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Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method.

Frontiers in pharmacology

Wati RK, de Graaf EF, Bogarín D, Heijungs R, van Vugt R, Smets EF, Gravendeel B.
PMID: 33776752
Front Pharmacol. 2021 Mar 12;11:586345. doi: 10.3389/fphar.2020.586345. eCollection 2020.

Necklace orchids (Coelogyninae, Epidendroideae) have been used in traditional medicine practices for centuries. Previous studies on a subset of unrelated orchid species utilized in these traditional practices revealed they possessed antimicrobial, anti-inflammatory, and anti-oxidant activity, providing experimental proof for...

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Wati RK, de Graaf EF, Bogarín D, et al. Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method. Front Pharmacol. 2021;11:586345doi: 10.3389/fphar.2020.586345.
Wati, R. K., de Graaf, E. F., Bogarín, D., Heijungs, R., van Vugt, R., Smets, E. F., & Gravendeel, B. (2020). Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method. Frontiers in pharmacology, 11586345. https://doi.org/10.3389/fphar.2020.586345
Wati, Richa Kusuma, et al. "Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method." Frontiers in pharmacology vol. 11 (2020): 586345. doi: https://doi.org/10.3389/fphar.2020.586345
Wati RK, de Graaf EF, Bogarín D, Heijungs R, van Vugt R, Smets EF, Gravendeel B. Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method. Front Pharmacol. 2021 Mar 12;11:586345. doi: 10.3389/fphar.2020.586345. eCollection 2020. PMID: 33776752; PMCID: PMC7994927.
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CSI Pollen: Diversity of Honey Bee Collected Pollen Studied by Citizen Scientists.

Insects

Brodschneider R, Kalcher-Sommersguter E, Kuchling S, Dietemann V, Gray A, Božič J, Briedis A, Carreck NL, Chlebo R, Crailsheim K, Coffey MF, Dahle B, González-Porto AV, Filipi J, de Graaf DC, Hatjina F, Ioannidis P, Ion N, Jørgensen AS, Kristiansen P, Lecocq A, Odoux JF, Özkirim A, Peterson M, Podrižnik B, Rašić S, Retschnig G, Schiesser A, Tosi S, Vejsnæs F, Williams G, van der Steen JJM.
PMID: 34821788
Insects. 2021 Nov 02;12(11). doi: 10.3390/insects12110987.

A diverse supply of pollen is an important factor for honey bee health, but information about the pollen diversity available to colonies at the landscape scale is largely missing. In this COLOSS study, beekeeper citizen scientists sampled and analyzed...

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Brodschneider R, Kalcher-Sommersguter E, Kuchling S, et al. CSI Pollen: Diversity of Honey Bee Collected Pollen Studied by Citizen Scientists. Insects. 2021;12(11)doi: 10.3390/insects12110987.
Brodschneider, R., Kalcher-Sommersguter, E., Kuchling, S., Dietemann, V., Gray, A., Božič, J., Briedis, A., Carreck, N. L., Chlebo, R., Crailsheim, K., Coffey, M. F., Dahle, B., González-Porto, A. V., Filipi, J., de Graaf, D. C., Hatjina, F., Ioannidis, P., Ion, N., Jørgensen, A. S., Kristiansen, P., Lecocq, A., Odoux, J. F., Özkirim, A., Peterson, M., Podrižnik, B., Rašić, S., Retschnig, G., Schiesser, A., Tosi, S., Vejsnæs, F., Williams, G., & van der Steen, J. J. M. (2021). CSI Pollen: Diversity of Honey Bee Collected Pollen Studied by Citizen Scientists. Insects, 12(11), . https://doi.org/10.3390/insects12110987
Brodschneider, Robert, et al. "CSI Pollen: Diversity of Honey Bee Collected Pollen Studied by Citizen Scientists." Insects vol. 12,11 (2021). doi: https://doi.org/10.3390/insects12110987
Brodschneider R, Kalcher-Sommersguter E, Kuchling S, Dietemann V, Gray A, Božič J, Briedis A, Carreck NL, Chlebo R, Crailsheim K, Coffey MF, Dahle B, González-Porto AV, Filipi J, de Graaf DC, Hatjina F, Ioannidis P, Ion N, Jørgensen AS, Kristiansen P, Lecocq A, Odoux JF, Özkirim A, Peterson M, Podrižnik B, Rašić S, Retschnig G, Schiesser A, Tosi S, Vejsnæs F, Williams G, van der Steen JJM. CSI Pollen: Diversity of Honey Bee Collected Pollen Studied by Citizen Scientists. Insects. 2021 Nov 02;12(11). doi: 10.3390/insects12110987. PMID: 34821788; PMCID: PMC8625907.
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The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model.

