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PubMed1998

New tools in an old trade: CS1 pilus morphogenesis.

CS1 pili serve as the prototype for a large class of serologically distinct pili associated with enterotoxigenic Escherichia coli that cause diarrhoea in humans. The four genes essential for CS1 pilus morphogenesis, cooB, A, C and D, are arranged in an operon and encode structural and assembly proteins unlike those of other pilus systems commonly associated with Gram-negative bacteria. CS1 pili are composed primarily of the major pilin subunit, CooA, which determines the serological type of the pilus. The major pilin subunit is assembled into pili by the proteins CooB, CooC and CooD. CooD is both a minor component found at the pilus tip and an essential assembly protein, whereas CooC is an outer membrane protein thought to be involved in pilin transport. CooB is a novel periplasmic chaperone-like protein that forms intermolecular complexes with and stabilizes the major and minor pilins. Unlike other pilin chaperones, CooB also stabilizes the outer membrane component of the assembly system, CooC. The proteins of CS1 pili have no significant homology to those of the well-characterized Pap (pyelonephritis-associated) pili and related systems, although most of the features of pilus morphogenesis are similar. Therefore, these appear to be among the rare cases of convergent evolution. Thus, for CS1 pili, enterotoxigenic E. coli use new protein 'tools' in the old 'trade' of forming functional pili.

Bacterial Proteins↗
PubMed2006

A Survey of the bacteriophage WO in the endosymbiotic bacteria Wolbachia.

Bacteriophages are common viruses infecting prokaryotes. In addition to their deadly effect, phages are also involved in several evolutionary processes of bacteria, such as coding functional proteins potentially beneficial to them, or favoring horizontal gene transfer through transduction. The particular lifestyle of obligatory intracellular bacteria usually protects them from phage infection. However, Wolbachia, an intracellular alpha-proteobacterium, infecting diverse arthropod and nematode species and best known for the reproductive alterations it induces, harbors a phage named WO, which has recently been proven to be lytic. Here, phage infection was checked in 31 Wolbachia strains, which induce 5 different effects in their hosts and infect 25 insect species and 3 nematodes. Only the Wolbachia infecting nematodes and Trichogramma were found devoid of phage infection. All the 25 detected phages were characterized by the DNA sequence of a minor capsid protein gene. Based on all data currently available, phylogenetic analyses show a lack of congruency between Wolbachia or insect and phage WO phylogenies, indicating numerous horizontal transfers of phage among the different Wolbachia strains. The absence of relation between phage phylogeny and the effects induced by Wolbachia suggests that WO is not directly involved in these effects. Implications on phage WO evolution are discussed.

Animals↗
PubMed2006

Differential induction of Leishmania donovani bi-subunit topoisomerase I-DNA cleavage complex by selected flavones and camptothecin: activity of flavones against camptothecin-resistant topoisomerase I.

Emergence of the bi-subunit topoisomerase I in the kinetoplastid family (Trypanosoma and Leishmania) has brought a new twist in topoisomerase research related to evolution, functional conservation and preferential sensitivities to the specific inhibitors of type IB topoisomerase family. In the present study, we describe that naturally occurring flavones baicalein, luteolin and quercetin are potent inhibitors of the recombinant Leishmania donovani topoisomerase I. These compounds bind to the free enzyme and also intercalate into the DNA at a very high concentration (300 microM) without binding to the minor grove. Here, we show that inhibition of topoisomerase I by these flavones is due to stabilization of topoisomerase I-DNA cleavage complexes, which subsequently inhibit the religation step. Their ability to stabilize the covalent topoisomerase I-DNA complex in vitro and in living cells is similar to that of the known topoisomerase I inhibitor camptothecin (CPT). However, in contrast to CPT, baicalein and luteolin failed to inhibit the religation step when the drugs were added to pre-formed enzyme substrate binary complex. This differential mechanism to induce the stabilization of cleavable complex with topoisomerase I and DNA by these selected flavones and CPT led us to investigate the effect of baicalein and luteolin on CPT-resistant mutant enzyme LdTOP1Delta39LS lacking 1-39 amino acids of the large subunit [B. B. Das, N. Sen, S. B. Dasgupta, A. Ganguly and H. K. Majumder (2005) J. Biol. Chem. 280, 16335-16344]. Baicalein and luteolin stabilize duplex oligonucleotide cleavage with LdTOP1Delta39LS. This observation was further supported by the stabilization of in vivo cleavable complex by baicalein and luteolin with highly CPT-resistant L.donovani strain. Taken together, our data suggest that the interacting amino acid residues of topoisomerase I may be partially overlapping or different for flavones and CPT. This study illuminates new properties of the flavones and provide additional insights into the ligand binding properties of L.donovani topoisomerase I.

