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PubMed1989

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.

Algorithms↗

PubMed2025

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.

SUMMARY: Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, a clonally evolving bacterium with a small accessory genome, as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read versus hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations. AVAILABILITY AND IMPLEMENTATION: Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.

Genome, Bacterial↗

PubMed1999

Circular epidemiology.

Circular epidemiology can be defined as the continuation of specific types of epidemiologic studies beyond the point of reasonable doubt of the true existence of an important association or the absence of such an association. Circular epidemiology is an extreme example of studies of the consistency of associations. A basic problem for epidemiology is the lack of a systematic approach to acquiring new knowledge to reach a goal of improving public health and preventive medicine. For epidemiologists, research support unfortunately is biased toward the continued study of already proven hypotheses. Circular epidemiology, however, freezes at one point in the evolution of epidemiologic studies, failing to move from descriptive to analytical case-control and longitudinal studies, for example, to experimental, clinical trials. Good epidemiology journals are filled with very well-conducted epidemiologic studies that primarily repeat the obvious or are variations on the theme.

Bias↗

PubMed2026

Toward life with a 19-amino acid alphabet through generative artificial intelligence design.

Because all known living organisms are made from at least 20 canonical amino acids, the feasibility of life using a more simplified alphabet remains unclear. In this work, we leveraged computational design and synthetic biology to explore building a cell from a 19-amino acid alphabet. Initial analyses suggested that isoleucine (Ile) may be dispensable, which we confirmed by directly replacing Ile residues in essential proteins in Escherichia coli. Critically, protein language models and structure-based models were necessary to redesign functional Ile-less proteins in most cases. We systematically replaced all 382 Ile residues from the ribosome and combined 21 redesigned subunits at a native genomic locus to produce a viable, evolutionarily stable cell. This work provides a roadmap to create the first 19-amino acid organism since early evolution.

Escherichia coli↗

PubMed2005

[Prevalence of tobacco dependency and its prevention in patients with persistent asthma].

OBJECTIVES: To analyse in patients with persistent bronchial asthma the prevalence of tobacco dependency and its degree; and to assess measures of prevention. DESIGN: Cross-sectional, descriptive study. SETTING: Allergy Service of the Lozano Blesa University Hospital, Zaragoza, Spain. PARTICIPANTS: A total of 121 patients, from systematic selection of asthmatics attending for consultation. MAIN MEASUREMENTS: Questionnaire filled out in the consulting room, recording social, demographic and clinical variables. RESULTS: A sample of 121 patients was obtained, 62.7% women and 37.3% men. They had 5.87 +/- 4.99 years mean evolution of asthma. 21.5% were daily smokers, 4.1% occasional smokers, 27.3% ex-smokers, and 47.1% non-smokers. The ages of starting to smoke were < 10 years old, 1.7%; 10-15, 30%; 15-20, 56.7%; 20-25, 6.7%, and > 25, 5% (P > .05). There were significant differences between gender and tobacco dependency and between age and tobacco dependency (P < .01 and P < .014, respectively). 96.8% of smokers thought that tobacco was harmful to their health. This figure was 100% in daily smokers and 80% in occasional smokers (P < .02). 83.9% of smokers had the intention of giving up. Counselling to give up was received from the specialist (41.9%), the primary care doctor (12.9%), and both (9.7% of cases). 35.5% received no counselling. CONCLUSIONS: The prevalence of tobacco dependency in patients with persistent asthma is lower than in the population as a whole; over a third receive no counselling about giving up. Interventions must be conducted in still healthy smokers and chronically ill patients in both primary and specialist care.

Adolescent↗

PubMed2005

[Prevalence of neuropathic pain in Spain: clinical, working and health care implications].

A narrative systematic medical literature review on prevalence of neuropathic pain (NP) in Spain from 1990 to 2004 was conducted. The average number of publications was 3 per year. Prevalence data varied depending on studied population, definition of pain/pathology and time of pain evolution. The most commonly studied pathologies included: mononeuropathies and polyneuropathies: 42%, multiple sclerosis: 35% and entrapment neuropathies: 16%. Some episodes of NP were left untreated. One third of patients with back pain receiving analgesic treatment still had high intensity pain. Future studies on the prevalence of NP should use work definitions and criteria reached by consensus. An awareness of the clinical presentation of NP and an appropriate and early treatment could minimize its clinical, working and health care implications. NP is a diverse and highly prevalent condition in Spain. Efforts should be conducted towards the achievement of diagnostic criteria consensus and higher rates of analgesic success.

