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PubMed2000

Neo-self antigens and the expansion of B-1 cells: lessons from atherosclerosis-prone mice.

The pathogenesis of atherosclerosis involves an inflammatory process that is modulated by the immune system, and within these complex responses we have discerned a possible role for an archetypic B-1 clone. We speculate that due to their immunogenicity and in vivo distribution the "neo"-self determinants created in oxidatively modified LDL are highly stimulatory for certain B-1 cell clones. These neo-self determinants, which can be created chemically, by somatic processes, may in fact represent the molecular analogues of somatic maturation, or even aging. These changes, including those on non-protein antigens induced by oxidative metabolism, amongst others, create neo-determinants against which the host no doubt can not develop rigorous B-cell tolerance. The onset of expression of these oxidative neo-determinants relatively late in development may well serve a useful function for the highly evolved mammalian immune system, as targeting by evolutionarily selected B-1 clones may facilitate the amplification of other useful antibody-mediated physiologic functions. As in the case of the T15 clone, these antibodies may aid in protection against common microbial pathogens. Hence we postulate that during the evolution of the adaptive immune system the neo-self antigenic milieu may have been exploited for the natural selection of primordial clonal specificities. The T15 B-1 clone may then illustrate a common paradigm in which there has been natural selection based on utility for the defense of the individual from environmental threats, as well as for possible "housekeeping" role(s) and the maintenance of cellular homeostasis.

Animals↗
PubMed2004

Phylogenetic analysis based on genome-scale metabolic pathway reaction content.

Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement. Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content. From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance). This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways. Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).

Archaea↗
PubMed1994

Dictyostelium discoideum, a lower eukaryote model for the study of DNA repair: implications for the role of DNA-damaging chemicals in the evolution of repair proficient cells.

The evolution of the ability of living cells to cope with stress is crucial for the maintenance of their genetic integrity. Yet low levels of mutation must remain to allow adaptation to environmental changes. The cellular slime mold D. discoideum is a good system for studying molecular aspects of the repair of lethal and mutagenic damage to DNA by radiation and chemicals. The wild-type strains of this soil microorganism are extremely resistant to DNA damaging agents. In nature the amoeboid cells in their replicative stage feed on soil bacteria and are exposed to numerous DNA-damaging chemicals produced by various soil microorganisms. It is probable that the evolution of repair systems in this organism and perhaps in others is a consequence of the necessity to cope with chemical damage which also confers resistance to radiation.

Animals↗
PubMed2004

Evolutionary dynamics of invasion and escape.

Whenever life wants to invade a new habitat or escape from a lethal selection pressure, some mutations may be necessary to yield sustainable replication. We imagine situations like (i) a parasite infecting a new host, (ii) a species trying to invade a new ecological niche, (iii) cancer cells escaping from chemotherapy, (iv) viruses or microbes evading anti-microbial therapy, and also (v) the repeated attempts of combinatorial chemistry in the very beginning of life to produce self-replicating molecules. All such seemingly unrelated situations have a common structure in terms of Darwinian dynamics: a replicator with a basic reproductive ratio less than one attempts to find some mutations that allow indefinite survival. We develop a general theory, based on multitype branching processes, to describe the evolutionary dynamics of invasion and escape.

Animals↗
PubMed2002

Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains.

Intraspecific variation in the 16S rRNA genes of 17 Mycoplasma agalactiae and eight Mycoplasma bovis isolates was investigated to determine the degree of sequence variation in these two species and to determine whether the polymorphisms in the 16S rRNA genes could be used for the construction of an evolutionary tree and as epidemiological markers. A high degree of variation was found within isolates (between operons) and between isolates of both species. In contrast to M. capripneumoniae no distinct evolutionary pattern could be seen, probably because there are functional systems for gene conversion in M. agalactiae and M. bovis. However, the non-European isolates of M. agalactiae shared three characteristic nucleotides and European isolates from the same or neighbouring countries were very similar. Differences within isolates included both polymorphic positions and sequence length differences between operons. The amount of variation within isolates of the respective species ranged from zero to seven polymorphisms for M. agalactiae and from zero to four polymorphisms for M. bovis. The high degree of variation suggests the potential for misdiagnosis of species in diagnostic PCR assays based on the 16S rRNA gene sequences. All isolates of both species had a thymidine in position 912 (E. coli numbering) that causes streptomycin resistance in several bacterial species and which is characteristic for the members of the hominis group. As expected, when five M. agalactiae and three M. bovis isolates were tested for streptomycin susceptibility, they all demonstrated streptomycin resistance. M. agalactiae and M. bovis were found to have high intraspecific variation in their 16S rRNA gene and the polymorphisms patterns indicate that gene conversion takes place.

