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PubMed2000

Lineage-specific loss and divergence of functionally linked genes in eukaryotes.

By comparing 4,344 protein sequences from fission yeast Schizosaccharomyces pombe with all available eukaryotic sequences, we identified those genes that are conserved in S. pombe and nonfungal eukaryotes but are missing or highly diverged in the baker's yeast Saccharomyces cerevisiae. Since the radiation from the common ancestor with S. pombe, S. cerevisiae appears to have lost about 300 genes, and about 300 more genes have diverged by far beyond expectation. The most notable feature of the set of genes lost in S. cerevisiae is the coelimination of functionally connected groups of proteins, such as the signalosome and the spliceosome components. We predict similar coelimination of the components of the posttranscriptional gene-silencing system that includes the recently identified RNA-dependent RNA polymerase. Because one of the functions of posttranscriptional silencing appears to be "taming" of retrotransposons, the loss of this system in yeast could have triggered massive retrotransposition, resulting in elimination of introns and subsequent loss of spliceosome components that become dispensable. As the genome database grows, systematic analysis of coordinated gene loss may become a general approach for predicting new components of functional systems or even defining previously unknown functional complexes.

Biological Evolution↗

PubMed1999

Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae.

Overlapping genes are defined, in this paper, as a pair of adjacent genes whose coding regions are partly overlapping. We systematically analyzed all overlapping genes in the genomes of two closely related species: Mycoplasma genitalium and Mycoplasma pneumoniae. Careful comparisons were made for homologous genes that are overlapped in one species but not in the other. This comparative analysis allows us to propose a model of how overlapping genes emerged in the course of evolution. It was found that overlapping genes were generated primarily due to the loss of a stop codon in either gene, in many cases, the absence of which resulted in elongation of the 3' end of the gene's coding region. More specifically, the loss of the stop codon took place as a result of the following events: deletion of the stop codon (64.4%), point mutation at the stop codon (4.4%), and frame shift at the end of the coding region (6.7%). Overlapping genes, in a sense, can be thought of as the results of evolutionary pressure to minimize genome size. However, our analysis indicates that many overlapping genes, at least in the genomes of M.genitalium and M.pneumoniae, are due to incidental elongation of the coding regions.

Genes, Bacterial↗

PubMed1999

Long-term follow-up of juvenile nasopharyngeal angiofibromas: analysis of recurrences.

OBJECTIVES: Juvenile nasopharyngeal angiofibroma often recurs if the tumor is large. This report is a long-term follow-up of these cases. It establishes the prognostic values of tumor extensions, analyzes the anatomic factors involved in recurrences, describes the spontaneous evolution of remnants based on a radiographic follow-up, and evaluates the pertinence of complex combined surgical approaches for invasive tumors and the value of complementary endoscopy. STUDY DESIGN: Retrospective review of 44 cases treated between 1985 and 1996. METHODS: Statistical analysis of the correlation between recurrence and tumor extension as evaluated by systematic analysis of 18 putative tumor extensions on preoperative computed tomography scans. RESULTS: Invasion of the skull base affected two-thirds of the patients, and the rate of recurrence was 27.5%. Extensions to the infratemporal fossa, sphenoid sinus, base of pterygoids and clivus, the cavernous sinus (medial), foramen lacerum, and anterior fossa were correlated with more frequent recurrence. Long-term radiographic follow-up revealed putative residual disease in nine asymptomatic patients: these remnants gradually involuted. CONCLUSIONS: The data in the current study emphasize the prognostic value of skull base invasion and the difficulty of complete resection of extended lesions. Tumor remnants detected in symptom-free patients should be kept under surveillance by repeated computed tomography scan, since involution may occur. Recurrent symptoms may be treated by radiotherapy (30 Gy) rather than by extended combined procedures. Endoscopic surgery should be combined with surgery for better control of skull base extensions.

Adolescent↗

PubMed1971

The photosynthetic unit in chlorella measured by repetitive short flashes.

