28 results on '"Detlef Groth"'
Search Results
2. Improving ramification detection of St. Nicolas House Analysis
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Seve Chen, Cédric Moris, and Detlef Groth
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St. Nicolas Analysis ,snha ,network reconstruction ,R-squared gaining ,linear model check ,graph estimation ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
The St. Nicolas House Analysis (SNHA) is a new graph estimation method for detection of extensive interactions among variables. It operates by ranking absolute bivariate correlation coefficients in descending order thereby creating hierarchic association chains. The latter characterizes dependence structures of interacting variables which can be visualized in a corresponding network graph as a chain of end-to-end connected edges representing direct relationships between the connected nodes. The important advantage of this relatively new approach is that it produces less false positive edges resulting from indirect or transitive associations than expected with standard correlation or linear model-based approaches. Here we aim to improve the detection of ramifications in graphs by addition of different data processing layers to SNHA. They include the combinations of the extensions R-squared gaining(RSG) and linear model check(LMC). SNHA together with these so-called extensions were benchmarked against default SNHA and other reference methods available for the programming language R. In the end combinations of RSG, LMC and Bootstrapping improve SNHA performance across different network types, albeit at the cost of longer computation time.
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- 2024
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3. Networks in Auxology – proceedings of the 31st Aschauer Soiree, held at Aschau, Germany, June 17th 2023
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Michael Hermanussen, Christiane Scheffler, Melanie Dammhahn, Detlef Groth, Cédric Moris, Tim Hake, Barry Bogin, Piotr Fedurek, Jesper Boldsen, Takashi Satake, Stef van Buuren, Jani Söderhäll, Chris Jefferies, Yehuda Limony, Jovanna Dahlgren, Julia Quitmann, Ingo Scheffler, Nino Nazirishvili, Ekaterine Kvaratskhelia, Annamaria Zsakai, Martin Musalek, Basak Koca Özer, Cansev Meşe Yavuz, Janina Tutkuviene, Laura Kasperiunaite, Simona Gervickaite, Sylvia Kirchengast, Slawomir Koziel, Aleksandra Gomula, Zbyszek Czapla, Antonia Rösler, Leslie Lieberman, Stephen Lieberman, and Martin Brüne
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Social hierarchies ,strategic growth adjustment ,Monte Carlo analysis ,life history strategy ,adherence and quality of life ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Twenty-seven scientists met for the annual Auxological conference held at Aschau, Germany, to particularly discuss the interaction between social factors and human growth, and to highlight several topics of general interest to the regulation of human growth. Humans are social mammals. Humans show and share personal interests and needs, and are able to strategically adjust size according to social position, with love and hope being prime factors in the regulation of growth. In contrast to Western societies, where body size has been shown to be an important predictor of socioeconomic status, egalitarian societies without formalized hierarchy and material wealth-dependent social status do not appear to similarly integrate body size and social network. Social network structures can be modeled by Monte Carlo simulation. Modeling dominance hierarchies suggests that winner-loser effects play a pivotal role in robust self-organization that transcends the specifics of the individual. Further improvements of the St. Nicolas House analysis using re-sampling/bootstrap techniques yielded encouraging results for exploring dense networks of interacting variables. Customized pediatric growth references, and approaches towards a Digital Rare Disease Growth Chart Library were presented. First attempts with a mobile phone application were presented to investigate the associations between maternal pre-pregnancy overweight, gestational weight gain, and the child’s future motor development. Clinical contributions included growth patterns of individuals with Silver-Russell syndrome, and treatment burden in children with growth hormone deficiency. Contributions on sports highlighted the fallacy inherent in disregarding the biological maturation status when interpreting physical performance outcomes. The meeting explored the complex influence of nutrition and lifestyle on menarcheal age of Lithuanian girls and emphasized regional trends in height of Austrian recruits. Examples of the psychosocial stress caused by the forced migration of modern Kyrgyz children and Polish children after World War II were presented, as well as the effects of nutritional stress during and after World War I. The session concluded with a discussion of recent trends in gun violence affecting children and adolescents in the United States, and aspects of life history theory using the example of "Borderline Personality Disorder." The features of this disorder are consistent with the notion that it reflects a "fast" life history strategy, with higher levels of allostatic load, higher levels of aggression, and greater exposure to both childhood adversity and chronic stress. The results were discussed in light of evolutionary guided research. In all contributions presented here, written informed consent was obtained from all participants in accordance with institutional Human investigation committee guidelines in accordance with the Declaration of Helsinki amended October 2013, after information about the procedures used.
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- 2023
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4. Attitude towards purchasing consumer items can be extracted from Demographic and health survey India-2019-2020 (NFHS 5)
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Singha Roy Soumyajit, Mithun Sikdar, Nitish Mondal, Christiane Scheffler, Detlef Groth, and Michael Hermanussen
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consumer items ,national health surveys ,associated chains ,gross domestic production ,antropometry ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background: National Health Surveys have been part of national health services in many countries, but their data are summary com- pilations and commonly used only for describing trends in health and living conditions. Aim: Tostatisticallydisclosenetworksofinteractingvariableswithin National Health Survey data. Sample and methods: We used anthropometric, educational, environ- mental and economic information of people of Sikkim, West Bengal, Telangana, and Gujarat, India, obtained by the Fifth Indian National Family Health Survey (NFHS-5). We applied a new statistical approach labeled as “St. Nicholas House Analysis” (SNHA). SNHA ranks absolute bivariate correlation coef- ficients in descending order according to magnitude. The method creates hierarchic “association chains” of correlation coefficients de- fined by sequences where reversing the start and end point does not alter the ordering of elements. Association chains characterize de- pendence structures within networks of extensively interacting variables. Results: SNHA disclosed fundamental differences in the network of anthropometric, educational, environmental and economic variables of the people of Sikkim, and the people of West Ben- gal, Telangana and Gujarat. Whereas relevant interactions among these variables were largely absent in the people of Sikkim, the variables formed characteristic star-shaped networks with wealth quintile and the possession of motorcycles in a strong central position, in the people of West Bengal, Telangana and Gujarat. Conclusion: Depicting association chains within net- works of extensively interacting variables such as health survey data appears to be a promising statisti- cal tool for disentangling the effects of environmen- tal circumstances, education, and social, economic, political and emotional (SEPE) factors on human growth.
