Paul-Bertram Kamp

The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing

Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora that has been recognized as causative agent of urinary tract infections. We report the analysis of the complete genome sequence of C. urealyticum DSM7109, which was initially recovered from a patient with alkaline-encrusted cystitis. The genome sequence was determined by a combination of pyrosequencing and Sanger technology. The chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and contains 2024 predicted coding sequences, of which 78% were considered as orthologous with genes in the Corynebacterium jeikeium K411 genome. Metabolic analysis of the lipid-requiring phenotype revealed the absence of a fatty acid synthase gene and the presence of a beta-oxidation pathway along with a large repertoire of auxillary genes for the degradation of exogenous fatty acids. A urease locus with the gene order ureABCEFGD may play a pivotal role in virulence of C. urealyticum by the alkalinization of human urine and the formation of struvite stones. Multidrug resistance of C. urealyticum DSM7109 is mediated by transposable elements, conferring resistances to macrolides, lincosamides, ketolides, aminoglycosides, chloramphenicol, and tetracycline. The complete genome sequence of C. urealyticum revealed a detailed picture of the lifestyle of this opportunistic human pathogen.

A biochip based on magnetoresistive sensors

The signal response of Bangs Laboratories magnetic markers with a mean diameter of 0.86 /spl mu/m on a spiral-shaped giant magnetoresistance sensor with a diameter of 70 /spl mu/m is investigated. The data show a linear dependence of the sensor signal on the surface coverage of the magnetic markers. The detection limit is reached at a coverage of about 5%, which corresponds to about 200 markers distributed across the surface of the sensor. The corresponding molecular binding of the analyte DNA and the magnetic markers show good selectivity and sensitivity.

A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data

Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.

Molecular Detection with Magnetic Labels and Magnetoresistive Sensors

For future lab-on-a-chip devices, compact and inexpensive detection units are required that directly translate the abundance of certain biomolecules into an electronic signal. By detecting specifically bound magnetic labels with magnetoresistive sensors, a versatile platform can be designed that fulfils those requirements and even enables on-chip manipulation of biomolecules by suitable magnetic gradient fields. Here, we present sensitive recognition of different types of magnetic labels by magnetoresistive sensors based both on giant magnetoresistance (GMR) and tunneling magnetoresistance (TMR). Hybridization experiments show that our prototype magnetoresistive biosensor can detect complex DNA with a length of one thousand base pairs down to a concentration of 24 pM. A direct comparison of our magnetoresistive and a standard fluorescent detection method clearly shows the advantage and competitiveness of our approach.

A biochip sensor based on giant and tunnel magnetoresistance

Summary form only given. Compared to the established fluorescent labeling method, the use of magnetic markers in biochip sensors has important advantages with respect to the detection of biomolecules at low concentrations. The magnetic markers are commercially available superparamagnetic microspheres. We demonstrate the applicability and functionality of both Giant Magnetoresistance (GMR) and Tunnel Magnetoresistance (TMR) sensors for detecting magnetic markers, also including corresponding molecular binding results with DNA. The GMR sensors consist of patterned Cu/NiFe multilayers in the second antiferromagnetic maximum, whose resistance vs. field dependencies can be tailored for large sensitivity (up to 3%/Oe). The experimental data are supported and understood by numerical simulations in a local field approach. Initial experiments with TMR sensors take advantage of the larger signal amplitude of around 40% and corresponding sensitivity of 12%/Oe.