Biomedical subjects

K Zahn

Publications and source records attributed to K Zahn.

At least 19 recordsLinked to original sources

PubMed2005

Experimental realization of a model glass former in 2D.

We have studied binary two-dimensional (2D) mixtures of superparamagnetic colloidal particles interacting through magnetic dipole moments, which were induced by an external magnetic field B. By tuning B the effective system temperature could be widely adjusted. Time-dependent particle coordinates measured by video-microscopy provide radial pair-distribution functions, mean-square displacements as well as evidence for heterogeneous dynamics. Characteristic features of 3D glass formers are observed experimentally in 2D for the first time.

Journal Article↗

PubMed2004

Elastic behavior of a two-dimensional crystal near melting.

Using positional data from video microscopy, we determine the elastic moduli of two-dimensional colloidal crystals as a function of temperature. The moduli are extracted from the wave-vector-dependent normal-mode spring constants in the limit q-->0 and are compared to the renormalized Young's modulus of the Kosterlitz-Thouless-Halperin-Nelson-Young theory. An essential element of this theory is the universal prediction that Young's modulus must approach 16 pi at the melting temperature. This is indeed observed in our experiment.

Journal Article↗

PubMed2003

Three-particle correlations in simple liquids.

We use videomicroscopy to follow the phase-space trajectory of a two-dimensional colloidal model liquid and calculate three-point correlation functions from the measured particle configurations. Approaching the fluid-solid transition by increasing the strength of the pair-interaction potential, one observes the gradual formation of a crystal-like local order due to triplet correlations, while being still deep inside the fluid phase. Furthermore, we show that in a strongly interacting system the Born-Green equation can be satisfied only with the full triplet correlation function but not with three-body distribution functions obtained from superposing pair correlations (Kirkwood superposition approximation).

Journal Article↗

PubMed2003

Elastic properties of 2D colloidal crystals from video microscopy.

Elastic constants of two-dimensional (2D) colloidal crystals are determined by measuring strain fluctuations induced by Brownian motion of particles. Paramagnetic colloids confined to an air-water interface of a pendant drop are crystallized under the action of a magnetic field, which is applied perpendicular to the 2D layer. Using video microscopy and digital image processing we measure fluctuations of the microscopic strain obtained from random displacements of the colloidal particles from their mean (reference) positions. From these we calculate system-size dependent elastic constants, which are extrapolated using finite-size scaling to obtain their values in the thermodynamic limit. The data are found to agree rather well with zero-temperature calculations.

Journal Article↗

PubMed2001

Mechanics of venom expulsion in Crotalus, with special reference to the role of the fang sheath.

A combination of anatomical and experimental preparations were used to explore the function of the venom delivery system in rattlesnakes (Crotalus). The distal end of the venom duct is compressed near the point where it empties into the venom chamber, a space surrounding the fang defined by the fang sheath. Within the venom chamber, the inner fang membrane lies obliquely over the base of the fang at least partially occluding the entrance orifice. When the fang is retracted the combination of the compressed venom duct and the spatial position of the inner fang membrane serve to inhibit or block venom flow. As the fang is erected beyond approximately 60 degrees (relative to the roof of the mouth) localized compression of the fang sheath decreases the size of the venom chamber, relieves the compressive force from the venom duct, and displaces the inner fang membrane away from the entrance orifice of the fang. Pressure recordings taken at different locations along the venom delivery system demonstrate that the venom gland produces suction during relaxation of the extrinsic glandular musculature. These findings suggest that the venom delivery system of Crotalus is both more flexible and more regulated than previously assumed.

Animals↗

PubMed2001

Structure, expression and products of the ribosomal RNA operons of Rhodopseudomonas palustris No. 7.

