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PubMed2004

Nucleotide diversity and linkage disequilibrium in loblolly pine.

Outbreeding species with large, stable population sizes, such as widely distributed conifers, are expected to harbor relatively more DNA sequence polymorphism. Under the neutral theory of molecular evolution, the expected heterozygosity is a function of the product 4N(e)mu, where N(e) is the effective population size and mu is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4N(e)r, where r is the per-generation recombination rate between adjacent sites. These parameters were estimated in the long-lived, outcrossing gymnosperm loblolly pine (Pinus taeda L.) from a survey of single nucleotide polymorphisms across approximately 18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4N(e)mu at silent and nonsynonymous sites were 0.00658 and 0.00108, respectively, and both were statistically heterogeneous among loci. By Tajima's D statistic, the site frequency spectrum of no locus was observed to deviate from that predicted by neutral theory. Substantial recombination in the history of the sampled alleles was observed and linkage disequilibrium declined within several kilobases. The composite likelihood estimate of 4N(e)r based on all two-site sample configurations equaled 0.00175. When geological dating, an assumed generation time (25 years), and an estimated divergence from Pinus pinaster Ait. are used, the effective population size of loblolly pine should be 5.6 x 10(5). The emerging narrow range of estimated silent site heterozygosities (relative to the vast range of population sizes) for humans, Drosophila, maize, and pine parallels the paradox described earlier for allozyme polymorphism and challenges simple equilibrium models of molecular evolution.

Animals↗

PubMed2004

Emergence of Talanin protein associated with human uric acid nephrolithiasis in the Hominidae lineage.

Recently, we identified a susceptibility locus for human uric acid nephrolithiasis (UAN) on 10q21-q22 and demonstrated that a novel gene (ZNF365) included in this region produces through alternative splicing several transcripts coding for four protein isoforms. Mutation analysis showed that one of them (Talanin) is associated with UAN. We examined the evolutionary conservation of ZNF365 gene through a comparative genomic approach. Searching for mouse homologs of ZNF365 transcripts, we identified a highly conserved mouse ortholog of ZNF365A transcript, expressed specifically in brain. We did not found a mouse homolog for ZNF365D transcript encoding the Talanin protein, even if we were able to identify the corresponding genomic region in mouse and rat not yet organized in canonical gene structure suggesting that ZNF365D was originated after the branching of hominoid from rodent lineage. In mouse and in most mammals, a functional uricase degrades the uric acid to allantoin, but uricase activity was lost during the Miocene epoch in hominoids. Searching for the presence of Talanin in Primates, we found a canonical intron-exon structure with several stop codons preventing protein production in Old World and New World monkeys. In humans, we observe expression and we have evidence that ZNF365D transcript produces a functional protein. It seems therefore that ZNF365D transcript emerged during primate evolution from a noncoding genomic sequence that evolved in a standard gene structure and assumed its role in parallel with the disappearance of uricase, probably against a disadvantageous excessive hyperuricemia.

Alternative Splicing↗

PubMed2005

Dynamics of CNS barriers: evolution, differentiation, and modulation.

(1) Three main barrier layers at the interface between blood and tissue protect the central nervous system (CNS): the endothelium of brain capillaries, and the epithelia of the choroid plexus (CP) and the arachnoid. The classical work on these barriers in situ until the 1970s laid the foundations for modern understanding. Techniques for brain endothelial cell isolation and culture pioneered by Ferenc Joó in the 1970s opened up new fields of examination, enabling study of mechanisms at the cellular and molecular level. (2) Astrocytic glial cells are closely associated with the brain endothelial barrier. During evolution the barrier appears to have shifted from the glial to the endothelial layer, in parallel with the increasing importance of the microvasculature and its regulation. Vestiges of the barrier potential of glia remain in the modern mammalian CNS. (3) Evolutionary evidence suggests that the advantage derived from ionic homeostasis around central synapses was the major selective pressure leading to refinement of CNS barrier systems. This is one element of the modern 'multitasking' barrier function. (4) While epithelia are constitutively able to form barriers at appropriate interfaces, the 'default' condition for endothelia is more leaky; inductive influences from associated cells especially astrocytes are important in generating the full blood-brain barrier (BBB) phenotype in brain capillaries. The underlying mechanisms are being elucidated at the molecular and genomics level. (5) The barrier layers of the nervous system can be modulated by a number of receptor-mediated processes, involving several signal transduction pathways, both calcium dependent and independent. Some agents acting as 'inducers' in the long term can act as 'modulators' in the short-term, with some overlap of signaling pathways. Modulating agents may be derived both from the blood and from cells associated with cerebral vessels. Less is known about the modulation of the CP. (6) The challenge for the next era of CNS barrier studies will be to apply new knowledge from proteomics and genomics to understanding the in vivo condition in physiology and pathology.

