TY - JOUR A1 - Groth, Detlef A1 - Reszka, R. A1 - Schenk, Jörg A. T1 - Polyethylene glycol-mediated transformation of escherichia coli is increased by room temperature incubation Y1 - 1996 ER - TY - JOUR A1 - Steinfath, Matthias A1 - Strehmel, Nadine A1 - Peters, Rolf A1 - Schauer, Nicolas A1 - Groth, Detlef A1 - Hummel, Jan A1 - Steup, Martin A1 - Selbig, Joachim A1 - Kopka, Joachim A1 - Geigenberger, Peter A1 - Dongen, Joost T. van T1 - Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach N2 - Biomarkers are used to predict phenotypical properties before these features become apparent and, therefore, are valuable tools for both fundamental and applied research. Diagnostic biomarkers have been discovered in medicine many decades ago and are now commonly applied. While this is routine in the field of medicine, it is of surprise that in agriculture this approach has never been investigated. Up to now, the prediction of phenotypes in plants was based on growing plants and assaying the organs of interest in a time intensive process. For the first time, we demonstrate in this study the application of metabolomics to predict agronomic important phenotypes of a crop plant that was grown in different environments. Our procedure consists of established techniques to screen untargeted for a large amount of metabolites in parallel, in combination with machine learning methods. By using this combination of metabolomics and biomathematical tools metabolites were identified that can be used as biomarkers to improve the prediction of traits. The predictive metabolites can be selected and used subsequently to develop fast, targeted and low-cost diagnostic biomarker assays that can be implemented in breeding programs or quality assessment analysis. The identified metabolic biomarkers allow for the prediction of crop product quality. Furthermore, marker-assisted selection can benefit from the discovery of metabolic biomarkers when other molecular markers come to its limitation. The described marker selection method was developed for potato tubers, but is generally applicable to any crop and trait as it functions independently of genomic information. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=1467-7644 U6 - https://doi.org/10.1111/j.1467-7652.2010.00516.x SN - 1467-7644 ER - TY - JOUR A1 - Hill, Natascha A1 - Leow, Alexander A1 - Bleidorn, Christoph A1 - Groth, Detlef A1 - Tiedemann, Ralph A1 - Selbig, Joachim A1 - Hartmann, Stefanie T1 - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information JF - Theory in biosciences N2 - Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary. KW - Mutual Information KW - Evolution KW - Gene structure Y1 - 2013 U6 - https://doi.org/10.1007/s12064-012-0173-0 SN - 1431-7613 VL - 132 IS - 2 SP - 93 EP - 104 PB - Springer CY - New York ER - TY - JOUR A1 - Vi, Son Lang A1 - Trost, Gerda A1 - Lange, Peggy A1 - Czesnick, Hjördis A1 - Rao, Nishta A1 - Lieber, Diana A1 - Laux, Thomas A1 - Gray, William M. A1 - Manley, James L. A1 - Groth, Detlef A1 - Kappel, Christian A1 - Lenhard, Michael T1 - Target specificity among canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA N2 - Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs. Y1 - 2013 U6 - https://doi.org/10.1073/pnas.1303967110 SN - 0027-8424 VL - 110 IS - 34 SP - 13994 EP - 13999 PB - NATL ACAD SCIENCES CY - WASHINGTON ER - TY - JOUR A1 - Hermanussen, Michael A1 - Alt, Christoph A1 - Staub, Kaspar A1 - Aßmann, Christian A1 - Groth, Detlef T1 - The impact of physical connectedness on body height in Swiss conscripts JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Background: Human populations differ in height. Recent evidence suggests that social networks play an important role in the regulation of adolescent growth and adult height. We further investigated the effect of physical connectedness on height. Material and methods: We considered Switzerland as a geographic network with 169 nodes (district capitals) and 335 edges (connecting roads) and studied effects of connectedness on height in Swiss conscript from 1884-1891, 1908-1910, and 2004-2009. We also created exponential-family random graph models to separate possible unspecific effects of geographic vicinity. Results: In 1884-1891, in 1908-1910, and in 2004-2009, 1st, 2nd and 3rd order neighboring districts significantly correlate in height (p<0.01). The correlations depend on the order of connectedness, they decline with increasing distance. Short stature districts tend to have short, tall stature districts tend to have tall neighbors. Random network analyses suggest direct road effects on height. Whereas in 1884-1891, direct road effects were only visible between 1st order neighbors, direct road effects extended to 2nd and 3rd in 1908-1910, and in 2004-2009, also to 4th order neighbors, and might reflect historic improvements in transportation. The spatial correlations did not significantly change when height was controlled for goiter (1884-1889) and for median per capita income (2006), suggesting direct road effects also in