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- 2023
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5. Significant, but not biologically relevant: Nosema ceranae infections and winter losses of honey bee colonies
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Vivian Schüler, Yuk-Chien Liu, Sebastian Gisder, Lennart Horchler, Detlef Groth, and Elke Genersch
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Biology (General) ,QH301-705.5 - Abstract
The analysis of a dataset collected over 15 years reveals no biological relevance of Nosema ceranae infections for colony losses; hence, N. ceranae is not considered a serious threat for honey bees in the background of Varroa destructor infestations.
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- 2023
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6. Environment, social behavior, and growth
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Michael Hermanussen, Christiane Scheffler, Aman Pulungan, Arup Ratan Bandyopadhyay, Jyoti Ratan Ghosh, Ayşegül Özdemir, Başak Koca Özer, Martin Musalek, Lidia Lebedeva, Elena Godina, Barry Bogin, Janina Tutkuviene, Milda Budrytė, Simona Gervickaite, Yehuda Limony, Sylvia Kirchengast, Peter Buston, Detlef Groth, Antonia Rösler, Nikolaos Gasparatos, Sergei Erofeev, Masiar Novine, Bárbara Navazo, Silvia Dahinten, Aleksandra Gomuła, Natalia Nowak-Szczepańska, and Sławomir Kozieł
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St. Nicolas House Analysis ,child growth ,body proportions ,social network ,public health ,migration ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Twenty-four scientists met for the annual Auxological conference held at Krobielowice castle, Poland, to discuss the diverse influences of the environment and of social behavior on growth following last year’s focus on growth and public health concerns (Hermanussen et al., 2022b). Growth and final body size exhibit marked plastic responses to ecological conditions. Among the shortest are the pygmoid people of Rampasasa, Flores, Indonesia, who still live under most secluded insular conditions. Genetics and nutrition are usually considered responsible for the poor growth in many parts of this world, but evidence is accumulating on the prominent impact of social embedding on child growth. Secular trends not only in the growth of height, but also in body proportions, accompany the secular changes in the social, economic and political conditions, with major influences on the emotional and educational circumstances under which the children grow up (Bogin, 2021). Aspects of developmental tempo and aspects of sports were discussed, and the impact of migration by the example of women from Bangladesh who grew up in the UK. Child growth was considered in particular from the point of view of strategic adjustments of individual size within the network of its social group. Theoretical considerations on network characteristics were presented and related to the evolutionary conservation of growth regulating hypothalamic neuropeptides that have been shown to link behavior and physical growth in the vertebrate species. New statistical approaches were presented for the evaluation of short term growth measurements that permit monitoring child growth at intervals of a few days and weeks.
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- 2023
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7. Human growth data analysis and statistics – the 5th Gülpe International Student Summer School
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Detlef Groth, Christiane Scheffler, and Michael Hermanussen
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Summer Schools ,Statistical Exercise ,Repetition ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
The Summer School in Gülpe (Ecological Station of the University of Potsdam) offers an exceptional learning opportunity for students to apply their knowledge and skills to real-world problems. With the guidance of experienced human biologists, statisticians, and programmers, students have the unique chance to analyze their own data and gain valuable insights. This interdisciplinary setting not only bridges different research areas but also leads to highly valuable outputs. The progress of students within just a few days is truly remarkable, especially when they are motivated and receive immediate feedback on their questions, problems, and results. The Summer School covers a wide range of topics, with this year’s focus mainly on two areas: understanding the impact of socioeconomic and physiological factors on human development and mastering statistical techniques for analyzing data such as changepoint analysis and the St. Nicolas House Analysis (SNHA) to visualize interacting variables. The latter technique, born out of the Summer School’s emphasis on gaining comprehensive data insights and understanding major relationships, has proven to be a valuable tool for researchers in the field. The articles in this special issue demonstrate that the Summer School in Gülpe stands as a testament to the power of practical learning and collaboration. Students who attend not only gain hands-on experience but also benefit from the expertise of professionals and the opportunity to engage with peers from diverse disciplines.
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- 2023
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8. In Python available: St. Nicolas House Algorithm (SNHA) with bootstrap support for improved performance in dense networks
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Tim Hake, Bernhard Bodenberger, and Detlef Groth
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Python ,correlation ,network reconstruction ,bootstrap ,St. Nicolas house algorithm ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
The St. Nicolas House algorithm (SNHA) finds association chains of direct dependent variables in a data set. The dependency is based on the correlation coefficient, which is visualized as an undirected graph. The network prediction is improved by a bootstrap routine. It enables the computation of the empirical p-value, which is used to evaluate the significance of the predicted edges. Synthetic data generated with the Monte Carlo method were used to firstly compare the Python package with the original R package, and secondly to evaluate the predicted network using the sensitivity, specificity, balanced classification rate and the Matthew's correlation coefficient (MCC). The Python implementation yields the same results as the R package. Hence, the algorithm was correctly ported into Python. The SNHA scores high specificity values for all tested graphs. For graphs with high edge densities, the other evaluation metrics decrease due to lower sensitivity, which could be partially improved by using bootstrap,while for graphs with low edge densities the algorithm achieves high evaluation scores. The empirical p-values indicated that the predicted edges indeed are significant.