Animals↗
PubMed2001

Antibiotic resistance in the absence of selective pressure.

Antibiotic resistance poses a serious threat to modern medical practice making treatment more difficult and is associated with increased mortality among patients infected with resistant organisms. There is clear evidence that acquisition of resistance is associated with a decrease in the fitness of the organisms at least in the short term. Evidence from in vitro experiments indicates that bacteria have the ability to adapt to this deficit and recover fitness on serial passage. More recent results show that identical organisms isolated from patients in outbreaks have an initial deficit but that adaptation occurs in vivo. Strategies directed towards controlling resistance must move beyond wishful thinking that supposes that these organisms will disappear merely with control of prescribing. In some cases, resistance will not disappear because there is no evolutionary disadvantage in being resistant once adaptation has taken place. It is important, therefore, that we direct our efforts towards preventing primary resistance emerging and in limiting the spread of resistant strains. Ultimately, we must look again to new drug discovery to improve our therapeutic armoury.

Adaptation, Physiological↗
PubMed2000

The effect of a commercial starter culture addition on the ripening of an artisanal goat's cheese (Cameros cheese).

The evolution of physicochemical parameters, and the most important microbial groups, were determined for the following three batches of 'Cameros' goat's milk cheese during ripening: Batch R elaborated with raw milk, Batch RS elaborated with raw milk and with the addition of a starter culture, and Batch PS elaborated with pasteurized milk and with the addition of the same culture. No differences in total solids (TS) or in the content of NaCl, fat and total nitrogen (expressed as percentages of TS) were found during the ripening. The pH, fat acidity and non-protein nitrogen (NPN, expressed as a percentage of TN) showed significant differences between the batches. The inoculated batches showed the fastest drop in pH at the beginning of the ripening period, but the cheeses of Batch R showed a higher degree of lipolysis and proteolysis. The addition of a starter influenced the microbiological quality of the cheeses. Differences in the counts of Enterobacteriaceae and faecal coliforms were found between Batches R and RS after 15 days. Staphylococcus aureus increased in number during the early period of ripening and attained a population above 6 log cfu g-1 in Batch R in the period from 5 to 10 days. However, enterotoxins were not detected in this Batch. Batch R showed lower values of lactic acid bacteria at the beginning of the ripening period, but no significant differences were found between batches in the period from 5 to 15 days of ripening. At the beginning of the ripening, Lactococcus was the main lactic acid bacteria, with L. lactis lactis being predominant. After 15 days, the lactic acid bacteria counts decreased in the three batches, especially in the cheeses of Batch PS (only 2.2 log cfu g-1 was found at 60 days), as lactococci (the only lactic acid bacteria present in Batch PS) are incapable of growing under the conditions found in cheeses at the end of their ripening period. At this time, Lactobacillus was the predominant genus in Batches R and RS, with L. plantarum predominant. No lactococci were found from day 30 in Batch R and from day 40 in Batch RS. The cheeses of Batch RS received the most favourable scores from the tasting panel for all attributes judged: cut appearance, colour, aroma, taste, texture and general acceptance.

Animals↗
PubMed1998

Antibiotic resistance caused by gram-negative multidrug efflux pumps.

Minimum inhibitory concentrations (MICs) of most lipophilic agents tend to be much higher against gram-negative than gram-positive bacteria. Multidrug efflux pumps that traverse both the inner and outer membranes make a major contribution to this intrinsic resistance of gram-negative bacteria. Such a pump is composed of at least three components, is energized by the proton-motive force, and can pump out not only an extremely wide variety of detergents, dyes, and antibiotics, but also those compounds, such as beta-lactams, that do not easily cross the cytoplasmic membrane. Increased expression of these pumps can raise the MICs to an impressive level. For example, 80% of carbenicillin-resistant clinical isolates of Pseudomonas aeruginosa from the British Isles owed their resistance to overexpression of an efflux pump and had carbenicillin MICs that were up to 2,000 times higher than that of the pump-deficient mutant strain.

