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 - TY - JOUR A1 - Hermanussen, Michael A1 - Assmann, Christian A1 - Staub, K. A1 - Groth, Detlef T1 - Monte Carlo simulation of body height in a spatial network JF - European journal of clinical nutrition N2 - BACKGROUND/OBJECTIVES: Recent evidence suggests clustering of human body height. We want to assess the consequences of connectedness in a spatial network on height clustering in an artificial society. SUBJECTS/METHODS: We used an agent-based computer modelling technique (Monte Carlo simulation) and compared simulated height in a spatial network with characteristics of the observed geographic height distribution of three historic cohorts of Swiss military conscripts (conscripted in 1884-1891; 1908-1910; and 2004-2009). RESULTS: Conscript height shows several characteristic features: (1) height distributions are overdispersed. (2) Conscripts from districts with direct inter-district road connections tend to be similar in height. (3) Clusters of tall and clusters of short stature districts vary over time. Autocorrelations in height between late 19th and early 21st century districts are low. (4) Mean district height depends on the number of connecting roads and on the number of conscripts per district. Using Monte Carlo simulation, we were able to generate these natural characteristics in an artificial society. Already 5% height information from directly connected districts is sufficient to simulate the characteristics of natural height distribution. Very similar observations in regular rectangular networks indicate that the characteristics of Swiss conscript height distributions do not so much result from the particular Swiss geography but rather appear to be general features of spatial networks. CONCLUSIONS: Spatial connectedness can affect height clustering in an artificial society, similar to that seen in natural cohorts of military conscripts, and strengthen the concept of connectedness being involved in the regulation of human height. Y1 - 2016 U6 - https://doi.org/10.1038/ejcn.2016.45 SN - 0954-3007 SN - 1476-5640 VL - 70 SP - 671 EP - 678 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Groth, Detlef T1 - Modeling a secular trend by Monte Carlo simulation of height biased migration in a spatial network JF - Anthropologischer Anzeiger : journal of biological and clinical anthropology ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - 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. KW - secular trend KW - body height KW - simulation KW - community effect KW - Monte Carlo method KW - network Y1 - 2017 U6 - https://doi.org/10.1127/anthranz/2017/0703 SN - 0003-5548 SN - 2363-7099 VL - 74 IS - 1 SP - 81 EP - 88 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Bents, Dominik A1 - Rybak, Alexander A1 - Groth, Detlef T1 - Spatial conscript body height correlation of Norwegian districts in the 19th century JF - Anthropologischer Anzeiger : journal of biological and clinical anthropology ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Background: We investigated height of Norwegian conscripts in view of the hypothesis of a "community effect on height" using autocorrelation analysis of district heights within a time-span of 20 years at the end of the 19th century and correlations between neighboring districts at this time. Material and methods: After digitalizing available body height data of Norwegian draftees in 1877-1878, 1880 (averaged as 1878), and 1895-1897 (averaged as 1896) we calculated the magnitude of autocorrelation of body height within the same municipality at different time points. Furthermore, we generated three different neighborhood networks, (1) based on Euclidean distances, (2) a minimum spanning tree build on those distances, (3) a network founded on real world road connections. The networks were used to determine the correlation between body height of neighboring districts depending on the number of edges required to connect two municipalities. Results: The autocorrelation value for body heights was around r = 0.5 (for all p < 0.001) in the years 1878 and 1896. The correlation between neighboring districts varied in the Euclidean distance based network between 0.47 and 0.27 approximately for both years in a sorted order, descending from nearest (0-50 km) to farthest (150-200 km, for all p < 0.001). First order neighbors in the minimum spanning tree network correlation was 0.36 in 1878 and 0.42 in 1896 (for all p < 0.001). The values of neighbor correlation in the road connection based network ranged in 1878 from 0.42 (first order neighbors) to 0.17 (forth order neighbors, for all p < 0.01) and in 1896 from 0.46 (first order neighbors) to 0.12 (forth order neighbors, for all p < 0.05). Conclusion: This initial study of Norwegian conscript height data from the 19th century showed significant medium sized effects for the within district autocorrelation between 1878 and 1896 as well as medium neighborhood correlation, slightly lower in comparison to a recent study regarding Swiss conscripts. Digitalizing more data from other years in this and later time spans as well as using older road and ship connections instead of the actual road data might stabilize and improve those