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- 2023
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9. Growth and Public Health Concerns
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Michael Hermanussen, Christiane Scheffler, Liza Wilke, Sonja Böker, Detlef Groth, Sylvia Kirchengast, Dominik Hagmann, Lidia Lebedeva, Elena Godina, Aleksandra Gomula, Jan M Konarski, Ayşegül Özdemir Başaran, Başak Koca Özer, Janina Tutkuviene, Simona Gervickaite, Dziugile Kersnauskaite, and Slawomir Koziel
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dominance ,prestige ,nutrition ,spatial difference ,developmental tempo ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Seventeen scientists met for this year’s conference on Auxology held at Krobielowice castle, Poland, to discuss growth and public health concerns. The regulation of growth is complex and besides metabolic and endocrine components including hypothalamic releasing factors, growth hormone and multiple downstream effectors, comprises the full spectrum of the psychosocial, economic and emotional environment including signaling dominance, competence, prestige, or subordination and indulgence, all of this being sensitive to urban or rural lifestyle, the political climate and with marked plasticity throughout history. New statistical techniques (St. Nicolas House Analysis) are presented for analyzing anthropometric variables for public health concerns. The impact of spatial differences on developmental tempo, growth in height, and the prevalence of childhood obesity are discussed as well as the impact of social mobility on obesity, and the benefits of the biopsychosocial status when getting along with socio-economic disasters and the COVID-19 pandemic.
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- 2022
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10. The arithmetic dilemma when defining thinness, overweight and obesity in stunted populations
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Michael Hermanussen, Masiar Novine, Christiane Scheffler, and Detlef Groth
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BMI ,stunting ,prevalence ,thinness ,obesity ,misclassification ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background: Critical cut-off values of BMI-for-age z-scores (BAZ) are used to define “thinness”, “overweight” and “obesity”, but the validity of these cut-off values needs to be questioned in populations that are shorter or taller than the reference. We hypothesized that the prevalence of thinness, overweight, and obesity depends on population height and performed a random simulation. Methods: We created virtual child populations aged 2-10 years with normally distributed height expressed as height-for-age z-scores (HAZ) and weight expressed as weight-for-age z-score (WAZ), based on WHO growth standards and references, with a correlation r=0.7 between height and weight. We adjusted weight-for-height and calculated BAZ. Results: BAZ depends on height and age. In short children (mean HAZ=-2 to HAZ=-3), the prevalence of thinness falls to less than 1% in the youngest and rises up to 10% (mean HAZ=-2) and up to 13% (mean HAZ=-3) at age 10 years. The prevalence of obesity rises to up to 7% in the shortest and youngest and falls close to zero at age 10. Short young children and tall older children are more prone to be misclassified as overweight. Conclusions: The prevalence of thinness, overweight and obesity depends on height and age. The coexistence of being short and being overweight – currently referred to as “double burden of malnutrition” – needs consideration as to what extent this condition is a health issue or reflects calculation artefacts. The arithmetic dilemma particularly affects young children in short populations. We suggest abstaining from defining “thinness”, “overweight”, or “obesity” by BMI z-scores. Different states of under- and malnutrition should rather be classified by direct or indirect measures of body fat.
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- 2022
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11. Network reconstruction based on synthetic data generated by a Monte Carlo approach
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Masiar Novine, Cecilie Cordua Mattsson, and Detlef Groth
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Monte Carlo method ,network reconstruction ,mcgraph ,random sampling ,linear enamel hypoplasia ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background: Network models are useful tools for researchers to simplify and understand investigated systems. Yet, the assessment of methods for network construction is often uncertain. Random resampling simulations can aid to assess methods, provided synthetic data exists for reliable network construction. Objectives: We implemented a new Monte Carlo algorithm to create simulated data for network reconstruction, tested the influence of adjusted parameters and used simulations to select a method for network model estimation based on real-world data. We hypothesized, that reconstructs based on Monte Carlo data are scored at least as good compared to a benchmark. Methods: Simulated data was generated in R using the Monte Carlo algorithm of the mcgraph package. Benchmark data was created by the huge package. Networks were reconstructed using six estimator functions and scored by four classification metrics. For compatibility tests of mean score differences, Welch’s t-test was used. Network model estimation based on real-world data was done by stepwise selection. Samples: Simulated data was generated based on 640 input graphs of various types and sizes. The real-world dataset consisted of 67 medieval skeletons of females and males from the region of Refshale (Lolland) and Nordby (Jutland) in Denmark. Results: Results after t-tests and determining confidence intervals (CI95%) show, that evaluation scores for network reconstructs based on the mcgraph package were at least as good compared to the benchmark huge. The results even indicate slightly better scores on average for the mcgraph package. Conclusion: The results confirmed our objective and suggested that Monte Carlo data can keep up with the benchmark in the applied test framework. The algorithm offers the feature to use (weighted) un- and directed graphs and might be useful for assessing methods for network construction.
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- 2022
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12. PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments
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Yen Hoang, Stefanie Gryzik, Ines Hoppe, Alexander Rybak, Martin Schädlich, Isabelle Kadner, Dirk Walther, Julio Vera, Andreas Radbruch, Detlef Groth, Sabine Baumgart, and Ria Baumgrass
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multi-parametric analysis ,re-analysis ,combinatorial protein expression ,high-dimensional cytometry data ,mass cytometry data ,pattern perception ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm “pattern recognition of immune cells (PRI)” to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4+T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data.
