Biomedical subjects

Markus Schmid

Publications and source records attributed to Markus Schmid.

At least 19 recordsLinked to original sources

PubMed2006

Deciphering the evolution and metabolism of an anammox bacterium from a community genome.

Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.

Anaerobiosis↗

PubMed2005

Integration of spatial and temporal information during floral induction in Arabidopsis.

Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering. Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction. A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).

Arabidopsis↗

PubMed2005

Diversity of flowering responses in wild Arabidopsis thaliana strains.

Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci.

Journal Article↗

PubMed2005

Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation.

In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, and NO3-) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs) and is commonly attributed to denitrification (reduction of nitrate to N2 by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N2) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions of the world ocean, the Benguela upwelling system. Our in situ experiments indicate that nitrate is not directly converted to N2 by heterotrophic denitrification in the suboxic zone. In the Benguela system, nutrient profiles, anammox rates, abundances of anammox cells, and specific biomarker lipids indicate that anammox bacteria are responsible for massive losses of fixed nitrogen. We have identified and directly linked anammox bacteria to the removal of fixed inorganic nitrogen in the OMZ waters of an open-ocean setting. We hypothesize that anammox could also be responsible for substantial nitrogen loss from other OMZ waters of the ocean.

Atlantic Ocean↗

PubMed2005

A gene expression map of Arabidopsis thaliana development.

Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

Arabidopsis↗

PubMed2005

Kinetics, diffusional limitation and microscale distribution of chemistry and organisms in a CANON reactor.

In the Completely Autotrophic Nitrogen removal Over Nitrite (CANON) process, aerobic and anaerobic ammonia oxidizing bacteria cooperate to remove ammonia in one oxygen-limited reactor. Kinetic studies, microsensor analysis, and fluorescence in situ hybridization on CANON biomass showed a partial differentiation of processes and organisms within and among aggregates. Under normal oxygen-limited conditions ( approximately 5 microM O2), aerobic ammonia oxidation (nitrification) was restricted to an outer shell (<100 microm) while anaerobic ammonia oxidation (anammox) was found in the central anoxic parts. Larger type aggregates (>500 microm) accounted for 68% of the anammox potential whereas 65% of the nitrification potential was found in the smaller aggregates (<500 microm). Analysis with O2 and NO2- microsensors showed that the thickness of the activity zones varied as a function of bulk O2 and NO2- concentrations and flow rate.

Aerobiosis↗

PubMed2005

Specific effects of microRNAs on the plant transcriptome.

Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.

Base Pairing↗

PubMed2005

Anammox organisms: enrichment, cultivation, and environmental analysis.

Anaerobic ammonium oxidation (anammox) is the microbial oxidation of ammonium with nitrite to dinitrogen gas under strict anoxic conditions mediated by planctomycete-like bacteria. Anammox is not only important in the oceanic nitrogen cycle, but can also contribute substantially to nitrogen removal in municipal and industrial wastewater treatment. This chapter addresses the enrichment and cultivation of anammox bacteria in a sequencing batch reactor (SBR) and a gas lift reactor. The reactors can be operated anoxically as an anammox reactor or as an oxygen-limited "completely autotrophic nitrogen removal over nitrite" (CANON) system. Pure cultures of anammox organisms have not yet been obtained, but anammox cells can be purified to more than 99.5% using a Percoll density gradient centrifugation protocol. Furthermore, we show how anammox communities in natural and man-made ecosystems can be identified and characterized using molecular methods such as fluorescence in situ hybridization (FISH) or Planctomycetes/anammox-specific polymerase chain reaction (PCR). Both techniques are based on retrieved 16S rRNA gene sequences. In addition to 16S rRNA, unique anammox ladderane lipids can also serve as biomarkers to determine the abundance of anammox organisms in environmental samples.

Anaerobiosis↗

PubMed2004

Nitrification and anammox with urea as the energy source.

