Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations.

Direct sequencing of segments of the envelope gene of human immunodeficiency virus type 1 proviruses in peripheral blood mononuclear cells has revealed that a cohort of hemophiliacs who were infected after exposure to a single common batch of factor VIII share closely related virus strains. Seventy-four sequences extending from hypervariable regions V4 through V5 from nine patients yielded a mean intrapatient nucleotide distance of 5.5%, while a mean of 4.2% was observed in 39 sequences of the V3 loop (six patients). Phylogenetic analysis revealed that sequences of six Edinburgh patients were particularly closely related and those from a patient infected in the United States were very distinct. The mean nucleotide distance among these six was 8.3%, while the mean distance from the U.S.-derived sequences was 25.5% in the V4-V5 region. The rate of sequence change across this patient group has been estimated to be 0.4% per year in the V4-V5 region and 0.5% per year in the V3 region, with at least a twofold range across patients. Only two inactivating nucleotide substitutions have been observed in a total of 42 kb of sequence obtained from the env and gag genes during this study.     

Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1.

Nucleotide sequences in three hypervariable regions of the human immunodeficiency virus type 1 (HIV-1) env gene were obtained by sequencing provirus present in peripheral blood mononuclear cells of HIV-infected individuals. Single molecules of target sequences were isolated by limiting dilution and amplified in two stages by the polymerase chain reaction, using nested primers. The product was directly sequenced to avoid errors introduced by Taq polymerase during the amplification process. There was extensive variation between sequences from the same individual as well as between sequences from different individuals. Interpatient variability was markedly less in individuals infected from a common source. A high proportion of amino acid substitutions in the hypervariable regions altered the number and positions of potential N-linked glycosylation sites. Sequences in two hypervariable regions frequently contained short (3- to 15-bp) duplications or deletions, and by amplifying peripheral blood mononuclear cell DNA containing 10(2) or 10(3) proviral molecules and analyzing the product by high-resolution electrophoresis, the total number and abundance of distinct length variants within an individual could be estimated, providing a more comprehensive analysis of the variants present than would be obtained by sequencing alone. Sequences from many individuals showed frequent amino acid substitutions at certain key positions for neutralizing-antibody and cytotoxic T-cell recognition in the immunodominant loop. The rates of synonymous and nonsynonymous nucleotide substitution in the region of this and flanking regions indicate that strong positive selection for amino acid change is operating in the generation of antigenic diversity.     

Isozyme and plastid DNA assessment of pedigrees of nineteenth century potato cultivars

Summary Isozyme and ctDNA RFLP patterns were determined for ten historically important potato cultivars (Solanum tuberosum ssp. tuberosuni) in order to relate and confirm their pedigrees. Isozyme polymorphism was detected at 11 of 13 loci examined, whereas only T-type cytoplasm, the predominant ctDNA of S. tuberosum ssp. tuberosum, was observed. Isozyme analysis indicated that potato cultivars previously presumed to be derived from open-pollinated berries of Garnet Chili and Early Rose were in fact the result of hybridizations. In addition, putative pedigrees of Irish Cobbler, White Rose, and Bliss Triumph were not supported. Garnet Chili, the first derivative of Rough Purple Chili, carries allozmyes at Mdh-1 and Pgm-2, which supports the Chilean origin of Rough Purple Chili. The identical ctDNA pattern among the cultivars may indicate a common maternal lineage that traces through Garnet Chili to Rough Purple Chili. The allozyme frequencies estimated from these cultivars provide a base from which subsequent introductions of Solanum species into the ssp. tuberosum gene pool can be assessed.Journal Article No. 000123     

Contrasting effects of substrate and grazer manipulations on picoplankton in oceanic and coastal waters off Brazil

In two contrasting regions off the coast of Brazil, picoplankton(<1 µm) responses to removal of larger grazers andto the additions of glucose and amino acids were determined.Effects of glucose and amino acid additions (1 µM) onparticulate nitrogen and chlorophyll a concentrations, and onrates of NH₄⁺ uptake and regeneration, were observed after 5h pre-incubation. In the oceanic waters, removal of the >1µm fraction had no significant effect on the chlorophylla of the picoplankton after 5 h. However, the addition of glucosestimulated both uptake and regeneration by a mean of 27%, andthe addition of arginine led to significant decreases in therates of NH₄⁺ uptake and regeneration. In contrast, in the coastalwaters, significant increases in chlorophyll and particulatenitrogen concentrations were found after 5 h incubation in boththe amended samples and in the controls, and mean rates of NH₄⁺uptake and regeneration were affected to a lesser degree bythe additions of either glucose or amino acids than in the oceanicwaters. The oceanic responses were suggestive of carbon limitationof heterotrophic bacteria. In the coastal region, on the otherhand, the supply of organic carbon and nitrogen was likely tohave been sufficient to meet the nutritional requirements ofthe heterotrophic bacteria and cyanobacteria. Grazing by largerorganisms on the picoplankton appeared to play a more significantrole in the nitrogen cycle in the coastal waters than in theoceanic waters.     

