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Papers by Daniel van der Lelie

... Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/4934\. Tit... more ... Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/4934. Title: Monitoring sulfate-reducing bacteria (SRB) using molecular tools during in situ immobilization of heavy metals. ...

International Journal of Phytoremediation, Apr 1, 2002

We investigated bacterial populations associated with the Zn hyperaccumulator Thlaspi caerulescen... more We investigated bacterial populations associated with the Zn hyperaccumulator Thlaspi caerulescens subsp. calaminaria grown in a soil collected from an abandoned Zn-Pb mine and smelter in Plombières, Belgium. The bacterial population of the nonrhizospheric soil consisted of typical soil bacteria, some exhibiting multiple heavy-metal resistance characteristics that often are associated with polluted substrates: 7.8% and 4% of the population survived

CRC Press eBooks, Sep 24, 1999

Gene Transfers and Environment, 1992

Alcaligenes eutrophus, a chemolithotrophic Gram-negative bacterium, is a good colonizer of pollut... more Alcaligenes eutrophus, a chemolithotrophic Gram-negative bacterium, is a good colonizer of polluted soils perfectly apt to survive in a variety of harsh conditions (Diels et al. 1989; Diels and Mergeay 1990). Therefore, strains of this species attracted our interest for various environmental applications. Using recombinant A.eutrophus CH34 (ATCC 43123) and A. eutrophus A5 strains, we were able to obtain concomitant expression of xenobiotic degrading genes (derived from the A5 chromosome) and heavy metal resistances encoded by the CH34 megaplasmids pMOL28 and pMOL30 (Mergeay et al. 1985; Springael Ph.D. thesis). Such strains look promising in bioremediation processes. In addition, research is going on to use CH34 or related strains in water and soil depollution and metal reclamation. Alcaligenes eutrophus was not only shown to be a good host for the expression of foreign genes, but also easily accessible for genetic manipulation by means of conjugaison. Having in mind to use A. eutrophus as a containment system for the release of recombinant DNA in the environment, this bacteria was also used as a recipient in a study to establish a model system assaying the intergeneric transmission and expression of cloned genes in soil samples (Top et al. 1990).

Phytoremediation of Contaminated Soil and Water, 1999

Biotechnology for Biofuels, 2011

Background To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industr... more Background To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms. Results From the metagenome sequences of an anaerobic microbial community actively decaying poplar biomass, we identified approximately 4,000 GHase homologs. Based on homology to GHase families/activities of interest and the quality of the sequences, candidates were selected for full-length cloning and subsequent expression. As an alternative strategy, a metagenome expression library was constructed and screened for GHase activities. These combined efforts resulted in the cloning of four novel GHases t...

Applied and Environmental Microbiology, 2006

We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughpu... more We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC , uvrB , and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully ...

International Journal of Phytoremediation, Mar 13, 2009

Nano Letters, 2007

We investigated the biocompatibility, specificity, and activity of a ligand-receptor-protein syst... more We investigated the biocompatibility, specificity, and activity of a ligand-receptor-protein system covalently bound to oxidized single-walled carbon nanotubes (SWNTs) as a model proof-of-concept for employing such SWNTs as biosensors. SWNTs were functionalized under ambient conditions with either the Knob protein domain from adenovirus serotype 12 (Ad 12 Knob) or its human cellular receptor, the CAR protein, via diimide-activated amidation. We confirmed the biological activity of Knob protein immobilized on the nanotube surfaces by using its labeled conjugate antibody and evaluated the activity and specificity of bound CAR on SWNTs, first, in the presence of fluorescently labeled Knob, which interacts specifically with CAR, and second, with a negative control protein, YieF, which is not recognized by biologically active CAR proteins. In addition, current-gate voltage (I-V(g)) measurements on a dozen nanotube devices explored the effect of protein binding on the intrinsic electronic properties of the SWNTs, and also demonstrated the devices' high sensitivity in detecting protein activity. All data showed that both Knob and CAR immobilized on SWNT surfaces fully retained their biological activities, suggesting that SWNT-CAR complexes can serve as biosensors for detecting environmental adenoviruses.

