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At least 289 records · Page 16Linked to original sources
PubMed2006

Intraspecific variation in survival and mitochondrial oxidative phosphorylation in wild-caught Drosophila simulans.

Lifespans of organisms vary greatly even among individuals of the same species. Under the framework of the free oxygen radical theory of aging, it is predicted that variation in individual lifespan within a species will correlate with variation in the accumulation of oxidative damage to cell components from reactive oxygen species. In this study we test the hypothesis that variation in survival of three wild-caught Drosophila simulans fly lines (HW09, NC48 and MD106) correlates with three key aspects of mitochondrial bioenergetics. The rank order of median survival was HW09 > MD106 > NC48. Young HW09 flies (11-18 days) had (i) highest ADP:O (quantity of oxygen consumed by mitochondria when provided with a quantity of ADP) when metabolizing both electron transport chain complex I and complex III substrates; (ii) lowest rate of mitochondrial hydrogen peroxide production from complex III; and (iii) highest cytochrome c oxidase activity from complex IV. Rate of hydrogen peroxide production increased and cytochrome c oxidase activity decreased in all lines in the age range 11-25 days. This is the first study to correlate natural variation in organism survival with natural variation in mitochondrial bioenergetics.

Adenosine Diphosphate↗
PubMed1974

A general model to account for enzyme variation in natural populations.

Approximate conditions for genetic polymorphism in temporally and spatially varying environments are presented for loci which are intermediate at the level of fitness or at the level of gene function. The conditions suggest that polymorphism will be more likely in more variable environments while unlikely in constant environments. Biochemical evidence is presented to justify the assumption of heterozygote intermediacy. Observations on natural populations are cited which substantiate the claim that allozymic polymorphism is primarily due to selection acting on environmental variation in gene function.

Animals↗
PubMed2006

Cellular reactivity to the p. Falciparum protein trap in adult kenyans: novel epitopes, complex cytokine patterns, and the impact of natural antigenic variation.

Malaria vaccines based on thrombospondin-related adhesive protein of Plasmodium falciparum (Pf TRAP) are currently undergoing clinical trials in humans. This study was designed to investigate naturally acquired cellular immunity to Pf TRAP in adults from a target population for future trials of TRAP-based vaccines in Kilifi, Kenya. We first tested reactivity to a panel of 53 peptides spanning Pf TRAP and identified 26 novel T-cell epitopes. A panel of naturally occurring polymorphic variant epitope peptides were made to the most commonly recognized epitope regions and tested for ability to elicit IFN-gamma, IL-4, and IL-10 production. These data provide for the first time a complex cytokine matrix mapping naturally induced T-cell responses to TRAP and suggest that T-cell responses boosted by vaccination with Pf TRAP could stimulate the release of competing pro- and anti-inflammatory cytokines. They further define polymorphic variants able to boost specific Th1, Th2, and possibly Tr1 reactivity.

Adult↗
PubMed1989

Electrophoretically detectable genetic variation in natural and hatchery stocks of Atlantic salmon in Finland.

To survey the genetic resources of Atlantic salmon (Salmo salar L.) stocks in Finland, an electrophoretic study was made of natural and hatchery stocks. The stocks were compared with the nearest stocks in the USSR, and the effects of hatchery rearing were evaluated. The genetic variation within and between stocks was measured from 20 samples, of which three (Kola, Neva and Onega) were from the USSR. Twenty-five enzyme loci were examined, of which six were polymorphic: AAT-4, IDH-3, ME-3, MDH-3, PGM-1, and SDH-1. The mean heterozygosity of all the populations was 4.2% (1.0-7.2). For the natural salmon stocks of the Arctic Ocean, the mean heterozygosity was 6.3%, for the natural stocks of Atlantic salmon in the Baltic 4.8%, for the hatchery stocks 3.6%, and for the lake salmon (Salmo salar m. sebago Girard) 1.8%. The results are in agreement with the hypothesis that the amount of variation depends on the effective population size and that culture diminishes variation by decreasing the effective population size. All the stocks originating from different rivers differed from each other with statistical significance. The most unique stocks were the River Kola stock and the lake salmon stock from Lake Saimaa. The genetic distances were consistent with the geographic distance between the rivers from which the stocks originated. Stress is laid on the importance in fish culture of maintaining separate stocks and using larger brood stocks.

