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PubMed2004

The phylogenetic position of Morotopithecus.

The phylogenetic relationship of the Ugandan Miocene hominoid Morotopithecus bishopi to fossil and living hominoids remains to be determined. In a cladistic approach to this question, we used three published Miocene character sets as the basis of a phylogenetic analysis: J. Hum. Evol. 29 (1995) 101; Function, Phylogeny, and Fossils: Miocene Hominoid Evolution and Adaptations, 1997, 389. Because these datasets often describe the same anatomy using different characters and states, three different datasets were created to reflect these alternatives. In addition, new postcranial characters describable in Morotopithecus were added to each of the above datasets and a fourth dataset was created using only postcranial characters. The most parsimonious tree(s) recovered in all analyses consistently placed Morotopithecus as a sister taxon to the extant great apes, with Hylobates sister to this clade. Morotopithecus was also consistently more derived than Proconsul, Afropithecus, and Kenyapithecus (as defined prior to the description of Equatorius), but less derived than Oreopithecus, Sivapithecus (only craniodentally) and Dryopithecus. These results imply that Morotopithecus is more derived than Hylobates. However, gibbons are believed to have branched off by at least 18 Ma while Morotopithecus is dated at >20.6 Ma. Possible explanations include: (1) the dating of the Morotopithecus material is too old; (2) the Hylobates divergence time has been underestimated; (3) the great ape condition, and not that of Hylobates, is primitive for hominoids; (4) the similarities of Morotopithecus and great apes are homoplasies. Given current evidence, the first possibility is unlikely, but it is not possible to choose definitively between the latter three possibilities. This conclusion is supported by the fact that despite the consistencies of the analyses, the addition of Morotopithecus and the use of different characters had a large effect on the placement of other Miocene taxa. This raises questions as to the robustness of the connections between Miocene taxa and extant hominoids since different results can be achieved by changing either a few characters, or by adding a single taxon. Many of the characters used to estimate phylogeny may need to be reassessed before a reliable assessment of the phylogenetic position of Morotopithecus can be achieved.

Animals↗
PubMed2006

The tryptophan oxidation pathway in mosquitoes with emphasis on xanthurenic acid biosynthesis.

Oxidation of tryptophan to kynurenine and 3-hydroxykynurenine (3-HK) is the major catabolic pathway in mosquitoes. However, 3-HK is oxidized easily under physiological conditions, resulting in the production of reactive radical species. To overcome this problem, mosquitoes have developed an efficient mechanism to prevent 3-HK from accumulating by converting this chemically reactive compound to the chemically stable xanthurenic acid. Interestingly, 3-HK is a precursor for the production of compound eye pigments during the pupal and early adult stages; consequently, mosquitoes need to preserve and transport 3-HK for compound eye pigmentation in pupae and adults. This review summarizes the tryptophan oxidation pathway, compares and contrasts the mosquito tryptophan oxidation pathway with other model species, and discusses possible driving forces leading to the functional adaptation and evolution of enzymes involved in the mosquito tryptophan oxidation pathway.

Alanine Transaminase↗
PubMed2006

A novel haem-binding interface in the 22 kDa haem-binding protein p22HBP.

The 22 kDa haem-binding protein, p22HBP, is highly expressed in erythropoietic tissues and binds to a range of metallo- and non-metalloporphyrin molecules with similar affinities, suggesting a role in haem regulation or synthesis. We have determined the three-dimensional solution structure of p22HBP and mapped the porphyrin-binding site, which comprises a number of loops and a alpha-helix all located on a single face of the molecule. The structure of p22HBP is related to the bacterial multi-drug resistance protein BmrR, and is the first protein with this fold to be identified in eukaryotes. Strikingly, the porphyrin-binding site in p22HBP is located in a similar position to the drug-binding site of BmrR. These similarities suggest that the broad ligand specificity observed for both BmrR and p22HBP may result from a conserved ligand interaction mechanism. Taken together, these data suggest that the both the fold and its associated function, that of binding to a broad range of small hydrophobic molecules, are ancient, and have been adapted throughout evolution for a variety of purposes.

Amino Acid Sequence↗
PubMed2006

Fitness of antimicrobial-resistant Campylobacter and Salmonella.

