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PubMed1975

[Neo and postnatal development of the cerebral cortex in mice. Ultrastructural study].

Maturation in the Purkinje cell (Pk) of the cerebellar cortex of developing mice (from birth up to weaning) was investigated by structural and especially ultrastructural studies. In comparison to the adult neuron, four developmental stages were identified by studying selective morphological features (shape and size of the Pk, neuronal environment) as well as specific characteristics of neuronal constituants, particularly the "nucleus-ribosome system". The stages are: early, intermediate and late neuroblasts and young neuron. The neuronogenesis of the Purkinje cell can be summarized as follows: (a) the nuclear maturation occurs early in the development and markedly preceeds that of several organelles in the perikaryon; (b) the cytoplasmic maturation extends gradually until the young neuron state was reached. Some structures such as the granular mass and the "spotted body" in the nucleus, the nuclear envelop including its two membranes, and the ribosomal components either free or attached to the Endoplasmic Reticulum seem to exert an important role during neuronal development. Maturation processes in the Purkinje cell are generally similar in both mouse and rat and, except for some morphological and/or chronological variables, comparable in others developing nerve cells. This model of neuronal maturation is used alone or in comparison to another model of neuro-behavioral evolution which was established concommitantly. Both of these models reveal to be very useful for the evaluation of the effects induced in the developing animal following the administration of neuropsychotropic drugs such as Hallucinogens and Narcotics.

Animals↗
PubMed2005

Molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria.

We report the cloning and functional characterization of an endo-beta-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. This is the first gene of this type from any nematode species. We show that a similar cDNA is also present in another closely related species B. mucronatus, but that similar sequences are not present in any other nematode studied to date. The B. xylophilus gene is expressed solely in the oesophageal gland cells of the nematode and the protein is present in the nematode's secretions. The deduced amino acid sequence of the gene is very similar to glycosyl hydrolase family 16 proteins. The recombinant protein, expressed in Escherichia coli, preferentially hydrolysed the beta-1,3-glucan laminarin, and had very low levels of activity on beta-1,3-1,4-glucan, lichenan and barley beta-glucan. Laminarin was degraded in an endoglucanase mode by the enzyme. The optimal temperature and pH for activity of the recombinant enzyme were 65 degrees C and pH 4.9. The protein is probably important in allowing the nematodes to feed on fungi. Sequence comparisons suggest that the gene encoding the endo-beta-1,3-glucanase was acquired by horizontal gene transfer from bacteria. B. xylophilus therefore contains genes that have been acquired by this process from both bacteria and fungi. These findings support the idea that multiple independent horizontal gene transfer events have helped in shaping the evolution of several different life strategies in nematodes.

Amino Acid Sequence↗
PubMed2006

An unusual mode of concerted evolution of the EGF-TM7 receptor chimera EMR2.

The epidermal growth factor (EGF)-TM7 receptors CD97, EMR1, EMR2, EMR3, and EMR4 form a group of adhesion class heptahelical molecules predominantly expressed by cells of the immune system. These receptors bind cellular ligands through EGF-like domains, localized N-terminal to a large extracellular region. Remarkably, EMR2 possesses a chimeric structure with a seven-span transmembrane (TM7) region most related to EMR3 and an EGF domain region nearly identical to CD97. By comparing EGF-TM7 receptors in primates and dogs, we identified an intriguing pattern of concerted evolution, apparently mediated by gene conversion, among EMR2 and the oppositely orientated and physically adjacent genes CD97 and EMR3. This concerted evolution has continuously maintained the chimeric structure of EMR2 since early mammal radiation. Most highly conserved between EMR2 and CD97 is the fourth EGF domain, which mediates binding to chondroitin sulfate, a ligand specificity shared by both receptors. Another ligand, CD55, is bound effectively only by CD97. We show that different molecular mechanisms (mutations vs. alternative splicing) prevent CD55 binding by EMR2 in hominoids. Our findings illustrate how various and partially opposing evolutionary events have shaped the structure and ligand specificity of a modern mammalian gene family.

Amino Acid Sequence↗
PubMed2003

Memory inflation: continuous accumulation of antiviral CD8+ T cells over time.

