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PubMed1978

Malignant lymphoplasmacytoid lymphomas. Clinical and evolutive data.

A series of 31 cases of malignant lymphoplasmacytoid lymphomas (excluding Waldenström disease) is analyzed. Two-thirds of the patients initially had localizations elsewhere than in the lymph nodes and presented clinical stage I or II. The median survival is around 4 years and is particularly favorable for stage I and II patients who have received an association of radiotherapy and systematic chemotherapy; the estimated "cure rate" for these patients is around 80%.

Adult↗

PubMed2001

A unified theory of enzyme kinetics based upon the systematic analysis of the variations of k(cat), K(M), and k(cat)/K(M) and the relevant DeltaG(0 not equal) values-possible implications in chemotherapy and biotechnology.

To elucidate the kinetic properties of critical enzymatic situations that have previously escaped classification, we performed a systematic analysis of all the possible variations of the kinetic constants k(cat,) K(M,) and k(sp) = k(cat)/K(M,) encompassing all aspects of enzymology. The equation gives a total of thirteen theoretically possible cases, comprising the reference case plus 12 different sets of variations, which can be divided into six principal cases and six specular ones. The six relevant cases are examined individually in the context of each of the main chapters of enzymology, i.e. as regards mechanism of action, specificity of substrate and isoenzyme, reversible and irreversible inhibition, and mutation of residues (enzyme evolution and enzyme engineering). Some critical cases where k(sp) does not hold as a specificity index are classified for the first time. Interestingly, the six possible cases correspond to the five known cases of reversible inhibition (competitive, non-competitive, incompetitive, mixed competitive/non-competitive, and mixed incompetitive/non-competitive) plus an additional case of biphasic nature (activation-inhibition), which is crucial for a full understanding of specificity and which leads us to propose some modification to the definition of enzyme specificity. The systematic approach to enzymology outlined herein could find practical applications in various sectors of biotechnology, including chemotherapy.

Binding, Competitive↗

PubMed2002

Molecular evolution of the period gene in sandflies.

The molecular evolution of the clock gene period was studied in Phlebotomine sandflies (Diptera: Psychodidae). Comparison of the synonymous and nonsynonymous substitution rates between sandflies and Drosophila revealed a significantly higher evolutionary rate in the latter in three of the four regions analyzed. The differences in rate were higher in the sequences flanking the Thr-Gly repetitive domain, a region that has expanded in Drosophila but remained stable and short in sandflies, a result consistent with the coevolutionary scenario proposed for this region of the gene. An initial phylogenetic analysis including eight neotropical sandfly species and one from the Old World was also carried out. The results showed that only the subgenus Nyssomyia is well supported by distance (neighbor-joining) and maximum parsimony analysis. The grouping of the other species from the subgenus Lutzomyia and Migonei group shows very low bootstrap values and is not entirely consistent with classical morphological systematics of the genus Lutzomyia.

Amino Acid Sequence↗

PubMed2005

A multidimensional approach for detecting species patterns in Malagasy vertebrates.

The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biologists, we employ a suite of methodological and analytical tools to investigate the vertebrate portion of Madagascar's fauna. Given that species are the fundamental unit of evolution, where micro- and macroevolutionary forces converge to generate biological diversity, a thorough understanding of species distribution and abundance is critical for understanding the evolutionary, ecological, and biogeographic forces that have shaped Malagasy vertebrate diversity. We illustrate the means by which we apply Mayr's "three basic tasks" of the systematist [Mayr, E. (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist (Harvard Univ. Press, Cambridge, MA)] to identify, classify, and study the organisms that together constitute Madagascar's vertebrate community. Using field inventory methods, specimen-based studies, and morphological and molecular analyses, we formulate hypotheses of species identity that then serve as the foundation for subsequent studies of biology and history. Our experience, as well as that of other investigators, has shown that much of the vertebrate species diversity in Madagascar is "cryptic" for both biological and practical reasons. Beyond issues of cryptic biological diversity, the resolution of species identity in Madagascar has been hampered because of a lack of vouchered comparative material at the population level. Through our activities, we are attempting to remedy these limitations while simultaneously enhancing research capacity in Madagascar.