Apparent size of the photosynthetic unit in Chlorella pyrenoidosa was estimated by the method of Emerson and Arnold: rate of oxygen evolution was measured under repetitive saturating flashes of about 10-microsecond duration separated by dark periods of 0.033 to 0.100 second. Cells used were taken from six steady state cultures maintained at different light intensities. Cell characteristics included a variation in chlorophyll content from 1 to 5%. Apparent size of the photosynthetic unit varied systematically with chlorophyll content in the range of 1560 to 2350 chlorophylls per O(2) per flash. Values for unit size showed no unusual statistical distribution and were not changed significantly by addition of low level background light at 645 or 705 nanometers. Maximal rate of unit turnover, calculated from light-saturated rate and unit size, varied inversely with chlorophyll content in the range of 70 to 180 per second.

Journal Article↗

PubMedDate not supplied

Phylogenetic networks: modeling, reconstructibility, and accuracy.

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

Algorithms↗

PubMed2026

A comprehensive overview of monkeypox virus disease.

BACKGROUND: Monkeypox (mpox), caused by monkeypox virus (MPXV), re-emerged as a major global public health concern in 2022, resulting in widespread transmission beyond traditionally endemic regions. As of March 2026, 181,164 confirmed cases and 492 deaths had been reported across 144 countries globally. The unprecedented geographic spread of the outbreak highlighted important knowledge gaps in disease surveillance, prevention, and control. Given the ongoing global circulation of MPXV and the risk of future outbreaks, this review provides a comprehensive synthesis of current evidence on MPXV and mpox. METHODS: The literature, surveillance data, and public health reports available up to March 2026 were systematically reviewed and synthesized. The review comprehensively assesses viral biology, genetic diversity, epidemiology, transmission dynamics, clinical manifestations, pathogenesis, laboratory diagnosis, infection during pregnancy, host immune responses, immune evasion mechanisms, therapeutic interventions, and prevention strategies. FINDINGS AND CONCLUSIONS: Globally, the decline in public immunity following the cessation of routine smallpox vaccination, together with ongoing viral evolution, may have contributed to the resurgence of mpox. Advances in genomic surveillance, diagnostics, and public health preparedness have strengthened outbreak response; however, important gaps remain in understanding long-term immunity and optimal treatment strategies. This review summarizes current evidence on MPXV and mpox and highlights priorities for future research and public health interventions.

Antiviral therapy↗

PubMed2001

Prospective follow-up of 33 asymptomatic patients with familial cerebral cavernous malformations.

BACKGROUND: Cerebral cavernous malformation (CCM) is one of the most common vascular malformations of the CNS. Familial CCM are increasingly diagnosed, but little is known about their natural history, especially in asymptomatic patients. OBJECTIVE: To determine the degree of spontaneous evolution of familial CCM in a population of 33 symptom-free patients. METHODS: During a previous national survey, the authors analyzed the clinical and MRI features of 173 patients from 57 unrelated French families, including 73 asymptomatic subjects. Of these 73 subjects, 33 prospectively underwent two serial clinical and MRI examinations. Cerebral MRI systematically included spin echo and gradient echo sequences. Occurrence of clinical symptoms and MRI changes of CCM, namely, hemorrhage, change in signal intensity, change in size, and appearance of new lesions, were recorded by means of comparison of the first and last MRI examinations. RESULTS: The 33 patients (234 CCM, mean 7.1 lesions/subject, range 1 to 85 lesions/subject) were followed during a mean period of 2.1 years (range 0.5 to 4.5 years). Two patients became symptomatic: One presented with brainstem hemorrhage and one with partial seizure. Comparison of the two serial MR images found changes in 15 patients (46%): 1) Bleeding occurred in three type II lesions (1.3%) in three patients (9.1%); 2) 30 new lesions appeared in 10 patients (30.3%); 3) change in signal intensity was observed in one lesion (0.4%) in one patient (3%); and 4) increase in size was observed in four lesions (1.7%) in three patients (9.1%). CONCLUSIONS: This prospective study confirms the dynamic nature of CCM. The appearance of new lesions in 30% of patients has to be retained as a hallmark of the familial condition.