Humans↗

PubMed2006

Retroposed elements as archives for the evolutionary history of placental mammals.

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as well as directional mutation pressure, can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics. By computationally scanning more than 160,000 chromosomal loci and judiciously selecting from only phylogenetically informative retroposons for experimental high-throughput PCR applications, we recovered 28 clear, independent monophyly markers that conclusively verify the earliest divergences in placental mammalian evolution. Using tests that take into account ancestral polymorphisms, multiple long interspersed elements and long terminal repeat element insertions provide highly significant evidence for the monophyletic clades Boreotheria (synonymous with Boreoeutheria), Supraprimates (synonymous with Euarchontoglires), and Laurasiatheria. More importantly, two retropositions provide new support for a prior scenario of early mammalian evolution that places the basal placental divergence between Xenarthra and Epitheria, the latter comprising all remaining placentals. Due to its virtually homoplasy-free nature, the analysis of retroposon presence/absence patterns avoids the pitfalls of other molecular methodologies and provides a rapid, unequivocal means for revealing the evolutionary history of organisms.

Animals↗

PubMed2005

Phylogeny and molecular evolution of the Drosophila hydei subgroup (Drosophila repleta group) inferred from the Xanthine dehydrogenase gene.

The hydei subgroup (Drosophila repleta group) consists of seven species divided into two complexes: bifurca and hydei, whose phylogenetic relationships are not well understood. To evaluate the molecular phylogeny of this subgroup, we analyzed 2085 bp of coding sequence of the Xanthine dehydrogenase gene in six available species of the hydei subgroup, with Drosophila buzzatii and Drosophila mulleri as an outgroup. For phylogenetic reconstruction we adopted a maximum-likelihood framework, based on the adjustment of descriptive models of nucleotide substitution to real data. We employed distance-based and weighted parsimony methods to construct candidate phylogenies. In all cases, we obtained only one completely resolved tree with strong statistical support for each node, that shows a phylogeny that is partially discordant with the proposed systematics of the subgroup. This tree suggests that the two species complexes are paraphyletic, as opposed to classic phylogenies using morphologic and cytologic traits. This discordance is discussed in relation to its implication for the evolutionary history of the hydei subgroup.

Animals↗

PubMed2001

Origin and evolution of African Polystoma (Monogenea: Polystomatidae) assessed by molecular methods.

Among Polystomatidae (Monogenea), the genus Polystoma, which mainly infests neobatrachian hosts, is the most diverse and occurs principally in Africa, from where half the species have been reported. Previous molecular phylogenetic studies have shown that this genus originated in South America, and later colonised Eurasia and Africa. No mention was made on dispersal corridors between Europe and Africa or of the origin of the African Polystoma radiation. Therefore, a molecular phylogeny was inferred from ITS1 sequences of 21 taxa comprising two species from America, seven representatives from Europe and 12 from Africa. The topology of the phylogenetic tree reveals that a single event of colonisation took place from Europe to Africa and that the putative host carrying along the ancestral polystome is to be found among ancestral pelobatids. Percentage divergences estimates suggest that some presumably distinct vesicular species in unrelated South African anurans and some neotenic forms found in several distinct hosts in Ivory Coast, could, in fact, belong to two single polystome species parasitising divergent hosts. Two main factors are identified that may explain the diversity of African polystomes: (i), we propose that following some degree of generalism, at least during the juvenile stages of both hosts and parasites, distinctive larval behaviour of polystomes engenders isolation between parasite populations that precludes sympatric speciations; (ii), cospeciation events between Ptychadena hosts and their parasites are another factor of diversification of Polystoma on the African continent. Finally, we discuss the systematic status of the Madagascan parasite Metapolystoma, as well as the colonisation of Madagascar by the host Ptychadena mascareniensis.

Africa↗

PubMed2003

Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes.