Animals↗
PubMed2026

Biocontrol potential and molecular basis of predation in a marine raptorial ciliate.

Predator-prey interactions are widespread across organisms and are key drivers of morphological and behavioral evolution. Despite this, predation remains poorly understood among microbial eukaryotes, mostly due to the absence of a tractable experimental system that allows quantitative, reproducible investigation. This study establishes the marine raptorial ciliate Chaenea vorax as a highly efficient predator, with Rosenzweig-MacArthur model simulations based on predation data showing that only a few dozen individuals can eliminate the vast majority of the facultatively pathogenic ciliate Uronema marinum within 1-2 days, providing a quantitative basis for developing predator-based biocontrol strategies in aquaculture. Genomic analysis shows that C. vorax possesses a highly fragmented macronuclear genome enriched with predation-related pathways, including calcium-mediated contractility, cellular proteolysis, toxin expulsion systems, among others. Transcriptomic profiling during predation events further demonstrates significant upregulation of genes involved in cytoskeletal remodeling, proteolytic activity, and cellular detoxification. Evolutionary analyses suggest that C. vorax has an extremely long evolutionary history, exceptionally high nucleotide diversity even among ciliates, and gene family expansions linked to predatory adaptation. Although the prey possesses certain defensive mechanisms (e.g. trichocysts), these are largely ineffective against short-term predation in closed aquatic environments. These findings provide fundamental insights into the molecular basis of predation in ciliates and suggest the potential utility of C. vorax in biocontrol applications targeting pathogenic ciliates.

Ciliophora↗
PubMed1996

The Garrod Lecture. Evasion of antibiotic action by bacteria.

Antibiotics have reduced the mortality from infectious diseases but not the prevalence of these diseases. Use, and often abuse, of antimicrobial agents encourages the evolution of bacteria toward resistance, often resulting in therapeutic failure. This evolution is due to the emergence of "new' resistance mechanisms and to the spread of well-characterized mechanisms of resistance to the majority of bacterial species. Bacterial resistance can be intrinsic or acquired. Intrinsic resistance is species or genus specific and delineates the spectrum of activity of the antibiotic. Acquired resistance is present in only certain strains of a species or of a genus. The latter results from mutation in a gene located in the host chromosome or a plasmid or from acquisition of new genetic information by a bacterium, mainly by conjugation or transformation. In this review, recent developments in the understanding of biochemical mechanisms and the genetics of resistance is considered for the clinically important antibiotic families.

Anti-Bacterial Agents↗
PubMed1999

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database.

The HIV RT and Protease Sequence Database is an on-line relational database that catalogues evolutionary and drug-related human immunodeficiency virus reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences including International Collaboration database submissions (e.g., GenBank) and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the anti-HIV drug treatment history of the individual from whom the isolate was obtained. The database is curated and sequences are annotated with data from 180 literature references. Users can retrieve additional data and view alignments of sequences sets meeting specific criteria (e.g., treatment history, subtype, presence of a particular mutation).

Anti-HIV Agents↗
PubMed1994

Evolution of Fusarium graminearum A3/5 grown in a glucose-limited chemostat culture at a slow dilution rate.

The evolution of Fusarium graminearum A3/5 grown in a glucose-limited chemostat at a dilution rate of 0.05 h-1 (doubling time of 13.9 h) was followed for 957 h or 69 generations. Periodic selection of advantageous mutants was monitored in the culture by determining increases and decreases in the concentration of cycloheximide-resistant macroconidia in the population. Six peaks in the concentration of cycloheximide-resistant macroconidia were observed representing five adaptive changes in the population; on average, an adaptive change occurred once every 148 +/- 22 h (mean +/- SE). The selection coefficient of strains present at the start of each increase in the concentration of cycloheximide-resistant macroconidia (i.e. after the establishment of a new advantageous strain) was determined relative to A3/5 and was found to increase progressively with time. When grown at a dilution rate of 0.05 h-1, the strain (A28-S) isolated from the last adaptive peak had a selection coefficient of 0.023 h-1 relative to A3/5, but A28-S lost its selective advantage when grown at a dilution rate of about 0.11 h-1 and was at a selective disadvantage when grown at a dilution rate higher than 0.11 h-1. The Km value (12 +/- 5 microM) for uptake of glucose by A28-S was significantly lower than that for A3/5. The spontaneous mutation rate from cycloheximide sensitivity to cycloheximide resistance was estimated to be 1.8 (+/- 0.2) x 10(-6) h-1 or 2.5 x 10(-5) generation.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Physiological↗
PubMed1994

Evolution of antibiotic resistance: several different amino acid substitutions in an active site loop alter the substrate profile of beta-lactamase.