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- 2022
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13. Growth during times of fear and emotional stress
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Christiane Scheffler, Alan D. Rogol, Mirela Iancu, Tomasz Hanc, Annang Giri Moelyo, Andrej Suchomlinov, Lidia Lebedeva, Yehuda Limony, Martin Musalek, Gudrun Veldre, Elena Z. Godina, Sylvia Kirchengast, Rebekka Mumm, Detlef Groth, Janina Tutkuviene, Sonja Böker, Basak Koca Ozer, Barbara Navazo, Laure Spake, Slawomir Koziel, and Michael Hermanussen
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stunting ,birth weight ,fear ,emotional stress ,economy ,SEPE ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Twenty-one scientists met for this year’s virtual conference on Auxology held at the University Potsdam, Germany, to discuss child and adolescent growth during times of fear and emotional stress. Growth within the broad range of normal for age and sex is considered a sign of good general health whereas fear and emotional stress can lead to growth faltering. Stunting is a sign of social disadvantage and poor parental education. Adverse childhood experiences affect child development, particularly in families with low parental education and low socioeconomic status. Negative effects were also shown in Indian children exposed prenatally and in early postnatal life to the cyclone Aila in 2009. Distrust, fears and fake news regarding the current Corona pandemic received particular attention though the effects generally appeared weak. Mean birth weight was higher; rates of low, very and extremely low birth weight were lower. Other topics discussed by the participants, were the influences of economic crises on birth weight, the measurement of self-confidence and its impact on growth, the associations between obesity, peer relationship, and behavior among Turkish adolescents, height trends in Indonesia, physiological neonatal weight loss, methods for assessing biological maturation in sportsmen, and a new method for skeletal age determination. The participants also discussed the association between acute myocardial infarction and somatotype in Estonia, rural-urban growth differences in Mongolian children, socio-environmental conditions and sexual dimorphism, biological mortality bias, and new statistical techniques for describing inhomogeneity in the association of bivariate variables, and for detecting and visualizing extensive interactions among variables.
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- 2021
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14. Growth, Nutrition and Economy
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Michael Hermanussen, Christiane Scheffler, Lidia Martin, Detlef Groth, James G. Waxmonsky, James Swanson, Natalia Nowak-Szczepanska, Aleksandra Gomula, Anna Apanasewicz, Jan M. Konarski, Robert M. Malina, Sylwia Bartkowiak, Lidia Lebedeva, Andrej Suchomlinov, Vsevolod Konstantinov, Werner Blum, Yehuda Limony, Raja Chakraborty, Sylvia Kirchengast, Janina Tutkuviene, Egle Marija Jakimaviciene, Ramune Cepuliene, Daniel Franken, Bárbara Navazo, Annang G. Moelyo, Takashi Satake, and Slawomir Koziel
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nutrition ,stunting ,socioeconomy ,education ,secular changes ,pubertal timing ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Twenty-three scientists met at Krobielowice, Poland to discuss the role of growth, nutrition and economy on body size. Contrasting prevailing concepts, re-analyses of studies in Indonesian and Guatemalan school children with high prevalence of stunting failed to provide evidence for an association between nutritional status and body height. Direct effects of parental education on growth that were not transmitted via nutrition were shown in Indian datasets using network analysis and novel statistical methods (St. Nicolas House Analysis) that translate correlation matrices into network graphs. Data on Polish children suggest significant impact of socioeconomic sensitivity on child growth, with no effect of maternal money satisfaction. Height and maturation tempo affect the position of a child among its peers. Correlations also exist between mood disorders and height. Secular changes in height and weight varied across decades independent of population size. Historic and recent Russian data showed that height of persons whose fathers performed manual work were on average four cm shorter than persons whose fathers were high-degree specialists. Body height, menarcheal age, and body proportions are sensitive to socioeconomic variables. Additional topics included delayed motherhood and its associations with newborn size; geographic and socioeconomic indicators related to low birth weight, prematurity and stillbirth rate; data on anthropometric history of Brazil, 1850-1950; the impact of central nervous system stimulants on the growth of children with attention-deficit/hyperactivity disorder; and pituitary development and growth hormone secretion. Final discussions debated on reverse causality interfering between social position, and adolescent growth and developmental tempo.
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- 2021
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15. Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception
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Stefanie Gryzik, Yen Hoang, Timo Lischke, Elodie Mohr, Melanie Venzke, Isabelle Kadner, Josephine Poetzsch, Detlef Groth, Andreas Radbruch, Andreas Hutloff, and Ria Baumgrass
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autoimmune disease ,cytokine expression ,multi-parametric analysis ,combinatorial protein expression ,cd4+ t cells ,high-dimensional flow cytometry ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21+ IFN-γhigh PD-1low CD40Lhigh CXCR5- Bcl-6- T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-α and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties.
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- 2020
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16. The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna
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Ina Maria Schedina, Detlef Groth, Ingo Schlupp, and Ralph Tiedemann
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Differential gene expression ,Gynogenesis ,Hybrid speciation ,Meiosis ,Poecilia formosa ,Poecilia latipinna ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna. Results We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR. Conclusions We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.
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- 2018
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17. Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany: Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis
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Sebastian Gisder, Vivian Schüler, Lennart L. Horchler, Detlef Groth, and Elke Genersch
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honey bee ,Apis mellifera ,Nosema spp. ,epidemiology ,replacement ,Microbiology ,QR1-502 - Abstract
The Western honey bee (Apis mellifera) is widely used as commercial pollinator in worldwide agriculture and, therefore, plays an important role in global food security. Among the parasites and pathogens threatening health and survival of honey bees are two species of microsporidia, Nosema apis and Nosema ceranae. Nosema ceranae is considered an emerging pathogen of the Western honey bee. Reports on the spread of N. ceranae suggested that this presumably highly virulent species is replacing its more benign congener N. apis in the global A. mellifera population. We here present a 12 year longitudinal cohort study on the prevalence of N. apis and N. ceranae in Northeast Germany. Between 2005 and 2016, a cohort of about 230 honey bee colonies originating from 23 apiaries was sampled twice a year (spring and autumn) resulting in a total of 5,600 bee samples which were subjected to microscopic and molecular analysis for determining the presence of infections with N. apis or/and N. ceranae. Throughout the entire study period, both N. apis- and N. ceranae-infections could be diagnosed within the cohort. Logistic regression analysis of the prevalence data demonstrated a significant increase of N. ceranae-infections over the last 12 years, both in autumn (reflecting the development during the summer) and in spring (reflecting the development over winter) samples. Cell culture experiments confirmed that N. ceranae has a higher proliferative potential than N. apis at 27° and 33°C potentially explaining the increase in N. ceranae prevalence during summer. In autumn, characterized by generally low infection prevalence, this increase was accompanied by a significant decrease in N. apis-infection prevalence. In contrast, in spring, the season with a higher prevalence of infection, no significant decrease of N. apis infections despite a significant increase in N. ceranae infections could be observed. Therefore, our data do not support a general advantage of N. ceranae over N. apis and an overall replacement of N. apis by N. ceranae in the studied honey bee population.
