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At least 451 records · Page 25Linked to original sources
PubMed2005

Neck dissections: radical to conservative.

BACKGROUND: Neck dissection is an important surgical procedure for the management of metastatic nodal disease in the neck. The gold standard of neck nodal management has been the radical neck dissection. Any modification in the neck dissection is always compared with this standard. Over the last few decades, in order to alleviate the morbidity of radical neck dissection, several modifications and conservative procedures have been advocated. These procedures retain certain lymphatic or non-lymphatic structures and have been shown not to compromise oncological safety. METHODS: A literature search of the Medline was carried out for all articles on neck dissections. The articles were systematically reviewed to analyze and trace the evolution of neck dissection. These were then categorized to address the nomenclature, management of node positive and node negative neck including those who had received chemoradiation. RESULTS: The present article discusses the neck nodal nomenclature, the radical neck dissection, its modifications and migration to more conservative procedures and possible advances in the near future. CONCLUSION: Radical neck dissection is now replaced with modified radical neck dissections in most situations. Attempts are being made to replace modified radical neck dissections with selective neck dissections for early node positivity. Sentinel node biopsy is being studied to address the issue of node negative neck. More conservative surgeries are likely to replace the 'radical' surgeries of bygone era. This process is facilitated by earlier detection of the disease and better understanding of cancer biology.

Journal Article↗
PubMed1989

[On some characteristics of Tahitian family groups. Standards, behavior, projection].

"[This is a] study of the evolution of the Tahitian family group through systematic analysis of a set of files of candidates for low cost housing. This first showed a set of frequently little-known standards: the normal nature of concubinage, relatively late marriage, the establishment of the family only considered as being effective with the third child, the generalization of adoption, etc. The trend towards nuclear families is then questioned. The nuclear family model is spreading rapidly and even appears to be consciously desired by many young couples. However, the extended family in various forms (with a tendency to favour matrilineal extensions) remains preponderant and conserves an essential social integration function in Tahitian society." (SUMMARY IN ENG)

Adoption↗
PubMed1996

Ancestral relationships of the major eukaryotic lineages.

Molecular systematics has revolutionized our understanding of microbial evolution. Phylogenetic frameworks relating all organisms in this biosphere can be inferred from comparisons of slowly evolving molecules such as the small and large subunit ribosomal RNAs. Unlike today's text book standard, the "Five Kingdoms" (plants, animals, fungi, protists and bacteria), molecular studies define three primary lines of descent (Eukaryotes, Eubacteria, and Archaebacteria). Within the Eukaryotes, the "higher" kingdoms (Fungi, Plantae, and Animalia) are joined by at least two novel complex evolutionary assemblages, the "Alveolates" (ciliates, dinoflagellates and apicomplexans) and the "Stramenopiles" (diatoms, oomycetes, labyrinthulids, brown algae and chrysophytes). The separation of these eukaryotic groups (described as the eukaryotic "crown") occurred approximately 10(9) years ago and was preceded by a succession of earlier diverging protist lineages, some as ancient as the separation of the prokaryotic domains. The molecular phylogenies suggest that multiple endosymbiotic events introduced plastids into discrete eukaryotic lineages.

Animal Population Groups↗
PubMed1998

Investigating catalytic processes with parahydrogen: evolution of zero-quantum coherence in AA'X spin systems

A systematic outline for the elucidation of the nature of hydrogenation intermediates with a lifetime too short to be directly detectable with standard NMR methods is presented. The method takes advantage of the special nature of the parahydrogen density operator and its inherent enhancement factor. The key aspect of these experiments is the evolution of zero-quantum coherence which is contained in the parahydrogen density operator. Analytical coherence transfer functions have been derived which describe the evolution of this zero-quantum coherence in spin systems consisting of three spins 1/2 that form an AA'X spin system. The analytical expressions presented form a basis for a thorough investigation of crucial catalytic steps. Copyright 1998 Academic Press.

Journal Article↗
PubMed2025

Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.

BACKGROUND: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution. RESULTS: In this study, we perform a systematic comparative analysis of centromeres in common wheat and its corresponding ancestral species, utilizing the latest comprehensive reference genome assembly available. Our findings reveal that wheat centromeres predominantly consist of five types of centromeric-specific retrotransposon elements (CRWs), with CRW1 and CRW2 being the most prevalent. We identify distinct evolutionary trajectories in the functional centromeres of each subgenome, characterized by variations in copy number, insertion age, and CRW composition. By utilizing CENH3-ChIP data across various ploidy levels, we uncover a series of CRW invasion events that have shaped the evolution of AA subgenome centromeres. Conversely, the evolutionary process of the DD subgenome centromeres involves their expansion from diploid to hexaploid wheat, facilitating adaptation to a larger genomic context. Integration of complete einkorn centromere assemblies and Aegilops tauschii pan-genomes further revealed subgenome-specific centromere evolutionary trajectories. By inclusion of synthetic hexaploid from S2-S3 generations, alongside 2x/6 × natural accessions, we demonstrate that DD subgenome centromere expansion represents a gradual evolutionary process rather than an immediate response to polyploidization. CONCLUSIONS: Our study provides a comprehensive landscape of centromere adaptation, evolution, and maturation, along with insights into how retrotransposon invasions drive centromere evolution in polyploid wheat.