Animals↗
PubMed1999

The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis.

Multilocus sequence typing (MLST) is a recently developed nucleotide sequence-based method for the definitive assignment of isolates within bacterial populations to specific clones. MLST uses the same principles as multilocus enzyme electrophoresis and provides data that can be used to investigate aspects of the population genetics and evolution of bacterial species. We used an MLST data set consisting of the sequences of approximately 450-bp fragments from seven housekeeping loci from a large strain collection of Neisseria meningitidis to estimate the relative impact of recombination compared with point mutation in the diversification of N. meningitidis clonal complexes. 126 meningococcal isolates were assigned to 10 clonal complexes, 9 of which contained minor clonal variants. The allelic variation within each complex was classified as a recombinational exchange or a putative point mutation through a comparison of the sequences of each variant allele with that of the allele typically found in the clonal complex. The nine clonal complexes contained a total of 23 allelic variants, and analysis of the sequences of these variant alleles revealed that a single nucleotide site in a meningococcal housekeeping gene is at least 80-fold more likely to change as a result of recombination than as a result of mutation. This value is estimated to be 10-50-fold for Escherichia coli and approximately 50-fold for Streptococcus pneumoniae.

Alleles↗
PubMed2026

Perturbing H-NS function reveals roles in restricting virulence heterogeneity and pathogen adaptation.

Xenogeneic silencers, such as histone-like nucleoid structuring protein (H-NS), are critical for maintaining horizontally acquired genes in bacterial genomes and minimizing fitness costs associated with inappropriate expression. For bacterial pathogens, this has enabled the acquisition of costly virulence regulons, with H-NS balancing the need for tight silencing with rapid expression in host environments. For Salmonella enterica serovar Typhimurium (STm), survival in these environments relies on phenotypic heterogeneity in virulence gene expression and evolutionary adaptation. Although complete loss of hns is highly deleterious in STm, how subtle impairments to this global silencer disrupt heterogeneity in virulence gene expression and alter adaptation to host environments remains poorly understood. Here, we identify an STm hns hypomorph strain and find that its reduced H-NS DNA-binding affinity increases the proportion of virulence-expressing cells, resulting in enhanced epithelial cell infection in vitro. Furthermore, through experimental evolution in intracellular-like conditions in vitro, we demonstrate that both wild-type and mutant populations converge on disrupting the SPI-2 virulence regulon to improve fitness; however, the mutant population also acquires distinct adaptive mutations to resolve the underlying dysregulation in gene expression. These results suggest that H-NS sets single-cell virulence activation thresholds and that even minor disruptions to its silencing function impact pathogen adaptation, highlighting its role as a critical evolutionary buffer.

Salmonella typhimurium↗
PubMed1987

[One-day surgery in an ENT practice].

The one-day surgery is not a new concept, but has become more frequent during the last years. Medical, psychosocial and especially economical reasons are the basis of this evolution. These different reasons having been analyzed, this evolution is illustrated by a personal experience and statistical data of the last ten years. Advantages and possible complications of the ambulatory surgery in our specialty are then discussed.

Adolescent↗
PubMed1983

Copper deficiency in Helianthus annuus L.: developmental and metabolic consequences, stomatal function and senescence.