Animals↗

PubMed2026

Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis).

Endogenous retroviruses (ERVs) are a dynamic and biologically significant component of vertebrate genomes, with integration events spanning deep evolutionary time. The crab-eating macaque (Macaca fascicularis) is an important non-human primate model for biomedical research because of its close phylogenetic relationship to humans and its conservation status as an endangered species. However, the ERV complement of its genome has not been systematically characterized. Using the current highest-quality chromosome-level genome assembly for this species, we performed a genome-wide, homology-based survey of relatively intact ERV proviruses in M. fascicularis. We identified 106 proviral loci distributed across all chromosomes. Phylogenetic reconstruction based on conserved reverse transcriptase domains classified these elements into β-, γ-, and unclassified lineages, with β- and γ-retroviral lineages predominating. LTR divergence-based dating indicated that these proviruses represent multiple waves of historical retroviral activity and span a broad range of integration ages. This curated dataset provides a high-confidence reference set for investigating the evolutionary history and genomic impact of preserved ERV proviruses in an endangered primate model; however, it does not include degraded ERV fragments or solo LTRs.

Animals↗

PubMed2001

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.

Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.

Algorithms↗

PubMed2005

Accurate measurement of 15N-13C residual dipolar couplings in nucleic acids.

New 3D HCN quantitative J (QJ) pulse schemes are presented for the precise and accurate measurement of one-bond 15N1/9-13C1', 15N1/9-13C6/8, and 15N1/9-13C2/4 residual dipolar couplings (RDCs) in weakly aligned nucleic acids. The methods employ 1H-13C multiple quantum (MQ) coherence or TROSY-type pulse sequences for optimal resolution and sensitivity. RDCs are obtained from the intensity ratio of H1'-C1'-N1/9 (MQ-HCN-QJ) or H6/8-C6/8-N1/9 (TROSY-HCN-QJ) correlations in two interleaved 3D NMR spectra, with dephasing intervals of zero (reference spectrum) and approximately 1/(2J(NC)) (attenuated spectrum). The different types of 15N-13C couplings can be obtained by using either the 3D MQ-HCN-QJ or TROSY-HCN-QJ pulse scheme, with the appropriate setting of the duration of the constant-time 15N evolution period and the offset of two frequency-selective 13C pulses. The methods are demonstrated for a uniformly 13C, 15N-enriched 24-nucleotide stem-loop RNA sequence, helix-35psi, aligned in the magnetic field using phage Pf1. For measurements of RDCs systematic errors are found to be negligible, and experiments performed on a 1.5 mM helix-35psi sample result in an estimated precision of ca. 0.07 Hz for 1D(NC), indicating the utility of the measured RDCs in structure validation and refinement. Indeed, for a complete set of 15N1/9-13C1', 15N1/9-13C6/8, and 15N1/9-13C2/4 dipolar couplings obtained for the stem nucleotides, the measured RDCs are in excellent agreement with those predicted for an NMR structure of helix-35psi, refined using independently measured observables, including 13C-1H, 13C-13C and 1H-1H dipolar couplings.

Adenine↗

PubMed1982

Ethnopharmacology versus chemosystematics in the search for biologically active principles in plants.

The chemicals to which Brazilian angiosperms owe their use in the preparation of arrow poisons, hallucinogens, fish poisons, drugs, stimulants, spices, perfumes and pigments are correlated with the systematic position of the species in which they occur. Most compounds are produced either by the primitive Magnoliidae (sensu Cronquist) or by the advanced Asteridae. The Rosidae-Dilleniidae, precisely the group of subclasses of widest distribution over the country, have heretofore yielded relatively few useful compounds. This fact can be rationalized by the presence in their species of massive quantities of gallo- and ellagitannins, general defences which make the presence of specific alleochemics superfluous. The natural occurrence of specific biologically active compounds is thus ecologically and systematically conditioned and it should be possible to build a system capable of predicting the existence and the nature of useful chemicals in plant taxa.

Animals↗

PubMed2003

Tracing floral adaptations from ecology to molecules.

