Biomedical subjects

Claus Nielsen

Publications and source records attributed to Claus Nielsen.

10 recordsLinked to original sources

PubMed2003

Patterns of gene expression: homology or homocracy?

Numerous papers over the years have stated that the original meaning of the term homology is historical and morphological and denotes organs/structures in two or more species derived from the same structure in their latest common ancestor. However, several more recent papers have extended the use of the term to cover organs/structures which are organised through the expression of homologous genes. This usage has created an ambiguity about the meaning of the term, and we propose to remove this by proposing a new term, homocracy, for organs/structures which are organised through the expression of identical patterning genes. We want to emphasise that the terms homologous and homocratic are not mutually exclusive. Many homologous structures are in all probability homocratic, whereas only a small number of homocratic structures are homologous.

Biological Evolution↗

PubMed2003

Synthesis of 2-methylsulfanyl-1H-imidazoles as novel non-nucleoside reverse transcriptase inhibitors (NNRTIs).

alpha-Aminoketone hydrochlorides 2a-d were synthesized by Dakin-West reaction from L-phenylalanine and L-cyclohexylalanine followed by hydrolysis in acidic medium. Treatment of 2a-d with aqueous potassium thiocyanate afforded 1, 3-imidazole-2-thiones 3a-d which were alkylated with methyl iodide to give 2-methylsulfanyl-1H-imidazoles 4a-d with 4-benzyl/4-cyclohexylmethyl and 5-ethyl/5-isopropyl substituents. Coupling of 4a-d with ethoxymethyl chloride or benzyloxymethyl chloride furnished N-1 5a-d and N-3 6a-h alkylated products. The synthesised compounds were tested for their activity against HIV-1. The most active compounds have a cyclohexylmethyl group in the 5-position of 6 and showed an activity against HIV-1 comparable to the activity of Nevirapine.

Cell Line↗

PubMed2003

Immunogenicity in Mamu-A*01 rhesus macaques of a CCR5-tropic human immunodeficiency virus type 1 envelope from the primary isolate (Bx08) after synthetic DNA prime and recombinant adenovirus 5 boost.

Envelopes of primary R5-tropic human immunodeficiency virus type 1 (HIV-1) isolates may be particularly relevant for vaccine purposes and should be evaluated for immunogenicity in animals including macaques before carrying out human vaccine trials. In the present study, the immunogenicities of synthetic HIV-1 env DNA vaccines, which had been derived from the early primary isolate Bx08 and contain humanized codons, were evaluated in mice, guinea pigs and rhesus macaques. Neutralization sensitivity of the HIV-1(Bx08) isolate was found to resemble that of other primary isolate prototypes. Immunogenicity of gp120 delivered as codon-optimized DNA vaccine was comparable to that of recombinant gp120 protein plus adjuvant in mice. Similarly, DNA vaccination of guinea pigs with synthetic gp140(Bx08) and gp150(Bx08) DNA induced a strong antibody response independent of the gene construct and DNA immunization route. Mamu-A*01 rhesus macaques were DNA vaccinated with synthetic gp150(Bx08) or gp140(Bx08) DNA and boosted with a replication-deficient recombinant human adenovirus type 5 expressing a synthetic gp120(Bx08) gene. DNA-vaccinated rhesus macaques developed specific CD8+ T lymphocyte responses and anti-rgp120(IIIb) antibody responses. Both the humoral and cellular responses were significantly improved following intramuscular boosting with the recombinant adenovirus. The demonstrated humoral and cellular immunogenicities of these HIV Bx08 Env vaccines in non-human primates encourages their further development as one component in candidate HIV vaccines for humans.

AIDS Vaccines↗

PubMed2002

Synthesis of novel N-1 (allyloxymethyl) analogues of 6-benzyl-1-(ethoxymethyl)-5-isopropyluracil (MKC-442, emivirine) with improved activity against HIV-1 and its mutants.

This paper reports the synthesis and the antiviral activities of a series of 6-arylmethyl-1-(allyloxymethyl)-5-alkyluracil derivatives, which can be viewed as analogues of the anti-HIV-1 drug emivirine (formerly MKC-442) from which they differ in the replacement of the ethoxymethyl group with variously allyloxymethyl moieties. The most active compounds N-1 allyloxymethyl- and N-1 3-methylbut-2-enyl substituted 5-ethyl-6-(3,5-dimethylbenzyl)uracils (12 and 13) showed activity against HIV-1 wild-type in the picomolar range with selective index of greater than 5 x 10(6) and activity in the submicromolar range against the clinically important Y181C and K103N mutant strains known to be resistant to emivirine. Structure-activity relationship studies established a correlation between the anti-HIV-1 activity and the substitution pattern of the N-1 allyloxymethyl group.

Anti-HIV Agents↗

PubMed2002

A new non-linear normalization method for reducing variability in DNA microarray experiments.

BACKGROUND: Microarray data are subject to multiple sources of variation, of which biological sources are of interest whereas most others are only confounding. Recent work has identified systematic sources of variation that are intensity-dependent and non-linear in nature. Systematic sources of variation are not limited to the differing properties of the cyanine dyes Cy(5) and Cy(3) as observed in cDNA arrays, but are the general case for both oligonucleotide microarray (Affymetrix GeneChips) and cDNA microarray data. Current normalization techniques are most often linear and therefore not capable of fully correcting for these effects. RESULTS: We present here a simple and robust non-linear method for normalization using array signal distribution analysis and cubic splines. These methods compared favorably to normalization using robust local-linear regression (lowess). The application of these methods to oligonucleotide arrays reduced the relative error between replicates by 5-10% compared with a standard global normalization method. Application to cDNA arrays showed improvements over the standard method and over Cy(3)-Cy(5) normalization based on dye-swap replication. In addition, a set of known differentially regulated genes was ranked higher by the t-test. In either cDNA or Affymetrix technology, signal-dependent bias was more than ten times greater than the observed print-tip or spatial effects. CONCLUSIONS: Intensity-dependent normalization is important for both high-density oligonucleotide array and cDNA array data. Both the regression and spline-based methods described here performed better than existing linear methods when assessed on the variability of replicate arrays. Dye-swap normalization was less effective at Cy(3)-Cy(5) normalization than either regression or spline-based methods alone.

