Geertje van Keulen

Geertje van Keulen
Swansea University | SWAN · Institute of Life Science "ILS"

About

54
Publications
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1,102
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Introduction
Geertje van Keulen currently works at the Institute of Life Science "ILS", Swansea University. Their most recent publication is 'Organic matter identifies the nano-mechanical properties of native soil aggregates.'

Publications

Publications (54)
Article
Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically...
Preprint
The Park Grass Experiment, is an international reference soil with an impressive repository of temperate grassland (meta)data, however, it still lacks documentation of its soil metaproteome. The identification of these proteins is crucial to our understanding of soil ecology and their role in major biogeochemical processes. However, protein extract...
Article
This article is part of a series on the 'A Sustainable Future' workshops. As such, all three articles share the same introduction and 'workshop background' written by the Chair of the Steering Group.
Article
Full-text available
Accurate measurement of the composition of complex samples is key for the safety and efficacy of a range of products used in daily life, with sample preparation a critical step in this workflow. QuEChERS is one such method, however published protocols do not explicitly address acidic, basic, neutral, and amphiphilic species in a single protocol and...
Conference Paper
Spatial variations at the nanoscale of soil aggregate surfaces and in the spatial organisation of soil organic matter (SOM) are critical to understanding the factors involved in soil composition and turnover. However, soil nanoscience has been hampered by the lack of suitable methods to determine soil biophysical properties at nanometre spatial res...
Article
Localized variations at the nanoscale in soil aggregates and in the spatial organisation of soil organic matter (SOM) are critical to understanding the factors involved in soil composition and turnover. However soil nanoscience has been hampered by the lack of suitable methods to determine soil biophysical properties at nanometre spatial resolution...
Conference Paper
Many environmental processes that have a major impact at the field-scale are determined by events occurring at the micro- and nanometer scales. Due to technical challenges, soil has only relatively recently been the focus of nanoscale studies. Recent advances in Atomic Force Microscopy (AFM) now allow the characterization of natural soil samples bo...
Conference Paper
Soil hydrophobicity can lead to reduced soil fertility and heightened flood risk caused by increased run-off. Soil hydrophobicity is a well-known phenomenon when induced by natural events such as wildfires and anthropogenic causes including adding organic wastes or hydrocarbon contaminants. This presentation concerns a much more subtle effect - the...
Conference Paper
Soil water repellency is a common phenomenon affecting the hydrological responses of many soil and land use types in different climates. This in turn leads to decreased water infiltration, reduced vegetation cover, fertiliser run off and soil erosion. The fundamental (biological) causes of (bulk) soil repellency and its dynamic behaviour remain poo...
Conference Paper
Soil metaproteomics, the systemic extraction and identification of proteins from a soil, is key to understanding the biological and physical processes that occur within the soil at a molecular level. Until recently, direct extraction of proteins from complex soils have yielded only dozens of protein identifications due to interfering substances, su...
Article
Full-text available
Although molecular techniques, including metagenomics, have revolutionized the study of microbial ecology, the sheer magnitude of soil microbial diversity has prevented full access to the scope and scale of relevant microbiology questions worth asking of this complex habitat. Indeed, we still lack the ability to link most microorganisms to their me...
Article
Recent developments in nanotechnology enable the imaging, quantification and manipulation of materials at the near-atomic level. The number of applications of atomic-force microscopy (AFM) in the life sciences is increasing, now allowing the integrated study of topological and quantitative nanoscale mechanical characterization of living cells and t...
Article
The actinomycetes are well-known bioactive natural product producers, comprising the Streptomycetes, the richest drug-prolific family in all kingdoms, producing therapeutic compounds for the areas of infection, cancer, circulation, and immunity. Completion and annotation of many actinomycete genomes has highlighted further how proficient these bact...
Article
