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PubMed1981

Evolutionary genetics of Metridium senile. II. Geographic patterns of allozyme variation.

Electrophoretic surveys have demonstrated that populations of the sea anemone Metridium senile along the northeast coast of the United States are polymorphic at four enzyme loci. Phosphoglucose isomerase (PGI) has two alleles in most populations, phosphoglucomutase (PGM) has three alleles, and two leucine aminopeptidase loci have two common alleles each. Phosphoglucose isomerase displays clinial variation and an apparent association with environmental temperature. Phosphoglucomutase shows clinial variation north of Cape Cod for two of the three alleles, while the two leucine aminopeptidase loci are not clinial. All loci show a great deal of variation in populations on Cape Cod, but there is no apparent systematic pattern of this variation. Temperature may be a selective agent in the maintenance of the PGI and PGM clines, although other possibilities cannot presently be completely excluded.

Alleles↗

PubMed2006

Protein interaction networks in plants.

Protein-protein interactions are fundamental to virtually every aspect of cellular functions. With the development of high-throughput technologies of both the yeast two-hybrid system and tandem mass spectrometry, genome-wide protein-linkage mapping has become a major objective in post-genomic research. While at least partial "interactome" networks of several model organisms are already available, in the plant field, progress in this respect is slow. However, even with comprehensive protein interaction data still missing, substantial recent advance in the graph-theoretical functional interpretation of complex network architectures might pave the way for novel approaches in plant research. This article reviews current progress and discussions in network biology. Emphasis is put on the question of what can be learned about protein functions and cellular processes by studying the topology of complex protein interaction networks and the evolutionary mechanisms underlying their development. Particularly the intermediate and local levels of network organization--the modules, motifs and cliques--are increasingly recognized as the operational units of biological functions. As demonstrated by some recent results from systematic analyses of plant protein families, protein interaction networks promise to be a valuable tool for a molecular understanding of functional specificities and for identifying novel regulatory components and pathways.

Biological Evolution↗

PubMed2006

Phylogenetics of Chinese Dryopteris (Dryopteridaceae) based on the chloroplast rps4-trnS sequence data.

Dryopteris is one of the largest and most taxonomically complex fern genera in the Dryopteridaceae, with 127 species occurring throughout temperate, sub-temperate, subtropical, and tropical China. Investigations of the evolutionary relationships of a subset of these Chinese Dryopteris species, using DNA sequence-based methods, specifically tested the monophyly of the genus and the validity of the previous subgeneric classifications. Sixty species of Dryopteris, four closely related non-Dryopteris and three species of Arachniodes, were used as outgroup taxa. The rps4-trnS region of the chloroplast genome was sequenced in these species for the first time. Both maximum parsimony (MP) and neighbor-joining (NJ) analyses identified six polyphyletic clades that contained Dryopteris species. These results were supported by a Bayesian analysis of the same data set. The phylogenetic patterns strongly suggest the polyphyletic status of Dryopteris; the monophyletic groupings of the species do not correspond with either Fraser-Jenkins [In: Bull Brit Mus (Nat Hist) Bot 14(3):183-218, 1986} or Wu (In: Flora Reipublica Popularis Sinicae Tomus 5 (1) pp 1-241, 2000] subgeneric classification of Dryopteris, except in a few specific cases. This work represents the first molecular systematic analyses of Chinese Dryopteris, and we propose the next steps necessary to recognize new subgenera of the genus.

Base Sequence↗

PubMed2004

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes.

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.

Animals↗

PubMed2000

Proteomics: applications in basic and applied biology.

The rapid evolution of proteomics has continued during the past year, with a series of innovations in the core technologies of two-dimensional electrophoresis and mass spectrometry, and a diversity of productive research programmes. Well-annotated proteomics databases are now emerging in a number of fields to provide a platform for systematic research, with particularly promising progress in clinical applications such as cardiology and oncology. Large-scale quantitative research, comparable in power and sensitivity to that achieved for gene expression, is thus becoming a reality at the protein level.

Databases, Factual↗

PubMed2002

Eternal vigilance on an Amazon floodplain.

Deep and puzzling evolutionary questions are still being raised by the unfashionable work of systematic biologists. James S. Albert describes some such work and argues why we need much more of it in the face of unprecedented loss of species through human activity.

Animals↗

PubMed2002

A molecular phylogeny for the South African limbless lizard taxa of the subfamily Acontinae (Sauria: Scincidae) with special emphasis on relationships within Acontias.