Order out of chaos in the nucleus

A report on the 'Nuclear architecture and control of gene expression' minisymposium at the first meeting of the European Life Scientists Organisation (ELSO), Geneva, Switzerland, September 2-6, 2000.     

Intronic gene conversion in the evolution of human X-linked color vision genes

Human red and green visual pigment genes are X-linked duplicate genes. To study their evolutionary history, introns 2 and 4 (1,987 and 1,552 bp, respectively) of human red and green pigment genes were sequenced. Surprisingly, we found that intron 4 sequences of these two genes are identical and that the intron 2 sequences differ by only 0.3%. The low divergences are unexpected because the duplication event producing the two genes is believed to have occurred before the separation of the human and Old World monkey (OWM) lineages. Indeed, the divergences in the two introns are significantly lower than both the synonymous divergence (3.2% +/- 1.1%) and the nonsynonymous divergence (2.0% +/- 0.5%) in the coding sequences (exons 1-6). A comparison of partial sequences of exons 4 and 5 of human and OWM red and green pigment genes supports the hypothesis that the gene duplication occurred before the human-OWM split. In conclusion, the high similarities in the two intron sequences might be due to very recent gene conversion, probably during evolution of the human lineage.      

Protein evolution of ANTP and PRD homeobox genes

Background  

Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes.     

HPLC based method for the measurement of the reduction of aflatoxin B<Subscript>1</Subscript> by bacterial cultures isolated from different African foods

The consumption of fermented foods contaminated with aflatoxin B₁ is linked to aflatoxicosis. Aflatoxicosis is a serious problem in developing countries with environmental conditions appropriate for the biosynthesis of AFB₁ byAspergillus flavus andAspergillus parasiticus. In Africa, especially in Ghana and Nigeria, there is a very high risk of liver cancer which is caused by the consumption of AFB₁-intoxicated, traditionally fermented maize and sorghum products. It is suggested that one way to diminish this health risk might be the reduction of the AFB₁ concentration in foods by bacteria. Especially bacteria used for food fermentation processes are of great importance, with a special emphasis on lactic acid bacteria which are involved in traditionally fermented African foods based on maize and sorghum.Most publications dealing with aflatoxin degradation by microorganisms describe a phosphate buffer test system for the performance of degradation experiments. In contrast to that, a test system based on physiological active bacterial and yeast cells has been developed, to assess food fermentation organisms for their ability to reduce the AFB₁ concentration in vitro. The aflatoxin B₁ concentration in test samples was quatitatively determined by HPLC.The assessment of lactic acid bacteria originating from different German and other European culture collections only showed a very slight reduction of the AFB₁ concentration from 3% to 12%. Screening experiments in which other bacterial genera and lactic acid bacteria, isolated from different African foods have been assessed, in most cases showed the same results. However, some bacterial strains, e.g. strains of the genusBacillus derived from European culture collections and strains of the genusLactobacillus isolated from African foods, caused a release of AFB₁ which was chemically bound before to components of the test medium and which therefore could not be extracted with chloroform.A process quite similar to that may happen during food fermentations. Different experiments showed that e.g. cellulose can bind AFB₁ very effectively. Cellulose and different other food components are well known to absorb AFB₁. During fermentation the cellulose and other AFB₁-absorbing components may be degraded and the AFB₁ will be released again.The only bacterial strain known as yet which is able to reduce the AFB₁ concentration in vitro and in different food comodities isNocardia corynebacteroides (formerFlavobacterium aurantiacum). Nevertheless the mechanism of this AFB₁ reduction is actually not well understood, it still has to be investigated. In the meantime several other bacterial strains, presumably from the taxonomic group of theActinomycetes could be proved to be effective reducers of the AFB₁ concentration in our in vitro test system. Because as yet no food relevant microorganism could be found, which is able to degrade AFB₁, these new strains in general offer the possibility for a genetic modification of food relevant microorganisms. This seems to be the way to come to starter cultures which are able to degrade AFB₁ during food fermentations.     

Effects of sex and dietary phosphorus level on the apparent metabolizable energy and nutrient digestibility in broiler chickens

The influence of sex of broilers and dietary phosphorus (P) level on energy utilization and apparent ileal digestibility of N, P and phytate-P were investigated. The AME_N was determined using 3- and 6-week old broilers, while the apparent ileal digestibility were determined only with 6-week old birds. Sex of broilers had no effect on the AME_N values determined during week 3. During week 6, the AME_N values for male broilers were higher (P?0.01) than those for the females. An interaction (P?0.05) between sex and dietary P level was also observed. AME_N values determined with male broilers were lower in the adequate-P diet compared to those in the low-P diet, whereas no effect of P level was observed in females. Female broilers tended (P?0.10) to have a higher ileal N digestibility than the males, but a significant (P?0.01) sex ×?P level interaction was observed. Males receiving the adequate-P diet had a lower N digestibility than those receiving the low-P diet, whereas the opposite was true in the females. Ileal phytate P degradation in males was higher than in females (0.282 vs. 0.234), but the differences were not significant. Increasing dietary P level increased ileal P digestibility in both the males and females, but the improvements were greater in the females, as indicated by a significant sex × P level interaction.