International journal of molecular sciences

MacKenzie KC, Garritsen R, Chauhan RK, Sribudiani Y, de Graaf BM, Rugenbrink T, Brouwer R, van Ijcken WFJ, de Blaauw I, Brooks AS, Sloots CEJ, Meeuwsen CJHM, Wijnen RM, Newgreen DF, Burns AJ, Hofstra RMW, Alves MM, Brosens E.
PMID: 34830235
Int J Mol Sci. 2021 Nov 16;22(22). doi: 10.3390/ijms222212354.

Patients with Hirschsprung disease (HSCR) do not always receive a genetic diagnosis after routine screening in clinical practice. One of the reasons for this could be that the causal mutation is not present in the cell types that are...

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MacKenzie KC, Garritsen R, Chauhan RK, et al. The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model. Int J Mol Sci. 2021;22(22)doi: 10.3390/ijms222212354.
MacKenzie, K. C., Garritsen, R., Chauhan, R. K., Sribudiani, Y., de Graaf, B. M., Rugenbrink, T., Brouwer, R., van Ijcken, W. F. J., de Blaauw, I., Brooks, A. S., Sloots, C. E. J., Meeuwsen, C. J. H. M., Wijnen, R. M., Newgreen, D. F., Burns, A. J., Hofstra, R. M. W., Alves, M. M., & Brosens, E. (2021). The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model. International journal of molecular sciences, 22(22), . https://doi.org/10.3390/ijms222212354
MacKenzie, Katherine C, et al. "The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model." International journal of molecular sciences vol. 22,22 (2021). doi: https://doi.org/10.3390/ijms222212354
MacKenzie KC, Garritsen R, Chauhan RK, Sribudiani Y, de Graaf BM, Rugenbrink T, Brouwer R, van Ijcken WFJ, de Blaauw I, Brooks AS, Sloots CEJ, Meeuwsen CJHM, Wijnen RM, Newgreen DF, Burns AJ, Hofstra RMW, Alves MM, Brosens E. The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model. Int J Mol Sci. 2021 Nov 16;22(22). doi: 10.3390/ijms222212354. PMID: 34830235; PMCID: PMC8624421.
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Reduced nest development of reared Bombus terrestris within apiary dense human-modified landscapes.

Scientific reports

Meeus I, Parmentier L, Pisman M, de Graaf DC, Smagghe G.
PMID: 33580131
Sci Rep. 2021 Feb 12;11(1):3755. doi: 10.1038/s41598-021-82540-6.

Wild bees are in decline on a local to global scale. The presence of managed honey bees can lead to competition for resources with wild bee species, which has not been investigated so far for human-modified landscapes. In this...

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Meeus I, Parmentier L, Pisman M, et al. Reduced nest development of reared Bombus terrestris within apiary dense human-modified landscapes. Sci Rep. 2021;11(1):3755doi: 10.1038/s41598-021-82540-6.
Meeus, I., Parmentier, L., Pisman, M., de Graaf, D. C., & Smagghe, G. (2021). Reduced nest development of reared Bombus terrestris within apiary dense human-modified landscapes. Scientific reports, 11(1), 3755. https://doi.org/10.1038/s41598-021-82540-6
Meeus, Ivan, et al. "Reduced nest development of reared Bombus terrestris within apiary dense human-modified landscapes." Scientific reports vol. 11,1 (2021): 3755. doi: https://doi.org/10.1038/s41598-021-82540-6
Meeus I, Parmentier L, Pisman M, de Graaf DC, Smagghe G. Reduced nest development of reared Bombus terrestris within apiary dense human-modified landscapes. Sci Rep. 2021 Feb 12;11(1):3755. doi: 10.1038/s41598-021-82540-6. PMID: 33580131; PMCID: PMC7881143.
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No more conventional reference electrode: transition time for determining chloride ion concentration.

