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PubMed2006

Variation in synonymous codon use and DNA polymorphism within the Drosophila genome.

A strong negative correlation between the rate of amino-acid substitution and codon usage bias in Drosophila has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. To further explore this possibility we have investigated polymorphism and divergence at three kinds of sites: synonymous, nonsynonymous and intronic in relation to codon bias in D. melanogaster and D. simulans. We confirmed that protein evolution is one of the main explicative parameters for interlocus codon bias variation (r(2) approximately 40%). However, intron or synonymous diversities, which could have been expected to be good indicators of local interference [here defined as the additional increase of drift due to selection on tightly linked sites, also called 'genetic draft' by Gillespie (2000)] did not covary significantly with codon bias or with protein evolution. Concurrently, levels of polymorphism were reduced in regions of low recombination rates whereas codon bias was not. Finally, while nonsynonymous diversities were very well correlated between species, neither synonymous nor intron diversities observed in D. melanogaster were correlated with those observed in D. simulans. All together, our results suggest that the selective constraint on the protein is a stable component of gene evolution while local interference is not. The pattern of variation in genetic draft along the genome therefore seems to be instable through evolutionary times and should therefore be considered as a minor determinant of codon bias variance. We argue that selective constraints for optimal codon usage are likely to be correlated with selective constraints on the protein, both between codons within a gene, as previously suggested, and also between genes within a genome.

Animals↗
PubMed1992

On the evolution of the bacterial major sigma factors.

The existence of internal sequence homologies between the N-terminal halves of the gram-negative bacterial major sigma factors and their C-terminal halves, which correspond to minor factors, is reported. In the case of Escherichia-Salmonella sigma-70, an apparent homology was even found between the C-terminal helix-turn-helix DNA-binding motif and the corresponding region of the peptide N half, which, however, is not directly engaged in promoter recognition. It is proposed that major sigma factors may have originated by duplication and fusion of a DNA unit related to the ancestral gene for the whole sigma family. Coevolution of major sigma structures and complex promoters is suggested.

Amino Acid Sequence↗
PubMed2005

The last common ancestor: what's in a name?

Twenty completely sequenced cellular genomes from the three major domains were analyzed using twice one-way BLAST searches in order to define the set of the most conserved protein-encoding sequences to characterize the gene complement of the last common ancestor of extant life. The resulting set is dominated by different putative ATPases, and by molecules involved in gene expression and RNA metabolism. DEAD-type RNA helicase and enolase genes, which are known to be part of the RNA degradosome, are as conserved as many transcription and translation genes. This suggests the early evolution of a control mechanism for gene expression at the RNA level, providing additional support to the hypothesis that during early cellular evolution RNA molecules played a more prominent role. Conserved sequences related to biosynthetic pathways include those encoding putative phosphoribosyl pyrophosphate synthase and thioredoxin, which participate in nucleotide metabolism. Although the information contained in the available databases corresponds only to a minor portion of biological diversity, the sequences reported here are likely to be part of an essential and highly conserved pool of proteins domains common to all organisms.

Evolution, Molecular↗
PubMed1993

A quantitative test of the neutral theory using pooled allozyme data.

Neutral theory predicts a positive correlation between the amount of polymorphism within species and evolutionary rate. Previous tests of this prediction using both allozyme and DNA data have led to conflicting conclusions about the influence of selection and mutation drift. It is argued here that quantitative conclusions about the adequacy of neutral theory can be obtained by analyzing genetic data pooled from many sources. Using this approach, a large database containing information on allozyme variation in over 1500 species is used to examine the relationship between heterozygosity and genetic distance. The results provide support for the hypothesis that a major percentage of protein variation can be explained by variation in neutral mutation rate, and a minor percentage by strong selection.

Animals↗
PubMedDate not supplied

[Neurologic follow-up of the premature infant with very low birth weight].