Animals↗

PubMed1980

[2 rules on the life cycle of trematodes in the ecosystem].

Rule I: The more advanced in its primary evolution a life cycle is, the greater the participation of the animal component in it is. Parallel to that, most often the direct effect of the non-living component of the ecosystem on the cycle running is decreased. Rule II: In the majority of secondarily evolved life cycles of trematodes the following occurred in comparison with their initial life cycle: a) either a decrease of the direct effect of the non-living component of the ecosystem on the cycle running; b) or a decrease of the participation of the animal component of the ecosystem in the cycle; c) or most often a decrease of both together.

Animals↗

PubMed2002

Analysis of mammalian brain architecture.

The mammalian brain is composed of several distinct parts which show different growth in evolution. Clark, Mitra and Wang found that the two main cortices of the brain - the cerebral (neo-) cortex and the cerebellum - show very different growth, and that whereas the ratio of neocortex volume to total brain volume increases with evolution, the cerebellum occupies a constant proportion in different species. Here I compare the surface areas of the two cortices in different species and find that these show a simple proportionality. Contrary to the conclusion drawn by Clark et al., this linear dependence of size implies that the two major cortices increase their computational capacity in parallel, suggesting a functional dependence of the one upon the other.

Animals↗

PubMedDate not supplied

[Comparative genetics and evolutionary morphology of symbiosis formed by plants with nitrogen-fixing microbes and endomycorrhizal fungi].

Results of comparative morphological and genetic analyses are described for two major plant-microbe endosymbioses: N2-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N2-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripheral in legumes but central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, whereas pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia that can be located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps composing four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. Origination of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g. inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). Analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N2-fixing symbioses. This evolution proceeded to a sufficient degree independently from the basic physiological function of nodules (symbiotic N2-fixation) and possibly a recruiting of plant genes that initially fulfilled various "non-symbiotic" functions into the genetic networks monitoring plant-microbe interactions.

Bacterial Physiological Phenomena↗

PubMed1997

The interplay between binding energy and catalysis in the evolution of a catalytic antibody.

Antibody catalysis provides an opportunity to examine the evolution of binding energy and its relation to catalytic function in a system that has many parallels with natural enzymes. Here we report such a study involving an antibody AZ-28 that catalyses an oxy-Cope rearrangement, a pericyclic reaction that belongs to a well studied and widely used class of reactions in organic chemistry. Immunization with transition state analogue 1 results in a germline-encoded antibody that catalyses the rearrangement of hexadiene 2 to aldehyde 3 with a rate approaching that of a related pericyclic reaction catalysed by the enzyme chorismate mutase. Affinity maturation gives antibody AZ-28, which has six amino acid substitutions, one of which results in a decrease in catalytic rate. To understand the relationship between binding and catalytic rate in this system we characterized a series of active-site mutants and determined the three-dimensional crystal structure of the complex of AZ-28 with the transition state analogue. This analysis indicates that the activation energy depends on a complex balance of several stereoelectronic effects which are controlled by an extensive network of binding interactions in the active site. Thus in this instance the combinatorial diversity of the immune system provided both an efficient catalyst for a reaction where no enzyme is known, as well as an opportunity to explore the mechanisms and evolution of biological catalysis.

Aldehydes↗

PubMed2002

Developmental genetics and evolution of symbiotic structures in nitrogen-fixing nodules and arbuscular mycorrhiza.

Genetic and molecular mechanisms of development are compared for two major plant-microbe endosymbioses: N(2)-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N(2)-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripherical in legumes or central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia and located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps comprising four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. The origin of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g., inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). An analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N(2)-fixing symbioses.

Actinomycetales↗

PubMed1977

[A comparative study of the difference in the evolution of refraction in the two eyes in patients with convergent strabismus (author's transl)].

In 329 cases of concomitant convergent strabismus, the alterations of refraction in the two eyes were compared over periods ranging from 10 to 30 years. In the group with unilateral strabismus (245 cases), a significant difference between the two eyes was observed. The change of refraction, if any, in the non-fixing eye (emmetropization or myopization) clearly lagged behind that in the fixing eye. This difference was particularly pronounced in the cases showing myopization. In the group with equivalent function of both eyes--alternating strabismus and cases with complete normalization, including functional normalization--a total of 84 cases, any emmetropization or myopization was found to run practically parallel in the two eyes. This shows that it is true of refraction, also that the genetically determined evolutive pattern may be modified by a functional abnormality.

Aging↗

PubMed1994

"Giant" tamarin from the Miocene of Colombia.