Campylobacter and Salmonella are the most commonly reported bacterial causes of human foodborne infections, and increasing proportions of these pathogens become resistant to medically important antimicrobial agents, imposing a burden on public health. Acquisition of resistance to antibiotics affects the adaptation and evolution of Salmonella and Campylobacter in various environments. Many resistance-conferring mutations entail a biological fitness cost, while others (e.g. fluoroquinolone resistance in Campylobacter) have no cost or even enhanced fitness. In Salmonella, the fitness disadvantage due to antimicrobial resistance can be restored by acquired compensatory mutations, which occur both in vitro and in vivo. The compensated or even enhanced fitness associated with antibiotic resistance may facilitate the spread and persistence of antimicrobial-resistant Salmonella and Campylobacter in the absence of selection pressure, creating a significant barrier for controlling antibiotic-resistant foodborne pathogens.

Animals↗
PubMed2005

Suppression of homologous and homeologous recombination by the bacterial MutS2 protein.

In addition to their role in DNA repair, recombination events are associated with processes aimed at providing the genetic variability needed for adaptation and evolution of a population. In bacteria, recombination is involved in the appearance of new variants by allowing the incorporation of exogenous DNA or the reshuffling of endogenous sequences. Here we show that HpMutS2, a protein belonging to the MutS2 family in Helicobacter pylori, is not involved in mismatch repair but inhibits homologous and homeologous recombination. Disruption of HpmutS2 leads to an increased efficiency of exogenous DNA incorporation. HpMutS2 has a selective affinity for DNA structures mimicking recombination intermediates with no specificity for homoduplex DNA or mismatches. The purified protein has an ATPase activity stimulated by the same DNA structures. Finally, we show that HpMutS2 inhibits DNA strand exchange reactions in vitro. Thus, MutS2 proteins are candidates for controlling recombination and therefore genetic diversity in bacteria.

Adenosine Triphosphatases↗
PubMed2026

Metagenomics indicates new taxa in Candidatus Saccharimonadia and proposal of Parviradicicola hetaonensis gen. nov. sp. nov. and Parviputeicola dengkouensis gen. nov. sp. nov. following the rules of the SeqCode.

Candidatus Saccharimonadia is a core lineage within the phylum Patescibacteriota (formerly the bacterial candidate phyla radiation, CPR), yet the class has long lacked a standardized, complete taxonomic framework. This nomenclatural gap severely hinders consistent academic exchange and global research into its diversity, evolutionary history, and ecological roles. Here, we recovered 29 medium- to high-quality Ca. Saccharimonadia metagenome-assembled genomes (MAGs) from groundwater, rhizosphere soil, and saline-alkali soil in the Hetao Irrigation District, Inner Mongolia, China, and performed integrated phylogenomic, genome size evolution, and metabolic analyses alongside reference genomes from the GTDB r220 database. Based on robust polyphasic taxonomic evidence (multi-dimensional phylogenetic analyses, widely accepted genome-wide ANI/AAI thresholds) and SeqCode rules, we formally propose two novel taxa: Parviradicicola hetaonensis gen. nov., sp. nov. (type material: txb011_bin.8.strictTS) and Parviputeicola dengkouensis gen. nov., sp. nov. (type material: sgl022_bin.19.origTS), plus two novel families and one novel order. We further identified potential drivers and important associations related to Ca. Saccharimonadia genome size evolution and adaptive metabolic traits. This work refines the Ca. Saccharimonadia taxonomic framework, providing critical genomic references for follow-up research.

Phylogeny↗
PubMed2005

[Intra cranial abscess and empyemas from E.N.T. origin].

OBJECTIVES: The purpose of this study was to evaluate the diagnosis criteria, the bacteriology and the evolution after adapted treatment of intracranial abscess of ENT origin. MATERIAL AND METHODS: It was a retrospective study from 1985 to 2003 concerning 22 patients who had brain abscesses secondary to an ENT infection. RESULTS: The infectious origin was sinusoid in 32% of cases, otologic in 32% of cases, pharyngeal or dental in 27% of cases and cutaneous in 9% of cases. The clinical symptoms were: fever in 55% of cases, headache in 73% of cases (Intra cranial hypertension syndrome in 23% of cases), epilepsy in 32% of cases and various other neurologic symptoms. Bacteria were identified in 82% of cases. In 50% of cases multibacterial associations were found. All the patients had bi antibiotherapy associated to surgical excision of the abscess (16 cases) or single (or more) punction (stereotaxic guided or not) of the abscess. 3 patients (14%) died and 50% are alive and well. CONCLUSION: The diagnosis of cerebral abscess is often difficult. The "classical" intracranial hypertension associated to high fever is usually incomplete and sometimes absent. There is no predominant bacteria involved and multibacterial infections are frequent. Despite abscesses are serious and potentially lethal, an early diagnosis, a medical (antibiotics) and surgical treatment (punction and/or surgical excision) may completely be cured in more than 50% of cases.