Analytica chimica acta

Abbas Y, de Graaf DB, Olthuis W, van den Berg A.
PMID: 24703217
Anal Chim Acta. 2014 Apr 22;821:81-8. doi: 10.1016/j.aca.2014.03.013. Epub 2014 Mar 14.

Ion selective electrodes (ISE) are used extensively for the potentiometric determination of ion concentrations in electrolytes. However, the inherent drift in these measurements and the requirement of a stable reference electrode restrict the feasibility of this method for long-term...

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Abbas Y, de Graaf DB, Olthuis W, et al. No more conventional reference electrode: transition time for determining chloride ion concentration. Anal Chim Acta. 2014;821:81-8doi: 10.1016/j.aca.2014.03.013.
Abbas, Y., de Graaf, D. B., Olthuis, W., & van den Berg, A. (2014). No more conventional reference electrode: transition time for determining chloride ion concentration. Analytica chimica acta, 82181-8. https://doi.org/10.1016/j.aca.2014.03.013
Abbas, Yawar, et al. "No more conventional reference electrode: transition time for determining chloride ion concentration." Analytica chimica acta vol. 821 (2014): 81-8. doi: https://doi.org/10.1016/j.aca.2014.03.013
Abbas Y, de Graaf DB, Olthuis W, van den Berg A. No more conventional reference electrode: transition time for determining chloride ion concentration. Anal Chim Acta. 2014 Apr 22;821:81-8. doi: 10.1016/j.aca.2014.03.013. Epub 2014 Mar 14. PMID: 24703217.
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Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry.

Analytical chemistry

Belov ME, Ellis SR, Dilillo M, Paine MRL, Danielson WF, Anderson GA, de Graaf EL, Eijkel GB, Heeren RMA, McDonnell LA.
PMID: 28613836
Anal Chem. 2017 Jul 18;89(14):7493-7501. doi: 10.1021/acs.analchem.7b01168. Epub 2017 Jun 28.

Matrix-Assisted Laser Desorption Ionization, MALDI, has been increasingly used in a variety of biomedical applications, including tissue imaging of clinical tissue samples, and in drug discovery and development. These studies strongly depend on the performance of the analytical instrumentation...

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Belov ME, Ellis SR, Dilillo M, et al. Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry. Anal Chem. 2017;89(14):7493-7501doi: 10.1021/acs.analchem.7b01168.
Belov, M. E., Ellis, S. R., Dilillo, M., Paine, M. R. L., Danielson, W. F., Anderson, G. A., de Graaf, E. L., Eijkel, G. B., Heeren, R. M. A., & McDonnell, L. A. (2017). Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry. Analytical chemistry, 89(14), 7493-7501. https://doi.org/10.1021/acs.analchem.7b01168
Belov, Mikhail E, et al. "Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry." Analytical chemistry vol. 89,14 (2017): 7493-7501. doi: https://doi.org/10.1021/acs.analchem.7b01168
Belov ME, Ellis SR, Dilillo M, Paine MRL, Danielson WF, Anderson GA, de Graaf EL, Eijkel GB, Heeren RMA, McDonnell LA. Design and Performance of a Novel Interface for Combined Matrix-Assisted Laser Desorption Ionization at Elevated Pressure and Electrospray Ionization with Orbitrap Mass Spectrometry. Anal Chem. 2017 Jul 18;89(14):7493-7501. doi: 10.1021/acs.analchem.7b01168. Epub 2017 Jun 28. PMID: 28613836.
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13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches .

Biotechnology and bioengineering

de Graaf AA, Marx A, Nielsen J, Sahm H, Schmidt K, Villadsen J, Wiechert W.
PMID: 10191397
Biotechnol Bioeng. 1998 Apr 05;58(2):254-7. doi: 10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c.

Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily on the...