Centromere↗
PubMed2006

The effects of early antiretroviral therapy and its discontinuation on the HIV-specific antibody response.

HIV-specific antibodies become detectable and continue to increase in frequency during primary infection. The effects of early antiretroviral treatment (ART) and its discontinuation on the evolution of this immune response have not been systematically analyzed. To investigate the associations between antibody titer, viral load, and ART, we used a less-sensitive enzyme-linked immunosorbant assay (LS-EIA) to measure changes in HIV-1-specific antibody levels in treated and untreated subjects undergoing primary infection. In this longitudinal study, antibody levels gradually increased in therapy-naive subjects, reaching a plateau approximately 40 weeks postinfection. In contrast, antibody titers remained low among subjects receiving ART. Subjects who discontinued ART exhibited a more rapid rise in antibody titers than therapy-naive subjects, suggesting the presence of an enhanced B cell response. These results demonstrate that early ART prevents the typical evolution of the HIV-1-specific antibody response and can alter the expected kinetics of this response in subjects discontinuing therapy.

Adult↗
PubMed1997

Molecular variation, evolution and geographical distribution of louping ill virus.

Following the demonstration that the tick-borne encephalitis (TBE) subgroup viruses are distributed as a cline across the Northern Hemisphere (Zanotto et al., 1995), we have analyzed the dispersal pattern of louping ill (LI) virus, the most westerly located member in the cline. A total number of 21 LI or LI-related virus E gene sequences have been used for a detailed molecular analysis of the evolution, phylogeny and geographical distribution of LI virus in the British Isles and Ireland. The results show that LI virus is genetically stable in general but minor differences enable its separation into four genetically distinct subtypes (genotypes) with clear geographical correlation, designated Type 1 in Scotland and England, Type 2 in Scotland, Type 3 in Wales and Type 4 in Ireland. These data demonstrate that geographically independent evolution of LI viruses has occurred. The molecular systematics and substitutional parameters analyses combined with the clinal distribution of the TBE virus complex allow the assignment of the origin for both Negishi (NEG) virus and a Norwegian isolate to the British Isles. Moreover, proposals for the classification of LI and LI-like viruses which cause encephalomyelitis in sheep, goat or cattle are presented.

Animals↗
PubMed1985

Evolutionary trends of the histological pattern in the teeth of Edentata (Xenarthra).

In a comparative study of the dental structure of Edentata, the central tissue was identified as a modified orthodentine, except in the Glyptodontidae where an osteodentine was found. Some evolutionary trends of the tissues in these teeth may have been related with the extinction of ground sloths. Comparative studies of the tissues in mammalian teeth seem to be good tests for systematics.

Animals↗
PubMed1999

Molecular systematics: Perfect SINEs of evolutionary history?

Short interspersed repetitive elements - SINEs - are being championed as near-perfect phylogenetic characters; they have recently been used with notable success to resolve some phylogenetic conundrums, but they do have certain limitations that restrict their use as 'perfect' characters for molecular systematics.

Animals↗
PubMed2005

Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations.

Metallo-beta-lactamases (MBLs) represent the latest generation of beta-lactamases. The structural diversity and broad substrate profile of MBLs allow them to confer resistance to most beta-lactam antibiotics. To explore the evolutionary potential of these enzymes, we have subjected the Bacillus cereus MBL (BcII) to a directed evolution scheme, which resulted in an increased hydrolytic efficiency toward cephalexin. A systematic study of the hydrolytic profile, substrate binding, and active-site features of the evolved lactamase reveal that directed evolution has shaped the active site by means of remote mutations to better hydrolyze cephalosporins with small, uncharged C-3 substituents. One of these mutations is found in related enzymes from pathogenic bacteria and is responsible for the increase in that enzyme's hydrolytic profile. The mutations lowered the activation energy of the rate-limiting step rather than improved the affinity of the enzyme toward these substrates. The following conclusions can be made: (i) MBLs are able to expand their substrate spectrum without sacrificing their inherent hydrolytic capabilities; (ii) directed evolution is able to mimic mutations that occur in nature; (iii) the metal-ligand strength is tuned by second-shell mutations, thereby influencing the catalytic efficiency; and (iv) changes in the position of the second Zn(II) ion in MBLs affect the substrate positioning in the active site. Overall, these results show that the evolution of enzymatic catalysis can take place by remote mutations controlling reactivity.

