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PubMed1998

The use of hierarchies as organizational models in systematics

A hierarchy is an abstract organizational model of inter-level relationships among entities. When isomorphic with nature, hierarchies are useful for organizing and manipulating our knowledge. Hierarchies have been used in biological systematics to represent several distinct, but interrelated, facets of the evolution of life with different organizational properties, and these distinctions have been confused by the rubric «the hierarchy of life». Evolution, as descent with modification, is inherently dualistic. The organizational structure of a hierarchy can be used to represent dualistic properties as inter-level relationships. Cladistics is monistic, with a singular focus on patterns of descent. Descent has conceptual priority over modification, but the organizational relationship is not exclusive. «Cladistic classification» is an oxymoron because cladistics lacks the class concepts needed to construct a classification, a point recognized by those who suggest abandoning Linnaean classification in favour of a newly devised monophyletic systematization. Cladistic analysis of descent can be supplemented with an analysis of modification that provides the class concepts needed to construct an evolutionary/phylogenetic classification. When a strong monophyletic pattern of modification is detected (in addition to its monophyletic pattern of descent), the criterion of subsequent modification provides the basis for formally recognizing a certain monophyletic group at a given rank, as opposed to a group that is one node more inclusive or one node less. The criterion of subsequent modification also permits detection of strong paraphyletic patterns of modification, when they exist. By setting standards of evidence needed to recognize paraphyletic groups, one concomitantly strengthens the basis for formally recognizing selective monophyletic groups.Copyright 1998 The Linnean Society of London

Journal Article↗

PubMed1992

Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus.

The length of the small subunit ribosomal DNA (SSU rDNA) differs significantly among individuals from natural populations of the ascomycetous lichen complex Cladonia chlorophaea. The sequence of the 3' region of the SSU rDNA from two individuals, chosen to represent the shortest and longest sequences, revealed multiple insertions within a region that otherwise aligned with a 520-nucleotide sequence of the SSU rDNA in Saccharomyces cerevisiae. The high degree of variability in SSU rDNA size can be accounted for by different numbers of insertions; one individual had two group I introns and the second had five introns, two of which were clearly related to introns at identical positions in the other individual. Yet, introns in different positions, whether within an individual or between individuals, were not similar in sequence. The distribution of introns at three of the positions is consistent with either intron loss or acquisition, and clearly indicates the dynamic variability in this region of the nuclear genome. All seven insertions, which ranged in size from 210 to 228 nucleotides, had the conserved sequence and secondary structural elements of group I introns. The variation in distribution and sequence of group I introns within a short highly conserved region of rDNA presents a unique opportunity for examining the molecular evolution and mobility of group I introns within a systematics framework.

Ascomycota↗

PubMed2002

Phenotype switching in polymorphic Tetrahymena: a single-cell Jekyll and Hyde.

For nearly half a century, phenotype switching in the group of polymorphic species of the ciliate genus Tetrahymena has been the subject of investigations of the underlying mechanisms, the accompanying biochemical and structural changes, and the evolution of polymorphic survival strategy. Beginning with the pioneering systematic studies by Furgason in 1940 of hymenostome ciliates, the experimental approach rapidly expanded to include investigations of growth, nutrition, physiology, morphology, and morphogenesis in the polymorphic species. Recently, with progress in elucidation of the novel signaling ligand and identification of elements of the subsequent signal transduction cascade, in addition to the growing catalog of intracellular events associated with differentiation in these unicellular eukaryotes, we have begun to address the mechanistic basis of polymorphism. This review summarizes and integrates the history and recent discoveries concerning Tetrahymena polymorphic cells. We are now poised to answer fundamental questions about this interesting pathway of cell differentiation.

Animals↗

PubMed2006

Poly(dimethylamino)ethyl methacrylate for use as a surfactant in the miniemulsion polymerization of styrene.