Many early reports of ITS region (ITS 1, 5.8S, and ITS 2) variation in flowering plants indicated that nrDNA arrays within individuals are homogeneous. However, both older and more recent studies have found intra-individual nrDNA polymorphism across a range of plant taxa including presumed non-hybrid diploids. In addition, polymorphic individuals often contain potentially non-functional nrDNA copies (pseudogenes). These findings suggest that complete concerted evolution should not be assumed when embarking on phylogenetic studies using nrDNA sequences. Here we (1). discuss paralogy in relation to species tree reconstruction and conclude that a priori determinations of orthology and paralogy of nrDNA sequences should not be made based on the functionality or lack of functionality of those sequences; (2). discuss why systematists might be particularly interested in identifying and including pseudogene sequences as a test of gene tree sampling; (3). examine the various definitions and characterizations of nrDNA pseudogenes as well as the relative merits and limitations of a subset of pseudogene detection methods and conclude that nucleotide substitution patterns are particularly appropriate for the identification of putative nrDNA pseudogenes; and (4). present and discuss the advantages of a tree-based approach to identifying pseudogenes based on comparisons of sequence substitution patterns from putatively conserved (e.g., 5.8S) and less constrained (e.g., ITS 1 and ITS 2) regions. Application of this approach, through a method employing bootstrap hypothesis testing, and the issues discussed in the paper are illustrated through reanalysis of two previously published matrices. Given the apparent robustness of the test developed and the ease of carrying out percentile bootstrap hypothesis tests, we urge researchers to employ this statistical tool. While our discussion and examples concern the literature on plant systematics, the issues addressed are relevant to studies of nrDNA and other multicopy genes in other taxa.

DNA, Ribosomal↗

PubMed2005

Evolution of nuclear shells due to the tensor force.

The monopole effect of the tensor force is presented, exhibiting how spherical single-particle energies are shifted as protons or neutrons occupy certain orbits. An analytic relation for such shifts is shown, and their general features are explained intuitively. Single-particle levels are shown to change in a systematic and robust way, by using the pi + rho meson exchange tensor potential, consistently with the chiral perturbation idea. Several examples are compared with experiments.

Journal Article↗

PubMed2004

Illness, injury, and disability among Shiwiar forager-horticulturalists: implications of health-risk buffering for the evolution of human life history.

Human life history is distinguished by long lifespan, delayed reproduction, intergenerational asymmetric benefit transfers from adults to juveniles and between adults, and a large brain able to engage in unprecedented levels of learning, reasoning, and insight. The evolution of these traits depends on relatively low human mortality. Understanding why humans have low mortality is therefore critical for understanding the evolution of key human traits. One explanation is that the evolution of food provisioning during periods of health crisis reduced mortality. This hypothesis turns on health risk having posed a significant adaptive problem that could be effectively buffered by healthcare provisioning. Unfortunately, the frequency, duration, and fitness effects of temporary disability are difficult to estimate based on osteological evidence alone, and systematic ethno-biological research on these issues among extant small-scale societies with little access to Western medical care is lacking. Here I present data on 678 injuries and illnesses suffered by 40 Shiwiar forager-horticulturalists, based on physical evidence and informant reports. A subsample of 17 individuals provided data on incidence and duration of disability for 215 pathological incidents. Results indicate that injury and illness occur frequently across the lifespan. Most living individuals have suffered temporarily disabling health crises likely to have been lethal without provisioning. The fitness effects of surviving these episodes are high, suggesting that the Shiwiar population structure and lifeway are dependent on infrequent extended provisioning to temporarily disabled individuals, and that provisioning of aid during healthcare crises effectively lowers mortality in this small-scale society.

Adolescent↗

PubMed2005

Structure and evolution of the mouse pregnancy-specific glycoprotein (Psg) gene locus.