The effects of copper deficiency on developmental morphology and on age related metabolic activity, water utilization, stomatal response to light and leaf senescence in the sunflower, Helianthus annuus L., were monitored by sampling single leaves representing each leaf pair at designated harvest times during much of the vegetative lifespan. Plants grown in nutrient solutions lacking copper exhibited no apparent abnormalities during early vegetative growth and leaf morphology differed little from controls. There were no significant differences in rates of respiratory oxygen uptake of basal leaves between minus copper and controls. The effects of copper deficiency on rates of photosynthetic oxygen evolution were related to leaf age: rates were lower than controls in young basal leaves but higher as these leaves approached senescence. Both respiration and photosynthesis were more susceptible to KCN inhibition in minus copper leaves than in controls. There were no differences in cumulative water use per plant during the first five weeks after transfer of seedlings to nutrient solutions and only minor differences in stomatal aperture and guard cell potassium levels in ambient greenhouse light. Both minus copper and control leaves exhibited a sequential loss of stomatal function. Decay in the turgor driven opening response to light preceded loss of light dependent uptake of potassium into guard cells. Both changes in stomatal response to light occurred before major breakdown of chlorophyll. Basal leaves of sunflowers grown in minus copper nutrient solution tended to be retained longer and exhibited delayed loss of chlorophyll.

Copper↗
PubMed2003

Evolutionary patterns of codon usage in the chloroplast gene rbcL.

In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum likelihood-ratio tests to compare the performance of two models, one in which a single codon is overrepresented and one in which two codons are overrepresented. The measure allowed us to analyze both the extent of bias in each lineage and the evolution of codon choice across the phylogeny. Despite predictions based primarily on the low G + C content of the chloroplast and the high functional importance of rbcL, we found large differences in the extent of bias, suggesting differential molecular selection that is clade specific. The seed plants and simple leafy liverworts each independently derived a low level of bias in rbcL, perhaps indicating relaxed selectional constraint on molecular changes in the gene. Overrepresentation of a single codon was typically plesiomorphic, and transitions to overrepresentation of two codons occurred commonly across the phylogeny, possibly indicating biochemical selection. The total codon bias in each taxon, when regressed against the total bias of each amino acid, suggested that twofold amino acids play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds compose a minority of residues in this gene. Those amino acids that contributed most to the total codon usage bias of each taxon are known through amino acid knockout and replacement to be of high functional importance. This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness.

Amino Acids↗
PubMed2006

The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test.

BACKGROUND: The evolution of alternatively spliced exons (ASEs) is of primary interest because these exons are suggested to be a major source of functional diversity of proteins. Many exon features have been suggested to affect the evolution of ASEs. However, previous studies have relied on the KA/KS ratio test without taking into consideration information sufficiency (i.e., exon length > 75 bp, cross-species divergence > 5%) of the studied exons, leading to potentially biased interpretations. Furthermore, which exon feature dominates the results of the KA/KS ratio test and whether multiple exon features have additive effects have remained unexplored. RESULTS: In this study, we collect two different datasets for analysis - the ASE dataset (which includes lineage-specific ASEs and conserved ASEs) and the ACE dataset (which includes only conserved ASEs). We first show that information sufficiency can significantly affect the interpretation of relationship between exons features and the KA/KS ratio test results. After discarding exons with insufficient information, we use a Boolean method to analyze the relationship between test results and four exon features (namely length, protein domain overlapping, inclusion level, and exonic splicing enhancer (ESE) frequency) for the ASE dataset. We demonstrate that length and protein domain overlapping are dominant factors, and they have similar impacts on test results of ASEs. In addition, despite the weak impacts of inclusion level and ESE motif frequency when considered individually, combination of these two factors still have minor additive effects on test results. However, the ACE dataset shows a slightly different result in that inclusion level has a marginally significant effect on test results. Lineage-specific ASEs may have contributed to the difference. Overall, in both ASEs and ACEs, protein domain overlapping is the most dominant exon feature while ESE frequency is the weakest one in affecting test results. CONCLUSION: The proposed method can easily find additive effects of individual or multiple factors on the KA/KS ratio test results of exons. Therefore, the system can analyze complex conditions in evolution where multiple features are involved. More factors can also be added into the system to extend the scope of evolutionary analysis of exons. In addition, our method may be useful when orthologous exons can not be found for the KA/KS ratio test.