In the present study, relationships among three genera Acontias, Acontophiops, and Typhlosaurus, that comprise the South African limbless lizard subfamily Acontinae, were assessed with partial sequences of the 16S rRNA mitochondrial DNA gene. In addition, relationships within Acontias were further investigated using sequence data from the cytochrome oxidase I gene (COI). Maximum likelihood and maximum parsimony analyses of the 16S rRNA mtDNA data revealed that within this subfamily, Typhlosaurus is basal while Acontophiops and Acontias are sister taxa. Based on the 16S rRNA mtDNA data, the relationships within Acontias placed A. meleagris orientalis as the sister taxon of A. percivali tasmani, with A. m. orientalis lineacauda morph and A. m. meleagrus being the sister taxa to this group. The small-bodied skinks A. lineatus lineatus and A. l. tristis formed a monophyletic group, with the medium-bodied species A. gracilicauda gracilicauda being their sister taxon. Analyses of the COI gene for Acontias place A. m. orientalis as the sister taxon of A. p. tasmani with both A. meleagris meleagris and A. m. orientalis lineacauda being distinct. In contrast to the 16S rRNA mtDNA data, the COI data placed A. g. gracilicauda as the sister taxon to these medium-bodied species; while the subspecies status of the small-bodied taxa A. l. lineatus and A. l. tristis is reaffirmed. Combined analysis of both gene fragments for Acontias taxa recovered the same clades as found using only COI data. Systematic affinities in Acontias are discussed. These results indicate that Acontias is more species rich than previously thought.

Animals↗

PubMed2006

Pandora's mycological box: molecular sequences vs. morphology in understanding fungal relationships and biodiversity.

Fundamental reappraisals of diverse traditional ideas in mycology have become necessary as a result of molecular insights. These different insights are discussed in relation to: the positions of microsporidia, slime moulds and oomycetes; the basal position of lichen fungi in the evolution of ascomycetes forming fruit bodies; remodelling of orders and families; changed generic concepts; the issue of whether permitting a dual nomenclature for the different states of pleomorphic fungi should be continued; and the recognition of additional cryptic species within a "species". The molecular data has necessitated a reassessment of the systematic importance of many types of characters. Also, the techniques open exciting horizons and undreamed of abilities through being able to identify non-sporing fungi in ecological samples and plant material, and revealing unexpected levels of diversity in hitherto little-explored habitats. Major advances in understanding how fungi operate through total genomic approaches can be anticipated as more are completely sequenced. The Pandora's box of molecular surprises is to be seen as one of blessings and not one of miseries and evils.

Agaricales↗

PubMed2002

Electrophoretic injection within microdevices.

The flexibility of the microfabricated format creates unique opportunities for study of the electrophoretic process. The present work utilizes digital images to capture the motion of DNA samples during pre-electrophoretic processes. A systematic study of DNA loading and strong sample stacking (sample concentration effects) was performed in order to analyze realistic DNA analysis conditions within microdevices. Using digital imaging and microscopy, DNA sample profiles within the injector were analyzed by deconvolving the geometrical intensity profile into different velocity groups. This analysis illustrates the evolution of molecular separation into distinct migrating populations within the injector itself. The present study performed DNA injections within microfabricated devices imposing run voltages between 85 and 850 V/cm. Data from 3 different offset lengths of a double-T cross-injector, 10 different applied voltages, and 2 different sample preparation protocols are presented.

DNA↗

PubMed2003

Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity.

Over a hundred families of non-long terminal repeat retrotransposons (non-LTRs) were found in the newly released Anopheles gambiae genome assembly during a reiterative and comprehensive search using the conserved reverse transcriptase (RT) domains of known non-LTRs as the starting queries. These families, which are defined by at least 20% amino acid sequence divergence in their RT domains, range from a few to approximately 2,000 copies and occupy at least 3% of the genome. In addition to having an unprecedented number of diverse families, A. gambiae non-LTRs represent 8 of the 15 previously defined clades plus two novel clades, Loner and Outcast, more than what has been reported for any genome. Five families were found belonging to the L1 clade, which had no invertebrate representatives to date. One unique family named Sponge contains only a complete open reading frame (ORF) for the Gag-like protein and appears to have been mobilized by a family of the CR1 clade. Although most families appear to be inactive as expected, all clades except R4 have families with characteristics suggesting recent activity. At least 21 families have multiple full-length copies with over 99% nucleotide identity and some or all of the following characteristics: target site duplications (TSDs), intact ORFs, and corresponding expressed sequence tags (ESTs). The incredible diversity and the maintenance of multiple recently active lineages within different clades indicate a complex evolutionary scenario. A. gambiae non-LTRs have the potential to be developed as tools for population genetic studies and genetic manipulations of this primary vector of the devastating disease malaria. The semi-automated reiterative search approach described here may be used with any genome assembly to systematically survey and characterize non-LTRs as well as other transposable elements that encode a conserved protein.