A novel Y-shaped macromonomer based on poly[(dimethylamino)ethyl methacrylate] (PDMAEMA) with a narrow molecular weight distribution was synthesized via oxyanion-initiated polymerization in which a potassium alcoholate of trimethylol propane allyl ether (2K-TMPAE) was used as a difunctional initiator. For the miniemulsion polymerization of styrene, this macromonomer acted well both as a comonomer carrying a reactive C=C double bond in its central section and as a pH-responsive polycationic surfactant in media with different pH values. The resulting microspheres composed of a hydrophobic polystyrene core and a hydrophilic PDMAEMA-protonated corona have shown spherical morphology and are quite stable. The nature of the reactive group, the amount of polymeric surfactant, and pH values in the aqueous medium have been systematically investigated during the miniemulsion polymerization by analyzing the evolution of the monomer conversions. The results of FTIR and (1)H NMR spectra demonstrated the generation of the functional particles. The analyses of TEM micrographs and dynamic light scattering (DLS) confirmed that the latices had a relatively narrow particle size distribution. The measurement of the zeta potential gave further evidence of the "hairy" particle structure. Because the reactive group is located in the central section of the macromonomer, the stabilization mechanism of the polymeric surfactant can be ascribed to (1) the absorption of two polycationic and hydrophilic tails that have electrostatic and steric stabilization to decrease the interface tension and (2) the copolymerization with the styrene monomer.

Journal Article↗

PubMed2026

Genomic characterization of aggressiveness in pituitary neuroendocrine tumors.

BACKGROUND: Aggressive evolution of PitNETs is rare; metastatic spread is even more. Defining aggressiveness and malignancy is challenging, subsequently hard to predict, and to understand. The aim was to provide a molecular definition of aggressiveness using genomic approaches. METHODS: PitNETs from 206 patients were included. Associations between 9 clinicopathological features of aggressiveness and PitNETs' omics were explored. Omics included transcriptome, DNA methylation, chromosomal alterations, and mutations. Clonal tumor evolution was monitored in 7 patients. RESULTS: Among the 9 clinicopathological features of aggressiveness, only rapid progression, progression after radiotherapy, Ki67/MIB1 proliferation index ≥10%, temozolomide treatment, metastases, and specific death were associated with specific omics signatures, while tumour maximal diameter ≥40 mm, cavernous, and sphenoid invasion were not. The omic signatures associated with these features of aggressiveness overlapped but remained distinct between corticotroph and mammo-somato-thyrotroph lineages. For each lineage, a common signature of aggressiveness was identified, associating a proliferative transcriptome signature and DNA hypermethylation. Alterations in specific genes were associated with aggressive features, including a novel PitNET gene, LRP1B, and known cancer genes (TP53, CDKN2A), while USP8 and GNAS alterations were not. Integration of gene alterations with methylome and transcriptome signatures isolated a subset of molecularly aggressive PitNETs. Molecular signatures were stable during the course of the disease, despite evolution toward aggressiveness and potential clonal divergence. CONCLUSION: This systematic analysis of clinicopathological features of aggressiveness using an integrated multiomic approach establishes a histomolecular definition of aggressiveness in PitNETs. Prospective cohort studies are needed to validate these molecular signatures and establish their prognostic value.

Humans↗

PubMed1988

Bacterial evolution.

The deliberate application of the methodology of contemporary molecular genetics to problems in bacterial systematics has led to a broad new understanding of the evolutionary history of both prokaryotes and eukaryotes. In this review, I discuss some of the major conclusions of this endeavour and try to predict future directions.

Animals↗

PubMed1986

[Congenital paravertebral arteriovenous fistulae in children and adolescents].