Flowers have long fascinated humans. The scientific study of floral biology unifies many diverse areas of research, ranging from systematics to ecology, and from genetics to molecular biology. Despite this unity, few plant species offer the experimental versatility to encompass all levels of biological investigation in a single system. An exception is the morning glory genus Ipomoea, in which a broad picture of floral evolution, ranging from ecology to molecular biology, is emerging.

Acyltransferases↗

PubMed2002

The high-fat Greek diet: a recipe for all?

OBJECTIVE: To examine critically the published results of dietary surveys on the fat content of the Greek diet, and to assess its evolution and its relationship to the health of the Greeks. To consider the implications of these findings for current views on the nature and health implications of the traditional Mediterranean diet and how best to define it for use in modern policy making. DESIGN: A systematic review of the literature on food consumption in Greece. SETTING: Greece. RESULTS: The first fully published data on the fat content of the Greek diet-the Seven Countries Survey-relates only to a small number of adult males in Crete and Corfu; the legitimacy of extrapolating these results to the rest of Greece is questioned. Earlier studies and chemical validation of intakes point to a lower fat content of the traditional diet than that inferred for Crete. Nearly all later surveys relate only to urban groups in Athens (mostly case-control hospital-based samples) and a variety of non-representative Cretan groups. Only two studies are larger and more representative, but one uses FAO food balance-sheets to reflect the national diet, and the other surveyed school-age children in three out of the 52 Greek counties. Unfortunately recent dietary studies have proved unreliable, given the continuing lack of national food composition tables with survey methods which proved inaccurate for dietary fat content. A progressive upward trend in total and saturated fat intake appears to have occurred with all health indicators in relation to fat indicating remarkable increases in adult and childhood obesity with attendant progressive deterioration in cardiovascular mortality and its risk factors, ie hypertension and diabetes. These data emphasise the need to alter current nutritional advice in Greece, particularly when it focuses on the promotion of olive oil and a high-fat diet. CONCLUSIONS: The findings reaffirm low-moderate fat policies for optimum health, within which olive oil can be an important component of the diet.

Adolescent↗

PubMed2006

The role of the airline transportation network in the prediction and predictability of global epidemics.

The systematic study of large-scale networks has unveiled the ubiquitous presence of connectivity patterns characterized by large-scale heterogeneities and unbounded statistical fluctuations. These features affect dramatically the behavior of the diffusion processes occurring on networks, determining the ensuing statistical properties of their evolution pattern and dynamics. In this article, we present a stochastic computational framework for the forecast of global epidemics that considers the complete worldwide air travel infrastructure complemented with census population data. We address two basic issues in global epidemic modeling: (i) we study the role of the large scale properties of the airline transportation network in determining the global diffusion pattern of emerging diseases; and (ii) we evaluate the reliability of forecasts and outbreak scenarios with respect to the intrinsic stochasticity of disease transmission and traffic flows. To address these issues we define a set of quantitative measures able to characterize the level of heterogeneity and predictability of the epidemic pattern. These measures may be used for the analysis of containment policies and epidemic risk assessment.

Aviation↗

PubMed2000

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

Agaricales↗

PubMed2026

Bibliometric analysis of retinoblastoma research over the past decade.

BACKGROUND: Retinoblastoma (RB), the most prevalent primary intraocular malignancy in children, has emerged as a model disease for exploring the molecular underpinnings of pediatric cancer. Over the past decade, research in this field has accelerated, propelled by advances in genomics, diagnostic imaging, targeted therapies, and global scientific collaboration. METHODS: This study systematically retrieved RB-related publications from 2015 to 2024 using the Web of Science Core Collection. A total of 4990 articles were included. CiteSpace and VOSviewer were employed to perform bibliometric and visual analyses across multiple dimensions, including countries, institutions, authors, journals, and thematic evolution. RESULTS: The United States and China were identified as the leading contributors, jointly accounting for over 40.55% of all publications. US-based journals led in both publication volume and citation impact, underscoring their global influence. Cluster analysis revealed 4 major research domains: clinical diagnosis, treatment, and prognosis; molecular mechanisms and signaling pathways; gene and protein function studies; and research methodologies and experimental models. CONCLUSION: RB research is transitioning into an era of precision oncology, characterized by molecular subtyping, novel therapeutic targets, and individualized treatment approaches. While diagnostic and therapeutic outcomes have markedly improved in high-income countries, significant disparities persist in low- and middle-income regions due to limited access to early detection and comprehensive care. Future priorities should include the refinement of preclinical models, investigation of drug resistance mechanisms, and promotion of international collaboration to standardize diagnostic and therapeutic strategies. These efforts are critical to improving global outcomes for children with RB.