Biotechnology for Biofuels, 2011

ACS Nano, 2011

We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) ... more We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

Due to its fundamental role in the induction, training, and function of the immune system, it is ... more Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include the gut microbiome in clinical trials and studies that aim to broaden our understanding of COVID-19. A clear link seems to exist between gut microbiome health and COVID-19 progression. Understanding the “gut-lung axes”, where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut microbiome composition toward proinflammatory functional dysbiosis will be critical in addressing COVID-19, including disease progression, the importance of preexisting conditions, and the risk for developing complications. These insights will help to identify biomarkers and druggable targets and develop intervention strategies based on live biotherapeutics and nutrition to overcome gut microbiome dysbiosis and restore intestinal homeostasis as contributing factors to COVID-19.

Nature Communications

Environmental factors, mucosal permeability and defective immunoregulation drive overactive immun... more Environmental factors, mucosal permeability and defective immunoregulation drive overactive immunity to a subset of resident intestinal bacteria that mediate multiple inflammatory conditions. GUT-103 and GUT-108, live biotherapeutic products rationally designed to complement missing or underrepresented functions in the dysbiotic microbiome of IBD patients, address upstream targets, rather than targeting a single cytokine to block downstream inflammation responses. GUT-103, composed of 17 strains that synergistically provide protective and sustained engraftment in the IBD inflammatory environment, prevented and treated chronic immune-mediated colitis. Therapeutic application of GUT-108 reversed established colitis in a humanized chronic T cell-mediated mouse model. It decreased pathobionts while expanding resident protective bacteria; produced metabolites promoting mucosal healing and immunoregulatory responses; decreased inflammatory cytokines and Th-1 and Th-17 cells; and induced i...

... Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/4934\. Tit... more ... Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/4934. Title: Monitoring sulfate-reducing bacteria (SRB) using molecular tools during in situ immobilization of heavy metals. ...

International Journal of Phytoremediation, Apr 1, 2002

We investigated bacterial populations associated with the Zn hyperaccumulator Thlaspi caerulescen... more We investigated bacterial populations associated with the Zn hyperaccumulator Thlaspi caerulescens subsp. calaminaria grown in a soil collected from an abandoned Zn-Pb mine and smelter in Plombières, Belgium. The bacterial population of the nonrhizospheric soil consisted of typical soil bacteria, some exhibiting multiple heavy-metal resistance characteristics that often are associated with polluted substrates: 7.8% and 4% of the population survived

CRC Press eBooks, Sep 24, 1999

Gene Transfers and Environment, 1992

Alcaligenes eutrophus, a chemolithotrophic Gram-negative bacterium, is a good colonizer of pollut... more Alcaligenes eutrophus, a chemolithotrophic Gram-negative bacterium, is a good colonizer of polluted soils perfectly apt to survive in a variety of harsh conditions (Diels et al. 1989; Diels and Mergeay 1990). Therefore, strains of this species attracted our interest for various environmental applications. Using recombinant A.eutrophus CH34 (ATCC 43123) and A. eutrophus A5 strains, we were able to obtain concomitant expression of xenobiotic degrading genes (derived from the A5 chromosome) and heavy metal resistances encoded by the CH34 megaplasmids pMOL28 and pMOL30 (Mergeay et al. 1985; Springael Ph.D. thesis). Such strains look promising in bioremediation processes. In addition, research is going on to use CH34 or related strains in water and soil depollution and metal reclamation. Alcaligenes eutrophus was not only shown to be a good host for the expression of foreign genes, but also easily accessible for genetic manipulation by means of conjugaison. Having in mind to use A. eutrophus as a containment system for the release of recombinant DNA in the environment, this bacteria was also used as a recipient in a study to establish a model system assaying the intergeneric transmission and expression of cloned genes in soil samples (Top et al. 1990).