The family Streptomycetaceae comprises the genera Streptomyces, Kitasatospora, and Streptacidiphilus that are very difficult to differentiate both with genotypic and phenotypic characteristics. A separate generic status for Kitasatospora and Streptacidiphilus is questionable. Members of the family can be characterized as non-acid-alcohol-fast actin...
Article
Full-text available
We report the 4,385,577-bp high-quality draft assembly of the bacterial symbiont Rhodococcus rhodnii strain LMG5362, isolated from the gut of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the principle vector of the protozoan Trypanosoma cruzi, the etiological agent of Chagas disease. This sequence might provide useful information for sub...
Article
Full-text available
Multiple-choice question (MCQ) examinations are increasingly used as the assessment method of theoretical knowledge in large class-size modules in many life science degrees. MCQ-tests can be used to objectively measure factual knowledge, ability and high-level learning outcomes, but may also introduce gender bias in performance dependent on topic,...
Data
Questions used in the student feedback Survey (S1) and Post-Survey (S2). (DOCX)
Article
Full-text available
Phylogenetic reconstruction revealed that most Actinobacterial orthologs of S. coelicolor SCO2837, encoding a metal-dependent galactose oxidase-like protein, are found within Streptomyces and were probably acquired by horizontal gene transfer from fungi. Disruption of SCO2837 (glxA) caused a conditional bld phenotype that could not be reversed by e...
Data
GC content (%) of Streptomyces and S. aurantiaca genomes and SCO2837 (glxA) orthologs used in GC content comparisons. Only assembled genome sequences were included. ORF name is indicated when more than one glxA-like sequence per genome is present. (DOC)
Data
Diagram representing SCO2837 (glxA) genetic locus and DNA fragments used in sub-cloning experiments. The position of transposon insertions is indicated by gray vertical arrows, while the putative promoter predicted by PromBase is indicated by a striped arrow with chromosome position indicated. Refer to [19] for a detailed map of Tn5062. (TIF)
Data
Neighbour-Joining Bootstrap phylogenetic tree generated using protein sequences displaying similar domain composition and organisation to GlxA. Numbers at branch nodes indicate bootstrap values. (TIF)
Article
Full-text available
Streptomyces coelicolor A3(2) synthesizes three membrane-associated respiratory nitrate reductases (Nars). During aerobic growth in liquid medium the bacterium was able to reduce 50 mM nitrate stoichiometrically to nitrite. Construction and analysis of a mutant in which all three narGHJI operons were deleted showed that it failed to reduce n...
Article
Full-text available
Soil water repellency is a common phenomenon affecting a wide range of soil and land use types in different climates and is considered "the norm rather than the exception with its degree being variable". In all but the most severe cases, soil water repellency is transient with soils wetting eventually after prolonged wet weather and returning, when...
Article
Full-text available
Streptomycetes are exploited for production of a wide range of secondary metabolites, and there is much interest in enhancing the level of production of these metabolites. Secondary metabolites are synthesized in dedicated biosynthetic routes, but precursors and co-factors are derived from the primary metabolism. High level production of antibiotic...
Article
The actinomycete Streptomyces coelicolor is an obligate aerobe that is found in soil and aqueous habitats. The levels of oxygen in these environments can vary considerably, which raises the question of how these bacteria survive during periods of anaerobiosis. Although S. coelicolor cannot grow in the complete absence of oxygen, we demonstrate here...
Article
Gas vesicles are gas-filled prokaryotic organelles that provide buoyancy in many planktonic (cyano)bacteria and halophilic archaea. Remarkably, more and more genomes of soil bacteria, especially those of actinomycetes, show gas vesicle gene (gvp) clusters often encoding homologues of at least the eight gvp genes essential for gas vesicle formation...
Article
Gas vesicles are gas-filled prokaryotic organelles that function as flotation devices. This enables planktonic cyanobacteria and halophilic archaea to position themselves within the water column to make optimal use of light and nutrients. Few terrestrial microbes are known to contain gas vesicles. Genome sequences that have become available recentl...
Article
Full-text available
Binding-protein-dependent secondary transporters make up a unique transport protein family. They use a solute-binding protein in proton-motive-force-driven transport. Only a few systems have been functionally analysed. The yiaMNO genes of Escherichia coli K-12 encode one family member that transports the rare pentose l-xylulose. Its physiological r...
Article
Full-text available