Urea is present in many ecosystems and can be used as an energy source by chemolithotrophic aerobic ammonia oxidizing bacteria (AOB). Thus the utilization of urea in comparison to ammonia, by AOB as well as anaerobic ammonia oxidizing (Anammox) bacteria was investigated, using enrichments cultures, inoculated with activated sludge, and molecular ecological methods. In batch enrichment cultures grown with ammonia a population established in 2 weeks, which was dominated by halophilic and halotolerant AOB as determined by fluorescence in situ hybridization (FISH) experiments, with the 16S rRNA targeting oligonucleotide probe NEU. In other batch enrichment cultures using urea, the AOB population was assessed by PCR amplification, cloning and phylogenetic analysis of amoA and ribosomal 16S rRNA genes. While only one of the 48 16S rRNA gene clones could be identified as AOB (Nitrosomonas oligotropha), the amoA approach revealed two more AOB, Nitrosomonas europaea and Nitrosomonas nitrosa to be present in the enrichment. FISH analysis of the enrichment with probe NEU and newly designed probes for a specific detection of N. oligotropha and N. nitrosa related organisms, respectively, showed that N. oligotropha-like AOB formed about 50% of the total bacterial population. Also N. nitrosa (about 15% of the total population) and N. europaea (about 5% of the total population) were relatively abundant. Additionally, continuous enrichments were performed under oxygen limitation. When ammonia was the energy source, the community in this reactor consisted of Anammox bacteria and AOB hybridizing with probe NEU. As the substrate was changed to urea, AOB related to N. oligotropha became the dominant AOB in this oxygen limited consortium. This resulted in a direct conversion of urea to dinitrogen gas, without the addition of organic carbon.

Aerobiosis↗

PubMed2004

ECG artifacts during intraoperative high-field MRI scanning.

High-field magnetic resonance imaging (MRI) (1.5 T) has recently been introduced into the neurosurgical operating room for intraoperative resection control and functional neuronavigational guidance. However, long-lasting neurosurgical procedures in an operating room equipped with a high-field MRI scanner raise new challenges to the anesthesiologist. In particular, monitoring of vital signs during anesthesia requires equipment compatible with working in close vicinity to the strong magnetic field. However, even MRI-compatible electrocardiographic (ECG) monitoring interferes with electromagnetic fields, so several ECG artifacts can be observed in static and pulsed magnetic fields. As shown in this study, pulsed high-frequency fields induce characteristic field frequency-based artifacts in the ECG that can imitate malignant arrhythmia or provoke ST-segment abnormalities. The knowledge of possible and characteristic ECG artifacts during high-field MRI is therefore essential to prevent misinterpretation. Moreover, interference-free parameters such as pulse oximetry or invasive blood pressure curves are highly relevant during intraoperative MRI scans.

Adult↗

PubMed2003

Dissection of floral induction pathways using global expression analysis.

Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.

Animals↗

PubMed2003

Genome-wide insertional mutagenesis of Arabidopsis thaliana.

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.

3' Untranslated Regions↗

PubMed2003

AthPEX10, a nuclear gene essential for peroxisome and storage organelle formation during Arabidopsis embryogenesis.

In yeasts and mammals, PEX10 encodes an integral membrane protein with a C3HC4 RING finger motif in its C-terminal domain and is required for peroxisome biogenesis and matrix protein import. In humans, its dysfunction in peroxisome biogenesis leads to severe Zellweger Syndrome and infantile Refsum disease. Here we show that dysfunction of a homologous gene in Arabidopsis leads to lethality at the heart stage of embryogenesis, impairing the biogenesis of peroxisomes, lipid bodies, and protein bodies. In a T-DNA insertion mutant disrupting the fourth exon of the AthPEX10 gene, ultrastructural analyses fail to detect peroxisomes characteristic for wild-type embryogenesis. Storage triacyl glycerides are not assembled into lipid bodies (oil bodies; oleosomes) surrounded by the phospholipid-protein monolayer membrane. Instead, the dysfunctional monolayer membranes, which derive from the bilayer membrane of the endoplasmic reticulum, accumulate in the cytosol. Concomitantly the transfer of the storage proteins from their site of synthesis at the endoplasmic reticulum to the vacuoles is disturbed. The mutant can be rescued by transformation with wild-type AthPEX10 cDNA. Transformants of wild-type Hansenula polymorpha cells with the AthPEX10 cDNA did produce the encoded protein without targeting it to peroxisomes. Additionally, the cDNA could not complement a Hansenula pex10 mutant unable to form peroxisomes. The ultrastructural knockout phenotype of AthPEX10p suggests that this protein in Arabidopsis is essential for peroxisome, oleosome, and protein transport vesicle formation.

Amino Acid Sequence↗

PubMed2003

Anaerobic ammonium oxidation by anammox bacteria in the Black Sea.

The availability of fixed inorganic nitrogen (nitrate, nitrite and ammonium) limits primary productivity in many oceanic regions. The conversion of nitrate to N2 by heterotrophic bacteria (denitrification) is believed to be the only important sink for fixed inorganic nitrogen in the ocean. Here we provide evidence for bacteria that anaerobically oxidize ammonium with nitrite to N2 in the world's largest anoxic basin, the Black Sea. Phylogenetic analysis of 16S ribosomal RNA gene sequences shows that these bacteria are related to members of the order Planctomycetales performing the anammox (anaerobic ammonium oxidation) process in ammonium-removing bioreactors. Nutrient profiles, fluorescently labelled RNA probes, 15N tracer experiments and the distribution of specific 'ladderane' membrane lipids indicate that ammonium diffusing upwards from the anoxic deep water is consumed by anammox bacteria below the oxic zone. This is the first time that anammox bacteria have been identified and directly linked to the removal of fixed inorganic nitrogen in the environment. The widespread occurrence of ammonium consumption in suboxic marine settings indicates that anammox might be important in the oceanic nitrogen cycle.