Phytoremediation of Contaminated Soil and Water, 1999

Biotechnology for Biofuels, 2011

Background To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industr... more Background To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms. Results From the metagenome sequences of an anaerobic microbial community actively decaying poplar biomass, we identified approximately 4,000 GHase homologs. Based on homology to GHase families/activities of interest and the quality of the sequences, candidates were selected for full-length cloning and subsequent expression. As an alternative strategy, a metagenome expression library was constructed and screened for GHase activities. These combined efforts resulted in the cloning of four novel GHases t...

Applied and Environmental Microbiology, 2006

We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughpu... more We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC , uvrB , and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully ...

International Journal of Phytoremediation, Mar 13, 2009

Nano Letters, 2007

We investigated the biocompatibility, specificity, and activity of a ligand-receptor-protein syst... more We investigated the biocompatibility, specificity, and activity of a ligand-receptor-protein system covalently bound to oxidized single-walled carbon nanotubes (SWNTs) as a model proof-of-concept for employing such SWNTs as biosensors. SWNTs were functionalized under ambient conditions with either the Knob protein domain from adenovirus serotype 12 (Ad 12 Knob) or its human cellular receptor, the CAR protein, via diimide-activated amidation. We confirmed the biological activity of Knob protein immobilized on the nanotube surfaces by using its labeled conjugate antibody and evaluated the activity and specificity of bound CAR on SWNTs, first, in the presence of fluorescently labeled Knob, which interacts specifically with CAR, and second, with a negative control protein, YieF, which is not recognized by biologically active CAR proteins. In addition, current-gate voltage (I-V(g)) measurements on a dozen nanotube devices explored the effect of protein binding on the intrinsic electronic properties of the SWNTs, and also demonstrated the devices' high sensitivity in detecting protein activity. All data showed that both Knob and CAR immobilized on SWNT surfaces fully retained their biological activities, suggesting that SWNT-CAR complexes can serve as biosensors for detecting environmental adenoviruses.

Biotechnology for Biofuels, 2011

ACS Nano, 2011

We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) ... more We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

Due to its fundamental role in the induction, training, and function of the immune system, it is ... more Due to its fundamental role in the induction, training, and function of the immune system, it is critical to include the gut microbiome in clinical trials and studies that aim to broaden our understanding of COVID-19. A clear link seems to exist between gut microbiome health and COVID-19 progression. Understanding the “gut-lung axes”, where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut microbiome composition toward proinflammatory functional dysbiosis will be critical in addressing COVID-19, including disease progression, the importance of preexisting conditions, and the risk for developing complications. These insights will help to identify biomarkers and druggable targets and develop intervention strategies based on live biotherapeutics and nutrition to overcome gut microbiome dysbiosis and restore intestinal homeostasis as contributing factors to COVID-19.

Nature Communications

Environmental factors, mucosal permeability and defective immunoregulation drive overactive immun... more Environmental factors, mucosal permeability and defective immunoregulation drive overactive immunity to a subset of resident intestinal bacteria that mediate multiple inflammatory conditions. GUT-103 and GUT-108, live biotherapeutic products rationally designed to complement missing or underrepresented functions in the dysbiotic microbiome of IBD patients, address upstream targets, rather than targeting a single cytokine to block downstream inflammation responses. GUT-103, composed of 17 strains that synergistically provide protective and sustained engraftment in the IBD inflammatory environment, prevented and treated chronic immune-mediated colitis. Therapeutic application of GUT-108 reversed established colitis in a humanized chronic T cell-mediated mouse model. It decreased pathobionts while expanding resident protective bacteria; produced metabolites promoting mucosal healing and immunoregulatory responses; decreased inflammatory cytokines and Th-1 and Th-17 cells; and induced i...