Animals↗

PubMed2005

A genome-wide survey of structural variation between human and chimpanzee.

Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for dramatic and irreversible mutation. The low-quality nature of the current chimpanzee genome assembly precludes the reliable identification of many of these differences. To circumvent this, we applied a method to optimally map chimpanzee fosmid paired-end sequences against the human genome to systematically identify sites of structural variation > or = 12 kb between the two species. Our analysis yielded a total of 651 putative sites of chimpanzee deletion (n = 293), insertions (n = 184), and rearrangements consistent with local inversions between the two genomes (n = 174). We validated a subset (19/23) of insertion and deletions using PCR and Southern blot assays, confirming the accuracy of our method. The events are distributed throughout the genome on all chromosomes but are highly correlated with sites of segmental duplication in human and chimpanzee. These structural variants encompass at least 24 Mb of DNA and overlap with > 245 genes. Seventeen of these genes contain exons missing in the chimpanzee genomic sequence and also show a significant reduction in gene expression in chimpanzee. Compared with the pioneering work of Yunis, Prakash, Dutrillaux, and Lejeune, this analysis expands the number of potential rearrangements between chimpanzees and humans 50-fold. Furthermore, this work prioritizes regions for further finishing in the chimpanzee genome and provides a resource for interrogating functional differences between humans and chimpanzees.

Animals↗

PubMed2002

The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis.

Reversible protein phosphorylation is critically important in the modulation of a wide variety of cellular functions. Several families of protein phosphatases remove phosphate groups placed on key cellular proteins by protein kinases. The complete genomic sequence of the model plant Arabidopsis permits a comprehensive survey of the phosphatases encoded by this organism. Several errors in the sequencing project gene models were found via analysis of predicted phosphatase coding sequences. Structural sequence probes from aligned and unaligned sequence models, and all-against-all BLAST searches, were used to identify 112 phosphatase catalytic subunit sequences, distributed among the serine (Ser)/threonine (Thr) phosphatases (STs) of the protein phosphatase P (PPP) family, STs of the protein phosphatase M (PPM) family (protein phosphatases 2C [PP2Cs] subfamily), protein tyrosine (Tyr) phosphatases (PTPs), low-M(r) protein Tyr phosphatases, and dual-specificity (Tyr and Ser/Thr) phosphatases (DSPs). The Arabidopsis genome contains an abundance of PP2Cs (69) and a dearth of PTPs (one). Eight sequences were identified as new protein phosphatase candidates: five dual-specificity phosphatases and three PP2Cs. We used phylogenetic analyses to infer clustering patterns reflecting sequence similarity and evolutionary ancestry. These clusters, particularly for the largely unexplored PP2C set, will be a rich source of material for plant biologists, allowing the systematic sampling of protein function by genetic and biochemical means.

Animals↗

PubMed1999

[Alcohol withdrawal syndrome in the hospital].

Contrary to widely held belief, physical dependency is not systematic in alcohol dependence. Alcohol withdrawal syndrome can appear even without stopping (or sharply decreasing) high or chronic alcohol intake. It occurs through revelation of a physicochemical cerebral response (membrane changes and decrease in modulation systems) to chronic intoxication. Given the differences in severity, the lability of symptoms and the rapid evolution of the syndrome, the repeated use of scales to evaluate intensity is suggested. Management should be based on this index in order to treat minor forms and to avoid a course to severe forms, which should be transferred to the intensive care unit.

Alcohol Withdrawal Delirium↗

PubMed1975

[Toxi-infectious shock pneumopathy. A morphological study (author's transl)].

The lungs of 68 septicaemic patients have been systematically studied and compared. The observed lesions include a whole range if alterations usually described in routine sampling of lungs in cases of deaths from diverse diseases. One lesion however appears more frequent and intense: infection of the pulmonary oedema. Inflammatory reactions are associated to acute arteritis at different stages of evolution which, in these patients, was more frequent in cases of shock.