Rhodopseudomonas palustris strains carry one or two ribosomal rRNA operons, and those with duplicated rrn operons grow faster. The two rrn operons in R. palustris No. 7 are virtually identical over a 54,70-bp stretch containing the genes for 16S rRNA, tRNAile, tRNAala, 23S rRNA and 5S rRNA, as well as the intergenic spacers and part of the extragenic spacer. In R. palustris, unlike most bacteria with multiple rrn operons, the putative promoter sequences of the two operons are highly diverged, suggesting possible functional differentiation. By simultaneous primer-extension analysis of both pre-rRNAs, we detected a two-fold higher level of expression from rrnA under photoautotrophic conditions. Alteration of the conditions of growth leads to changes in the relative levels of expression of the two operons. Within the 5,470-bp segment, only two sequence differences are found between the 23S rRNA genes; one is at the center of the 23S rRNA molecule and affects a site of unknown function, and the other is within or immediately adjacent to sequences involved in processing of the 5' 23S rRNA IVS. In vitro processing of 5' IVS-containing 23S rRNA precursors from each operon does not reveal any detectable difference between them. The 5' ends of the mature 16S, 23S, and 5S rRNAs were determined by primer-extension analysis, and the 3' end of 23S rRNA was determined by RNA linker ligation-mediated cDNA cloning. The 5' and 3' ends of the R. palustris 23S rRNA molecule are extensively processed, suggesting that, unlike the situation in the established eubacterial model, these ends cannot basepair.

Base Sequence↗

PubMed2001

New LightCycler PCR for rapid and sensitive quantification of parvovirus B19 DNA guides therapeutic decision-making in relapsing infections.

Detection of parvovirus B19 DNA offers diagnostic advantages over serology, particularly in persistent infections of immunocompromised patients. A rapid, novel method of B19 DNA detection and quantification is introduced. This method, a quantitative PCR assay, is based on real-time glass capillary thermocycling (LightCycler [LC]) and fluorescence resonance energy transfer (FRET). The PCR assay allowed quantification over a dynamic range of over 7 logs and could quantify as little as 250 B19 genome equivalents (geq) per ml as calculated for plasmid DNA (i.e., theoretically >or=5 geq per assay). Interrater agreement analysis demonstrated equivalence of LC-FRET PCR and conventional nested PCR in the diagnosis of an active B19 infection (kappa coefficient = 0.83). The benefit of the new method was demonstrated in an immunocompromised child with a relapsing infection, who required an attenuation of the immunosuppressive therapy in addition to repeated doses of immunoglobulin to eliminate the virus.

Child↗

PubMed2001

Venom flow in rattlesnakes: mechanics and metering.

The functional morphology of venom injection in Crotalus atrox was explored using high-speed digital videography combined with direct recording of venom flow using perivascular flow probes. Although venom flow was variable, in most strikes the onset of venom flow was coincidental with fang penetration, and retrograde flow (venom suction) was observed prior to fang withdrawal. The duration of venom flow was consistently less than the duration of fang penetration. The occurrence of retrograde flow, 'dry bites' (which accounted for 35 % of the strikes) and unilateral strikes all support a hypothesis for venom pooling in the distal portion of the venom-delivery system. No significant difference in temporal or volumetric aspects of venom flow were found between defensive strikes directed at small and large rodents. With the species and size of target held constant, the duration of venom flow, maximum venom flow rate and total venom volume were all significantly lower in predatory than in defensive strikes.

Animals↗

PubMed2000

Divergent mechanisms of 5' 23S rRNA IVS processing in the alpha-proteobacteria.

Widespread occurrence of a separate small RNA derived from the 5'-end of 23S rRNA and of an intervening sequence (IVS) which separates this domain from the main segment of 23S rRNA in the alpha-proteobacteria implies that processing reactions which act to excise the IVS are also maintained in this group. We previously characterized the first example of processing of this IVS in Rhodopseudomonas palustris, which is classified with the Bradyrhizobia In this case, IVS excision occurs by a multistep process and RNase III appears to act at an early step. Here, we characterize in vivo and in vitro IVS processing in two other related, but phenotypically distinct, Bradyrhizobia We also examine in vivo and in vitro processing of rRNA precursors from a more distantly related alpha-proteobacterium, Rhodobacter sphaeroides which produces a separate 5' 23S rRNA domain but has different sequences in the 5' 23S rRNA IVS. The details of the in vivo processing of all of the Bradyrhizobial rRNAs closely resemble the R. palustris example and in vitro studies suggest that all of the Bradyrhizobia utilize RNase III in the first step of IVS cleavage. Remarkably, in vivo and in vitro studies with R.sphaeroides indicate that initial IVS cleavage uses a different mechanism. While the mechanism of IVS cleavage differs among these alpha-proteobacteria, in all of these cases the limits of the internal segments processed in vivo are almost identical and occur far beyond the initial cleavage sites within the IVSs. We propose that these bacteria possess common secondary maturation pathways which enable them to generate similarly processed 23S rRNA 5'- and 3'-ends.