findings. KW - body height KW - correlation KW - Norway KW - conscripts KW - community effect on height Y1 - 2017 U6 - https://doi.org/10.1127/anthranz/2017/0700 SN - 0003-5548 SN - 2363-7099 VL - 74 IS - 1 SP - 65 EP - 69 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Gisder, Sebastian A1 - Schüler, Vivian A1 - Horchler, Lennart L. A1 - Groth, Detlef A1 - Genersch, Elke T1 - Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany BT - Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis JF - Frontiers in cellular and infection microbiology N2 - 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 degrees 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. KW - honey bee KW - Apis mellifera KW - Nosema spp. KW - epidemiology KW - replacement Y1 - 2017 U6 - https://doi.org/10.3389/fcimb.2017.00301 SN - 2235-2988 VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Gomula, Aleksandra A1 - Koziel, Slawomir A1 - Groth, Detlef A1 - Bielicki, Tadeusz T1 - The effect of neighboring districts on body height of Polish conscripts JF - Anthropologischer Anzeiger : journal of biological and clinical anthropology ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - The aim of the study was to investigate the correlation of heights of conscripts living in neighboring districts in Poland. The study used 10% of a nationally representative sample of 26,178 males 18.5-19.5 years old examined during the National survey of Polish conscripts conducted in 2001. The sample represented all regions and social strata of the country and included 354 different districts within 16 voivodships (provinces). Analyses were performed with the R statistical software. A small but significant correlation (0.24, p < 0.0001) was observed for height between 1st order neighboring districts. Correlations decreased with increased distances between neighboring districts, but remained significant for 7th node neighbors (0.18, p < 0.0001). Regarding voivodships (provinces), average height showed a geographical trend from the northwest (relatively tall) to the southeast (relatively short), and the correlation was stronger for first order neighboring provinces (0.796, p < 0.001). This study revealed clusters of tall people and short people, providing a support for hypothesis of the community effect in height. Small correlations between 1st order neighbors than in another country (Switzerland) may be associated with differences in geography, since in Poland there are no natural barriers (e.g., mountains) and road infrastructure is well-developed. KW - body height KW - community effect KW - Polish conscripts Y1 - 2017 U6 - https://doi.org/10.1127/anthranz/2017/0701 SN - 0003-5548 SN - 2363-7099 VL - 74 IS - 1 SP - 71 EP - 76 PB - Schweizerbart CY - Stuttgart ER - TY - GEN A1 - Koziel, Slawomir A1 - Hermanussen, Michael A1 - Gomula, Alexandra A1 - Swanson, James A1 - Kaczmarek, Maria A1 - El-Shabrawi, Mortada A1 - Elhusseini, Mona A1 - Satake, Takashi A1 - Martinovic Klaric, Irena A1 - Scheffler, Christiane A1 - Morkuniene, Ruta A1 - Godina, Elena A1 - Sasa, Missoni A1 - Tutkuviene, Janina A1 - Siniarska, Anna A1 - Nieczuja-Dwojacka, Joanna A1 - Nunez, Javier A1 - Groth, Detlef A1 - Barbieri, Davide T1 - Adolescence - a Transition to Adulthood Proceedings of the 24th Aschauer Soiree, held at Jurata, Poland, November 5th 2016 T2 - Pediatric Endocrinology Reviews N2 - Eighteen scientists met at Jurata, Poland, to discuss various aspects of the transition from adolescence to adulthood. This transition is a delicate period facing complex interactions between the adolescents and the social group they belong to. Social identity, group identification and identity signalling, but also stress affecting basal salivary cortisol rhythms, hypertension, inappropriate nutrition causing latent and manifest obesity, moreover, in developing and under-developed countries, parasitosis causing anaemia thereby impairing growth and development, are issues to be dealt with during this period of the human development. In addition, some new aspects of the association between weight, height and head circumference in the newborns were discussed, as well as intrauterine head growth and head circumference as health risk indicators. KW - Strategic growth adjustment KW - BMI KW - Growth faltering KW - Secular trend KW - Obesity KW - Growth modelling Y1 - 2017 SN - 1565-4753 VL - 14 IS - 3 SP - 326 EP - 334 PB - Medical Media CY - Netanya ER - TY - JOUR A1 - Schedina, Ina Maria A1 - Groth, Detlef A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna JF - BMC Genomics N2 - 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. KW - Differential gene expression KW - Gynogenesis KW - Hybrid speciation KW - Meiosis KW - Poecilia formosa KW - Poecilia latipinna KW - Poecilia mexicana Y1 - 2018 U6 - https://doi.org/10.1186/s12864-017-4382-2 SN - 1471-2164 VL - 19 IS - 12 SP - 1 EP - 18 PB - BioMed Central CY - London ER - TY - GEN A1 - Schedina, Ina Maria A1 - Groth, Detlef A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 412 KW - Differential gene expression KW - Gynogenesis KW - Hybrid speciation KW - Meiosis KW - Poecilia formosa KW - Poecilia latipinna KW - Poecilia mexicana Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409299 ER -