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Biomedical subjects

A K Kleinschmidt

Publications and source records attributed to A K Kleinschmidt.

At least 19 recordsLinked to original sources
PubMed1995

Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences.

Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity. Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da (N,d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N,d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da (N,d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth. We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da (N,d0) within limitations (d0 = constant (average) coupling probability).

Animals↗
PubMed1995

HSV type 1 genome variants from persistently productive infections in Raji and BJAB cell lines.

We studied possible genomic changes occurring in herpes simplex virus type 1 (HSV-1) during long-term cell culture which served as a model system for persistence and latency studies as introduced earlier. Sixteen HSV-1 reisolates were isolated from persistently productive HSV-1 (strains F and AK)-infected Burkitt lymphoma cell lines Raji and BJAB at four different times. They were roughly characterized in plaque morphology, plaque size, and infectivity. The viral reisolate DNAs revealed deletions and insertions of up to 1,150 base pairs in fragments BamHI-B, -E, -F, -J, -V, -X, and in the L-terminal and junction fragments S and K. Results were confirmed by additional restriction enzyme analyses and DNA sequencing of selected genomic regions between map units 0.642-0.650, 0.763-0.778 and 0.887-0.934. There was a progressive increase in genomic variability over a three-year period. However, changes in DNA fragment size occurred at different rates, with some reisolates showing stability over several months. The selective pressure for HSV-1 (F and AK) genomic changes was stronger in Raji than in BJAB cells, and stronger for F than for AK strain.

Animals↗
PubMed1991

The size of small polydisperse circular DNA (spcDNA) in angiofibroma-derived cell cultures from patients with tuberous sclerosis (TSC) differs from that in fibroblasts.

Cell cultures were derived from angiofibromas of three patients with tuberous sclerosis (TSC), from the unaffected skin of these patients, and from the skin of five healthy donors. The length distributions of the small polydisperse circular DNA (spcDNA) fraction of these cell cultures were then analyzed. Nearly half the spcDNA molecules from the angiofibroma cultures were longer than 0.4 micron, whereas only about 7% exceeded this threshold in the spcDNA preparations from the skin fibroblast cultures. The percentage of the larger size class of spcDNA showed an increase at higher numbers of in vitro passages in all three types of cultures, but this effect was much more conspicuous in the angiofibroma-derived cultures than in those from the skin fibroblasts. An age-dependent increase in the overall amount of spcDNA was only seen in the angiofibroma-derived cultures. Our earlier finding of elevated amounts of spcDNA in angiofibroma cultures was confirmed in cultures from an additional TSC patient.

Adult↗
PubMed1991

Herpes simplex virus type 1 long-term persistence, latency, and reactivation in infected Burkitt lymphoma cells.

The two herpes simplex virus type 1 (HSV-1) strains F and AK which differ in virus-cell interaction and in DNA organization, were used to establish persistently productive infections in Burkitt lymphoma-derived cell lines BJAB and Raji. Four such lines could be maintained over a period of three years. Like the uninfected parental lines, the persistently infected cells display a cyclic pattern of cell proliferation. The expression of HSV-1-specific antigens proved to be variable. As a consequence, virus yields also vary within a subcultivation period. Pooled human HSV antisera, when continuously present, suppress virus production (inducible latency) and support cell proliferation to higher rates. By contrast, removal of the antiserum after a certain period of cultivation leads to virus reactivation with a delay of 8 to 20 days. After cultivation periods of more than 3 to 12 weeks, replacement of HSV antiserum does no longer result in virus reactivation and even inducers fail to reactivate.

Antibodies, Viral↗
PubMed1981

Viroid structure.

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Base Composition↗
PubMed1979

Structural and biological properties of mycoplasmavirus MVL3: an unusual virus-procaryote interaction.

The kinetics of adsorption and growth of mycoplasmavirus MVL3 in Acholeplasma laidlawii 1305/68 host cells have been studied with one-step growth, premature lysis, and single-burst experiments. The virus was found to kill infected host cells. Virus release starts 90 min after infection and continues for about 10 to 15 h. Hence, virus production is unlike the classical lytic bacteriophages and instead resembles nonlytic cytocidal animal viruses. Structural details of the virus are described, and the molecular weight of the viral linear DNA has beenfound to be 26 x 10(6).

Acholeplasma laidlawii↗
PubMed1976

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures.

Viroids are uncoated infectious RNA molecules pathogenic to certain higher plants. Four different highly purified viroids were studied. By ultracentrifugation, thermal denaturation, electron microscopy, and end group analysis the following features were established: (i) the molecular weight of cucumber pale fruit viroid from tomato is 110,000, of citrus exocortis viroid from Gynura 119,000, of citrus exocortis viroid from tomato 119,000 and of potato spindle tuber viroid from tomato 127,000. (ii) Viroids are single-stranded molecules. (iii) Virods exhibit high thermal stability, cooperativity, and self-complementarity resulting in a rod-like native structure. (iv) Viroids are covalently closed circular RNA molecules.

Centrifugation↗
PubMed1975

Electron microscopic studies of proteoglycan aggregates from bovine articular cartilage.

Proteoglycan aggregates from bovine articular cartilage have been visualized by electron microscopy of mixed proteoglycan-cytochrome c monolayers. The proteoglycan aggregates consist of proteoglycan subunits arising laterally at fairly regular intervals (20 to 30 nm) from the opposite sides of an elongated filamentous structure. The filamentous backbone in individual aggregates varies in length from 400 to 4000 nm. The individual proteoglycan subunits in the aggregate vary in length from 100 to 400 nm. However, there is no difference in the average size of the proteoglycan subunits associated with the largest or smallest aggregates. The sizes of the individual aggregates are determined mainly by the lengths of their filamentous backbones. The stoichiometry of binding of subunits to filament, calculated from the data reported here, is close to that for the binding of subunits to hyaluronic acid reported by others.

Animals↗
PubMed1974

Locating interrupted hydrogen bonding in the secondary structure of PM2 circular DNA by comparative denaturation mapping.

Previous studies with HCHO have revealed a reaction with superhelical DNA that strongly suggests that this DNA consists of small regions of interrupted secondary structure. To map these sites in PM2 DNA, the following set of experiments was performed using electron microscopy. (i) A denaturation map of nicked form II was obtained using Inman's alkaline-HCHO conditions. (ii) The superhelical form I was reacted with HCHO at 30 C until equilibrium was achieved at the interrupted sites (3.6% reactivity). The excess HCHO was removed rapidly and X-ray treatment was employed to nick these prereacted molecules. These form II molecules containing HCHO (form II HCHO) were also subjected to denaturation mapping. It would be expected that the HCHO-unpaired regions would serve as induction sites for the propagation of melting. Hence, depending on the location of the induction sites; we would anticipate either the creation of new regions of melting or a normal denaturation map shifted to lower pH values. Comparison of the development of progressive denaturation of form II and form II HCHO reveals that the latter is the case. The denaturation maps of form II are highly organized patterns of adenine-thymine (AT)-rich regions, with a total of five regions at extreme pH conditions. There are six highly organized regions for form II HCHO, i.e., smaller adjacent loops, at low denaturation conditions where no denaturation is seen for form II. These coalesce into the pattern for form II containing four of five A-T-rich regions observed for form II. Hence we conclude that the regions of altered hydrogen bonding in superhelical PM2 DNA are four to six in number and they map in the A-T-rich regions of the DNA.

Bacteriophages↗