Biomedical subjects

Peter de Groot

Publications and source records attributed to Peter de Groot.

7 recordsLinked to original sources

PubMed2006

Stroboscopic white-light interference microscopy.

The principle of stroboscopic motion freezing of oscillating objects extends directly to interference microscopes that use coherence as part of the measurement principle. Analysis shows, however, that the fringe contrast loss for out-of-plane motion in stroboscopic interferometry is a wavelength-dependent phenomenon, which can alter the apparent nominal center wavelength of the white-light source. As in monochromatic systems, the key adjustable parameter is the duty cycle, equal to the product of the vibrational frequency and the pulse width. This theoretical study provides detailed graphs of expected errors as a function of the duty cycle, including fringe contrast loss, apparent wavelength shift, and measurement error.

Algorithms↗

PubMed2005

Generating fringe-free images from phase-shifted interferometry data.

Weighted averaging of a sequence of phase-shifted interference patterns yields a fringe-free intensity image that can be useful for machine vision, lateral metrology, defect detection, and other supplementary tasks in a surface-profiling interferometer. Coefficients for effective fringe-removal algorithms follow from a Fourier analysis of phase-shifting errors. Theoretical and experimental examples illustrate the substantially improved performance of a well-designed weighted average over a simple linear sum of data frames.

Journal Article↗

PubMed2005

An unusual Tn21-like transposon containing an ars operon is present in highly arsenic-resistant strains of the biomining bacterium Acidithiobacillus caldus.

A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain of the moderately thermophilic, sulfur-oxidizing, biomining bacterium Acidithiobacillus caldus. This strain originated from a commercial plant used for the bio-oxidation of gold-bearing arsenopyrite concentrates. Continuous selection for arsenic resistance over many years had made the bacterium resistant to high concentrations of arsenic. Sequence analysis indicated that TnAtcArs is 12 444 bp in length and has 40 bp terminal inverted repeat sequences and divergently transcribed resolvase and transposase genes that are related to the Tn21-transposon subfamily. A series of genes consisting of arsR, two tandem copies of arsA and arsD, two ORFs (7 and 8) and arsB is situated between the resolvase and transposase genes. Although some commercial strains of At. caldus contained the arsDA duplication, when transformed into Escherichia coli, the arsDA duplication was unstable and was frequently lost during cultivation or if a plasmid containing TnAtcArs was conjugated into a recipient strain. TnAtcArs conferred resistance to arsenite and arsenate upon E. coli cells. Deletion of one copy of arsDA had no noticeable effect on resistance to arsenite or arsenate in E. coli. ORFs 7 and 8 had clear sequence similarity to an NADH oxidase and a CBS-domain-containing protein, respectively, but their deletion did not affect resistance to arsenite or arsenate in E. coli. TnAtcArs was actively transposed in E. coli, but no increase in transposition frequency in the presence of arsenic was detected. Northern hybridization and reporter gene studies indicated that although ArsR regulated the 10 kb operon containing the arsenic-resistance genes in response to arsenic, ArsR had no effect on the regulation of genes associated with transposition activity.

Acidithiobacillus↗

PubMed2004

Signal modeling for low-coherence height-scanning interference microscopy.

We propose a computationally efficient theoretical model for low-coherence interferometric profilers that measure surface heights by scanning the optical path difference of the interferometer. The model incorporates both geometric and spectral effects by means of an incoherent superposition of ray bundles through the interferometer spanning a range of wavelengths, incident angles, and pupil plane coordinates. This superposition sum is efficiently performed in the frequency domain, followed by a Fourier transform to generate the desired simulated interference signal. Example applications include white-light interferometry, high-numerical-aperture microscopy with a near-monochromatic light source, and interference microscopy for thickness and topography analysis of thin-film structures and other complex surface features.

Journal Article↗

PubMed2004

Silencing of the pollen-specific gene NTP303 and its family members in tobacco affects in vivo pollen tube growth and results in male sterile plants.

In seed plants, successful fertilization requires correct regulation of pollen tube growth. At germination and during growth, the pollen tube interacts with tissues from the pistil while the pollen tube extends via tip growth. Despite the fact that much research has been devoted to the mechanisms regulating pollen tube growth, many aspects are currently unknown. Previously, we have isolated a pollen-specific gene from tobacco--NTP303--that probably functions during pollen tube growth. NTP303 is part of a family of five members. Its expression is regulated both at the transcriptional and at the translational level. While NTP303 transcripts accumulate to high levels between early bi-cellular and mature pollen stages, NTP303 protein is hardly detectable until germination and pollen tube growth. In order to elucidate the role and function of NTP303 in the pollen tube, we studied the effect of NTP303 gene silencing on pollen function. Therefore, we have transformed tobacco plants with NTP303 co-suppression and anti-sense gene constructs. In these plants, the kanamycin resistance trait--which was linked to the NTP303-silencing gene--was not transmitted through the male gametophyte. This indicated that lowering the transcript level of NTP303 and/or its family members interferes with pollen function. Because we could not find a readily distinguishable phenotype in pollen from the hemizygous anti-sense and co-suppression plants, we rescued the defective pollen to produce doubled haploid plants that were homozygous for the NTP303 anti-sense gene. We found that in pollen from these plants the transcript levels of all NTP303 family members were reduced. Although pollen and pollen tubes from these plants appeared completely normal in vitro, the pollen tubes showed slower growth rates in vivo and arrested in the style before they reached the ovary, so that fertilization failed. These data demonstrate that NTP303 and its family members are essential for normal pollen tube growth and indicate several possible functions.

Down-Regulation↗

PubMed2002

Determination of fringe order in white-light interference microscopy.

Combining phase and coherence information for improved precision in white-light interference microscopy requires a robust strategy for dealing with the inconsistencies between these two types of information. We correct for these inconsistencies on every measurement by direct analysis of the difference map between the coherence and the phase profiles. The algorithm adapts to surface texture and noise level and dynamically compensates for optical aberrations, distortions, diffraction, and dispersion that would otherwise lead to incorrect fringe order. The same analysis also provides the absolute height data that are essential to relational measurements between disconnected surfaces.

Journal Article↗

PubMed2002

Optical interferometry for measurement of the geometric dimensions of industrial parts.

We describe an instrument for the measurement of surface flatness, parallelism, and size (thickness) of plane-parallel parts in a single measurement to 1sigma gauge capability of 0.02, 0.03, and 0.06 microm, respectively. A low-coherence IR profiler viewing both sides of the part simultaneously, believed to be novel, accommodates a wide variety of industrial surface finishes, including machined, ground, or lapped parts, with a 75-mm field of view and 15,000 pixels per side. A heterodyne laser displacement gauge together with an integrated zeroing system allows for a range of part sizes from 0 to 100 mm.

Journal Article↗