surgical pathology: sampling bias, heterogeneity and statistical uncertainty Although several articles on the methodological aspects of mitotic counting have been published, the effects of macroscopic sampling and tumour heterogeneity have not been discussed in any detail. In this review the essential elements for a standardized mitotic counting protocol are described, including microscopic calibration, specific morphological criteria, macroscopic selection, counting procedure, effect of biological variation, threshold, and the setting of an area of uncertainty (,grey area'). We propose that the use of a standard area for mitotic quantification and of a grey area in mitotic counting protocols will facilitate the application of mitotic counting in diagnostic and prognostic pathology. [source] Karl Pearson and the Establishment of Mathematical StatisticsINTERNATIONAL STATISTICAL REVIEW, Issue 1 2009M. Eileen Magnello Summary At the end of the nineteenth century, the content and practice of statistics underwent a series of transitions that led to its emergence as a highly specialised mathematical discipline. These intellectual and later institutional changes were, in part, brought about by a mathematical-statistical translation of Charles Darwin's redefinition of the biological species as something that could be viewed in terms of populations. Karl Pearson and W.F.R. Weldon's mathematical reconceptualisation of Darwinian biological variation and "statistical" population of species in the 1890s provided the framework within which a major paradigmatic shift occurred in statistical techniques and theory. Weldon's work on the shore crab in Naples and Plymouth from 1892 to 1895 not only brought them into the forefront of ideas of speciation and provided the impetus to Pearson's earliest statistical innovations, but it also led to Pearson shifting his professional interests from having had an established career as a mathematical physicist to developing one as a biometrician. The innovative statistical work Pearson undertook with Weldon in 1892 and later with Francis Galton in 1894 enabled him to lay the foundations of modern mathematical statistics. While Pearson's diverse publications, his establishment of four laboratories and the creation of new academic departments underscore the plurality of his work, the main focus of his life-long career was in the establishment and promulgation of his statistical methodology. [source] Ratio-dependent significance thresholds in reciprocal 15N-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatmentPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2009Sylwia Kierszniowska Abstract Metabolic labeling of plant tissues with 15N has become widely used in plant proteomics. Here, we describe a robust experimental design and data analysis workflow implementing two parallel biological replicate experiments with reciprocal labeling and series of 1:1 control mixtures. Thereby, we are able to unambiguously distinguish (i) inherent biological variation between cultures and (ii) specific responses to a biological treatment. The data analysis workflow is based on first determining the variation between cultures based on 15N/14N ratios in independent 1:1 mixtures before biological treatment is applied. In a second step, ratio-dependent SD is used to define p -values for significant deviation of protein ratios in the biological experiment from the distribution of protein ratios in the 1:1 mixture. This approach allows defining those proteins showing significant biological response superimposed on the biological variation before treatment. The proposed workflow was applied to a series of experiments, in which changes in composition of detergent resistant membrane domains was analyzed in response to sucrose resupply after carbon starvation. Especially in experiments involving cell culture treatment (starvation) prior to the actual biological stimulus of interest (resupply), a clear distinction between culture to culture variations and biological response is of utmost importance. [source] Modulation of cancer cell line differentiation: A neglected proteomic analysis with potential implications in pathophysiology, diagnosis, prognosis, and therapy of cancerPROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2008Roberto Scatena Professor Abstract The recent development of compounds that induce cell differentiation in various types of cancer cells has enabled the molecular mechanisms governing this kind of induced cancer regression to be investigated. Moreover, this approach to investigating the pathophysiology of neoplasia represents a promising experimental model for proteomic analysis of cancer cells. Modulating neoplastic cell differentiation grade may reveal cytodifferentiation-related protein expression changes, and doing so in vitro has the advantage of less biological variation. Hence, this analysis brings attention to molecular targets of the so-called differentiating factors (i.e., retinoids, hybrid polar compounds, tyrosine kinase inhibitors, etc.) as well as proteins that are frequently associated with differentiation/dedifferentiation processes. The in vitro study of these proteins and of their pathogenetic roles in cancer may ultimately result in the discovery of cancer biomarkers with diagnostic, prognostic, and therapeutic applications. [source] Further analysis of the population history of ancient EgyptiansAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2009Michael A. Schillaci Abstract The origins of state formation in ancient Egypt have been the focus of recent research utilizing biological data to test hypotheses regarding in situ development of local groups, or large-scale in-migration, possibly by an invading army. The primary goal of the present research is to further test these hypotheses. Our secondary goal is to compare different distance measures and assess how they might affect interpretation of population history. We analyze craniodental nonmetric data using several different measures