Retinoblastoma↗

PubMed2015

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Adaptation, Biological↗

PubMed1979

Enflurane in renal transplantation: report of 375 cases.

Our experience to date covers 675 kidney grafts performed in the Transplantation Department of the University of Louvain. The evolution of our anaesthesia methods has led us since the end of 1973 to conduct 375 transplantations with enflurane. The patients, aged between 18 months and 50 years, receive a conventional premedication, do not receive corticoids preoperatively nor undergo dialysis immediately prior to operation, but systematically receive a 5-unit transfusion beforehand. Having successively abandoned gallamine, succinylcholine, thiopentone and finally halothane, our present anaesthetic protocol is as follows: induction under benzodiazepines, fentanyl and enflurane, intubation under laryngeal anaesthesia. Maintenance: enflurane (2--3 MAC hours) in open circuit, pancuronium (0.02 mg/kg/h) and occasionally fentanyl. Details and comparative advantages are discussed. This anaesthesia technique combined with the systematic administration of antilymphocytic and antithymocytic serum in the postoperative period, and particularly the preliminary transfusion (producing blocking antibodies), has provided us, using cadaver kidney, with a survival rate of 96% at 6 months, 86% at 1 year and 80% at 2 years, the longest presently being 15 years.

Adolescent↗

PubMed1978

Engineering aspects of ECMO technology.

The primary areas of extracorporeal membrane oxygenation (ECMO) technology with engineering components are: biomaterials, oxygenator design, ECMO physiology and total system design. The evolution of ECMO has been largely empirical, with many innovations introduced directly from clinical experience and observation. Major advances are needed in both materials ans oxygenator design if current hematologic hazards are to be reduced. Optimization of ECMO systems has not been attempted in any systematic way because the basic physiology is not well enough understood to define the rationales for optimum control and management strategies. Once these strategies have been developed and tested, currently available automation technology can be applied to make the ECMO system system simpler and safer for clinical use.

Engineering↗

PubMedDate not supplied

[Systematics on the threshold of the XXI century. Traditional principles and fundamentals from today's point of view].

Systematics as regarded is a purely theoretical domain of biology, and its product, system, as a specific biological theory, or a topologo-genetic model of the biota. Linnaeus was the first to introduce the idea of system and the systematic approach into the natural history. The advent of evolutionism brought new meaning to the old term "affinity", so Linnaeus' slogan of natural system got new life, and Linnaeus taxonomy assimilated the evolutionary ideology quite naturally and much easier than many other departments of biology. The difference between natural and artificial systems is remaining, and it is in their goals, as formulated by Linnaeus: heuristic of the former and cataloguing of the latter. Linnaeus' clairvoyance discovered the existence of an infrageneric level of genetic integration provable by naturalists' experience. He chose for it the designation of "species" and laid it down as primary, basic unit of his system. This is plainly evident from his own writings; the story about Linnaean species being products of a logical division of genera is a pure fiction. Modern populational model of species, by 3 important criteria, appears to be more akin to the Linneaean one than to the ideas of Lamarckism and early Darwinism. Systematic approach focuses rather on the interrelations among elements and their relative position, then on the properties and qualities of separately treated individual elements. In the development of systematics the aspect of "nexification" (study of connections) has been continuously gaining attention especially regarding the nomenclature where connotation has been totally forced out by denotation.

Biological Evolution↗

PubMed2006

[Evolutionary significance of chromosome architecture for epigenetic control of eukaryote development and phylogeny].

The significance of the spatial organization of chromosomes in germline tissue as a positional system controlling segregation in oogenesis is considered. The history of the problem is reviewed. The author's data on reorganization of chromosome structure in germline tissue considered in terms of systemic mutations are systematized. The notion of specific morphogenetic field based on chromosome structure, which controls ooplasmic segregation and subsequent developmental stages, is developed.

Animals↗