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- 2017
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18. Growth, Nutrition and Economy : Proceedings of the 27th Aschauer Soiree, held at Krobielowice, Poland, November 16th 2019
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Andrej Suchomlinov, Sylvia Kirchengast, Raja Chakraborty, Sylwia Bartkowiak, Slawomir Koziel, Robert M. Malina, Lidia Lebedeva, Takashi Satake, Egle Marija Jakimaviciene, Daniel Franken, Christiane Scheffler, Michael Hermanussen, Detlef Groth, Aleksandra Gomula, Jan M. Konarski, James M. Swanson, Ramune Cepuliene, Yehuda Limony, Lidia Martin, Werner F. Blum, Natalia Nowak-Szczepanska, Bárbara Navazo, Vsevolod Konstantinov, Janina Tutkuviene, Anna Apanasewicz, Annang G. Moelyo, and James G. Waxmonsky
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education ,Body proportions ,socioeconomy ,secular changes ,pubertal timing ,stunting ,Anthropometry ,Affect (psychology) ,medicine.disease ,Growth hormone secretion ,Low birth weight ,nutrition ,Economy ,Mood disorders ,medicine ,Social position ,Nutrition ,Stunting ,Socioeconomy ,Education ,Secular changes ,Pubertal timing ,Ciencias Naturales ,medicine.symptom ,Psychology ,Socioeconomic status - Abstract
Twenty-three scientists met at Krobielowice, Poland to discuss the role of growth, nutrition and economy on body size. Contrasting prevailing concepts, re-analyses of studies in Indonesian and Guatemalan school children with high prevalence of stunting failed to provide evidence for an association between nutritional status and body height. Direct effects of parental education on growth that were not transmitted via nutrition were shown in Indian datasets using network analysis and novel statistical methods (St. Nicolas House Analysis) that translate correlation matrices into network graphs. Data on Polish children suggest significant impact of socioeconomic sensitivity on child growth, with no effect of maternal money satisfaction. Height and maturation tempo affect the position of a child among its peers. Correlations also exist between mood disorders and height. Secular changes in height and weight varied across decades independent of population size. Historic and recent Russian data showed that height of persons whose fathers performed manual work were on average four cm shorter than persons whose fathers were high-degree specialists. Body height, menarcheal age, and body proportions are sensitive to socioeconomic variables. Additional topics included delayed motherhood and its associations with newborn size; geographic and socioeconomic indicators related to low birth weight, prematurity and stillbirth rate; data on anthropometric history of Brazil, 1850-1950; the impact of central nervous system stimulants on the growth of children with attention-deficit/hyperactivity disorder; and pituitary development and growth hormone secretion. Final discussions debated on reverse causality interfering between social position, and adolescent growth and developmental tempo., Facultad de Ciencias Naturales y Museo
- Published
- 2021
19. Chain Reversion for Detecting Associations in Interacting Variables—St. Nicolas House Analysis
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Detlef Groth, Christian Aßmann, and Michael Hermanussen
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association chains ,Rank (linear algebra) ,Health, Toxicology and Mutagenesis ,media_common.quotation_subject ,Association (object-oriented programming) ,lcsh:Medicine ,Bivariate analysis ,01 natural sciences ,Article ,Correlation ,010104 statistics & probability ,03 medical and health sciences ,Statistics ,0101 mathematics ,Spurious relationship ,030304 developmental biology ,Mathematics ,Statistical hypothesis testing ,media_common ,0303 health sciences ,Variables ,data matrices ,lcsh:R ,Public Health, Environmental and Occupational Health ,Linear model ,bivariate correlation coefficients ,network graphs ,St. Nicolas House Analysis - Abstract
(1) Background: We present a new statistical approach labeled as “St. Nicolas House Analysis” (SNHA) for detecting and visualizing extensive interactions among variables. (2) Method: We rank absolute bivariate correlation coefficients in descending order according to magnitude and create hierarchic “association chains” defined by sequences where reversing start and end point does not alter the ordering of elements. Association chains are used to characterize dependence structures of interacting variables by a graph. (3) Results: SNHA depicts association chains in highly, but also in weakly correlated data, and is robust towards spurious accidental associations. Overlapping association chains can be visualized as network graphs. Between independent variables significantly fewer associations are detected compared to standard correlation or linear model-based approaches. (4) Conclusion: We propose reversible association chains as a principle to detect dependencies among variables. The proposed method can be conceptualized as a non-parametric statistical method. It is especially suited for secondary data analysis as only aggregate information such as correlations matrices are required. The analysis provides an initial approach for clarifying potential associations that may be subject to subsequent hypothesis testing.