Cell Line↗

PubMed2002

Sodium turnover rate determines sensitivity to acute copper and silver exposure in freshwater animals.

The mechanisms of acute copper and silver toxicity in freshwater organisms appear similar. Both result in inhibition of branchial sodium (and chloride) uptake initiating a cascade of effects leading to mortality. The inhibition of the branchial Na/K-ATPase in the basolateral membrane is generally accepted as the key component responsible for the reduced sodium uptake. We propose that branchial carbonic anhydrase and the apical sodium channel may also be important targets for both copper and silver exposure. Several attempts have been made to predict metal sensitivity. A prominent example is the geochemical-biotic ligand model. The geochemical-biotic ligand modeling approach has been successful in explaining variations in tolerance to metal exposure for specific groups of animals exposed at different water chemistries. This approach, however, cannot explain the large observed variation in tolerance to these metals amongst different groups of freshwater animals (i.e. Daphnia vs. fish). Based on the detailed knowledge of physiological responses to acute metal exposure, the present review offers an explanation for the observed variation in tolerance. Smaller animals are more sensitive than large animals because they exhibit higher sodium turnover rates. The same relative inhibition of sodium uptake results in faster depletion of internal sodium in animals with higher sodium turnover. We present a way to improve predictions of acute metal sensitivity, noting that sodium turnover rate is the key predictor for variation in acute copper and silver toxicity amongst groups of freshwater animals. We suggest that the presented sodium turnover model is used in conjunction with the Biotic Ligand Model for risk management decisions.

Animals↗

PubMed2002

Cell-associated HIV DNA measured early during infection has prognostic value independent of serum HIV RNA measured concomitantly.

Using data from the Danish AIDS Cohort of HIV-infected homosexual men established in the 1980s, the prognostic value of early HIV DNA loads was evaluated. In addition to DNA measurements, concomitant serum HIV RNA levels, CD4 cell counts and CCR5 genotypes were determined. The patients were divided into 3 groups, according to whether their cell-associated HIV DNA load was < or = 100, 500 or > or = 2,500 DNA copies/10(6) peripheral blood mononuclear cells. Clinical progression rates differed significantly between the groups (p < 0.005). Cell-associated HIV DNA load had prognostic value independent of serum HIV RNA (p < 0.02). However, when HIV DNA, HIV RNA and CD4 cell counts were all included in a Cox model, only serum HIV RNA had independent prognostic value. Patients heterozygous for the CCR5 delta 32 allele had significantly lower HIV DNA loads than those homozygous for the normal allele (p < 0.05). The interplay between HIV RNA and DNA levels is discussed, together with the possibility that cell-associated HIV DNA load is a marker of the HIV RNA peak seen shortly after primary HIV infection.

Cohort Studies↗

PubMed2002

What cell lineages tell us about the evolution of spiralia remains to be seen.

Cell-lineage trees may contain information about spiralian phylogeny, as proposed by Guralnick and Lindberg (2001). Here we discuss this possibility further and conclude that the cell-division pattern must be known in greater detail and the coding methods refined before a possible phylogenetic signal can be identified.

Animals↗

PubMed2002

Observations on the relations among occlusion effect, compliance, and vent size.

In a clinical experiment, it was found that there is a high correlation between the compliance measured by tympanometry and the minimum size of the earmold vent, which just solves the client's occlusion problem related to his/her own voice when using a hearing aid. For ears with sensorineural hearing losses, compliance explained 59 percent of the variation in vent size, whereas the average low-frequency hearing loss explained as little as 0.3 percent. In a laboratory experiment, the objective occlusion effect measured with the participants' own voices showed a similar relationship with compliance. Whereas the former relationship between compliance and vent size may be explained by a simple model, the latter relationship turns out to be the opposite of what a first-order model predicts. Hence, compliance must be indicative of another aspect of the occlusion mechanism, which has a more profound influence on the observed occlusion effect than compliance itself.

Acoustic Impedance Tests↗

PubMedDate not supplied

Defining phyla: morphological and molecular clues to metazoan evolution.

None of the supraspecific taxonomic categories can be defined objectively. Each taxon should of course be monophyletic, but there is no morphological or molecular character that identifies, for example, the phylum level. This has led some authors to abandon the Linnaean categories, but they appear to be practical "handles" in daily communication. It has been proposed that each phylum exhibits a characteristic Bauplan, but the identification of such "types" have in practice proved difficult or impossible for several phyla. Monophyly of some of the approximately 30 morphology-based phyla has been put in question by molecular studies, but recent reports clearly show that the 18S rRNA molecule, which has been used extensively in phylogenetic analyses, cannot be used alone in identifying phyla (or other higher taxonomic groups). Some higher taxa, for example Chordata, Vertebrata, and Echinodermata, consistently show up as monophyletic in the analyses, whereas molluscan and annelidan subgroups just as consistently are mixed with each other and with a number of other protostomian phyla in varying patterns.

Animals↗