Animals↗
PubMed1993

Measurement of rRNA Variations in Natural Communities of Microorganisms on the Southeastern U.S. Continental Shelf.

The development of a clear understanding of the physiology of marine prokaryotes is complicated by the difficulties inherent in resolving the activity of various components of natural microbial communities. Application of appropriate molecular biological techniques offers a means of overcoming some of these problems. In this regard, we have used direct probing of bulk RNA purified from selective size fractions to examine variations in the rRNA content of heterotrophic communities and Synechococcus populations on the southeastern U.S. continental shelf. Heterotrophic communities in natural seawater cultures amended with selected substrates were examined. Synechococcus populations were isolated from the water column by differential filtration. The total cellular rRNA content of the target populations was assayed by probing RNA purified from these samples with an oligonucleotide complementing a universally conserved region in the eubacterial 16S rRNA (heterotrophs) or with a 1.5-kbp fragment encoding the Synechococcus sp. strain WH 7803 16S rRNA (cyanobacteria). The analyses revealed that heterotrophic bacteria responded to the addition of glucose and trace nutrients after a 6-h lag period. However, no response was detected after amino acids were added. The cellular rRNA content increased 48-fold before dropping to a value 20 times that detected before nutrients were added. Variations in the rRNA content from Synechococcus spp. followed a distinct diel pattern imposed by the phasing of cell division within the irradiance cycle. The results indicate that careful application of these appropriate molecular biological techniques can be of great use in discerning basic physiological characteristics of selected natural populations and the mechanisms which regulate growth at the subcellular level.

Journal Article↗
PubMed1998

Natural abundance variations in stable isotopes and their potential uses in animal physiological ecology.

Chemical, biological, and physical processes lead to distinctive "isotopic signatures" in biological materials that allow tracing of the origins of organic substances. Isotopic variation has been extensively used by plant physiological ecologists and by paleontologists, and recently ecologists have adopted the use of stable isotopes to measure ecosystem patterns and processes. To date, animal physiological ecologists have made minimal use of naturally occurring stable isotopes as tracers. Here we provide a review of the current and potential uses of naturally occurring stable isotopes in animal physiological ecology. We outline the physical and biological processes that lead to variation in isotopic abundance in plants and animals. We summarize current uses in animal physiological ecology (diet reconstruction and animal movement patterns), and suggest areas of research where the use of stable isotopes can be fruitful (protein balance and turnover and the allocation of dietary nutrients). We argue that animal physiological ecologists can benefit from including the measurement of naturally occurring stable isotopes in their battery of techniques. We also argue that animal physiologists can make an important contribution to the emerging field of stable isotopes in biology by testing experimentally the plethora of assumptions upon which the techniques rely.

Animal Nutritional Physiological Phenomena↗
PubMed1991

Histoplasma variation and adaptive strategies for parasitism: new perspectives on histoplasmosis.

This review summarizes the biology of Histoplasma capsulatum in relation to a wide variety of corresponding pathologies in histoplasmosis. Features of these disease syndromes can be explained in part by natural variations within the fungal population and adaptations made by individual organisms to specific environments. H. capsulatum grows as mycelia and conidia in the soil; once inhaled, the organism undergoes a dramatic morphological and physiological conversion to a yeast form. The yeasts proliferate within the phagolysosomes of macrophages, using a variety of specific strategies for intracellular survival. Even avirulent strains or variants are able to avoid being killed by macrophages and instead establish inapparent or persistent infections. The ingested avirulent organisms assume enlarged shapes similar in appearance to those seen in histological sections of tissues from patients with histoplasmosis. Respiratory tract epithelial cells also appear to play a role in persistence: within them yeasts undergo phenotypic switching akin to the phase variation observed in other pathogens. This particular change involves the loss or modification of cell wall alpha-(1,3)-glucan, which is also correlated with the spontaneous appearance of avirulent variants. The repertoire of adaptive responses and natural variations within this species probably evolved from the need to adjust to a wide range of dynamic environments. In combination with the immune status of the host, these characteristics of H. capsulatum appear to influence the epidemiology, extent, and persistence of histoplasmosis.