Alphaproteobacteria↗

PubMed2000

Dynamic criteria for melting in two dimensions

The two-dimensional (2D) melting transition is analyzed on the basis of the long-time behavior of a modified Lindemann parameter in 2D gamma(L)(t) and the bond-angular correlation function g(6)(t). Using video microscopy complete positional data are obtained over five decades in time for an ensemble of superparamagnetic colloidal particles confined to an air-water interface. We find that each of the three phases (solid/hexatic/isotropic liquid) is uniquely characterized by the long-time behavior of gamma(L)(t), g(6)(t), and the non-Gaussian parameter of the relative neighbor-neighbor displacement.

Journal Article↗

PubMed2000

Functional subdivision of the venom gland musculature and the regulation of venom expulsion in rattlesnakes.

A combination of histology, whole muscle force physiology, glycogen depletion, and venom expulsion analyses using transonic probes to measure venom flow and fluid pressure transducers to measure venom pressure was performed on the m. compressor glandulae and m. pterygoideus glandulae. The m. pterygoideus glandulae has less than one-third the cross-sectional area of the m. compressor glandulae, and produces approximately one-fifth the total twitch and tetanic force; however, in situ surface stimulation of the muscle produces venom flow and pressure levels that are similar to those produced by the m. compressor glandulae. The similarity in venom output following stimulation reflects in part the functional role of the larger m. compressor glandulae in jaw adduction, but also the functional subdivisions within this muscle. The m. compressor glandulae is divided into a series of columnar fascicles that run from the surface of the muscle to the venom gland. The combined results of clearing and staining and glycogen depletion studies suggest that these fascicles may represent functional compartments. Identical stimulations applied to different regions of the m. compressor glandulae result in up to a six-fold difference in venom expulsion. This functional specialization may play a role in the regulation of venom flow during offensive and defensive strikes.

Animals↗

PubMed2000

"Micrognathozoa: A new class with complicated jaws like those of rotifera and Gnathostomulida:" journal of morphology, volume 246, number 1, october 2000

The cover caption for the October issue of Journal of Morphology (Volume 246, Number 1) incorrectly listed the size of the cover specimen, Limnognathia maerski, as 128 cm in length. This is incorrect. The correct length is 128 &mgr;m. The correct cover caption is: The type species, Limnognathia maerski nov. gen. et sp. of a new group of animals, Micrognathozoa, from Greenland was photographed using differential interference contract microscopy, Nomarski technique. Anterior of the specimen is at the top of the figure. Different internal structures such as the pharyngeal apparatus with jaws and the ovaria with eggs are seen in three dimensions. The long, stiff sensoria are best seen when the animal is living as here in this photomicrograph. This specimen is only 128 &mgr;m in length. The color in this image is not the true color of the transparent animal but is a reflection of the Nomarski technique. Photomicrograph by Reinhardt M. Kristensen. See R. M. Kristensen and P. Funch, page 1. The Editor regrets this error.

Journal Article↗

PubMed2000

Sequence analysis of the cryptic plasmid pMG101 from Rhodopseudomonas palustris and construction of stable cloning vectors.

A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of alpha-proteobacteria.

Bacterial Proteins↗

PubMed1999

Characterization of a separate small domain derived from the 5' end of 23S rRNA of an alpha-proteobacterium.