A nearly complete but badly crushed skull and mandible of Lagonimico conclucatus, gen. et sp. nov. is described from the La Victoria Formation, Colombia. The specimen is of middle Miocene age and dates from about 13.5 Ma. Features of the dentition suggest Lagonimico is a sister group to living Callitrichinae (Saguinus, Leontopithecus, Callithrix, and Cebuella). These features include having elongate compressed lower incisors, a reduced P2 lingual moiety, and the absence of upper molar hypocones. The new taxon also has autapomorphies, such as a relatively deep jaw, that rule it out of the direct ancestry of any living callitrichine. This animal is assigned to a new tribe of the callitrichine clade. The orbits of L. conclucatus are small, suggesting diurnal habits. Inflated, low-crowned (bunodont) cheek teeth with short, rounded shearing crests, as well as premolar simplification and M3 size reduction, suggest fruit- or gum-eating adaptations, as among many living callitrichines. Procumbent and slightly elongate lower incisors suggest this species could use its front teeth as a gouge, perhaps for harvesting tree gum. Estimates from jaw size suggest Lagonimico weighed about 1,200 g, about the size of Callicebus, the living titi monkey of South America. Judged from tooth size and jaw length, Lagonimico would have been slightly smaller than Callicebus, but still larger than Callimico or any living callitrichine. Therefore, many of the distinctive anatomical features of the callitrichine clade, sometimes explained by phyletic dwarfing, may have evolved at larger body size. Evolutionary size reduction may have occurred in parallel in callitrichines and Callimico.

Animals↗

PubMed1999

Almost pure I(alpha) cellulose in the cell wall of Glaucocystis.

Crystalline features of cellulose microfibrils in the cell walls of Glaucocystis (Glaucophyta) were studied by combined spectroscopy and diffraction techniques, and the results were compared with those of Oocystis (Chlorophyta). Although these algae are grouped into two different classes, by the composition of their chloroplasts for instance, their cell walls are quite similar in size and morphology. The most striking features of their cellulose crystallites are that they have the highest cellulose I(alpha) contents reported to date. In particular, the I(alpha) fraction of cellulose from Glaucocystis was found to be as high as 90% from (13)C NMR analysis. The mode of preferential orientation of cellulose crystallites in their cell walls is also interesting; equatorial 0.53-nm lattice planes were oriented parallel to the cell surface in the case of Glaucocystis, while the 0.62-nm planes were parallel to the Oocystis cell surface. Such a structural variation provides another link to the evolution of cellulose structure, biosynthesis, and its biocrystallization mechanism.

Cell Wall↗

PubMed2004

Molecular diagnosis in lymphoma.

The evolution of our ability to diagnose and classify lymphomas in an increasingly refined manner has paralleled the development of novel technologic approaches, with contemporary practice dependent upon the harnessing of a plethora of data that include microscopic, immunophenotypic, and genetic information. Although each of these components is currently indispensable, there is a purported progressive improvement in biologic objectivity as one maneuvers through these respective technologies. Accordingly, and in particular given the rapid pace at which key insights into lymphoma biology are emerging with microarray and other cutting-edge technologies, the role of molecular genetic testing is assuming even greater relevance. The ability to diagnose and classify lymphomas more accurately, precisely, and rationally by incorporating molecular data ought to lead to the development of more appropriate directed therapies.

Antigens, Neoplasm↗

PubMed1991

Mechanism of low serum sodium levels in Mediterranean spotted fever.

Prominent degrees of hyponatremia are detected in the severe forms of Mediterranean spotted fever and the intensity of this abnormality parallels the severity of the infectious process. In order to determine the incidence, degree and evolution of hyponatremia in 110 patients with Mediterranean spotted fever and to explore the feasible renal mechanism that could lead to this phenomenon, serum and urinary osmolality and levels of urea, creatinine and electrolytes were measured in samples obtained at selected points (up to the fifth week) in the course of the disease, and parameters of renal function were calculated. Mean serum sodium levels of 135.6 +/- 5.5 mEq/l were detected during the acute phase of the infection. At this point, 42 patients (38.2%) had sodium concentrations less than or equal to 135 mEq/l. After recovery, mean serum sodium values were 142.5 +/- 2.5. The analysis of the parameters of renal function indirectly rules out an inappropriate antidiuretic hormone secretion or renal failure as the cause of hyponatremia. As tubular incompetence to reabsorb sodium is also rejected in these patients, a shifting of sodium to the interstitial or intracellular space may account for the phenomenon.

Adolescent↗

PubMed1990

The complete structure of the rat VIP gene.