- Published
- 2021
20. Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception
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Josephine Poetzsch, Elodie Mohr, Ria Baumgrass, Stefanie Gryzik, Detlef Groth, Yen Hoang, Melanie Venzke, Andreas Hutloff, Timo Lischke, Andreas Radbruch, and Isabelle Kadner
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0301 basic medicine ,Mouse ,Autoimmunity ,Lymphocyte Activation ,CXCR5 ,Pattern Recognition, Automated ,Pathogenesis ,Mice ,Immunology and Inflammation ,0302 clinical medicine ,T-Lymphocyte Subsets ,Lupus Erythematosus, Systemic ,Biology (General) ,cd4+ t cells ,B-Lymphocytes ,Mice, Inbred NZB ,biology ,General Neuroscience ,T-Lymphocytes, Helper-Inducer ,General Medicine ,Flow Cytometry ,Cell biology ,medicine.anatomical_structure ,Medicine ,Female ,medicine.symptom ,multi-parametric analysis ,Research Article ,combinatorial protein expression ,QH301-705.5 ,T cell ,Science ,Inflammation ,autoimmune disease ,General Biochemistry, Genetics and Molecular Biology ,high-dimensional flow cytometry ,03 medical and health sciences ,Immune system ,medicine ,Animals ,cytokine expression ,B cell ,Autoimmune disease ,CD40 ,General Immunology and Microbiology ,Interleukins ,Cell Biology ,medicine.disease ,Antigens, Differentiation ,Coculture Techniques ,030104 developmental biology ,biology.protein ,Immunologic Memory ,030215 immunology - Abstract
Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21+ IFN-γhigh PD-1low CD40Lhigh CXCR5- Bcl-6- T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-α and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties.
- Published
- 2020
21. Influence of the A/T polymorphism of the FTO gene and sport specializations on the body composition of young Russian athletes
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Maria F Zaharova, Detlef Groth, O. I. Parfenteva, and Christiane Scheffler
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biology ,Athletes ,business.industry ,nutritional and metabolic diseases ,Regression analysis ,General Medicine ,biology.organism_classification ,FTO gene ,Physical activity level ,Polymorphism (computer science) ,Anthropology ,ddc:570 ,Cohort ,Aerobic exercise ,Medicine ,Animal Science and Zoology ,business ,Body mass index ,human activities ,Ecology, Evolution, Behavior and Systematics ,Institut für Biochemie und Biologie ,Demography - Abstract
Background: The polymorphism in FTO gene (rs9939609) is known to be associated with higher BMI and body fat mass content. However, environmental factors can modify this effect. The purpose of the present study was to investigate an association between sport specialization and the rs9939609 SNP in FTO gene in the cohort of professional and amateur young athletes. Methods: A total number of 250 young individuals 8-18 years old living in Moscow or Moscow district participated in the study. Individuals were divided into 3 groups in accordance with their physical activity level: control group (n = 49), amateurs (n = 67) and professionals (n = 137). Amateur and professional athletes were subdivided into groups according to their sport specialization. Quantile regression was used as a regression model, where the dependent (outcome) variable was BMI, along with percentage of body fat mass, and the independent variables (predictors) were the rs9939609 SNP in FTO gene, physical activity (active versus inactive), sport specialization (aerobic, intermittent sports and martial arts), nationality, level of sport experience (in years), gender and percentage of free fat mass content. Results: The regression analysis revealed that physical activity and sport specialization had greater impact compared to FTO allele in the group of physically active individuals. Physical activity, in particular aerobic, had negative associations with body fat mass and BMI. The rs9939609 SNP in FTO gene is associated with physical activity and aerobic activity. The magnitude of association becomes significantly larger at the upper quantiles of the body fat mass distribution. Conclusion: Physical activity and sport specialization explained more variance in body composition of physically active young individuals compared to the FTO polymorphism. Effect of interaction of physical activity, in particular aerobic, with the FTO polymorphism on body composition of young athletes was found.
- Published
- 2019
22. Modeling a secular trend by Monte Carlo simulation of height biased migration in a spatial network
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Detlef Groth
- Subjects
Adult ,Male ,Human Migration ,Standard deviation ,Anthropology, Physical ,Young Adult ,Spatial network ,ddc:570 ,Statistics ,Humans ,Computer Simulation ,Ecology, Evolution, Behavior and Systematics ,Institut für Biochemie und Biologie ,Mathematics ,Network model ,Models, Statistical ,Geography ,Human migration ,business.industry ,Null model ,Simulation modeling ,General Medicine ,Body Height ,Secular variation ,Military Personnel ,Anthropology ,Animal Science and Zoology ,Centrality ,business ,Monte Carlo Method ,Switzerland - Abstract
Background: In a recent Monte Carlo simulation, the clustering of body height of Swiss military conscripts within a spatial network with characteristic features of the natural Swiss geography was investigated. In this study I examined the effect of migration of tall individuals into network hubs on the dynamics of body height within the whole spatial network. The aim of this study was to simulate height trends. Material and methods: Three networks were used for modeling, a regular rectangular fishing net like network, a real world example based on the geographic map of Switzerland, and a random network. All networks contained between 144 and 148 districts and between 265-307 road connections. Around 100,000 agents were initially released with average height of 170 cm, and height standard deviation of 6.5 cm. The simulation was started with the a priori assumption that height variation within a district is limited and also depends on height of neighboring districts (community effect on height). In addition to a neighborhood influence factor, which simulates a community effect, body height dependent migration of conscripts between adjacent districts in each Monte Carlo simulation was used to re-calculate next generation body heights. In order to determine the direction of migration for taller individuals, various centrality measures for the evaluation of district importance within the spatial network were applied. Taller individuals were favored to migrate more into network hubs, backward migration using the same number of individuals was random, not biased towards body height. Network hubs were defined by the importance of a district within the spatial network. The importance of a district was evaluated by various centrality measures. In the null model there were no road connections, height information could not be delivered between the districts. Results: Due to the favored migration of tall individuals into network hubs, average body height of the hubs, and later, of the whole network increased by up to 0.1 cm per iteration depending on the network model. The general increase in height within the network depended on connectedness and on the amount of height information that was exchanged between neighboring districts. If higher amounts of neighborhood height information were exchanged, the general increase in height within the network was large (strong secular trend). The trend in the homogeneous fishnet like network was lowest, the trend in the random network was highest. Yet, some network properties, such as the heteroscedasticity and autocorrelations of the migration simulation models differed greatly from the natural features observed in Swiss military conscript networks. Autocorrelations of district heights for instance, were much higher in the migration models. Conclusion: This study confirmed that secular height trends can be modeled by preferred migration of tall individuals into network hubs. However, basic network properties of the migration simulation models differed greatly from the natural features observed in Swiss military conscripts. Similar network-based data from other countries should be explored to better investigate height trends with Monte Carlo migration approach.