The most recent studies on premature infants with low birth weights (less than 1500 grams) and extremely low birth weights (less than 1000 grams), other than confirming the spectacular drop in mortality in these subjects, have evaluated their neuropsychic development and the extent of the handicaps over the long term. The major handicaps (cerebral paralysis, mental retardation) have considerably decreased in the survivors, if one makes exception for cases with birth weights less than 750 grams (which present sequelae in high percentages, even if reported differently in the few works published). Minor handicaps (neuropsychological and behavioral defects) are maintained on relatively high levels (20-30% of subjects that survive). There is no doubt that the handicaps of these children may in large part be lead back to ischemic cerebral injuries and/or hemorrhages, well documented today in their evolution from neuroradiological technologies. The mechanism of neurological damage is, however, complex, both in its origin and in its development. Other factors contribute to this as well, among which environmental conditions seem to have an importance that can't be ignored. This applies especially for minor handicaps, which clearly predominate in premature infants of less advantaged social classes. At any rate, the neuropsychic development of premature infants with low birth weights is very individualized and difficult to predict, also because there is still much uncertainty about the value of neonatal prognostic indexes. In the course of the first year of life, neuromotor anomalies can be detected that then spontaneously disappear. In other cases, a more delayed recuperation, even if partial, can be obtained with delays in neuromotor development.(ABSTRACT TRUNCATED AT 250 WORDS)

Central Nervous System↗
PubMed1995

Moving up the hierarchy: a hypothesis on the evolution of a genetic sex determination pathway.

A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency-dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the hierarchy up to the first. The possible applicability of the model to the other well-characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some tests are proposed.

Animals↗
PubMed2002

In vitro molecular evolution of antibody genes mimicking receptor revision.

Antibody evolution in vivo proceeds mainly by stepwise improvements, accomplished by single base pair substitutions. Lately, receptor revision, i.e. exchange of large parts of the V gene for another sequence, has been suggested to provide a complementary route for affinity maturation. By employing a receptor revision like evolution process in vitro using combinatorial libraries and phage display selection, we demonstrate here that maturation of a clone may preferentially proceed through exchange of a large gene segment rather than via minor sequence changes. These modifications of a CD40-specific human antibody fragment outline how receptor revision like events may provide an advantage to a particular clonotype put under selective pressure.

Amino Acid Sequence↗
PubMed1975

[Regulating and limiting factors in evolution].

It is shown in a literature review, that in the Typostrophic Theory autonomous mechnisms in the organism are considered as the factors which play a decisive role in orienting and controlling the evolutionary process. Selection is a controlling factor of only minor importance. The synthetic Theory, on the other side, says that phylogenetic changes are not random or controlled by "internal factors" but can always be considered as adaptive remodellings. They are achieved by selection acting on the variation within populations. Ecological, historical and "bautechnische" (fabricational) factors are considered as limiting mechanisms in the evolutionary process. They are discussed in detail in the text.

Adaptation, Biological↗
PubMed2002

Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.

Here, we analyse Escherichia coli enzymes involved in small molecule metabolism (SMM). We introduce the concept of pathway distance as a measure of the number of distinct metabolic steps separating two SMM enzymes, and we consider protein homology (as determined by assigning enzymes to structural and sequence families) and gene interval (the number of genes separating two genes on the E. coli chromosome). The relationships between these three contexts (pathway distance, homology and chromosomal localisation) is investigated extensively. We make use of these relationships to suggest possible SMM evolution mechanisms. Homology between enzyme pairs close in the SMM was higher than expected by chance but was still rare. When observed, homologues usually conserved their reaction mechanism and/or co-factor binding rather than shared substrate binding. The correlation between pathway distance and gene intervals was clear. Enzymes catalysing nearby SMM reactions were usually encoded by genes close by on the E. coli chromosome. We found many co-regulated blocks of three to four genes (usually non-homologous) encoding enzymes occurring within four metabolic steps of one another; nearly all of these blocks formed part of known or predicted operons. The "inline reuse" of enzymes (i.e. the use of the same enzyme to catalyse two or more different steps of a metabolic pathway) is also discussed: of these enzymes, four were multifunctional (i.e. catalysed a different reaction in each instance), nine had multiple substrate specificity (i.e. catalysed the same reaction on different substrates in each instance) and one catalysed the same reaction on the same substrate but as part of two different complexes. We also identified 59 sets of isozymic proteins most commonly duplicated to function under different conditions, or with a different preferred substrate or minor substrate. In addition to transcriptional units, isozymes and inline reuse of enzymes provide mechanisms for controlling the SMM network. Our data suggest that several pathway evolution mechanisms may occur in concert, although chemistry-driven duplication/recruitment is favoured. SMM exploits regulatory strategies involving chromosomal location, isozymes and the reuse of enzymes.

Chromosomes, Bacterial↗
PubMed2001

Determination by capillary electrophoresis of total and available niacin in different development stage of raw and processed legumes: comparison with high-performance liquid chromatography.