Adolescent↗
PubMed2002

When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum.

Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox.

Bacteriophages↗
PubMed1998

Give us this day our daily germs.

Modern vaccinations, fear of germs and obsession with hygiene are depriving the immune system of the information input upon which it is dependent. This fails to maintain the correct cytokine balance and fine-tune T-cell regulation, and may lead to increased incidences of allergies and autoimmune diseases. If humans continue to deprive their immune systems of the input to which evolution has adapted it, it may be necessary to devise ways of replacing it artificially.

Adult↗
PubMed2000

Disaptation and recovery in the evolution of Antarctic fishes.

The radiation of notothenioid fishes provides an excellent system to explore issues of evolution and adaptation. Most studies emphasize adaptation to the extreme Antarctic environment; however, recent work provides cogent examples of disaptation or evolutionary loss of function. The nature and extent of regressive change is revealed by subsequent adaptive recovery. Ancestral notothenioids were benthic but some became secondarily pelagic through the retention of larval characters. Paedomorphosis has produced detrimental changes in lateral-line sensory systems that have been made good by compensatory adaptation. In the icefish family, compensatory adaptation has followed the loss of the oxygen-binding pigments haemoglobin and myoglobin.

Journal Article↗
PubMed1998

A comparative study of the beta-adrenoceptors in higher visual centres of birds.

This report describes the distribution of beta-adrenergic receptors in the telencephalic visual nuclei of chick, duck, pigeon, parakeet and goldfinch using [3H]CGP 12177 (4-3-t-butylamino-2-hydroxypropoxy-[5,7(3)H] benzimidazol-2-one) as a radioligand. The results reveal a predominance of the beta2-adrenoceptor subtype in all the species studied and that this subtype fits the pharmacological profile described for mammals. It is also demonstrated that the autoradiographic interspecific differences described in previous studies are due to changes in Bmax, while KD values remain in a similar range (0.1-0.6 nM). The distribution of beta-adrenoceptors was fairly similar in the areas of the visual Wulst of all five species studied while striking differences were found in the ectostriatum, the higher centre of the tectofugal pathway. Our findings support a role for ectostriatal beta-adrenoceptors in the visual adaptation and evolution of birds.

Adrenergic beta-Agonists↗
PubMed1997

The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules.

BACKGROUND: Protein disulfide isomerase (PDI), a multifunctional protein of the endoplasmic reticulum, catalyzes the formation, breakage and rearrangement of disulfide bonds during protein folding. Dissection of this protein into its individual domains has confirmed the presence of the a and a' domains, which are homologous to thioredoxin, having related structures and activities. The a and a' domains both contain a -Cys-Gly-His-Cys- active-site sequence motif. The remainder of the molecule consists primarily of two further domains, designated b and b' which are thought to be sequence repeats on the basis of a limited sequence similarity. The functions of the b and b' domains are unknown and, until now, the structure of neither domain was known. RESULTS: Heteronuclear nuclear magnetic resonance (NMR) methods have been used to determine the global fold of the PDI b domain. The protein has an alpha/beta fold with the order of the elements of secondary structure being beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-beta5+ ++-alpha4. The strands are all in a parallel arrangement with respect to each other, except for beta4 which is antiparallel. The arrangement of the secondary structure elements of the b domain is identical to that found in the a domain of PDI and in the ubiquitous redox protein thioredoxin; the three-dimensional folding topology of the b domain is also very similar to that of these proteins. CONCLUSIONS: Our determination of the global fold of the b domain of PDI by NMR reveals that, like the a domain, the b domain contains the thioredoxin motif, even though the b domain has no significant amino-acid sequence similarities to any members of the thioredoxin family. This observation, together with indications that the b' domain adopts a similar fold, suggests that PDI consists of active and inactive thioredoxin modules. These modules may have been adapted during evolution to provide PDI with its complete spectrum of enzymatic activities.

Amino Acid Sequence↗
PubMed1998

Single-clone and mixed-clone infections versus host environment in Crithidia bombi infecting bumblebees.