We demonstrate the presence of a separate processed domain derived from the 5' end of 23S rRNA in ribosomes of Rhodopseudomonas palustris, a member of the alpha-++proteobacteria. Previous sequencing studies predicted intervening sequences (IVS) at homologous positions within the 23S rRNA genes of several alpha-proteobacteria, including R.palustris, and we find a processed 23S rRNA 5' domain in unfractionated RNA from several species. 5.8S rRNA from eukaryotic cytoplasmic large subunit ribosomes and the bacterial processed 23S rRNA 5' domain share homology, possess similar structures and are both derived by processing of large precursors. However, the internal transcribed spacer regions or IVSs separating them from the main large subunit rRNAs are evolutionarily unrelated. Consistent with the difference in sequence, we find that the site and mechanism of IVS processing also differs. Rhodopseudomonas palustris IVS-containing RNA precursors are cleaved in vitro by Escherichia coli RNase III or a similar activity present in R.palustris extracts at a processing site distinct from that found in eukaryotic systems and this results in only partial processing of the IVS. Surprisingly, in a reaction unlike characterized cases of eubacterial IVS processing, an RNA segment larger than the corresponding DNA insertion is removed which contains conserved sequences. These sequences, by analogy, serve to link the 23S rRNA 5' rRNA domains or 5.8S rRNAs to the main portion of other prokaryotic 23S rRNAs or to eukaryotic 28S rRNAs, respectively.

Alphaproteobacteria↗

PubMed1999

Molecular and functional characterization of the Rhodopseudomonas palustris no. 7 phosphoenolpyruvate carboxykinase gene.

The pckA gene, encoding the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PEPCK), was cloned by PCR amplification from the purple nonsulfur bacterium Rhodopseudomonas palustris No. 7. Sequencing of a 2.5-kb chromosomal SmaI-PstI fragment containing the structural gene revealed an open reading frame encoding 537 amino acids, homologous to known pckA genes. Primer extension analysis identified a transcriptional start site 72 bp upstream of the pckA initiation codon and an upstream sequence similar to sigma70 promoters. Studies of a pckA-lacZ gene fusion indicated that when cells were grown in minimal media with various carbon sources, such as succinate, malate, pyruvate, lactate, or ethanol, under both anaerobic light and aerobic dark conditions, the pckA gene was induced in log phase, irrespective of the carbon source. A R. palustris No. 7 PEPCK-deficient strain showed growth characteristics identical to those of the wild-type strain either anaerobically in the light or aerobically in the dark when a C4-dicarboxylic acid, such as succinate or malate, was used as a carbon source. These results indicate that in R. palustris No. 7, an alternative gluconeogenic pathway may exist in addition to PEPCK.

Amino Acid Sequence↗

PubMed1999

Ex-chiral pool synthesis and pharmacological aspects of 3-pyrrolidinylisoxazoles.

Employing the dopamine autoreceptor agonist (-)-3-PPP (3) as well as the cholinergic receptor ligands 4 and 5 as lead compounds the 3-pyrrolidinylisoxazoles 2a,b as well as its optical antipodes ent 2a,b were synthesized from (R)-aspartic acid (6) and (S)-aspartic acid (ent-6), respectively. Pharmacological properties of the target compounds were evaluated employing dopamine D2 receptor binding studies and functional experiments on muscarinic M2 receptors.

Animals↗

PubMed1997

Structural and functional analysis of the phosphoenolpyruvate carboxylase gene from the purple nonsulfur bacterium Rhodopseudomonas palustris No. 7.

The ppc gene, encoding phosphoenolpyruvate carboxylase (PEPC), from Rhodopseudomonas palustris No. 7 was cloned and sequenced. Primer extension analysis identified a transcriptional start site 42 bp upstream of the ppc initiation codon. An R. palustris No. 7 PEPC-deficient strain showed a slower doubling time compared with the wild-type strain either anaerobically in the light or aerobically in the dark, when pyruvate was used as a carbon source.

Amino Acid Sequence↗

PubMed1996

Modulation of lambda integrase synthesis by rare arginine tRNA.

Lambda's int gene contains an anomalously high frequency of the rare arginine codons AGA and AGG when compared to genes of Escherichia coli or to the rest of phage lambda. These are the least frequent codons in genes of E. coli and are recognized by the rarest tRNAs. The presence of these codons reduces the translation rate and, depending on the context, this can strongly modulate translational efficiency by a variety of mechanisms. In this study, we show that expression of the natural int gene may also be modulated by rare arginine codon usage, and we explore this mechanism.

Amino Acid Sequence↗