Animals↗
PubMed1998

Phenotypic study of resistance of beta-lactamase-inhibitor-resistant TEM enzymes which differ by naturally occurring variations and by site-directed substitution at Asp276.

At this time an amino acid substitution at position 276 in the TEM-1 enzyme is associated with an additional substitution at position 69 in natural beta-lactamase-inhibitor-resistant (IRT) beta-lactamases. The effect of the Asn276-->Asp substitution on resistance was assessed with the Asn276Asp variant, generated by site-directed mutagenesis. The mutant was resistant to beta-lactamase inhibitors, but the MICs of amoxicillin combined with clavulanic acid or tazobactam were strikingly different for E. coli strains producing the Asn276Asp variant and those producing naturally occurring IRTs with single or double substitutions. The inhibitory effects of clavulanic acid and tazobactam were the same in IRTs with substitutions at position 69 (IRT-5 and IRT-6). The effect of clavulanic acid on the MICs of amoxicillin for the Asn276Asp variant was greater than that of tazobactam. In IRTs with double substitutions, at positions 69 plus 276 (IRT-4, IRT-7, and IRT-8) or 69 plus 275 (IRT-14), tazobactam was a more potent inhibitor than clavulanic acid. The effect of the Asn276-->Asp substitution on the values of the kinetic constants and the concentration required to inhibit by 50% the hydrolysis of benzylpenicillin confirms that this single mutation is responsible for resistance to beta-lactamase inhibitors. Molecular modeling of the Asn276Asp mutant shows that Asp276 can form two salt bonds with Arg244 close to the penicillin-binding cavity. The addition of the Asp276 mutation to that preexisting at position 69 confers a higher selective advantage to bacteria, as shown by the reduction in beta-lactamase inhibitor efficiencies of the double variants. Therefore, the emergence of multiple mutations in TEM beta-lactamases by virtue of the use of beta-lactamase inhibitors increases selection pressure resulting in the convergent evolution of resistant strains.

Amoxicillin↗
PubMed2006

Natural genetic variation of freezing tolerance in Arabidopsis.

Low temperature is a primary determinant of plant growth and survival. Using accessions of Arabidopsis (Arabidopsis thaliana) originating from Scandinavia to the Cape Verde Islands, we show that freezing tolerance of natural accessions correlates with habitat winter temperatures, identifying low temperature as an important selective pressure for Arabidopsis. Combined metabolite and transcript profiling show that during cold exposure, global changes of transcripts, but not of metabolites, correlate with the ability of Arabidopsis to cold acclimate. There are, however, metabolites and transcripts, including several transcription factors, that correlate with freezing tolerance, indicating regulatory pathways that may be of primary importance for this trait. These data identify that enhanced freezing tolerance is associated with the down-regulation of photosynthesis and hormonal responses and the induction of flavonoid metabolism, provide evidence for naturally increased nonacclimated freezing tolerance due to the constitutive activation of the C-repeat binding factors pathway, and identify candidate transcriptional regulators that correlate with freezing tolerance.

Acclimatization↗
PubMed2002

Effect of sequence polymorphism and drug resistance on two HIV-1 Gag processing sites.