Adolescent↗

PubMed1999

[Diagnosis and virologic monitoring of HIV infection].

The new challenge of the diagnosis of HIV infection concerns the treatment since an early diagnosis permits to start antiretroviral therapy with the aim to block the evolution to aids. The virological diagnosis may be done easily using new sensitive and specific techniques. Using the test of detection of p24 antigenemia and HIV-RNA in plasma, it is easy to approach the diagnosis of primary infection. The tests for HIV viral load are now largely available and they must be systematically included in the follow-up of infected persons.

AIDS Serodiagnosis↗

PubMedDate not supplied

[May Medically Assisted Procreation (MAP) be relevant for homosexual women? Study among 147 gynaeco-logists involved in MAP techniques].

The second part of the twentieth century has seen societal modifications as well as evolution of medical techniques allowing now thinking human procreation in terms of choices or even rights. Certain voices require sometimes Medically Assisted Procreation (MAP) for lesbians. Even though society did not allow such a possibility in France, it seemed interesting to question about it professionals actively involved in the use of MAP techniques. Through systematic internet queries, we obtained a list of one hundred private or public french medical institutions with a unit for the treatment of sterility. A telephone call to their secretary allowed us to individualize those doctors who did practice MAP. A sample of 147 medical doctors practicing MAP was then drawn. They were questioned with a clinical instrument including 20 ended-questions in order to assess their opinions on: homosexual women with a desire of a child; possibility for these clinicians to intervene with a donor insemination in such situations; developmental risk for such children. One hundred twenty five (85%) accepted to answer. Nine percent of these gynaecologists still consider homosexuality as pathological, and 10% as deviant - contrary to international classifications of mental disorders - and 5% deny good maternal abilities to homosexual women. Before the so-called french laws of bioethics in 1994, none of them had practiced a donor insemination for a lesbian couple, though 4% had realized some for single homosexual women. Two third of them do not agree opening donor insemination to homosexual women though for half of them, the anonymity of a donor is not perceived as prejudicial to the child. Eighty-seven percent of these gynaecologists think that a child brought up by homosexual parents is at risk for developmental disorder, the configuration supposed the most pathogenic being when the birth results from a donor insemination. The supposedly most important risk factors are thought to be the marginality of an homosexual family and the lack of a paternal figure at home. However, for 68% of the clinicians, this role can be taken by another male figure. These reasons make the gynaecologists reluctant to participate actively in the constitution of such a kind of family by the practice of a donor insemination. Even though demands of lesbian couples were not listed as an indication of donor insemination in the laws of bioethics, this does not seem to lessen the number of these demands in this population, and moreover if the law would allow this indication, half of these doctors would agree to practice it. The expression of the desire of a child by homosexual women and their request for its realization through medical techniques places the clinicians at the center of an ethical reflexion fed more by personal affects rather than scientific studies - however available - on the development of children brought up by an homosexual couple. Indeed, these studies indicate that these children suffer more from a societal view than parental sexual orientation, and it seems therefore appropriate to shed light on it in order to alleviate the weight of a stigmatization without any clinical argument founding it until now.

Adult↗

PubMedDate not supplied

[Use of botulinum toxin in the preventive and palliative treatment of the hips in children with infantile cerebral palsy].

INTRODUCTION: The bilateral spastic cerebral palsy (CP) usually produces hip abnormalities, already presents in many cases before 2 years of age, whose diagnostic requires X ray because clinical exam do not detect some of them. The prognosis of CP hip disorders with conventional treatment is bad, progressive, and limits the possibility of independent gait. Botulin toxin type A infiltrated in adductors, medial ischiotibials and iliopsoas, in addition to physiotherapy and orthosis, gives better results. PATIENTS, METHODS AND RESULTS: In our cases (98 cases, 193 hips) the natural evolution before (BT A) treatment had been of progressive lateral migration of femoral head (86% got worse, and 11,4% became luxated), and after the onset of it the progression stopped in 74% of hips and reverted in other 14%. CONCLUSIONS: It is very important to start early the BT A treatment and infiltrate systematically every 3 4 months in order to obtain good results. Stopping the treatment increase the chances of subluxation or luxation. BT A is also a good treatment for hip pain in spastic CP.