Alternative Splicing↗
PubMed1994

Adenoid cystic carcinoma of the head and neck.

Adenoid cystic carcinoma of the head and neck is relatively rare and is characterized by slow evolution, multiple recurrences, protracted clinical course, and late distant metastasis. This article presents its peculiar clinical course, response to therapy, and long-term treatment results by analyzing 67 cases treated from 1979 to 1991 at the Seoul (Korea) National University Hospital. The most common primary site was the parotid gland in the major salivary glands and the nose and paranasal sinuses in the minor salivary glands. The local control rate was 71.1% at 5 years and 44.3% at 8 years. Late-occurring distant metastases did not allow a plateau in survival curves, even after 8 years. Our study also revealed that surgery combined with postoperative radiotherapy could yield better local control.

Adult↗
PubMed1989

Multifunctional cytokines in haemopoiesis.

The number of cytokine molecules identified and cloned grows almost weekly. Studies using pure preparations have shown that single entities, e.g. TGF beta and IL-1 act on a wide variety of target cells whereas other cytokines, e.g. G-CSF have a more restricted target cell population. The outcome of stimulation of a cell by a cytokine depends on the target cell type, the presence of other coexisting cytokines and, as the release of cytokines may be targeted in the direction of the stimulus, the orientation of producer and target cells. These modulating phenomena may enable a small number of cytokines to specifically define a much larger number of responses, so that maximum 'value' is obtained from the successful evolution of cytokine and receptor molecules. The current nomenclature has little regard for this, the names of cytokines often deriving from the first property observed in vitro. In many cases these are not the most important properties of the molecule and can be misleading, e.g. transforming growth factor beta, which is growth inhibitory in some systems; the antiviral action of interferon gamma is relatively minor compared to its role as a macrophage activation factor; and interleukin-1 is produced by, and acts on, many cells outside the lymphohaemopoietic system. In addition, although there is often a high degree of homology, the repertoire of activities may vary between species. For example, IL-5 is a growth factor for eosinophils, both in humans and mice, however, in the mouse it also acts as a B-cell differentiation factor--a property which has been less easy to identify in human IL-5.(ABSTRACT TRUNCATED AT 250 WORDS)

Activins↗
PubMed1999

Comparative analysis of KRAB zinc finger proteins in rodents and man: evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes.

Although the KRAB zinc finger proteins probably constitute the single largest class of transcription factors within the human genome, almost nothing is known about their biological function. To increase our knowledge about this interesting and relatively unexplored family of potent transcriptional repressors, we here present the cloning, structural analysis, and expression study of three novel mouse KRAB zinc finger proteins. In addition, we present an extensive comparative analysis of various members of this gene family based on the structure of the common KRAB A motif. At least three larger subfamilies of KRAB zinc finger proteins are identified: one carrying the classical KRAB A motif only, another holding both a classical KRAB A and a classical KRAB B motif, and a third holding a classical KRAB A and a highly divergent KRAB B domain, named b. A large variation both in size and in primary amino acid sequence was observed in the linker region between the KRAB domain and the C-terminally located zinc finger repeats. This variability indicates that this region is of minor importance for the biological function of KRAB-containing zinc finger proteins. The fact that in many zinc finger genes, the entire or almost the entire linker region is composed of degenerate finger motifs substantiates this conclusion. The absence of identifiable KRAB A and B motifs in the genome of yeast, Saccharomyces cerevisiae, indicates a relatively late appearance of the KRAB domain in evolution and may suggest that the biological functions are restricted to multicellular organisms. In addition, we show that the expression of individual members of one subfamily of KRAB zinc finger genes is restricted to specific hematopoietic cell lineages. This finding suggests that KRAB zinc finger proteins may play a role in lineage commitment, possibly silencing leakage transcription from nonlineage-expressed genes.

Amino Acid Sequence↗
PubMed2005

Cooperation, social networks, and the emergence of leadership in a prisoner's dilemma with adaptive local interactions.