- Published
- 2017
23. Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions
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Wei Chen, E Gralinska, M Jargosch, Detlef Groth, S Kröger, U Klotz, Ria Baumgrass, U Leser, Joachim Selbig, and Zhuo Fang
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0301 basic medicine ,Cellular differentiation ,Gene regulatory network ,Computational biology ,Biology ,Cell fate determination ,Mice ,03 medical and health sciences ,Th2 Cells ,Genetics ,Animals ,Gene Regulatory Networks ,Receptors, Cytokine ,Molecular Biology ,Transcription factor ,Institut für Biochemie und Biologie ,STAT6 ,NFIL3 ,GATA3 ,Cell Differentiation ,General Medicine ,Systems Integration ,030104 developmental biology ,Cytokines ,STAT6 Transcription Factor ,Biological network - Abstract
Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation. We focused on transcription factors (TFs), cytokines, and cytokine receptors and delineated 59 positively and 41 negatively STAT6-regulated genes, which were used to construct a transcriptional network around STAT6. The network illustrates that important and well-known TFs for Th2 cell differentiation are positively regulated by STAT6 and act either as activators for Th2 cells (e.g., Gata3, Atf3, Satb1, Nfil3, Maf, and Pparg) or as suppressors for other Th cell subpopulations such as Th1 (e.g., Ar), Th17 (e.g., Etv6), or iTreg (e.g., Stat3 and Hif1a) cells. Moreover, our approach reveals 11 TFs (e.g., Atf5, Creb3l2, and Asb2) with unknown functions in Th cell differentiation. This fact together with the observed enrichment of asthma risk genes among those regulated by STAT6 underlines the potential value of the data integration strategy used here. Thus, our results clearly support the opinion that data integration is a useful tool to delineate complex physiological processes.
- Published
- 2016
24. Height and skeletal morphology in relation to modern life style
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Detlef Groth, Christian Aßmann, Christiane Scheffler, and Michael Hermanussen
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Elbow breadth ,Adult ,Male ,Adolescent ,Physiology ,Body height ,Human Factors and Ergonomics ,Review ,Growth ,Biology ,Adult age ,Adult height ,Modern life ,Young Adult ,Japan ,Reference Values ,Physiology (medical) ,Humans ,Orthopedics and Sports Medicine ,Community effect ,ddc:610 ,Young adult ,Pelvic breadth ,Child ,Life Style ,Institut für Biochemie und Biologie ,Life style ,Community effect in height ,Public Health, Environmental and Occupational Health ,Growth spurt ,Body Height ,Anthropology ,Female ,Mathematisch-Naturwissenschaftliche Fakultät ,Demography - Abstract
Height and skeletal morphology strongly relate to life style. Parallel to the decrease in physical activity and locomotion, modern people are slimmer in skeletal proportions. In German children and adolescents, elbow breadth and particularly relative pelvic breadth (50th centile of bicristal distance divided by body height) have significantly decreased in recent years. Even more evident than the changes in pelvic morphology are the rapid changes in body height in most modern countries since the end-19th and particularly since the mid-20th century. Modern Japanese mature earlier; the age at take-off (ATO, the age at which the adolescent growth spurt starts) decreases, and they are taller at all ages. Preece-Baines modelling of six national samples of Japanese children and adolescents, surveyed between 1955 and 2000, shows that this gain in height is largely an adolescent trend, whereas height at take-off (HTO) increased by less than 3 cm since 1955; adolescent growth (height gain between ATO and adult age) increased by 6 cm. The effect of globalization on the modern post-war Japanese society ("community effect in height") on adolescent growth is discussed., Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 869
- Published
- 2015
25. Transcriptomics-Aided dissection of the intracellular and extracellular roles of microcystin in microcystis aeruginosa PCC 7806
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J. Merijn Schuurmans, Detlef Groth, A. Katharina Makower, Yvonne Zilliges, Elke Dittmann, Hans C. P. Matthijs, Aquatic Microbiology (IBED, FNWI), and Aquatic Ecology (AqE)
- Subjects
Microcystis ,Microcystins ,Mutant ,Secondary Metabolism ,Microcystin ,Real-Time Polymerase Chain Reaction ,Applied Microbiology and Biotechnology ,Microbiology ,Bacterial Proteins ,Gene cluster ,Environmental Microbiology ,Extracellular ,polycyclic compounds ,Microcystis aeruginosa ,Secondary metabolism ,Institut für Biochemie und Biologie ,chemistry.chemical_classification ,Ecology ,biology ,Gene Expression Profiling ,Microarray Analysis ,biology.organism_classification ,Cell biology ,chemistry ,international ,Gene Deletion ,Metabolic Networks and Pathways ,Intracellular ,Food Science ,Biotechnology - Abstract
Recent studies have provided evidence for both intracellular and extracellular roles of the potent hepatotoxin microcystin (MC) in the bloom-forming cyanobacterium Microcystis . Here, we surveyed transcriptomes of the wild-type strain M. aeruginosa PCC 7806 and the microcystin-deficient Δ mcyB mutant under low light conditions with and without the addition of external MC of the LR variant (MC-LR). Transcriptomic data acquired by microarray and quantitative PCR revealed substantial differences in the relative expression of genes of the central intermediary metabolism, photosynthesis, and energy metabolism. In particular, the data provide evidence for a lower photosystem I (PSI)-to-photosystem II (PSII) ratio and a more pronounced carbon limitation in the microcystin-deficient mutant. Interestingly, only 6% of the transcriptional differences could be complemented by external microcystin-LR addition. This MC signaling effect was seen exclusively for genes of the secondary metabolism category. The orphan polyketide synthase gene cluster IPF38-51 was specifically downregulated in response to external MC-LR under low light. Our data suggest a hierarchical and light-dependent cross talk of secondary metabolites and support both an intracellular and an extracellular role of MC in Microcystis .