Streptomyces coelicolor is an obligate aerobic, filamentous soil-dwelling bacterium. Remarkably, the genome of S. coelicolor has three copies of the narGHJI operon that encodes respiratory nitrate reductase. This review summarizes our current views on the requirements for multiple nitrate reductases in S. coelicolor.
Article
Streptomycetes are complex soil bacteria capable of producing aerial reproductive mycelium and secondary metabolites. We observed novel phenomena such as an extended life cycle including flotation and anaerobiosis using standing liquid cultures. This paper describes an improved method for isolating good quality RNA from standing liquid cultures of...
Article
Methods used to date for the isolation of DNA from polyacrylamide gels are elution based, time-consuming and with low yield in DNA. This paper describes an improved system employing polyacrylamide gels made of a meltable matrix. The new system was successfully applied to in situ DNA footprinting following gel retardation assays.
Article
Full-text available
The LysR-type transcriptional regulator CbbR controls the expression of the cbb and gap-pgk operons in Xanthobacter flavus, which encode the majority of the enzymes of the Calvin cycle required for autotrophic CO2 fixation. The cbb operon promoter of this chemoautotrophic bacterium contains three potential CbbR binding sites, two of which partially...
Article
Full-text available
Streptomyces coelicolor differentiates on solid agar media by forming aerial hyphae that septate into spores. We here show that differentiation also occurs in standing liquid minimal media. After a period of submerged growth, hyphae migrate to the air interface, where they become fixed by a rigid reflecting film. Colonies that result from these hyp...
Article
The filamentous bacteria Streptomyces coelicolor and Streptomyces lividans exhibit a complex life cycle. After a branched submerged mycelium has been established, aerial hyphae are formed that may septate to form chains of spores. The aerial structures possess several surface layers of unknown nature that make them hydrophobic, one of which is the...
Article
Full-text available
The levels of reduced and oxidized nicotinamide adenine dinucleotides were determined in Xanthobacter flavus during a transition from heterotrophic to autotrophic growth. Excess reducing equivalents are rapidly dissipated following induction of the Calvin cycle, indicating that the Calvin cycle serves as a sink for excess reducing equivalents. The...
Article
The vitellogenin-binding protein (VBP) is a member of the proline and acidic-region rich (PAR) family of bZip transcription factors. PAR is located N-terminally to the DNA-binding domain. VBP binds to specific sites within the 300-bp 5'-flanking region of the chicken-liver-specific estrogen-dependent very-low-density apolipoprotein gene (apoVLDL II...
Article
Full-text available
Autotrophic growth of Xanthobacter flavus is dependent on the fixation of carbon dioxide via the Calvin cycle and on the oxidation of simple organic and inorganic compounds to provide the cell with energy. Maximal induction of the cbb and gap-pgk operons encoding enzymes of the Calvin cycle occurs in the absence of multicarbon substrates and the pr...
Article
Full-text available
The last decade has seen significant advances in our understanding of the physiology, ecology, and molecular biology of chemoautotrophic bacteria. Many ecosystems are dependent on CO2 fixation by either free-living or symbiotic chemoautotrophs. CO2 fixation in the chemoautotroph occurs via the Calvin-Benson-Bassham cycle. The cycle is characterized...
Article
Full-text available
The expression of the cbb and gap-pgk operons of Xanthobacter flavus encoding enzymes of the Calvin cycle is regulated by the transcriptional regulator CbbR. In order to identify other genes involved in the regulation of these operons, a mutant was isolated with a lowered activity of a fusion between the promoter of the cbb operon and the reporter...
Article
Activation of the very low density apolipoprotein II (apoVLDL II) gene in chicken liver by estrogen results in the binding of a variety of nuclear proteins including members of the steroid receptor superfamily and the bZip superfamily to the immediate 5' flanking region. In the present study, we have identified a bZip protein from chicken liver as...
Article
Autotrophic bacteria and plants are able to convert the greenhouse gas carbon dioxide, CO2, into cell material. Although there are a number of metabolic pathways supporting autotrophic growth, the Calvin cycle is the most widely distributed of these. CO2 fixation requires a large amount of energy which originates from light or chemical oxidation, s...

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Projects

Projects (3)
Project
To determine the switch to soil hydrophobicity (water repellency) at many scales from fieldscale to nanoscale. Model this data through a simulation software called Pore Expert.