Amino Acid Substitution↗
PubMed1995

A simulation test of Smith's "Degrees of freedom" correction for comparative studies.

Computer simulation was used to test Smith's (1994) correction for phylogenetic nonindependence in comparative studies. Smith's method find effective N, which is computed using nested analysis of variance, and uses this value in place of observed N as the baseline degrees of freedom (df) for calculating statistical significance levels. If Smith's formula finds the correct df, distributions of computer-generated statistics from simulations with observed N nonindependent species should match theoretical distributions (from statistical tables) with the df based on effective N. The computer program developed to test Smith's method simulates character evolution down user-specified phylogenies. Parameters were systematically varied to discover their effects on Smith's method. In simulations in which the phylogeny and taxonomy were identical (tests of narrow-sense validity), Smith's method always gave conservative statistical results when the taxonomy had fewer than five levels. This conservative departure gave way to a liberal deviation in type I error rates in simulations using more than five taxonomic levels, except when species values were nearly independent. Reducing the number of taxonomic levels used in the analysis, and thereby eliminating available information regarding evolutionary relationships, also increased type I error rates (broad-sense validity), indicating that this may be inappropriate under conditions shown to have high type I error rates. However, the use of taxonomic categories over more accurate phylogenies did not create a liberal bias in all cases in the analysis performed here. The effect of correlated trait evolution was ambiguous but, relative to other parameters, negligible.

Analysis of Variance↗
PubMed1989

Interactive analysis of phylogeny and character evolution using the computer program MacClade.

Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.

Animals↗
PubMed1995

The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species.

The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, beta, gamma, delta, epsilon proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.

Amino Acid Sequence↗
PubMed2006

Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms.

Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous protein-coding genes, limiting the use of nucleotide sequences to study the evolution and epidemiology of this bacterial pathogen. To systematically examine single nucleotide polymorphisms (SNPs) at a genome scale, we designed comparative genome sequencing microarrays and analyzed 1199 chromosomal genes (a total of 1,167,948 bp) and 92,721 bp of the large virulence plasmid (pO157) of eleven outbreak-associated STEC O157 strains. We discovered 906 SNPs in 523 chromosomal genes and observed a high level of DNA polymorphisms among the pO157 plasmids. Based on a uniform rate of synonymous substitution for Escherichia coli and Salmonella enterica (4.7x10(-9) per site per year), we estimate that the most recent common ancestor of the contemporary beta-glucuronidase-negative, non-sorbitolfermenting STEC O157 strains existed ca. 40 thousand years ago. The phylogeny of the STEC O157 strains based on the informative synonymous SNPs was compared to the maximum parsimony trees inferred from pulsed-field gel electrophoresis and multilocus variable numbers of tandem repeats analysis. The topological discrepancies indicate that, in contrast to the synonymous mutations, parts of STEC O157 genomes have evolved through different mechanisms with highly variable divergence rates. The SNP loci reported here will provide useful genetic markers for developing high-throughput methods for fine-resolution genotyping of STEC O157. Functional characterization of nucleotide polymorphisms should shed new insights on the evolution, epidemiology, and pathogenesis of STEC O157 and related pathogens.

Chromosome Mapping↗
PubMed2000

Some aspects of plant karyology and karyosystematics.

The significance of the 4C value (where C is the amount of DNA in the unreplicated haploid genome) in angiosperm plants is discussed. The DNA amount is a stable feature used in biosystematics. Although this parameter varies even in closely related taxa, there is no correlation between the DNA amount and the structural and functional organization of plants. The role of DNA amount, including "excess" DNA, in plant evolution is considered. Some rules governing the distribution of DNA amount among different plant taxa are postulated, together with the possibility of using the data in systematics, phylogeny, and solutions of problems of genetic apparatus organization and evolution. The decrease in DNA value per genome during plant evolution and the high level of species formation in taxa with large DNA values have been shown. Plant taxa with a small DNA value per genome have a high percentage and higher degree of polyploidy. The nature of the differential staining of euchromatin and heterochromatin bands of prophase and metaphase chromosomes is also discussed. Data that could explain the mechanism of heterochromatin visualization under cold pretreatment of cells are reviewed. Phenomena involved in the arrangement of chromocenters in interphase nuclei and chromosomes in metaphase during consecutive cell generations are discussed.

Gene Expression Regulation, Plant↗