BACKGROUND: The pregnancy-specific glycoprotein (Psg) genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea) gene family, which is a member of the immunoglobulin gene (Ig) superfamily. In rodents and primates, but not in artiodactyls (even-toed ungulates / hoofed mammals), there have been independent expansions of the Psg gene family, with all members expressed exclusively in placental trophoblast cells. For the mouse Psg genes, we sought to determine the genomic organisation of the locus, the expression profiles of the various family members, and the evolution of exon structure, to attempt to reconstruct the evolutionary history of this locus, and to determine whether expansion of the gene family has been driven by selection for increased gene dosage, or diversification of function. RESULTS: We collated the mouse Psg gene sequences currently in the public genome and expressed-sequence tag (EST) databases and used systematic BLAST searches to generate complete sequences for all known mouse Psg genes. We identified a novel family member, Psg31, which is similar to Psg30 but, uniquely amongst mouse Psg genes, has a duplicated N1 domain. We also identified a novel splice variant of Psg16 (bCEA). We show that Psg24 and Psg30 / Psg31 have independently undergone expansion of N-domain number. By mapping BAC, YAC and cosmid clones we described two clusters of Psg genes, which we linked and oriented using fluorescent in situ hybridisation (FISH). Comparison of our Psg locus map with the public mouse genome database indicates good agreement in overall structure and further elucidates gene order. Expression levels of Psg genes in placentas of different developmental stages revealed dramatic differences in the developmental expression profile of individual family members. CONCLUSION: We have combined existing information, and provide new information concerning the evolution of mouse Psg exon organization, the mouse Psg genomic locus structure, and the expression patterns of individual Psg genes. This information will facilitate functional studies of this complex gene family.

Alternative Splicing↗

PubMed1995

Mammalian mitochondrial DNA evolution: a comparison of the cytochrome b and cytochrome c oxidase II genes.

The evolution of two mitochondrial genes, cytochrome b and cytochrome c oxidase subunit II, was examined in several eutherian mammal orders, with special emphasis on the orders Artiodactyla and Rodentia. When analyzed using both maximum parsimony, with either equal or unequal character weighting, and neighbor joining, neither gene performed with a high degree of consistency in terms of the phylogenetic hypotheses supported. The phylogenetic inconsistencies observed for both these genes may be the result of several factors including differences in the rate of nucleotide substitution among particular lineages (especially between orders), base composition bias, transition/transversion bias, differences in codon usage, and different constraints and levels of homoplasy associated with first, second, and third codon positions. We discuss the implications of these findings for the molecular systematics of mammals, especially as they relate to recent hypotheses concerning the polyphyly of the order Rodentia, relationships among the Artiodactyla, and various interordinal relationships.

Animals↗

PubMed2003

Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G + C content.

There is a long-standing debate in molecular evolution concerning the putative importance of GC content in adapting the thermal stabilities of DNA and RNA. Most studies of this relationship have examined broad-scale compositional patterns, for example, total GC percentages in genomes and occurrence of GC-rich isochores. Few studies have systematically examined the GC contents of individual orthologous genes from differently thermally adapted species. When this has been done, the emphasis has been on comparing large numbers of genes in only a few species. We have approached the GC-adaptation temperature hypothesis in a different manner by examining patterns of base composition of genes encoding lactate dehydrogenase-A (ldh-a) and alpha-actin (alpha-actin) from 51 species of vertebrates whose adaptation temperatures ranged from -1.86 degrees C (Antarctic fishes) to approximately 45 degrees C (desert reptile). No significant positive correlation was found between any index of GC content (GC content of the entire sequence, GC content of the third codon position [GC(3)], and GC content at fourfold degenerate sites [GC(4)]) and any index of adaptation temperature (maximal, mean, or minimal body temperature). For alpha-actin, slopes of regression lines for all comparisons did not differ significantly from zero. For ldh-a, negative correlations between adaptation temperature and total GC content, GC(3), and GC(4) were observed but were shown to be due entirely to phylogenetic influences (as revealed by independent contrast analyses). This comparison of GC content across a wide range of ectothermic ("cold-blooded") and endothermic ("warm-blooded") vertebrates revealed that frogs of the genus Xenopus, which have commonly been used as a representative cold-blooded species, in fact are outliers among ectotherms for the alpha-actin analyses, raising concern about the appropriateness of choosing these amphibians as representative of ectothermic vertebrates in general. Our study indicates that, whereas GC contents of isochores may show variation among different classes of vertebrates, there is no consistent relationship between adaptation temperature and the percentage of thermal stability-enhancing G + C base pairs in protein-coding genes.

Actins↗

PubMed1994

A review of 76 patients with myelodysplastic syndromes treated with danazol.

