5813
2015
eng
conferenceobject
0
--
--
--
A new approach for honeybee breeding - genomic selection
44th Apimondia International Apicultural congress, 2015. Daejeon, South Korea
yes
Kaspar Bienefeld
lange
Andreas Spötter
Norbert Reinsch
Manfred Mayer
Pooja Gupta
Numerical Mathematics
Gupta, Pooja
no-project
5814
2013
eng
doctoralthesis
0
--
--
--
Integrating high-density marker information into the genetic evaluation of the honey bee
Christof Schütte
Pooja Gupta
lange
Kaspar Bienefeld
Numerical Mathematics
Computational Systems Biology
no-project
Freie Universität Berlin
5815
2013
eng
poster
0
--
--
--
Mathematical modeling of the Smad and Non-Smad BMP signaling pathways in context of cell density
Computational Models in biology and medicine, 2013, Dresden, Germany
no
Pooja Gupta
Pooja gupta
Susanna Röblitz
Carola Krause
Petra Knaus
Christof Schütte
Numerical Mathematics
Computational Systems Biology
Gupta, Pooja
Röblitz, Susanna
Schütte, Christof
BMPsys
5816
2014
eng
conferenceobject
0
--
--
--
Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density
10th International BMP conference, 2014, Berlin, Germany
yes
Pooja Gupta
lange
Carola Krause
Paul Rikeit
Susanna Röblitz
Petra Knaus
Christof Schütte
Numerical Mathematics
Computational Systems Biology
Gupta, Pooja
Röblitz, Susanna
Schütte, Christof
BMPsys
MODAL-MedLab
MODAL-Gesamt
5835
2016
eng
541
547
54(5)
article
0
--
--
--
A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour – illustrated by the hygienic behaviour towards Varroa infestation
Journal of Apicultural Research
yes
Kaspar Bienefeld
Pooja Gupta
Fred Zautke
Pooja Gupta
Numerical Mathematics
Gupta, Pooja
no-project
4966
2013
eng
doctoralthesis
0
--
--
2013-02-28
Integrating high-density marker information into the genetic evaluation of the honey bee
http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000093870
Christof Schütte
Pooja Gupta
Steffen Prohaska
Numerical Mathematics
Freie Universität Berlin
6259
2017
2017
eng
179
188
41
article
0
--
--
--
In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements
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.
Toxicology in Vitro
1438-0064
yes
urn:nbn:de:0297-zib-62666
Pooja Gupta
Erlinda Körnig
Annika Gramatke
Ralf Einspanier
Christof Schütte
Max von Kleist
Jutta Sharbati
eng
uncontrolled
Real-time cell analyzer
eng
uncontrolled
Toxicity
eng
uncontrolled
Mathematical modeling
Cell biology
Systems biology, networks
Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) [See also 80A30]
Numerical Mathematics
Computational Systems Biology
Gupta, Pooja
Schütte, Christof
MODAL-MedLab
MODAL-Gesamt
6266
2017
eng
reportzib
0
--
--
--
In silicio cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements
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.
1438-0064
urn:nbn:de:0297-zib-62666
To appear in ...
Pooja Gupta
Paulina Bressel
Annika Gramatke
Ralf Einspanier
Christof Schütte
Max von Kleist
Jutta Sharbati
ZIB-Report
17-08
eng
uncontrolled
Real-time cell analyzer
eng
uncontrolled
Toxicity
eng
uncontrolled
Mathematical modeling
eng
uncontrolled
IC_{50}
Cell biology
Systems biology, networks
Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) [See also 80A30]
Numerical Mathematics
Gupta, Pooja
Schütte, Christof
MODAL-MedLab
MODAL-Gesamt
https://opus4.kobv.de/opus4-zib/files/6266/zibreport_17-08.pdf
5836
2016
eng
220
227
3
107
article
0
--
--
--
Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)
Journal of Heredity
yes
Andreas Spötter
Pooja Gupta
Pooja Gupta
Manfred Mayer
Norbert Reinsch
Kaspar Bienefeld
Numerical Mathematics
Gupta, Pooja
no-project
5593
2015
eng
837
847
11
article
0
--
--
--
Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands
Beilstein J. Org. Chem.
yes
Koschek
Marcus Weber
Vedat Durmaz
Krylova
Wieczorek
Pooja Gupta
Richter
Alexander Bujotzek
Fischer
Rainer Haag
Freund
Marcus Weber
Rademann
Numerical Mathematics
Computational Molecular Design
Durmaz, Vedat
Weber, Marcus
Matheon-A19
Salsa-Klimm
SFB765-C2
6854
2012
eng
323
332
2
12
article
0
--
--
--
Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica)
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.
10.1111/j.1755-0998.2011.03106.x
yes
Andreas Spötter
Pooja Gupta
Pooja Gupta
Nürnberg
Norbert Reinsch
Kaspar Bienefeld
Numerical Mathematics
Gupta, Pooja
7148
2019
eng
9
article
0
2019-02-07
2019-02-07
--
Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections
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.
Scientific Reports in Nature
10.1038/s41598-018-38141-x
yes
Pooja Gupta
Erlinda Körnig
Sarah Peter
Markus Jung
Astrid Lewin
Georg Hemmrich-Stanisak
Andre Franke
Max von Kleist
Christof Schütte
Ralf Einspanier
Soroush Sharbati
Jennifer zur Bruegge
Numerical Mathematics
Gupta, Pooja
Schütte, Christof
MODAL-MedLab
MODAL-Gesamt
6358
2012
eng
article
0
--
--
--
Simulating a base population in honey bee for molecular genetic studies
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
Genetics Selection Evolution
10.1186/1297-9686-44-14
yes
Pooja Gupta
Paulina Bressel
Tim Conrad
Andreas Spötter
Norbert Reinsch
Kaspar Bienefeld
Numerical Mathematics
Visual Data Analysis
Gupta, Pooja
Conrad, Tim
MODAL-MedLab
Visual and Data-centric Computing
6351
2013
eng
36
14
article
0
--
--
--
Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)
BMC Genetics
10.1186/1471-2156-14-36
yes
Pooja Gupta
Paulina Bressel
Norbert Reinsch
Andreas Spötter
Tim Conrad
Kaspar Bienefeld
Numerical Mathematics
Visual Data Analysis
Gupta, Pooja
Conrad, Tim
MODAL-MedLab
Visual and Data-centric Computing