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de Graaf AA, Marx A, Nielsen J, et al. 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches . Biotechnol Bioeng. 1998;58(2):254-7doi: 10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c.
de Graaf AA, Marx, A., Nielsen, J., Sahm, H., Schmidt, K., Villadsen, J., & Wiechert, W. (1998). 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches . Biotechnology and bioengineering, 58(2), 254-7. https://doi.org/10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c
de Graaf AA, et al. "13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches ." Biotechnology and bioengineering vol. 58,2 (1998): 254-7. doi: https://doi.org/10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c
de Graaf AA, Marx A, Nielsen J, Sahm H, Schmidt K, Villadsen J, Wiechert W. 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches . Biotechnol Bioeng. 1998 Apr 05;58(2):254-7. doi: 10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c. PMID: 10191397.
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Determination of physiological parameters for endogenous glucose production in individuals using diurnal data.

BMC biomedical engineering

van Stee MF, Krishnan S, Groen AK, de Graaf AA.
PMID: 32903378
BMC Biomed Eng. 2019 Nov 15;1:29. doi: 10.1186/s42490-019-0030-z. eCollection 2019.

BACKGROUND: Triple tracer meal experiments used to investigate organ glucose-insulin dynamics, such as endogenous glucose production (EGP) of the liver are labor intensive and expensive. A procedure was developed to obtain individual liver related parameters to describe EGP dynamics...

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van Stee MF, Krishnan S, Groen AK, et al. Determination of physiological parameters for endogenous glucose production in individuals using diurnal data. BMC Biomed Eng. 2019;1:29doi: 10.1186/s42490-019-0030-z.
van Stee, M. F., Krishnan, S., Groen, A. K., & de Graaf, A. A. (2019). Determination of physiological parameters for endogenous glucose production in individuals using diurnal data. BMC biomedical engineering, 129. https://doi.org/10.1186/s42490-019-0030-z
van Stee, Mariël F, et al. "Determination of physiological parameters for endogenous glucose production in individuals using diurnal data." BMC biomedical engineering vol. 1 (2019): 29. doi: https://doi.org/10.1186/s42490-019-0030-z
van Stee MF, Krishnan S, Groen AK, de Graaf AA. Determination of physiological parameters for endogenous glucose production in individuals using diurnal data. BMC Biomed Eng. 2019 Nov 15;1:29. doi: 10.1186/s42490-019-0030-z. eCollection 2019. PMID: 32903378; PMCID: PMC7422590.
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Religious radicalization: social appraisals and finding radical redemption in extreme beliefs.

Current opinion in psychology

de Graaf BA, van den Bos K.
PMID: 33017747
Curr Opin Psychol. 2021 Aug;40:56-60. doi: 10.1016/j.copsyc.2020.08.028. Epub 2020 Sep 10.

In this article, we review the psychology of religion and radicalization. In doing so, we note that both macro-level approaches (that study structural conditions in society) and micro-level approaches (that focus on psychological coping and personal appraisal of individual...

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de Graaf BA, van den Bos K. Religious radicalization: social appraisals and finding radical redemption in extreme beliefs. Curr Opin Psychol. 2020;40:56-60doi: 10.1016/j.copsyc.2020.08.028.
de Graaf, B. A., & van den Bos, K. (2021). Religious radicalization: social appraisals and finding radical redemption in extreme beliefs. Current opinion in psychology, 4056-60. https://doi.org/10.1016/j.copsyc.2020.08.028
de Graaf, Beatrice A, and van den Bos, Kees. "Religious radicalization: social appraisals and finding radical redemption in extreme beliefs." Current opinion in psychology vol. 40 (2021): 56-60. doi: https://doi.org/10.1016/j.copsyc.2020.08.028
de Graaf BA, van den Bos K. Religious radicalization: social appraisals and finding radical redemption in extreme beliefs. Curr Opin Psychol. 2021 Aug;40:56-60. doi: 10.1016/j.copsyc.2020.08.028. Epub 2020 Sep 10. PMID: 33017747.
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Solvent-free synthesis of rechargeable solid oxygen reservoirs for clean hydrogen oxidation.