The available and total niacin evolution during maturation of yellow pea lupine (Lupinus luteus L., cv. Juno), pea (Pisum sativum L., cv. Ergo), faba bean (Vicia faba sp. minor Harz, cv. Tibo) and in germinated and high-pressure heated peas (Pisum sativum L., cv. Esla) have been determined by capillary electrophoresis (CE). The results have been compared with those obtained by high-performance liquid chromatography (HPLC). The values obtained by CE were similar to those obtained by HPLC. Maturation of seeds significantly reduced the available and total niacin content in legumes. The available/total niacin ratio during seed maturation depends on the type of legume. In faba beans and peas, a reduction was observed which was more pronounced in the case of peas. For lupine seeds, the ripening produced an increase (34%) in the available/total niacin ratio 50 days after flowering (DAF). Pea germination produced an overall increase in available and total niacin content although the available/total niacin ratio decreased. High pressure heating of pea yielded an increase in the available niacin content and available/total niacin ratio but the total niacin content did not change.

Chromatography, High Pressure Liquid↗
PubMed2004

Neuroprotective functions of prion protein.

The normal function of prion protein (PrP) is usually disregarded at the expense of the more fascinating role of PrP in transmissible prion diseases. However, the normal PrP may play an important role in cellular function in the central nervous system, since PrP is highly expressed in neurons and motifs in the sequence of PrP are conserved in evolution. The finding that prion null mice do not have a significant overt phenotype suggests that the normal function of PrP is of minor importance. However, the absence of PrP in cells or in vivo contributes to an increased susceptibility to oxidative stress or apoptosis-inducing insults. An alternative explanation is that the PrP normal function is so important that it is redundant. Probing into the characteristics of PrP has revealed a number of features that could mediate important cellular functions. The neuroprotective actions so far identified with PrP are initiated through cell surface signaling, antioxidant activity, or anti-Bax function. Here, we review the characteristics of the PrP and the evidence that PrP protects against neurodegeneration and neuronal cell death.

Animals↗
PubMed2003

Continuous irradiation and flash-photolysis studies of new[3H]naphtho[2,1-b]pyrans linked by covalent bonds to oligothiophene units. Effect of thiophene substituents on the photochromism.

The influence of oligothiophene substituents on five new [3H]naphtho[2,1-b]pyrans has been investigated using flash photolysis and continuous irradiation techniques. Photochromic properties strongly depend on the number and position of the thienyl units. Thienyl substitution increases the UV/visible absorbance of the lower energy transition of both the naphthopyran and merocyanine isomers. The rate constants of the thermal fading processes also increase with the number of thiophenic entities. Although several minor photoisomers, whose relative amounts depend on the irradiation conditions could be involved, it has been assumed that under continuous monochromatic irradiation, the evolution of the photochromic reaction can be described by the formation of only one photoisomer. Under these conditions, quantum yields of photocolouration and molar absorption coefficients of the non-isolable photomerocyanine isomer were evaluated by photokinetic analysis. Flash-photolytic colourability can be interpreted using continuous irradiation parameters. A linear correlation has been established between experimental and calculated colourability. This result shows that similar photochromic reactions leading to similar photoisomers are triggered either by polychromatic flash photolysis or by continuous monochromatic irradiation.

Journal Article↗
PubMed1999

High deferral rate for maternal-neonatal donor pairs for an allogeneic umbilical cord blood bank.

BACKGROUND: To fully evaluate the safety and efficacy of umbilical cord blood (UCB) as a source of hematopoietic progenitor cells, UCB banks are being established worldwide to provide a readily accessible resource of stem and progenitor cells for allogeneic transplantation. Guidelines for UCB donor criteria have been proposed to minimize the possibility of disease transmission to UCB recipients. STUDY DESIGN AND METHODS: In preparation for the establishment of an allogeneic UCB bank, 285 maternal-neonatal donor pairs were evaluated in our tertiary-care hospital, which was chosen because of the high percentage of African Americans among the maternal population. Maternal, neonatal, and family histories were obtained by confidential interview and medical record review to determine the number of eligible donor pairs on the basis of a conservative interpretation of proposed donor criteria. RESULTS: Only 44 percent of donor pairs were considered eligible. The most common deferral factors were maternal, and they included fever at delivery, history of chronic disease, and history of sexually transmitted disease. In most cases, more than one deferral factor was identified. CONCLUSIONS: High-risk maternal populations, which may provide access to ethnic minorities targeted for some UCB banks, may contain low percentages of eligible donors. Further refinement of donor criteria will be important in the evolution of UCB banking and transplantation.