These arteriovenous fistulae (AVF) situated in the paravertebral area present as a murmur which explains their cardiological orientation. They are characterised by the presence of one or more afferent paravertebral arteries giving rise to collateral vessels irrigating the bone marrow. The aim of this study of 13 cases was to study the diagnostic and therapeutic problems, and the evolution of this particular localisation of AVF. Two groups of paravertebral AVF were individualised: - Cervical AVF in which the vertebral artery was always involved (7 cases). Four were simple (only one fistula) and three were complex, having several afferent arteries. Two presented as a rapidly growing vascular tumour. Two caused an asymptomatic angiographic vertebral steal syndrome. Two simple forms were obturated by a detachable balloon and one by surgical excision. Two complex forms were treated by embolisation and surgery. Total closure of the AVF was obtained in all cases without complications. - Dorso-lumbar AVF (6 cases). The afferent vessels are the intercostal (D6 to D8) or lumbar (L2 to L4) arteries. Anatomically, these are extra-medullary fistulae with an extra or intra-vertebral venous drainage. Enlargement in an adjacent conjugating foramen forms a tumour which may narrow the spinal canal (1 case diagnosed by CAT) or erode the vertebral body, so compromising the spinal support. Spontaneous closure of the AVF was observed in 1 case. Three cases were treated surgically with good results; two patients are waiting for embolisation. A review of the literature provides complementary information on the long-term evolution of these AVF and confirms the need for systematic therapy as demonstrated in our study.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

PubMed1995

[Ocular involvement in dermatomyositis. Apropos of the case of a 15-year-old girl].

We relate the case of a 15 years old girl who suffered a sudden and severe bilateral lowering of the eyesight, on the occasion of a dermatomyositis. The evolution, over a year, showed a remission of the systematic appearances but there was a limited recovery of the eyesight, the diffuse retinal lesions are the sign of a more extensive vascular problem, found in case of paediatric dermatomyositis.

Adolescent↗

PubMed1993

Cholesterol--a model system to relate medical needs with analytical performance.

The evolution of cholesterol testing provides an example of a systematic approach that developed to relate the medical use of a laboratory test with the analytical performance requirements for that test. Laboratories today have the capability to perform cholesterol testing with the accuracy and precision necessary to meet medical needs. This statement can be made because (a) a standard diagnostic process has been established by the National Cholesterol Education Program; (b) an accuracy base is provided through a reference method that is readily available to manufacturers and laboratories; (c) the precision of analytical systems has been improved by manufacturers; (d) operating specifications for all such systems can be established, with statistical quality-control rules to ensure adequate within-run method performance; and (e) analytical performance is monitored by proficiency testing by using national quality requirements defined by CLIA '88 for acceptability. This cholesterol model provides a logical and scientific approach that should be applicable with other analytes to assure that the analytical performance of the laboratory test satisfies medical needs.

Chemistry, Clinical↗

PubMed1989

The evolution strategy--a search strategy used in individual optimization of electrical parameters for therapeutic carotid sinus nerve stimulation.

Optimization problems, arising in the search for parameters and/or techniques of functional electrostimulation (FES), disproportionally increase when multiple electrodes, electrode configurations, electrical parameters, and stimulation modes may be applied. When computational or investigational effort precludes systematic studies in FES, we propose to apply and evaluate Rechenberg's evolution strategy, which in technical use and numerical optimization has been valid in comparison to more traditional methods. This strategy implements mutation and selection processes in analogy to biological evolution. The effect of combined multiple input variables on a quality function (Q) is experimentally evaluated. The actual computed value of Q serves as a selection criterion for those input variable combinations which lead Q to approach a target value (maximization), similar to a hill-climbing procedure. In radiofrequency controlled, therapeutic electrical carotid sinus nerve stimulation (CSNS), we varied (mutated) combinations of pulse frequency and pulse amplitude parameters, according to the evolution strategy, in individual patients. CSNS lowers blood pressure and decreases heart rate. Q was computed from blood pressure and heart rate responses to CSNS. The strategy individually optimized electrical parameters to achieve large depressor responses upon CSNS. Although, in contrast to technical usage, only two input variables were investigated, and biomedical experience with the evolution strategy is limited so far, its potential use in other fields of FES, especially when more input variables are to be optimized, is discussed and encouraged.

Algorithms↗

PubMedDate not supplied

[Evaluation of nursing care systematization through the phases of nursing process performance and registration in a teaching hospital].