- Published
- 2015
26. GOblet: Annotation of anonymous sequence data with Gene Ontology and Pathway terms
- Author
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Detlef Groth, Stefanie Hartmann, Georgia Panopoulou, Albert J. Poustka, and Steffen Hennig
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Genome ,Computational Biology ,Data processing, computer science, computer systems ,General Medicine ,Algorithms ,Metabolic Networks and Pathways ,Software ,TP248.13-248.65 ,Signal Transduction ,Biotechnology - Abstract
SummaryThe functional annotation of genomic data has become a major task for the ever-growing number of sequencing projects. In order to address this challenge, we recently developed GOblet, a free web service for the annotation of anonymous sequences with Gene Ontology (GO) terms. However, to overcome limitations of the GO terminology, and to aid in understanding not only single components but as well systemic interactions between the individual components, we have now extended the GOblet web service to integrate also pathway annotations. Furthermore, we extended and upgraded the data analysis pipeline with improved summaries, and added term enrichment and clustering algorithms. Finally, we are now making GOblet available as a stand-alone application for high-throughput processing on local machines. The advantages of this frequently requested feature is that a) the user can avoid restrictions of our web service for uploading and processing large amounts of data, and that b) confidential data can be analysed without insecure transfer to a public web server. The stand-alone version of the web service has been implemented using platform independent Tcl-scripts, which can be run with just a single runtime file utilizing the Starkit technology. The GOblet web service and the stand-alone application are freely available at http://goblet.molgen.mpg.de.
- Published
- 2008
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27. Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells
- Author
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Wasco Wruck, Detlef Groth, Thore C. Brink, Yasmin Babaie, Ralf Herwig, Boris Greber, James Adjaye, Thomas G. Burdon, and Hans Lehrach
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Pluripotent Stem Cells ,Homeobox protein NANOG ,Rex1 ,Cellular differentiation ,Apoptosis ,Biology ,Transfection ,Chromatin remodeling ,Suppression, Genetic ,SOX2 ,Transforming Growth Factor beta ,medicine ,Humans ,Cell Lineage ,Gene Regulatory Networks ,Hedgehog Proteins ,Blastocyst ,RNA, Small Interfering ,Induced pluripotent stem cell ,Embryonic Stem Cells ,reproductive and urinary physiology ,Receptors, Notch ,Gene Expression Profiling ,Cell Differentiation ,Cell Biology ,Embryonic stem cell ,Trophoblasts ,Cell biology ,Fibroblast Growth Factors ,Wnt Proteins ,medicine.anatomical_structure ,Bone Morphogenetic Proteins ,embryonic structures ,Molecular Medicine ,RNA Interference ,biological phenomena, cell phenomena, and immunity ,Octamer Transcription Factor-3 ,Metabolic Networks and Pathways ,Signal Transduction ,Developmental Biology - Abstract
The POU domain transcription factor OCT4 is a key regulator of pluripotency in the early mammalian embryo and is highly expressed in the inner cell mass of the blastocyst. Consistent with its essential role in maintaining pluripotency, Oct4 expression is rapidly downregulated during formation of the trophoblast lineage. To enhance our understanding of the molecular basis of this differentiation event in humans, we used a functional genomics approach involving RNA interference-mediated suppression of OCT4 function in a human ESC line and analysis of the resulting transcriptional profiles to identify OCT4-dependent genes in human cells. We detected altered expression of >1,000 genes, including targets regulated directly by OCT4 either positively (NANOG, SOX2, REX1, LEFTB, LEFTA/EBAF DPPA4, THY1, and TDGF1) or negatively (CDX2, EOMES, BMP4, TBX18, Brachyury [T], DKK1, HLX1, GATA6, ID2, and DLX5), as well as targets for the OCT4-associated stem cell regulators SOX2 and NANOG. Our data set includes regulators of ACTIVIN, BMP, fibroblast growth factor, and WNT signaling. These pathways are implicated in regulating human ESC differentiation and therefore further validate the results of our analysis. In addition, we identified a number of differentially expressed genes that are involved in epigenetics, chromatin remodeling, apoptosis, and metabolism that may point to underlying molecular mechanisms that regulate pluripotency and trophoblast differentiation in humans. Significant concordance between this data set and previous comparisons between inner cell mass and trophectoderm in human embryos indicates that the study of human ESC differentiation in vitro represents a useful model of early embryonic differentiation in humans.
- Published
- 2006
28. GOblet: a platform for Gene Ontology annotation of anonymous sequence data
- Author
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Detlef Groth, Steffen Hennig, and Hans Lehrach
- Subjects
Web server ,DNA, Complementary ,Sequence analysis ,Sequence Homology ,Biology ,computer.software_genre ,Bioinformatics ,Annotation ,Mice ,User-Computer Interface ,Software ,Data sequences ,Sequence Analysis, Protein ,Genetics ,Animals ,Humans ,Databases, Protein ,Java applet ,Internet ,Information retrieval ,business.industry ,Articles ,Sequence Analysis, DNA ,Plants ,Invertebrates ,Genes ,The Internet ,business ,computer ,Gene ontology annotation - Abstract
GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms. It uses a variety of different protein databases (human, murines, invertebrates, plants, sp-trembl) and their respective GO mappings. The user selects the appropriate database and alignment threshold and thereafter submits single or multiple nucleotide or protein sequences. Results are shown in different ways, e.g. as survey statistics for the main GO categories for all sequences or as detailed results for each single sequence that has been submitted. In its newest version, GOblet allows the batch submission of sequences and provides an improved display of results with the aid of Java applets. All output data, together with the Java applet, are packed to a downloadable archive for local installation and analysis. GOblet can be accessed freely at http://goblet.molgen.mpg.de.
- Published
- 2004
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