Cooperative behavior among a group of agents is studied assuming adaptive interactions. Each agent plays a Prisoner's Dilemma game with its local neighbors, collects an aggregate payoff, and imitates the strategy of its best neighbor. Agents may punish or reward their neighbors by removing or sustaining the interactions, according to their satisfaction level and strategy played. An agent may dismiss an interaction, and the corresponding neighbor is replaced by another randomly chosen agent, introducing diversity and evolution to the network structure. We perform an extensive numerical and analytical study, extending results in M. G. Zimmermann, V. M. Eguíluz, and M. San Miguel, Phys. Rev. E 69, 065102(R) (2004). We show that the system typically reaches either a full-defective state or a highly cooperative steady state. The latter equilibrium solution is composed mostly by cooperative agents, with a minor population of defectors that exploit the cooperators. It is shown how the network adaptation dynamics favors the emergence of cooperators with the highest payoff. These "leaders" are shown to sustain the global cooperative steady state. Also we find that the average payoff of defectors is larger than the average payoff of cooperators. Whenever "leaders" are perturbed (e.g., by addition of noise), an unstable situation arises and global cascades with oscillations between the nearly full defection network and the fully cooperative outcome are observed.

Journal Article↗
PubMedDate not supplied

Percutaneous cholecystostomy for acute cholecystitis in critically ill patients.

BACKGROUND/AIMS: The aim of this study was to ascertain the therapeutic efficacy of percutaneous cholecystostomy in a selected group of high-risk patients who were physiologically unable to tolerate an open procedure. METHODOLOGY: We reviewed the hospital records of 11 critically ill patients who underwent percutaneous cholecystostomy for acute cholecystitis during the intensive care unit course of major underlying diseases. RESULTS: Percutaneous cholecystostomy was easily performed in all cases (feasibility rate: 100%). No procedure-related death was recorded and minor complications occurred in 2 patients (18%). Percutaneous cholecystostomy led to resolution of the sepsis in all but 1 patient with gangrenous calcolous cholecystitis who required emergent cholecystectomy (success rate: 91%). Percutaneous cholecystostomy was the permanent treatment in all patients with acalcolous cholecystitis. Among patients with calcolous cholecystitis, 4 underwent delayed elective cholecystectomy, 1 required no further treatment, and 2 eventually died from the evolution of their underlying diseases. After a mean follow-up of 25 months (range: 12-32 months), none of the patients managed non-operatively required surgery or re-hospitalization. CONCLUSIONS: Ease of performance, low complication rate, and high success rate make percutaneous cholecystostomy the procedure of choice for critically ill patients with acute cholecystitis. Whenever possible, percutaneous cholecystostomy should be followed by elective cholecystectomy. However, especially in acalcolous cholecystitis, it may constitute the definitive treatment.

Acute Disease↗
PubMed2005

Contributions of marginal offspring to reproductive success of Nazca booby (Sula granti) parents: tests of multiple hypotheses.

While obligate siblicide is a phylogenetically widespread behavior, known from plants, insects, birds, and other taxa, with important implications for life history evolution, comprehensive evaluations of its costs and benefits to parents are rare. We used 12 years of breeding and band resight data to evaluate the importance of several potential benefits that marginal offspring (the usual victims of obligate siblicide) could provide to parent Nazca boobies (Sula granti), a seabird. We found no evidence for the resource-tracking hypothesis: 99.95% of two-chick broods were reduced to one chick before fledging, and the single exceptional brood probably lost one chick between fledging and independence. Behavioral observations indicated that siblicidal aggression caused most mortality of marginal chicks, and at least contributed to the remainder. We also found no evidence that marginal offspring provide a food resource for other family members. Marginal chicks benefit parents via adoption into other families, and possibly also in the context of progeny choice, but these benefits are minor compared to the insurance that marginal chicks provide against early failure of core (first-hatched) offspring. Further evaluation of the Insurance Egg Hypothesis showed that marginal and core offspring are functionally equivalent in the absence of sibling interactions, and that core offspring incur no detectable costs from behaving siblicidally. Nazca boobies are truly obligate brood reducers, with parents receiving principally insurance benefits from marginal offspring, but many birds and other taxa exhibiting persistent, unconditional sibling aggression do not exhibit universal brood reduction. Insurance is only one of several potential benefits that marginal offspring can confer on parents, and a multi-hypothesis approach to decompose the different types of benefits is required to understand the evolution of clutch size in other obligately siblicidal species.

