@inproceedings{BienefeldSpoetterReinschetal., author = {Bienefeld, Kaspar and Sp{\"o}tter, Andreas and Reinsch, Norbert and Mayer, Manfred and Gupta, Pooja}, title = {A new approach for honeybee breeding - genomic selection}, series = {44th Apimondia International Apicultural congress, 2015. Daejeon, South Korea}, booktitle = {44th Apimondia International Apicultural congress, 2015. Daejeon, South Korea}, language = {en} } @phdthesis{Gupta, author = {Gupta, Pooja}, title = {Integrating high-density marker information into the genetic evaluation of the honey bee}, language = {en} } @misc{GuptaRoeblitzKrauseetal., author = {Gupta, Pooja and R{\"o}blitz, Susanna and Krause, Carola and Knaus, Petra and Sch{\"u}tte, Christof}, title = {Mathematical modeling of the Smad and Non-Smad BMP signaling pathways in context of cell density}, series = {Computational Models in biology and medicine, 2013, Dresden, Germany}, journal = {Computational Models in biology and medicine, 2013, Dresden, Germany}, language = {en} } @inproceedings{GuptaKrauseRikeitetal., author = {Gupta, Pooja and Krause, Carola and Rikeit, Paul and R{\"o}blitz, Susanna and Knaus, Petra and Sch{\"u}tte, Christof}, title = {Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density}, series = {10th International BMP conference, 2014, Berlin, Germany}, booktitle = {10th International BMP conference, 2014, Berlin, Germany}, language = {en} } @article{BienefeldZautkeGupta, author = {Bienefeld, Kaspar and Zautke, Fred and Gupta, Pooja}, title = {A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour - illustrated by the hygienic behaviour towards Varroa infestation}, series = {Journal of Apicultural Research}, volume = {54(5)}, journal = {Journal of Apicultural Research}, pages = {541 -- 547}, language = {en} } @phdthesis{Gupta, author = {Gupta, Pooja}, title = {Integrating high-density marker information into the genetic evaluation of the honey bee}, language = {en} } @article{GuptaGramatkeEinspanieretal.2017, author = {Gupta, Pooja and Gramatke, Annika and Einspanier, Ralf and Sch{\"u}tte, Christof and von Kleist, Max and Sharbati, Jutta}, title = {In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements}, series = {Toxicology in Vitro}, volume = {41}, journal = {Toxicology in Vitro}, issn = {1438-0064}, pages = {179 -- 188}, year = {2017}, abstract = {Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence's real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50\% inhibitory concentration IC50 on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC50 values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA's in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master.}, language = {en} } @misc{GuptaGramatkeEinspanieretal., author = {Gupta, Pooja and Gramatke, Annika and Einspanier, Ralf and Sch{\"u}tte, Christof and von Kleist, Max and Sharbati, Jutta}, title = {In silicio cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62666}, abstract = {Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence's real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50\% inhibitory concentration IC_{50} on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC_{50} values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA's in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master.}, language = {en} } @article{SpoetterGuptaMayeretal., author = {Sp{\"o}tter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)}, series = {Journal of Heredity}, volume = {107}, journal = {Journal of Heredity}, number = {3}, pages = {220 -- 227}, language = {en} } @article{KoschekDurmazKrylovaetal., author = {Koschek, and Durmaz, Vedat and Krylova, and Wieczorek, and Gupta, Pooja and Richter, and Bujotzek, Alexander and Fischer, and Haag, Rainer and Freund, and Weber, Marcus and Rademann,}, title = {Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands}, series = {Beilstein J. Org. Chem.}, volume = {11}, journal = {Beilstein J. Org. Chem.}, pages = {837 -- 847}, language = {en} } @article{SpoetterGuptaNuernbergetal., author = {Sp{\"o}tter, Andreas and Gupta, Pooja and N{\"u}rnberg, and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica)}, volume = {12}, number = {2}, doi = {10.1111/j.1755-0998.2011.03106.x}, pages = {323 -- 332}, abstract = {Honey bees are exposed to a number of damaging pathogens and parasites. The most destructive among them, affecting mainly the brood, is Varroa destructor. A promising approach to prevent its spread is to breed for Varroa-tolerant honey bees. A trait that has been shown to provide significant resistance against the Varroa mite is hygienic behaviour, a behavioural response of honey bee workers to brood diseases in general. This study reports the development of a 44K SNP assay, specifically designed for the analysis of hygienic behaviour of individual worker bees (Apis mellifera carnica) directed against V. destructor. Initially, 70 000 SNPs chosen from a large set of SNPs published by the Honey Bee Genome Project were validated for their suitability in the analysis of the Varroa resistance trait 'uncapping of Varroa-infested brood'. This was achieved by genotyping of pooled DNA samples of trait bearers and two trait-negative controls using next-generation sequencing. Approximately 36 000 of these validated SNPs and another 8000 SNPs not validated in this study were selected for the construction of a SNP assay. This assay will be employed in following experiments to analyse individualized DNA samples in order to identify quantitative trait loci (QTL) involved in the control of the investigated trait and to evaluate and possibly confirm QTL found in other studies. However, this assay is not just suitable to study Varroa tolerance, it is as well applicable to analyse any other trait in honey bees. In addition, because of its high density, this assay provides access into genomic selection with respect to several traits considered in honey bee breeding. It will become publicly available via AROS Applied Biotechnology AS, Aarhus, Denmark, before the end of the year 2011.}, language = {en} } @article{GuptaPeterJungetal., author = {Gupta, Pooja and Peter, Sarah and Jung, Markus and Lewin, Astrid and Hemmrich-Stanisak, Georg and Franke, Andre and von Kleist, Max and Sch{\"u}tte, Christof and Einspanier, Ralf and Sharbati, Soroush and zur Bruegge, Jennifer}, title = {Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections}, series = {Scientific Reports in Nature}, volume = {9}, journal = {Scientific Reports in Nature}, doi = {10.1038/s41598-018-38141-x}, abstract = {Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection.}, language = {en} } @article{GuptaConradSpoetteretal., author = {Gupta, Pooja and Conrad, Tim and Sp{\"o}tter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Simulating a base population in honey bee for molecular genetic studies}, series = {Genetics Selection Evolution}, journal = {Genetics Selection Evolution}, doi = {10.1186/1297-9686-44-14}, abstract = {Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding values estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has distinct genetic and reproductive biology characteristics. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee.  Results: Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) ?2 statistics for Hardy- Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion: We developed a software program that takes into account the genetic and reproductive biology characteristics specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html}, language = {en} } @article{GuptaReinschSpoetteretal., author = {Gupta, Pooja and Reinsch, Norbert and Sp{\"o}tter, Andreas and Conrad, Tim and Bienefeld, Kaspar}, title = {Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)}, series = {BMC Genetics}, volume = {14}, journal = {BMC Genetics}, number = {36}, doi = {10.1186/1471-2156-14-36}, language = {en} }