Botulinum Toxins, Type A↗

PubMed2003

[Variability in neurology care. Tools for quality improvement].

Medical practice variability is a common problem that can reduce the quality of health assistance. We can introduce several tools, like protocols (P), clinical practice guidelines (CPG) and clinical pathways (CP) that allow us to reduce it. CPG must be based in a review of medical evidence and it is the main difference with P. Also it will be more expensive to develop, and its final implementation is more difficult. On the other hand, P are born from simple consensus and its application are easier and widely in medicine. CP have recently appeared in the medical world to try to resolve the problems of the applications of P and CPG in clinical daily practice. They describe in detail medical attention in a systematic, temporal way. They are very similar to a process management and facilitate the interaction of all medical picture actors (manager, health personal and patients). One of the limitations of this tool is that it has not widely application. It is more useful in complex, frequent, very expensive medical process, with known predictable clinical evolution. Once developed, the control and the temporal improvement of these processes. It is very probable that the development of these tools can increase the quality of neurological assistance in Spain in the next future.

Critical Pathways↗

PubMed1980

[Rapid determination of MB fraction of serum creatine kinase in the diagnosis of acute myocardial infarction (author's transl)].

The behaviour of the myocardial fraction of creatine kinase has been studied in a group of 80 patients diagnosed as having an acute myocardial infarction. The method of selective activation with dithiothreitol was employed. This technique enables the isoenzyme quantification in less than 15 minutes, which represents a great advantage in comparison to other complex methods used in the past. According to the time of evolution of the infarction the patients were classified into four groups and comparative statistical studies were carried out between these groups and the group of 20 normal controls. The early increase of the myocardial fraction is stressed, even when creatine kinase is still within normal limits. Literature on this topic is reviewed and a systematic determination of the myocardial fraction of serum creatine kinase in the intensive Coronary Units is recommended in order to certainly diagnose myocardial infarction as soon as possible.

Creatine Kinase↗

PubMed2006

A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns.

BACKGROUND: Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. RESULTS: We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305) and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not involved in the integration or excision of island 4305. CONCLUSION: The "clone-and-transfer" approach of evolutionary study identifies genes whose expression patterns indicate the existence of genera-specific regulatory mechanisms that influence the expression of horizontally-transferred DNA sections. The results provide key information that can be used to facilitate the identification of these regulatory mechanisms.

Bacteria↗

PubMed1999

Pervasiveness of gene conservation and persistence of duplicates in cellular genomes.

In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed a significant correlation between duplication and conservation. Systematic comparisons of predicted proteomes of 23 organisms (including 20 that have been completely sequenced), have allowed us to quantify the degree of ancestral duplication within each genome and the level of conservation between genomes, using threshold values calculated for individual organisms. Statistical analysis of various gene proportions revealed interesting trends in gene structure and evolution, such as that (a) more than one-quarter (25%-66%) of the predicted ORF products of the surveyed organisms are not unique, indicating a high level of ancestral duplications; (b) levels of exclusive conservation within Bacteria are higher than those within the eukaryal or archaeal domains; and (c) at least one-half (47-99%) of the total predicted ORF products in the surveyed genomes have one or several highly significant matches in another genome. Significant matches are based on simulations taking into account the mean size of ORF products and the composition of each target organism's proteome. The methodology we have developed ensures stability and comparability of our results as the number of completely sequenced genomes increases.

Base Sequence↗

PubMed1995

Effects of GABAB receptor antagonists on two models of focal epileptogenesis.