The HIV-1 proteinase (PR) has proved to be a good target for antiretroviral therapy of AIDS, and various PR inhibitors are now in clinical use. However, there is a rapid selection of viral variants bearing mutations in the proteinase that are resistant to clinical inhibitors. Drug resistance also involves mutations of the nucleocapsid/p1 and p1/p6 cleavage sites of Gag, both in vitro and in vivo. Cleavages at these sites have been shown to be rate limiting steps for polyprotein processing and viral maturation. Furthermore, these sites show significant sequence polymorphism, which also may have an impact on virion infectivity. We have studied the hydrolysis of oligopeptides representing these cleavage sites with representative mutations found as natural variations or that arise as resistant mutations. Wild-type and five drug resistant PRs with mutations within or outside the substrate binding site were tested. While the natural variations showed either increased or decreased susceptibility of peptides toward the proteinases, the resistant mutations always had a beneficial effect on catalytic efficiency. Comparison of the specificity changes obtained for the various substrates suggested that the maximization of the van der Waals contacts between substrate and PR is the major determinant of specificity: the same effect is crucial for inhibitor potency. The natural nucleocapsid/p1 and p1/p6 sites do not appear to be optimized for rapid hydrolysis. Hence, mutation of these rate limiting cleavage sites can partly compensate for the reduced catalytic activity of drug resistant mutant HIV-1 proteinases.

Amino Acid Sequence↗
PubMed2004

Naturally occurring genetic variation in Arabidopsis thaliana.

Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down to the molecular level has now become feasible, especially in model species like Arabidopsis, where several genes accounting for natural variation have already been identified. Dissecting this variation requires first a quantitative trait locus (QTL) analysis, which in Arabidopsis has proven very effective by using recombinant inbred lines (RILs). Second, identifying the particular gene and the nucleotide polymorphism underlying QTL is the major challenge, and is now feasible by combining high-throughput genetics and functional genomic strategies. The analysis of Arabidopsis natural genetic variation is providing unique knowledge from functional, ecological, and evolutionary perspectives. This is illustrated by reviewing current research in two different biological fields: flowering time and plant growth. The analysis of Arabidopsis natural variation for flowering time revealed the identity of several genes, some of which correspond to genes with previously unknown function. In addition, for many other traits such as those related to primary metabolism and plant growth, Arabidopsis QTL analyses are detecting loci with small effects that are not easily amenable by mutant approaches, and which might provide new insights into the networks of gene regulation.

Arabidopsis↗
PubMed2001

Invasion without a bottleneck: Microsatellite variation in natural and invasive populations of the brown mussel Perna perna (L).

Population-level genetic diversity of the brown mussel Perna perna was investigated using nuclear microsatellite markers in 6 natural and 6 invasive populations. A total of 448 individuals from 12 populations spanning the natural and introduced ranges of the brown mussel were scored for 2 polymorphic microsatellite loci. Wright's hierarchical F statistics ( F(ST)), Hardy-Weinberg equilibrium, Nei's genetic distance, and other descriptive statistics were used to quantify geographic population subdivision, and to estimate the number of migrants per generation. F(ST) values (0.007-0.042) revealed that genetic partitioning among populations was low. Microsatellite data revealed a slight difference in observed heterozygosity and no statistically significant differences in expected heterozygosity or allelic diversity between natural and introduced populations. Effective numbers of migrants ( N(em)) per generation ranged from 6 to 35 individuals. The potential significance of an invasive species with high genetic variation in terms of the risk of establishment and conservation implications is discussed.

Journal Article↗
PubMed2004

Genetic analysis of genome-wide variation in human gene expression.

Natural variation in gene expression is extensive in humans and other organisms, and variation in the baseline expression level of many genes has a heritable component. To localize the genetic determinants of these quantitative traits (expression phenotypes) in humans, we used microarrays to measure gene expression levels and performed genome-wide linkage analysis for expression levels of 3,554 genes in 14 large families. For approximately 1,000 expression phenotypes, there was significant evidence of linkage to specific chromosomal regions. Both cis- and trans-acting loci regulate variation in the expression levels of genes, although most act in trans. Many gene expression phenotypes are influenced by several genetic determinants. Furthermore, we found hotspots of transcriptional regulation where significant evidence of linkage for several expression phenotypes (up to 31) coincides, and expression levels of many genes that share the same regulatory region are significantly correlated. The combination of microarray techniques for phenotyping and linkage analysis for quantitative traits allows the genetic mapping of determinants that contribute to variation in human gene expression.

Alleles↗