In order to understand how TEM-1 beta-lactamase substrate specificity can be altered by mutation, amino acid residues 161 through to 170 were randomly mutagenized to sample all possible amino acid substitutions. The 161-170 region includes a portion of an omega loop structure, which is involved in the formation of the active-site pocket. The percentage of random sequences that provide bacterial resistance to either ampicillin or to the extended-spectrum cephalosporin ceftazidime was determined. It was found that the sequence requirements for wild-type levels of ampicillin resistance are much more stringent than the sequence requirements for ceftazidime resistance. Surprisingly, more than 50% of all amino acid substitutions in the 161-170 region result in levels of ceftazidime resistance at least three times greater than wild type. In addition, by increasing the level of the selection for ceftazidime resistance, substitutions that result in a greater than 100-fold increase in ceftazidime resistance were identified. Characterization of altered beta-lactamase enzymes indicated that while their catalytic efficiency (kcat/Km) for ceftazidime hydrolysis is higher, the enzymes are poorly expressed relative to wild-type TEM-1 beta-lactamase.

Amino Acid Sequence↗
PubMed2004

Co-composting of PAH-contaminated soil with poultry manure.

AIMS: To investigate the effects of co-composting poultry manure with soil contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs), on the degradation of selected PAHs in a static-pile compost system. METHODS: Mispah form (Food & Agricultural Organisation, FAO : lithosol) soil contaminated with PAHs was co-composted with poultry manure for 19 months. The soil was mixed with wood chips in a ratio of 1:1 to improve aeration and then mixed with poultry manure in a ratio of 4:1. A data logger measured temperature monthly. Residual concentrations of selected PAHs in the compost were determined monthly by gas chromatography/flame ionisation detection (GC/FID). Moisture, pH, ash content and C:N ratios were also monitored monthly. Microbial activity was measured by measuring CO(2) evolution. CONCLUSIONS: The results obtained in this experiment have shown that co-composting poultry manure with PAH-contaminated soil is capable of removing large concentrations of high molecular weight PAH from contaminated soil to levels below 1 mg kg(-1) in 19 months. SIGNIFICANCE AND IMPACT OF THE STUDY: The paper adds to the body of knowledge necessary for the development of a cost effective technology for the remediation of soil contaminated with high molecular weight PAHs by providing information on the behaviour of selected PAHs and factors such as nutrient ratio, temperature and pH during composting.

Animals↗
PubMed1991

Trophic relationships between Saccharomyces cerevisiae and Lactobacillus plantarum and their metabolism of glucose and citrate.

Glucose and citrate are two major carbon sources in fruits or fruit juices such as orange juice. Their metabolism and the microorganisms involved in their degradation were studied by inoculating with an aliquot of fermented orange juice a synthetic model medium containing glucose and citrate. At pH 3.6, their degradation led, first, to the formation of ethanol due to the activity of yeasts fermenting glucose and, eventually, to the formation of acetate resulting from the activity of lactobacilli. The yeast population always outcompeted the lactobacilli even when the fermented orange juice used as inoculum was mixed with fermented beet leaves containing a wider variety of lactic acid bacteria. The evolution of the medium remained similar between pH 3.3 and 5.0. At pH 3.0 or below, the fermentation of citrate was totally inhibited. Saccharomyces cerevisiae and Lactobacillus plantarum were identified as the only dominant microorganisms. The evolution of the model medium with the complex microbial community was successfully reconstituted with a defined coculture of S. cerevisiae and L. plantarum. The study of the fermentation of the defined model medium with a reconstituted microbial community allows us to better understand the behavior not only of fermented orange juice but also of many other fruit fermentations utilized for the production of alcoholic beverages.

Citrates↗