Vasoactive intestinal polypeptide (VIP) is a regulatory neuropeptide/neurotransmitter of 28 amino acids involved in a wide variety of physiological functions. Using synthetic oligodeoxynucleotide probes related to the rat VIP-cDNA, we have isolated and characterized the gene encoding the rat pre-pro VIP/PHI-27 and compared it to the human VIP gene. The rat VIP gene spanned 7400 base pairs, and contained 7 exons interrupted by 6 introns. 100% identity was found between the gene exons and the cDNA sequence. Differences in sizes of introns 2, 4 and 5 (shorter in the rat gene) are the reason for the shorter rat gene compared with the human gene of 8837 base pairs. Comparison of the genes in the two species showed a high homology in the exon sequences, 80-90% in exons 2, 4, 5, 6 and 30-50% in exons 1 and 7. In addition, the exon-intron junctions shared high identity between the genes. The rat untranslated exon 1 had little homology (30%) with human exon 1 and was 13 base pairs shorter. Interestingly, the 160 base pairs at the 5'-flanking region upstream of the cap-site share more than 75% identity between the two genes, including the exact position of TATA-boxes in positions -28, -145, -155, a cAMP-responsive element in position -80 and a CAAT sequence in position -127. The conservation of the 5'-flanking region of the VIP gene in parallel with the conservation of its coding exons emphasize the importance of these sequences during evolution.

Amino Acid Sequence↗

PubMed1979

Oestrogen-induced increase in uterine cGMP content: a true hormonal action?

The dependency of the oestrogen-induced increase in uterine cGMP content towards the cytosol-nuclear receptor system was investigated. The following observations were made: (1) With oestradiol-17 beta (E2-17 beta), U11-100A (UA) or CI-628 (CI) the cGMP response elicited in the uterus of immature rats followed a course that was parallel to (yet delayed by about 1 h from it) the known time-course evolution of nuclear occupancy by the complex formed by each compound with the oestrogen-receptor. (2) While a marked (about 2-fold) increase in uterine cGMP content was obtained with 0.1 microgram E2-17 beta, oestradiol-17 alpha (E2-17 alpha) given at the same dose had no effect on uterine cGMP. (3) The 2--3 h response to E2-17 beta (or to UA) could not be obtained in animals that had received a first injection of E2-17 beta, 2 h, or of one of the anti-oestrogens UA or tamoxifen, 20--22 h prior to the test injection of E2-17 beta. Those 3 treatments have in common that, at the time indicated, they create a state of depletion in the uterine cytosolic receptor population. The cGMP response to E2-17 beta was restored 20--22 h following a first injection of E2-17 beta. This time is known, in this case, to correspond to full replenishment of the cytosol-receptor population. In all those tests, the wet weight increase, measured in the same organs, behaves exactly as did the cGMP response. These results support the conclusion that the increase in uterine cGMP after oestrogen administration to the immature rat, represents a true hormonal action which, like other uterotrophic actions of oestrogens, involves binding of the hormone by the cytosol receptor.

Animals↗

PubMed2004

Structural delineation of the calcineurin-NFAT interaction and its parallels to PP1 targeting interactions.

Calcineurin is a phosphoprotein phosphatase that channels intracellular Ca signals into multiple biological pathways. Calcineurin is known to interact directly with its substrate nuclear factor of activated T cells (NFAT or NFATc), with other substrates, and with several targeting and scaffold proteins including AKAP79 and Cabin1/cain. The calcineurin-NFAT interaction depends on recognition of a PxIxIT sequence motif present in NFAT-family proteins and in certain other calcineurin-interacting proteins. Here, we define the structural basis for the interaction of calcineurin with NFAT and with other proteins possessing the PxIxIT motif. The calcineurin-PxIxIT contact has a direct parallel in the contact of protein phosphatase 1 with its regulatory proteins, suggesting that the evolution of these related phosphatases involved local remodelling of an ancestral docking site.

Amino Acid Sequence↗

PubMed2005

Organization of chromatin in the interphase mammalian cell.

The use of imaging techniques has become an essential tool in cell biology. In particular, advances in fluorescence microscopy and conventional transmission electron microscopy have had a major impact on our understanding of chromatin structure and function. In this review we attempt to chart the conceptual evolution of models describing the organization and function of chromatin in higher eukaryotic cells, in parallel with the advances in light and electron microscopy over the past 50 years. In the last decade alone, the application of energy filtered transmission electron microscopy (EFTEM), also referred to as electron spectroscopic imaging (ESI), has provided many new insights into the organization of chromatin in the interphase nucleus. Based on ESI imaging of chromatin in situ, we propose a 'lattice' model for the organization of chromatin in interphase cells. In this model, the chromatin fibers of 10 and 30nm diameter observed by ESI, produce a meshwork that accommodates an extensive and distributed interchromosomal (IC) space devoid of chromatin. The functional implications of this model for nuclear activity are discussed.

Animals↗

PubMed1997

Modern science and the explosion of new knowledge.

The technological evolution of mankind accelerated enormously after the institutionalization of science in the 19th century. In parallel with the vast number of beneficial effects derived from the scientific revolution, the explosion of new knowledge and its centralization in only a few countries has generated a number of complex situations that present major challenges for the modern science. These include the asymmetrical distribution in the planet of young people and science, the super-specialization derived from the information overload and the difficulties in teaching the vast amount of new knowledge generated each year by science.

Journal Article↗