This descriptive study was carried out in a teaching hospital at São Paulo city and had as objective to identify the phases performance and registration of nursing care systematization and the most frequent nursing diagnoses. Data were collected retrospectively from 135 patients records of three units: Cardiology, Adult Infectious Diseases and Neurosurgery, from January to July, 2002. The phases: history, nursing diagnoses, prescription, evolution and assessment were performed and registered in the three units, however, it was verified systematization gaps performance related to nursing diagnoses registered without the realization of nursing history and nursing prescriptions without evolution. The most frequent nursing diagnosis in the three units was risk for infection.

Hospitals, Teaching↗

PubMed2001

Changing views of brain evolution.

Although brain studies began in ancient Egypt, speculations on vertebrate brain evolution occurred only much later, after the publication of Darwin's Origin of Species in 1859. Subsequently, views of brain evolution have been shaped by a complex interplay of theory and technique. Darwin's theory allowed the variation in brain size and complexity to be re-interpreted within an evolutionary context, albeit an erroneous pre-Darwinian context based on scala naturae. With the development of histological techniques, research shifted to descriptions of cellular structure, cellular aggregates and their putative interconnections. In spite of these technical advances, brain evolution continued to be viewed within the context of scala naturae. Following the publication of The Comparative Anatomy of the Nervous System of Vertebrates by Ariëns Kappers, Huber, and Crosby in 1936, there followed a period of stasis, after which biological views of evolution were radically altered by the confluence of genetics, paleontology, and systematics, termed the Evolutionary Synthesis. Against this background, the development of new experimental techniques for establishing neural connections resulted in a new flowering of comparative neuroanatomy. While comparative descriptive and experimental studies of brain organization continue, the rapprochement of embryology and genetics is fueling a new renaissance that promises to increase our understanding of brain evolution and its genetic basis.

Animals↗

PubMed2004

Protein dynamics and the immunological evolution of molecular recognition.

While it is accepted that protein flexibility plays a role in protein folding, catalysis, and molecular recognition, few techniques are capable of the rigorous measurement of protein motions required to quantify flexibility. Three-pulse photon echo shift spectroscopy can be used to measure the time scale of protein motions, and we have used this technique, along with steady-state spectroscopy and binding and structural data, to examine the immunological evolution of protein flexibility in an anti-fluorescein antibody. Two light chain somatic mutations increase affinity for fluorescein by 12-fold but also significantly affect flexibility. Specifically, a rigidification of the protein is seen in each of three observable motions; two slower motions undergo decreased amplitudes of displacement, by 3- and 20-fold, respectively, in response to an applied force, and the distribution associated with the amplitude of a faster motion is narrowed upon somatic mutation. The somatic mutations appear to rigidify the antibody-fluorescein complex by more strongly anchoring fluorescein to the protein and by more tightly packing the complex. The data demonstrate that in addition to affinity, antibody dynamics are systematically manipulated during affinity maturation, and they imply that the evolution of protein flexibility may be a central component of the immune response. The results also reflect the type of protein rigidification that may be important for other biological interactions, such as protein-protein, protein-ligand or protein-drug, and enzyme-substrate recognition.

5' Untranslated Regions↗

PubMed1998

Do we understand the evolution of genomic imprinting?

The conflict theory is the only hypothesis to have attracted any critical attention for the evolution of genomic imprinting. Although the earliest data appeared supportive, recent systematic analyses have not confirmed the model's predictions. The status of theory remains undecided, however, as post-hoc explanations can be provided as to why these predictions are not borne out.

Animals↗

PubMed2005

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development.

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.

Anatomy, Comparative↗

PubMed2003

At the feet of the dinosaurs: the early history and radiation of lizards.