Blood Banks↗
PubMed2000

Priapism in a sickle cell prepuberal child.

Between 1985 and 1995, six sickle cell children listed SS were hospitalized in our department for priapism persisting after 24 hours of medical treatment. Two cases regressed after 6 hours of treatment follow-up. Four children were treated by a corpus cavernosum puncture, through the gland, leading to priapism detumescence in 3 cases. In one of our cases, the persistence of priapism induced us to perform a spongiocavernous anastomosis at the 72nd hour. One of the children developed a cerebrovascular accident 10 days after the beginning of the priapism. The other children have been re-examined. They have not presented any reccurence and have normal erection after puberty. Starting from a literature review, we explain the principles we adopted. The physiopathology of priapism in sickle cell patients remains unclear, for both high and low flows do exist. In addition to the risks related to blood products, the treatment by transfusional exchange involves neurological risks and must not delay any surgery. Analgesic treatment is often required. Corpus cavernosum puncture is efficient, with no fibrosis risk. In case of failure, a cavernospongious shunt, with a biopsy needle, can be performed at the same time. Surgical anastomoses are then proposed in case of priapism persistence. General evolution is satisfactory. But the sickle cell patient's priapism needs a long-term follow-up in order to recognise any minor recurrences. The latter could be the principal cause of fibrosis and impotency.

Child↗
PubMed2004

Identification and kinetics analysis of a novel heparin-binding site (KEDK) in human tenascin-C.

The interaction between tenascin-C (TN-C), a multi-subunit extracellular matrix protein, and heparin was examined using a surface plasmon resonance-based technique on a Biacore system. The aims of the present study were to examine the affinity of fibronectin type III repeats of TN-C fragments (TNIII) for heparin, to investigate the role of the TNIII4 domains in the binding of TN-C to heparin, and to delineate a sequence of amino acids within the TNIII4 domain, which mediates cooperative heparin binding. At a physiological salt concentration, and pH 7.4, TNIII3-5 binds to heparin with high affinity (K(D) = 30 nm). However, a major heparin-binding site in TNIII5 produces a modest affinity binding at a K(D) near 4 microm, and a second site in TNIII4 enhances the binding by several orders of magnitude, although it was far too weak to produce an observable binding of TNIII4 by itself. Moreover, mutagenesis of the KEDK sequence in the TNIII4 domain resulted in the significant reduction of heparin-binding affinity. In addition, residues in the KEDK sequences are conserved in TN-C throughout mammalian evolution. Thus the structure-based sequence alignment, mutagenesis, and sequence conservation data together reveal a KEDK sequence in TNIII4 suggestive of a minor heparin-binding site. Finally, we demonstrate that TNIII4 contains binding sites for heparin sulfate proteoglycan and enhances the heparin sulfate proteoglycan-dependent human gingival fibroblast adhesion to TNIII5, thus providing the biological significance of heparin-binding site of TNIII4. These results suggest that the heparin-binding sites may traverse TNIII4-5 and thus require KEDK in TNIII4 for optimal heparin-binding.

Amino Acid Sequence↗
PubMed1999

The modern hippocratic tradition. Some messages for contemporary medicine.

Hippocrates (5th century B.C.), the most prominent physician of antiquity, was born in the small Greek island of Kos, which is near the coast of Asia Minor. Before his era, medicine was practiced as an empirical art and had a religious nature. Hippocratic medicine represents the landmark for the evolution of Western medicine. This "father" of rational medicine assimilated the accumulated knowledge of the past and formed a diagnostic system based on clinical observation and logical reasoning. The great physician attributed diseases to natural causes, believed in the healing power of nature, and gave special emphasis to the prevention and prognosis of illnesses. He treated patients as psychosomatic entities (a holistic medical approach) in relation to their natural environment. In his treatises, Hippocrates defined the ethical principles guiding medical practice. His entire work was inspired by humanistic ideals and an undeviating dedication to the patient. Modern medicine can derive valuable lessons from the Hippocratic tradition. For the coming 21st century, medicine more than ever senses the need to combine the concepts of humanistic values and the Hippocratic messages with the technologic "imperative" (power). This bond is necessary to the improvement of medicine in the future because, currently, the enormous biomedical technology so far has contributed little to the traditionally human fields of psychosomatic and functional disturbances, posing new dilemmas and threatening scientific problems.

Ethics, Medical↗