BACKGROUND: Treatment of myelodysplastic syndromes (MDSs) remains unsatisfactory. A limited number of reports provide contradictory information on whether danazol, a synthetic androgen, may be useful in patients with MDS. METHODS: Between 1984 and 1992, 76 patients were treated with danazol (Danatrol, Winthrop) in an open nonrandomized study. Clinical status, blood counts, differential marrow cell counts, transfusion requirements, and liver enzymes were monitored at 3-month intervals during and 6 months after discontinuation of therapy. The authors present the retrospective analysis of this cohort of patients. RESULTS: This study shows a limited usefulness of danazol in patients with MDS. Blood counts were not significantly changed during danazol administration; neither were transfusion requirements. Overall survival and the rate of leukemic transformation were not affected when compared with 50 untreated patients or with data available in the literature. An increase in platelet numbers in four patients and in hemoglobin level in one patient was observed; these patients were unremarkable and were not transfused before initial danazol therapy; therefore, changes in blood counts were of limited clinical significance. The search for subgroups of patients likely to have a favorable response was unsuccessful. Side effects of danazol were limited. In addition, this study provides information on the frequency of antiplatelet antibodies and other autoantibodies in patients with MDS. CONCLUSIONS: This study does not support a positive effect of danazol in patients with MDS during long term follow-up. Anecdotal positive evolution in a few patients cannot be formally ascribed to danazol. These results should be interpreted by comparison with previous publications that report on small numbers of patients with limited follow-up. Based on these data, the authors cannot recommend the systematic use of danazol in MDS.

Adult↗

PubMed2004

Rationale and strategies for implementing community-based transfer protocols for primary percutaneous coronary intervention for acute ST-segment elevation myocardial infarction.

The focus for the initial approach to the treatment of acute ST-segment elevation myocardial infarction (STEMI) has shifted toward extending the benefits of mechanical reperfusion with primary percutaneous coronary intervention (PCI) to patients who present to community hospitals that have no interventional capabilities. Several randomized clinical trials have shown that transferring STEMI patients to tertiary centers for primary PCI leads to better outcomes than when fibrinolytic therapy is administered at community hospitals. Furthermore, potent pharmacologic reperfusion regimens that enhance early reperfusion of the infarct vessel before primary PCI may enhance the positive result of the transfer approach. Despite these promising findings, several obstacles have hindered the adoption of patient-transfer strategies in the U.S., including greater distances between community and tertiary hospitals, a lack of integrated emergency medical services, and the medical community's limited experience with centralized acute myocardial infarction (AMI) care networks. Nonetheless, the implementation of system-wide changes in the care of STEMI patients analogous to the creation of trauma networks could facilitate the creation and ongoing evaluation of dedicated patient transfer strategies and better early invasive care in the U.S. Within this context, a systematic, stepwise approach to the creation of AMI care networks and to the development of standard nomenclature and performance indicators is necessary to guide quality assurance monitoring and future research efforts as the care of STEMI patients is redefined. Consequently, this current evolution of reperfusion strategies has the potential to further reduce morbidity and mortality for patients presenting with STEMI.

Angioplasty, Balloon, Coronary↗

PubMed2004

Evolutionary optimization for robust hierarchical computation of the rotation centres of kinematic chains from reduced ranges of motion the lower spine case.

A novel technique based on evolutionary optimization is proposed here to compute the average rotation centres (RCs) of ball joints linked into kinematic chains using 3D trajectories of the markers attached to the external surface of the corresponding articulated structures. The chain is hierarchically solved by iteratively minimizing the variance of the marker distances from the actual RC through an evolutional strategy method (ESM) from proximal to distal joints. In particular, the technique is compared to the non-rigid sphere-fitting method, recently proposed in literature and implemented through a closed-form solution (CFS), in conditions of random and systematic noise superimposed to the marker coordinates. Results from simulated motions showed that, in case of small range of motion (5 degrees , 10 degrees ) the performance of CFS is really unreliable whereas ESM provided satisfactory accuracy. Error propagation along the kinematic chain was found to be negligible. Also in the case of systematic errors, ESM provides an accuracy that is sensibly better than that of the CFS. As a case study, ESM was applied to the in vivo computation of the RCs of the vertebrae in the lower spine region using a specific marker protocol. A set of spine movements by a normal adult male, recorded by an optoelectronic motion capture system, were processed with the developed method. The variability of the estimated average RCs was small (few millimeters) in agreement with the literature data from cadaveric studies and X-ray imaging.

Algorithms↗