of biological distance, as well as a method for estimating group diversity using multidimensional scaling of distance estimates. Patterns of biological variation and population relationships were interpreted in temporal and geographic contexts. The results of our analyses suggest that the formation of the ancient Egyptian state likely included a substantial in situ process, with some level of contribution by outside migrants probable. The higher level of population structure in Lower Egypt, relative to Upper Egypt, suggests that such influence and migration by outsiders may not have been widespread geographically. These findings support, but serve to refine further those obtained by the second author in a previous study. Moreover, our comparison of distance measures indicates that the choice of measure can influence identification and interpretation of the microevolutionary processes shaping population history, despite being strongly correlated with one another. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] How race becomes biology: Embodiment of social inequalityAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2009Clarence C. Gravlee Abstract The current debate over racial inequalities in health is arguably the most important venue for advancing both scientific and public understanding of race, racism, and human biological variation. In the United States and elsewhere, there are well-defined inequalities between racially defined groups for a range of biological outcomes,cardiovascular disease, diabetes, stroke, certain cancers, low birth weight, preterm delivery, and others. Among biomedical researchers, these patterns are often taken as evidence of fundamental genetic differences between alleged races. However, a growing body of evidence establishes the primacy of social inequalities in the origin and persistence of racial health disparities. Here, I summarize this evidence and argue that the debate over racial inequalities in health presents an opportunity to refine the critique of race in three ways: 1) to reiterate why the race concept is inconsistent with patterns of global human genetic diversity; 2) to refocus attention on the complex, environmental influences on human biology at multiple levels of analysis and across the lifecourse; and 3) to revise the claim that race is a cultural construct and expand research on the sociocultural reality of race and racism. Drawing on recent developments in neighboring disciplines, I present a model for explaining how racial inequality becomes embodied,literally,in the biological well-being of racialized groups and individuals. This model requires a shift in the way we articulate the critique of race as bad biology. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Contact in the Andes: Bioarchaeology of systemic stress in colonial Mórrope, PeruAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Haagen D. Klaus Abstract The biocultural interchange between the Eastern and Western Hemispheres beginning in the late fifteenth century initiated an unprecedented adaptive transition for Native Americans. This article presents findings from the initial population biological study of contact in the Central Andes of Peru using human skeletal remains. We test the hypothesis that as a consequence of Spanish colonization, the indigenous Mochica population of Mórrope on the north coast of Peru experienced elevated systemic biological stress. Using multivariate statistical methods, we examine childhood stress reflected in the prevalence of linear enamel hypoplasias and porotic hyperostosis, femoral growth velocity, and terminal adult stature. Nonspecific periosteal infection prevalence and D30+/D5+ ratio estimations of female fertility characterized adult systemic stress. Compared to the late pre-Hispanic population, statistically significant patterns of increased porotic hyperostosis and periosteal inflammation, subadult growth faltering, and depressed female fertility indicate elevated postcontact stress among both children and adults in Mórrope. Terminal adult stature was unchanged. A significant decrease in linear enamel hypoplasia prevalence may not indicate improved health, but reflect effects of high-mortality epidemic disease. Various lines of physiological, archaeological, and ethnohistoric evidence point to specific socioeconomic and microenvironmental factors that shaped these outcomes, but the effects of postcontact population aggregation in this colonial town likely played a fundamental role in increased morbidity. These results inform a model of postcontact coastal Andean health outcomes on local and regional scales and contribute to expanding understandings of the diversity of indigenous biological variation in the postcontact Western Hemisphere. Am J Phys Anthropol, 2009. © 2008 Wiley-Liss, Inc. [source] Dietary variation and stress among prehistoric Jomon foragers from JapanAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2007Daniel H. Temple Abstract Current archaeological evidence indicates that greater dietary reliance on marine resources is recorded among the eastern Jomon, while plant dependence prevailed in western/inland Japan. The hypothesis that the dietary choices of the western/inland Jomon will be associated with greater systemic stress is tested by comparing carious tooth and enamel hypoplasia frequencies between the eastern and western/inland Jomon. Demographic collapse coincides with climate change during the Middle to Late Jomon period, suggesting dwindling resource availability. It is hypothesized that this change was associated with greater systemic stress and/or dietary change among the Middle to Late Jomon. This hypothesis is tested by comparing enamel hypoplasia and carious tooth frequencies between Middle to Late and Late to Final Jomon foragers. Enamel hypoplasia was significantly more prevalent among the western/inland Jomon. Such findings are consistent with archaeological studies that argue for greater plant consumption and stresses associated with seasonal resource depletion among the western/inland Jomon. Approximately equivalent enamel hypoplasia frequencies between Middle to Late and Late to Final Jomon foragers argues against a demographic collapse in association with diminished nutritional returns. Significant differences in carious tooth frequencies are, however, observed between Middle to Late and Late to Final Jomon foragers. These results suggest a subsistence shift during the Middle to Late Jomon period, perhaps in response to a changed climate. The overall patterns of stress documented by this study indicate wide-spread environmentally directed biological variation among the prehistoric Jomon. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc. [source] Phenotypic approaches for understanding patterns of intracemetery biological variationAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue S43 2006Christopher M. Stojanowski Abstract This paper reviews studies of phenotypic inheritance and microevolutionary processes in archaeological populations using data on cranial and dental phenotypic variation, often referred to as paleogenetics or biodistance analysis. The estimation of biological distances between populations, or among individuals within populations, is one component of bioarchaeological research on past populations. In this overview, five approaches that focus on morphological variation within cemeteries are summarized: kinship and cemetery structure analysis, postmarital residence analysis, sample aggregate phenotypic variability, temporal microchronology, and age-structured phenotypic variation. Previous research, theoretical justifications, and methods are outlined for each topic. Case studies are presented that illustrate these theoretical and methodological bases, as well as demonstrate the kinds of inferences possible using these approaches. Kinship and cemetery structure analysis seeks to identify the members of family groups within larger cemeteries or determine whether cemeteries were kin-structured. Analysis of sex-specific phenotypic variation allows estimation of postmarital residence practices, which is important for understanding other aspects of prehistoric social organization. Analysis of aggregate phenotypic variability can be used to infer site formation processes or cemetery catchment area. The study of temporal microchronologies can be used to evaluate provisional archaeological chronologies or study microevolutionary processes such as adaptive selection or changing patterns of gene flow. Finally, age-structured phenotypic variation can be reflective of selection processes within populations or it can be used as a measure of morbidity, growth arrest, and early mortality within past populations. Use of phenotypic data as a genotypic proxy is theoretically sound, even at small scales of analysis. Yrbk Phys Anthropol 49:49,88, 2006. © 2006 Wiley-Liss, Inc. [source] Changes in biological anthropology: Results of the 1998 American Association of Physical Anthropology Membership SurveyAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2002Trudy R. Turner Abstract In response to the results of the 1996 survey of the membership of the American Association of Physical Anthropology (AAPA), the Executive Committee of the Association sponsored a follow-up survey designed to assess gender and specialty differences in training, employment, academic status, mentoring, and research support. A total of 993 questionnaires was analyzed, representing approximately 62% of the 1998 membership of the Association. There has been a marked shift in the number of males and females in the discipline from the 1960s to the 1990s. While 51.2% of all respondents are female and 48.8% are male, 70% of the students are female. Chi-square tests indicate significant differences between males and females by highest degree, age, status, obtaining a tenure-track position, receiving tenure, and taking nontenure-track employment before receiving a tenure-track position. In recent years, there has been an increasing number of females in the ranks of assistant and associate professors; however, this is not true for the rank of professor. There are also significant differences between males and females by specialty within the discipline: researchers in primatology, human biological variation, skeletal biology, and paleopathology are primarily female, while researchers in human and primate evolution are increasingly female. Am J Phys Anthropol 118:111,116, 2002. © 2002 Wiley-Liss, Inc. [source] Considering Dependencies Amongst Genes Helps to Adjust the Significance Rank of DEGsCHINESE JOURNAL OF CHEMISTRY, Issue 7 2010Qi Liu Abstract Lists of differentially expressed genes (DEGs) detected often show low reproducibility even in technique replicate experiments. The reproducibility is even lower for those real cancer data with large biological variations and limited number of samples. Since existing methods for identifying differentially expressed genes treat each gene separately, they cannot circumvent the problem of low reproducibility. Considering correlation structures of genes may help to mitigate the effect of errors on individual gene estimates and thus get more reliable lists of DEGs. We borrowed information from large amount of existing microarray data to define the expression dependencies amongst genes. We use this prior knowledge of dependencies amongst genes to adjust the significance rank of DEGs. We applied our method and four popular ranking algorithms including mean fold change (FC), SAM, t-statistic and Wilcoxon rank sum-test on two cancer microarray datasets. Our method achieved higher reproducibility than other methods across a range of sample sizes. Furthermore, our method obtained higher accuracy than other methods, especially when the sample size is small. The results demonstrate that considering the dependencies amongst genes helps to adjust the significance rank of genes and find those truly differentially expressed genes. [source] | |||||||||||||