The acute effects of two GABAB receptor antagonists (phaclofen and CGP-35348) were studied in two types of epileptogenic activity: that produced by intracortical injections of baclofen and that appearing after withdrawal of chronic intracerebral GABA infusion (the GABA-withdrawal syndrome, GWS). Intracortical baclofen induced two types of electrographic paroxysmal discharges: one consisting of single spike-and-wave (pattern I) and another of polyspike-and-wave patterns (pattern II). Both patterns showed similar latencies and temporal evolution of spike frequency discharges. Phaclofen, applied directly into the baclofen-induced epileptogenic focus, suppressed pattern II but was ineffective in modifying both pattern I and the GWS. CGP-35348, administered systemically, inhibited both patterns I and II. Intracortical microinjection of baclofen or phaclofen in rats showing a GWS had no effect, nor the systematically given CGP 35348. These results indicate a differential participation of GABAB receptors in GABA-related epileptic syndromes of cortical origin.

Animals↗

PubMed2000

Towards a new evolutionary synthesis.

New concepts and information from molecular developmental biology, systematics, geology and the fossil record of all groups of organisms, need to be integrated into an expanded evolutionary synthesis. These fields of study show that large-scale evolutionary phenomena cannot be understood solely on the basis of extrapolation from processes observed at the level of modern populations and species. Patterns and rates of evolution are much more varied than had been conceived by Darwin or the evolutionary synthesis, and physical factors of the earth's history have had a significant, but extremely varied, impact on the evolution of life.

Journal Article↗

PubMed1975

Nonprevalence of biochemical fossils in kerogen from pre-Phanerozoic sediments.

Evidence of biochemical and geochemical evolution was sought in insoluble carbonaceous matter from 30 selected pre-Phanerozoic sediments ranging in age from about 3.8 to about 0.7 x 10(9) years. The carbon isotope ratios observed were in the range of -20 to -32 per mil with reference to the Peedee belemnite standard, similar to those previously reported. No systematic trends are obvious to us. Stepwise pyrolysis-gas-chromatography showed only molecules with fewer than 8 carbon atoms at the level of sensitivity of 10(-9) g of organics in a 10 mg rock sample. Carbon, hydrogen, and nitrogen analyses showed noncarbonate carbon from less than 0.1% to more than 3%, with very small amounts of N. The H/C (atomic) ratios on HCl-leached and HF-treated samples were generally less than 0.3. Evidence of low pyrolysis yields (micro-analysis) and low H/C atomic ratios (macro-analysis) implies that the carbonaceous solids in even the least metamorphosed of these ancient sediments have evolved far toward amorphous carbon or graphite and do not yield useful "biochemical fossils."

Journal Article↗

PubMed1999

Age-associated alteration of muscle oxygenation measured by near infrared spectroscopy during exercise.

The influence of ageing on the capacity to increase muscle oxygen delivery during exercise is unclear. This was investigated by comparing the evolution of Near InfraRed Spectroscopy (NIRS) in 10 old (67 +/- 5 years, Old group) and 13 young subjects (27 +/- 4 years, Young group), during a progressive maximal exercise. The NIRS probe was placed on the vastus lateralis; muscle oxygen saturation - IR-SmO(2) - values were expressed on a scale using an arterial occlusion as the lower reference point and the subsequent reactive hyperaemia as the upper reference point. Resting IR-SmO( 2) was found to be significantly lower in the Old as co mpared to the Young group. During exercise, VO(2) increased similarly as a function of the workload whereas IR-SmO(2) decreased faster in old subjects than in young ones. Conversely, when expressed at the same percentage of VO( 2max), IR-SmO(2) followed a similar evolution in both groups from rest to maximal exercise (27.3 +/- 16.7 vs 24.3 +/- 12.9% decrease, in Old and Young group, respectively, NS). Thus, the initial difference remained constant between the two groups. During recovery, the time to recover the signal variation was not different between the two groups. We concluded that Old subjects demonstrate a systematic lower muscle oxygen saturation than Young ones. This difference could be explained by an age related decrease in muscle blood flow limiting O(2) supply.

Adult↗