Animals↗
PubMed2004

Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation.

Recently there has been much interest in assessing the role of alternative splicing in evolution. We have sought to measure functional selection pressure on alternatively spliced single-exon skips, by calculating the fraction that are an exact multiple of 3 nt in length and therefore preserve protein reading-frame in both the exon-inclusion and exon-skip splice forms. The frame-preservation ratio (defined as the number of exons that are an exact multiple of three in length, divided by the number of exons that are not) was slightly above random for both constitutive exons and alternatively spliced exons as a whole in human and mouse. However, orthologous exons that were observed to be alternatively spliced in the expressed sequence tag data from two or more organisms showed a substantially increased bias to be frame-preserving. This effect held true only for exons within the protein coding region, and not the untranslated region. In five animal genomes (human, mouse, rat, zebrafish, Drosophila), we observed an association between these conserved alternative splicing events and increased selection pressure for frame-preservation. Surprisingly, this effect became stronger as a function of decreasing exon inclusion level: for alternatively spliced exons that were included in a majority of the gene's transcripts, the frame-preservation bias was no higher than that of constitutive exons, whereas for alternatively spliced exons that were included in only a minority of the gene's transcripts, the frame-preservation bias increased nearly 20-fold. These data indicate that a subpopulation of modern alternative splicing events was present in the common ancestors of these genomes, and was under functional selection pressure to preserve the protein reading frame.

Alternative Splicing↗
PubMed2004

The 14-3-3 proteins in the teleost fish rainbow trout (Oncorhynchus mykiss).

We report studies of 14-3-3 genes in rainbow trout, adding to current understanding of the molecular evolution of this multigene family and its functional importance in fish. Ten genes were identified that are apparent duplicates of five ancestors. The duplicated 14-3-3 genes diverged rapidly and their cladogram is markedly different from the phylogenetic tree. The mean rate of nonsynonymous divergence of trout 14-3-3 genes is one order of magnitude greater than that of mammalian genes. An evolutionarily recent genome duplication in salmonid fish relaxed functional constraints, and selection favored establishment of novel isoforms. Differences in tissue distribution of 14-3-3 genes were minor; however, results of 31 microarray experiments showed divergence of expression profiles, which was related to structural divergence of the duplicates. We observed remarkable coordination of expression of all isoforms in our study of stress response in the brain. Profiles of the 14-3-3 genes correlated with a large group of chaperones and genes involved in cell communication and signal transduction. We studied embryonic expression of 14-3-3 genes and found abundant transcripts in the rapidly growing and differentiating parts of embryos such as eyes, tail bud and yolk syncytium during somitogenesis and in gills and pectoral fins after completion of somitogenesis. Consistent expression was observed in the neural crest, which is known to have high morphogenetic potential.

14-3-3 Proteins↗
PubMed1986

Somatic evolution of variable region structures during an immune response.

Immunization of strain A mice with p-azophenylarsonate-conjugated protein stimulates B cells that synthesize anti-p-azophenylarsonate antibodies. A large fraction of these cells produce antibodies with variable (V) regions encoded by a single heavy chain V gene segment together with multiple combinations of diversity, heavy chain joining, light chain variable, and light chain joining gene segments. Early in the immune response, these V regions are not somatically mutated. One of these V regions is initially expressed by only a minority of the responding B cells but binds p-azophenylarsonate with the highest affinity. After a secondary immunization, B cells synthesizing mutated derivatives of this single V region dominate the response and bind p-azophenylarsonate with even higher affinity than does the unmutated V region. These results suggest that antigen directs both the expression of the immune repertoire and the amplification of V region diversity by a sequential process of clonal selection of B cells expressing receptor antibodies encoded by unmutated V genes, induction of mutation in the V genes expressed by the selected cells, and reselection of B cells expressing antibodies with mutated V regions of higher affinity.

Animals↗