Current theories assume that adaptive parasite evolution explains variation in the level of virulence and parasite success. In particular, mixed-genotype infections by parasites should generally be more virulent, and faster multiplying strains more successful, either because fixed strategies have evolved or because parasites facultatively alter virulence in response to co-infecting competitors. We compared several measures of parasite success and virulence between single-clone and mixed-clone infections of 2 strains of the trypanosome Crithidia bombi in its bumblebee host, Bombus terrestris. Contrary to expectation, we could not find differences between single-clone and mixed-clone infections in parasite prevalence, infection success, duration and clearance rate. However, a clearly significant effect of colony on infection intensity was present, and the colony effect emerged in virtually all other measures. We thus conclude that host environment as defined by the family (colony) genotype and thus host heterogeneity are more important in determining parasite virulence than the parasite characteristics. This does not invalidate modern theories of parasite evolution but suggests that variation in both hosts and parasites must be taken into account in more detail.

Animals↗
PubMed1999

Adherence of pathogenic mycoplasmas to host cells.

The significant genome compaction in mycoplasmas was made possible by adoption of a parasitic lifestyle. During their evolution and adaptation to a parasitic mode of life the mycoplasmas have developed various genetic systems enabling their attachment to host tissues as well as a highly plastic set of variable surface proteins. The generation of a versatile surface coat through high-frequency phase and size variation provides the organism with a useful tool for immune system avoidance, allowing the mycoplasmas to escape antibody attack, explaining why these minute organisms are such successful parasites.

Adhesins, Bacterial↗
PubMed1993

Four systems for emotion activation: cognitive and noncognitive processes.

The significant role of emotions in evolution and adaptation suggests that there must be more than 1 mechanism for generating them. Nevertheless, much of current emotion theory focuses on cognitive processes (appraisal, attribution, and construal) as the sole, or primary, means of eliciting emotions. As an alternative to this position, the present model describes 4 types of emotion-activating systems, 3 of which involve noncognitive information processing. From an evolutionary-developmental perspective, the systems maybe viewed as a loosely organized hierarchical arrangement, with neural systems, the simplest and most rapid, at the base and cognitive systems, the most complex and versatile, at the top. The emotion-activating systems operate under a number of constraints, including genetically influenced individual differences. The hierarchical organization of the systems for generating emotions provides an adaptive advantage.

Arousal↗
PubMed1992

Basic emotions, relations among emotions, and emotion-cognition relations.

From the cognitive theory perspective that emotions are cognition dependent and contain cognitive components, Ortony and Turner (1990) questioned the validity of the concept of basic emotions. They argued that the so-called basic emotions were neither psychologically or biologically "primitive" nor "irreducible building blocks" for generating the "great variety of emotional experiences." In the biosocial theory tradition, researchers have identified multiple noncognitive activators of emotion and demonstrated the usefulness of defining the essential components of emotion as phenomena that do not require cognitive mediators or constituents. In this framework, emotions are seen as basic because their biological and social functions are essential in evolution and adaptation. Particular emotions are called basic because they are assumed to have innate neural substrates, innate and universal expressions, and unique feeling-motivational states. The great variety of emotional experiences is explained as a function of emotion-cognition interactions that result in affective-cognitive structures.

Arousal↗
PubMed2006

Deciphering principles of transcription regulation in eukaryotic genomes.

Transcription regulation has been responsible for organismal complexity and diversity in the course of biological evolution and adaptation, and it is determined largely by the context-dependent behavior of cis-regulatory elements (CREs). Therefore, understanding principles underlying CRE behavior in regulating transcription constitutes a fundamental objective of quantitative biology, yet these remain poorly understood. Here we present a deterministic mathematical strategy, the motif expression decomposition (MED) method, for deriving principles of transcription regulation at the single-gene resolution level. MED operates on all genes in a genome without requiring any a priori knowledge of gene cluster membership, or manual tuning of parameters. Applying MED to Saccharomyces cerevisiae transcriptional networks, we identified four functions describing four different ways that CREs can quantitatively affect gene expression levels. These functions, three of which have extrema in different positions in the gene promoter (short-, mid-, and long-range) whereas the other depends on the motif orientation, are validated by expression data. We illustrate how nature could use these principles as an additional dimension to amplify the combinatorial power of a small set of CREs in regulating transcription.

Computational Biology↗