Adult↗

PubMed1998

[Malaria in infants in a rural area of maritime Guinea (Guinea Conakry). II. Development of antimalarial antibodies and malaria during the first year of life].

A transversal investigation carried out on 551 children and a longitudinal study of 55 infants showed the disappearance of maternal anti-plasmodium antibodies during the first year of life. Out of 212 new-borns surveyed for one year, 59 (28%) were infested by Plasmodium, but never during the first two months of life. This infestation was not related to the age of the infant nor to the season. For 46% of cases, infestation was completely asymptomatic, for 18% of cases respiratory signs were present and for 20% digestive signs not specific to malaria. Fever was present in 14 cases (24%) and isolated in 6 cases. Only 7 infants received a specific antimalarial treatment. Evolution under medical surveillance was favourable in all cases. These findings prove the difficulties inherent to the diagnosis of malaria, especially in the absence of laboratories for diagnosing other infections--such as typhoid--which do not appear in sanitary statistics. The findings also raise the question as to the efficiency of systematic antimalarial treatment in case of fever in the infant or child. Asymptomatic parasitemia can be explained by the existence of antitoxic immunity different from antiplasmodia immunity.

Aging↗

PubMedDate not supplied

[Sleep in infantile autism].

INTRODUCTION: Analysis of nocturnal sleep in infantile autism has been presented in various studies. However, there has been no systematization including the different structural and paroxystic alterations at the same time as permitting the development of a general theory of the effect of sleep on prognosis and treatment, particularly in a spectrum in which there is currently no definite solution. DEVELOPMENT: A systematic review was made of the literature obtained from publications included in MEDLINE and web pages of the last 25 years using the key words: autism, Asperger's disorder, sleep, childhood and Rett's syndrome. Altogether 21 papers fulfllled criteria for inclusion. Disorders of sleep in infantile autism were classified into three types: immaturity of sleep, showing a destructured polysomnographic recording and negative correlation with the level of development; functional alterations of sleep with early waking and difficulty in going to sleep being the disorders most frequently seen; and paroxystic alterations with epileptiform discharges being the commonest, without necessarily occurring together with seizures. The opinions stated on questionnaires and the data observed on the polysomnography were not in agreement. CONCLUSIONS: Analysis of the literature has permitted us to make an initial classification of sleep disorders in autistic children, and has shown a marked presence of these disorders in the evolution of autistic children. It is necessary that further studies being done, polysomnographic rather than by means of questionnaires, for two reasons: clinical and in order to obtain more precise classification.

Autistic Disorder↗

PubMed2000

Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators.

Members of the SOX family of transcription factors are found throughout the animal kingdom, are characterized by the presence of a DNA-binding HMG domain, and are involved in a diverse range of developmental processes. Previous attempts to group SOX genes and deduce their structural, functional, and evolutionary relationships have relied largely on complete or partial HMG box sequence of a limited number of genes. In this study, we have used complete HMG domain sequence, full-length protein structure, and gene organization data to study the pattern of evolution within the family. For the first time, a substantial number of invertebrate SOX sequences have been included in the analysis. We find support for subdivision of the family into groups A-H, as has been suggested in some previous studies, and for the assignment of two new groups, I and J. For vertebrate genes, it appears that relatedness as suggested by HMG domain sequence is congruent with relatedness as indicated by overall structure of the full-length protein and intron-exon structure of the genes. Most of the SOX groups identified in vertebrates were represented by a single SOX sequence in each invertebrate species studied. We have named anonymous sequences and, where appropriate, have suggested systematic names for some previously identified sequences. In addition, we identify an HMG domain signature motif which may be considered representative of the SOX family. Based on our data, we propose a robust phylogeny of SOX genes that reflects their evolutionary history in metazoans.

Amino Acid Sequence↗

PubMed2006

Systematic derivation of coarse-grained fluctuating hydrodynamic equations for many Brownian particles under nonequilibrium conditions.

We study the statistical properties of many Brownian particles under the influence of both a spatially homogeneous driving force and a periodic potential with period l in a two-dimensional space. In particular, we focus on two asymptotic cases lint< >l , where lint represents the interaction length between two particles. We derive fluctuating hydrodynamic equations describing the evolution of a coarse-grained density field defined on scales much larger than l for both cases. Using the obtained equations, we calculate the equal-time correlation functions of the density field to the lowest order of the interaction strength. We find that the system exhibits long-range correlation of the type r-d (d=2) for the case lint>>l , while no such behavior is observed for the case lint<<l .

Journal Article↗