goiter-allowed-for height and income-allowed-for height. Conclusion: Height in a district depends on height of physically connected neighboring districts. The association decreases with increasing distance in the net. The present data suggest that people can be short because their neighbors are short; or tall because their neighbors are tall (community effect on growth). Psycho-biological effects seem to control growth and development within communities that go far beyond our current understanding of growth regulation. KW - body height KW - connectedness KW - community effect KW - conscripts KW - Switzerland Y1 - 2014 U6 - https://doi.org/10.1127/0003-5548/2014/0466 SN - 0003-5548 VL - 71 IS - 4 SP - 313 EP - 327 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Schwarte, Sandra A1 - Wegner, Fanny A1 - Havenstein, Katja A1 - Groth, Detlef A1 - Steup, Martin A1 - Tiedemann, Ralph T1 - Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana JF - Plant molecular biology : an international journal of fundamental research and genetic engineering N2 - Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts. KW - Arabidopsis thaliana KW - Divergent evolution KW - Intraspecific genetic variation KW - Positive selection KW - Starch metabolizing enzymes KW - Transcript levels Y1 - 2015 U6 - https://doi.org/10.1007/s11103-015-0293-2 SN - 0167-4412 SN - 1573-5028 VL - 87 IS - 4-5 SP - 489 EP - 519 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Makower, A. Katharina A1 - Schuurmans, J. Merijn A1 - Groth, Detlef A1 - Zilliges, Yvonne A1 - Matthijs, Hans C. P. A1 - Dittmann-Thünemann, Elke T1 - Transcriptomics-Aided dissection of the intracellular and extracellular roles of microcystin in microcystis aeruginosa PCC 7806 JF - Applied and environmental microbiology N2 - 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 Delta 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. Y1 - 2015 U6 - https://doi.org/10.1128/AEM.02601-14 SN - 0099-2240 SN - 1098-5336 VL - 81 IS - 2 SP - 544 EP - 554 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Hermanussen, Michael A1 - Scheffler, Christiane A1 - Groth, Detlef A1 - Aßmann, Christian T1 - Height and skeletal morphology in relation to modern life style JF - Journal of physiological anthropology N2 - 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. KW - Pelvic breadth KW - Elbow breadth KW - Growth KW - Adult height KW - Community effect in height Y1 - 2015 U6 - https://doi.org/10.1186/s40101-015-0080-4 SN - 1880-6805 VL - 34 PB - BioMed Central CY - London ER - TY - JOUR A1 - Jargosch, M. A1 - Kroeger, S. A1 - Gralinska, E. A1 - Klotz, Ulrike A1 - Fang, Z. A1 - Chen, W. A1 - Leser, U. A1 - Selbig, Joachim A1 - Groth, Detlef A1 - Baumgrass, Ria T1 - Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions JF - Genetics and molecular research N2 - 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 Hifla) 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. KW - Data integration KW - Th2 cells KW - Gene regulatory network KW - STAT6 KW - Transcription factors Y1 - 2016 U6 - https://doi.org/10.4238/gmr.15028493 SN - 1676-5680 VL - 15 PB - FUNPEC CY - Ribeirao Preto ER - TY - GEN A1 - Hermanussen, Michael A1 - Ipsen, Josefin A1 - Mumm, Rebekka A1 - Assmann, Christian A1 - Quitmann, Julia A1 - Gomula, Aleksandra A1 - Lehmann, Andreas A1 - Jasch, Isabelle A1 - Tassenaar, Vincent A1 - Bogin, Barry A1 - Satake, Takashi A1 - Scheffler, Christiane A1 - Nunez, Javier A1 - Godina, Elena A1 - Hardeland, Ruediger A1 - Boldsen, Jesper L. A1 - El-Shabrawi, Mortada A1 - Elhusseini, Mona A1 - Barbu, Carmen Gabriela A1 - Pop, Ralucca A1 - Soederhaell, Jani A1 - Merker, Andrea A1 - Swanson, James A1 - Groth, Detlef T1 - Stunted Growth. Proceedings of the 23rd Aschauer Soiree, Held at Aschauhof, Germany, November 7th 2015 T2 - Pediatric Endocrinology Reviews N2 - Twenty-four scientists met at Aschauhof, Altenhof, Germany, to discuss the associations between child growth and development, and nutrition, health, environment and psychology. Meta-analyses of body height, height variability and household inequality, in historic and modern growth studies published since 1794, highlighting the enormously flexible patterns of child and adolescent height and weight increments throughout history which do not only depend on genetics, prenatal development, nutrition, health, and economic circumstances, but reflect social interactions. A Quality of Life in Short Stature Youth Questionnaire was presented to cross-culturally assess health-related quality of life in children. Changes of child body proportions in recent history, the relation between height and longevity in historic Dutch samples and also measures of body height in skeletal remains belonged to the topics of this meeting. Bayesian approaches and Monte Carlo simulations offer new statistical tools for the study of human growth. KW - Adolescent growth KW - Peer group KW - Growth hormone KW - Community effect KW - Body height Y1 - 2016 SN - 1565-4753 VL - 13 SP - 756 EP - 767 PB - Medical Media CY - Netanya ER -