Anaerobiosis↗

PubMed2003

Characterization of activated sludge flocs by confocal laser scanning microscopy and image analysis.

In this study we present a new approach to determine volumes, heterogeneity factors, and compositions of the bacterial population of activated sludge flocs by 3D confocal imaging. After staining the fresh flocs with fluorescein-isothiocyanate, 75 stacks of images (containing approx. 3000 flocs) were acquired with a confocal laser scanning microscope. The self-developed macro 3D volume and surface determination for the KS 400 software package combined the images of one stack to a 3D image and calculated the real floc volume and surface. We determined heterogeneity factors like the ratio of real floc surface to the surface of a sphere with the respective volume and the fractal dimension (D(f)). According to their significant influence on floc integrity and quality, we also investigated the chemical composition of flocs and quantified their bacterial population structure by using group-specific rRNA-targeted probes for fluorescence in situ hybridization. By a settling experiment we enriched flocs with poor settling properties and determined the above-mentioned parameters. This approach revealed shifts in floc volume, heterogeneity, and bacterial and chemical composition according to the settling quality of the flocs.

Bacteria↗

PubMed2003

New concepts of microbial treatment processes for the nitrogen removal in wastewater.

Many countries strive to reduce the emissions of nitrogen compounds (ammonia, nitrate, NOx) to the surface waters and the atmosphere. Since mainstream domestic wastewater treatment systems are usually already overloaded with ammonia, a dedicated nitrogen removal from concentrated secondary or industrial wastewaters is often more cost-effective than the disposal of such wastes to domestic wastewater treatment. The cost-effectiveness of separate treatment has increased dramatically in the past few years, since several processes for the biological removal of ammonia from concentrated waste streams have become available. Here, we review those processes that make use of new concepts in microbiology: partial nitrification, nitrifier denitrification and anaerobic ammonia oxidation (the anammox process). These processes target the removal of ammonia from gases, and ammonium-bicarbonate from concentrated wastewaters (i.e. sludge liquor and landfill leachate). The review addresses the microbiology, its consequences for their application, the current status regarding application, and the future developments.

Industrial Microbiology↗

PubMed2003

Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria.

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.

Anaerobiosis↗

PubMed2002

Subunit gamma of the oxaloacetate decarboxylase Na(+) pump: interaction with other subunits/domains of the complex and binding site for the Zn(2+) metal ion.

The oxaloacetate decarboxylase Na(+) pump of Klebsiella pneumoniae is an enzyme complex composed of the peripheral alpha subunit and the two integral membrane-bound subunits beta and gamma. The alpha subunit consists of the N-terminal carboxyltransferase domain and the C-terminal biotin domain, which are connected by a flexible proline/alanine-rich linker peptide. To probe interactions between the two domains of the alpha subunit and between alpha-subunit domains and the gamma subunit, the relevant polypeptides were synthesized in Escherichia coli and subjected to copurification studies. The two alpha-subunit domains had no distinct affinity toward each other and could, therefore, not be purified as a unit on avidin-sepharose. The two domains reacted together catalytically, however, performing the carboxyl transfer from oxaloacetate to protein-bound biotin. This reaction was enhanced up to 6-fold in the presence of the Zn(2+)-containing gamma subunit. On the basis of copurification with different tagged proteins, the C-terminal biotin domain but not the N-terminal carboxyltransferase domain of the alpha subunit formed a strong complex with the gamma subunit. Upon the mutation of gamma H78 to alanine, the binding affinity to subunit alpha was lost, indicating that this amino acid may be essential for formation of the oxaloacetate decarboxylase enzyme complex. The binding residues for the Zn(2+) metal ion were identified by site-directed and deletion mutagenesis. In the gamma D62A or gamma H77A mutant, the Zn(2+) content of the decarboxylase decreased to 35% or 10% of the wild-type enzyme, respectively. Less than 5% of the Zn(2+) present in the wild-type enzyme was found if the two C-terminal gamma-subunit residues H82 and P83 were deleted. Corresponding with the reduced Zn(2+) contents in these mutants, the oxaloacetate decarboxylase activities were diminished. These results indicate that aspartate 62, histidine 77, and histidine 82 of the gamma subunit are ligands for the catalytically important Zn(2+) metal ion.

Base Sequence↗