Lizards, snakes and amphisbaenians together constitute the Squamata, the largest and most diverse group of living reptiles. Despite their current success, the early squamate fossil record is extremely patchy. The last major survey of squamate palaeontology and evolution was published 20 years ago. Since then, there have been major changes in systematic theory and methodology, as well as a steady trickle of new fossil finds. This review examines our current understanding of the first 150 million years of squamate evolution in the light of the new data and changing ideas. Contrary to previous reports, no squamate fossils are currently documented before the Jurassic. Nonetheless, indirect evidence predicts that squamates had evolved by at least the middle Triassic, and had diversified into existing major lineages before the end of this period. There is thus a major gap in the squamate record at a time when key morphological features were evolving. With the exception of fragmentary remains from Africa and India, Jurassic squamates are known only from localities in northern continents (Laurasia). The situation improves in the Early Cretaceous, but the southern (Gondwanan) record remains extremely poor. This constrains palaeobiogeographic discussion and makes it difficult to predict centres of origin for major squamate clades on the basis of fossil evidence alone. Preliminary mapping of morphological characters onto a consensus tree demonstrates stages in the sequence of acquisition for some characters of the skull and postcranial skeleton, but many crucial stages--most notably those relating to the acquisition of squamate skull kinesis--remain unclear.

Animals↗

PubMed2025

Rapid replacement of blaKPC variant in ST11 carbapenem-resistant and hypervirulent Klebsiella pneumoniae contributed to ceftazidime/avibactam resistance during severe in vivo infection.

OBJECTIVES: Hypervirulent ceftazidime/avibactam (CAZ/AVI)-resistant Klebsiella pneumoniae (Kp) has emerged; however, its dynamic within-host evolution and competitive features are uncharacterized. This study aimed to clarify the systematic microevolution characteristics of the rapid transformation of blaKPC variants during long-term infection. METHODS: Thirty-nine Kp strains were isolated from a single patient with severe recurrent osteomyelitis during a 2-year period. Whole-genome sequencing and in vitro evolution assay was performed. Microbiological characteristics were examined through antimicrobial susceptibility testing, plasmid stability, growth curve, in vitro competition and Galleria mellonella larvae lethality assays. RESULTS: Among all the clinical Kp isolates, 37 were carbapenem-resistant Kp (CRKP), including 25 CAZ-/AVI-resistant Kp. All isolates belonged to the ST11-K47. During in vivo evolution, the blaKPC variant and its amplification emerged. Twenty-four isolates (24/39, 61.5%) harboured a novel blaKPC variant, blaKPC-144. All five Kp isolates carried blaKPC-2 in 2021. Surprisingly, 24 blaKPC-144-harbouring isolates (70.6%, 24/34) and 10 blaKPC-2-harboring isolates were identified in 2023, indicating rapid changing of blaKPC. Kp4 carried two copies of blaKPC-2, and Kp10-1 exhibited a 1.94-fold increase in the blaKPC-144 copy number. Similarly, in vitro, the blaKPC copy number increased upon exposure to low CAZ/AVI concentrations. However, at higher concentrations (4/1 mg/L), the blaKPC copy number increased significantly, and blaKPC mutations emerged simultaneously. The competition assay indicated that the blaKPC-144-harboring isolates exhibited a superior competitive capacity. CONCLUSIONS: The blaKPC amplification and mutation emerged simultaneously or sequentially during in vivo and in vitro evolution. Kp isolates harbouring blaKPC-144, conferring resistance to CAZ/AVI, exhibited a competitive advantage, promoting the rapid replacement of blaKPC-2.

Klebsiella pneumoniae↗

PubMed1991

Molecular evolution and phylogeny of the Drosophila virilis species group as inferred by two-dimensional electrophoresis.

Systematic relationship among the 12 species of the Drosophila virilis species group, and Drosophila robusta, were investigated by the use of two-dimensional electrophoresis (2-DE). A total of 389 protein characters (about 200 loci) were scored and analyzed both phylogenetically and phenetically. The resulting phylogeny was found to be largely concordant with the current views of evolution among these species based on other independent morphological, chromosomal, electrophoretic, and immunological data sets, although some notable differences were observed. The 2-DE data also appeared to be useful for constructing a molecular clock to date the absolute times of divergence among the species. It appears from this analysis that the evolution of the major clades within the species group occurred about 20 million years ago. Previous suggestions that the rate of molecular evolution was different between the virilis and montana phylads was not confirmed. The technique of 2-DE seems to be an excellent tool for reconstructing phylogenies and should be particularly valuable for examining relatively closely related species.

Animals↗