Angewandte Chemie (International ed. in English)

Rothenberg G, de Graaf EA, Bliek A.
PMID: 12888959
Angew Chem Int Ed Engl. 2003 Jul 28;42(29):3366-8. doi: 10.1002/anie.200351545.

No abstract available.

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Rothenberg G, de Graaf EA, Bliek A. Solvent-free synthesis of rechargeable solid oxygen reservoirs for clean hydrogen oxidation. Angew Chem Int Ed Engl. 2003;42(29):3366-8doi: 10.1002/anie.200351545.
Rothenberg, G., de Graaf, E. A., & Bliek, A. (2003). Solvent-free synthesis of rechargeable solid oxygen reservoirs for clean hydrogen oxidation. Angewandte Chemie (International ed. in English), 42(29), 3366-8. https://doi.org/10.1002/anie.200351545
Rothenberg, Gadi, et al. "Solvent-free synthesis of rechargeable solid oxygen reservoirs for clean hydrogen oxidation." Angewandte Chemie (International ed. in English) vol. 42,29 (2003): 3366-8. doi: https://doi.org/10.1002/anie.200351545
Rothenberg G, de Graaf EA, Bliek A. Solvent-free synthesis of rechargeable solid oxygen reservoirs for clean hydrogen oxidation. Angew Chem Int Ed Engl. 2003 Jul 28;42(29):3366-8. doi: 10.1002/anie.200351545. PMID: 12888959.
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Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments.

Biotechnology and bioengineering

Wiechert W, de Graaf AA.
PMID: 18636449
Biotechnol Bioeng. 1997 Jul 05;55(1):101-17. doi: 10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P.

The extension of metabolite balancing with carbon labeling experiments, as described by Marx et al. (Biotechnol. Bioeng. 49: 11-29), results in a much more detailed stationary metabolic flux analysis. As opposed to basic metabolite flux balancing alone, this method...

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Wiechert W, de Graaf AA. Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol Bioeng. 1997;55(1):101-17doi: 10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P.
Wiechert, W., & de Graaf, A. A. (1997). Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnology and bioengineering, 55(1), 101-17. https://doi.org/10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P
Wiechert, W, and de Graaf, A A. "Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments." Biotechnology and bioengineering vol. 55,1 (1997): 101-17. doi: https://doi.org/10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P
Wiechert W, de Graaf AA. Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol Bioeng. 1997 Jul 05;55(1):101-17. doi: 10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P. PMID: 18636449.
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Diagnostic markers based on a computational model of lipoprotein metabolism.

Journal of clinical bioinformatics

van Schalkwijk DB, van Ommen B, Freidig AP, van der Greef J, de Graaf AA.
PMID: 22029862
J Clin Bioinforma. 2011 Oct 26;1(1):29. doi: 10.1186/2043-9113-1-29.

BACKGROUND: Dyslipidemia is an important risk factor for cardiovascular disease and type II diabetes. Lipoprotein diagnostics, such as LDL cholesterol and HDL cholesterol, help to diagnose these diseases. Lipoprotein profile measurements could improve lipoprotein diagnostics, but interpretational complexity has...

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van Schalkwijk DB, van Ommen B, Freidig AP, et al. Diagnostic markers based on a computational model of lipoprotein metabolism. J Clin Bioinforma. 2011;1(1):29doi: 10.1186/2043-9113-1-29.
van Schalkwijk, D. B., van Ommen, B., Freidig, A. P., van der Greef, J., & de Graaf, A. A. (2011). Diagnostic markers based on a computational model of lipoprotein metabolism. Journal of clinical bioinformatics, 1(1), 29. https://doi.org/10.1186/2043-9113-1-29
van Schalkwijk, Daniël B, et al. "Diagnostic markers based on a computational model of lipoprotein metabolism." Journal of clinical bioinformatics vol. 1,1 (2011): 29. doi: https://doi.org/10.1186/2043-9113-1-29
van Schalkwijk DB, van Ommen B, Freidig AP, van der Greef J, de Graaf AA. Diagnostic markers based on a computational model of lipoprotein metabolism. J Clin Bioinforma. 2011 Oct 26;1(1):29. doi: 10.1186/2043-9113-1-29. PMID: 22029862; PMCID: PMC3305892.
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