CD8+ T lymphocytes play an important role in the control of intracellular pathogens during both acute and persistent infections. This is particularly true in the case of persistent herpesviruses such as human CMV, which are typified by large virus-specific CD8+ T cell populations during viral latency. To understand the origin of these populations and the factors shaping them over time, we investigated the CD8+ T cell response after murine CMV (MCMV) infection. The kinetics of the acute response were characterized by rapid expansion of activated T cells, followed by a contraction phase. Thereafter, we observed a striking pattern, where MCMV-specific memory CD8+ T cells steadily accumulated over time, with 20% of all CD8+ T cells at 1 year specific for one MCMV epitope. Accumulation of MCMV-specific CD8+ T lymphocytes was seen in all organs tested and was associated with continuous activation of specific CD8+ T lymphocytes, primarily within lymph nodes. The pattern of accumulation was observed in only two of five epitopes tested, and was accompanied by a gradual restriction in usage of the variable region of the TCR beta-chain over time. This novel pattern of a virus-specific CD8+ T cell response suggests that continuous or repetitive exposure to Ag can slowly mold memory T cell populations over time. This may be relevant for understanding the evolution of the large human CMV-specific CD8+ T cell populations seen in humans.

Animals↗
PubMed2001

Phylogenetic relationships among rodent Eimeria species determined by plastid ORF470 and nuclear 18S rDNA sequences.

Phylogenetic analyses for 10 rodent Eimeria species from different host genera based on plastid ORF470 and nuclear 18S rDNA sequences were done to infer the evolutionary relationships of these rodent Eimeria species and their correlation to morphology and host specificity. The phylogenies based on both data sets clearly grouped the 10 rodent Eimeria species into two major lineages, which reflect more their morphological differences than host specificity. Species in lineage A have spheroidal to subspheroidal sporulated oocysts, are similar in size (18-29 x 17-23; xbar = 22 x 20 microm), have an oocyst residuum and one-two polar granules; these include Eimeria albigulae (Neotoma), Eimeria arizonensis (Peromyscus, Reithrodontomys), Eimeria onychomysis (Onychomys) and Eimeria reedi (Perognathus). Species in lineage B, including Eimeria falciformis (Mus), Eimeria langebarteli (Reithrodontomys), Eimeria nieschulzi (Rattus), Eimeria papillata (Mus), Eimeria separata (Rattus) and Eimeria sevilletensis (Onychomys) have different shapes (ovoid, ellipsoid, elongated ellipsoid, etc.), differ greatly in size (10-27 x 9-24; xbar = 19 x 16 microm) and all lack an oocyst residuum. Thus, The oocyst residuum was the most determinant feature that differentiated the two lineages. The accession numbers of ORF470 of E. albigulae, E. arizonensis, E. falciformis, E. nieschulzi, E. onychomysis, E. papillata, E. reedi, E. separata, E. sevilletensis, E. langebarteli are AF311630-AF311639 and 18S rDNA of E. langebarteli, E. papillata, E. reedi, E. separata, E. sevilletensis are AF311640-AF311644.

Animals↗
PubMedDate not supplied

[The modelling of the initiation of genetic damages from low doses of ionizing radiation in eukaryotic cells based on the concept of the existence of evolutionary reserve cells].

The model predicting quantitatively a dose response for genetic lesions in low dose range is presented. The model is based on the concept of programmed initiation of the genetic damage in the subpopulation of specific cells of "evolutionary reserve" (CER). It is demonstrated that complex shape of dose-response curve results from superposition of processes in different subpopulations within exposed cell population, mainly in CER. The model allows us to explain the minimum observed in the dose-response curve at doses corresponding to one (on the average) event of energy deposition per CER with spontaneous aberrations. The equation for dose-response function for dicentrics describes satisfactory experimental observations. Advantage of proposed equation is that it does not deal with free parameters to fit the data. They are determined independently by using known physical and biological characteristics. The data described allow us to suggest that sensitive body for CER is a cell as a whole. Probably, programmed initiation of genetic lesions in CER requires both two hits at cell membrane and radiation effect on cell nucleus.

Animals↗
PubMed2000

Molecular characterization of human tensin.

Tensin is a focal-adhesion molecule that binds to actin filaments and interacts with phosphotyrosine-containing proteins. To analyse tensin's function in mammals, we have cloned tensin cDNAs from human and cow. The isolated approx. 7.7-kb human cDNA contains an open reading frame encoding 1735 amino acid residues. The amino acid sequence of human tensin shares 60% identity with chicken tensin, and contains all the structural features described previously in chicken tensin. This includes the actin-binding domains, the Src homology domain 2, and the region similar to a tumour suppressor, PTEN. Two major differences between human and chicken tensin are (i) the lack of the first 54 residues present in chicken tensin, and (ii) the addition of 34- and 38-residue inserts in human and bovine tensin. In addition, our interspecies sequencing data have uncovered the presence of a glutamine/CAG repeat that appears to have expanded in the course of evolution. Northern-blot analysis reveals a 10-kb message in most of the human tissues examined. An additional 9-kb message is detected in heart and skeletal muscles. The molecular mass predicted from the human cDNA is 185 kDa, although both endogenous and recombinant human tensin migrate as 220-kDa proteins on SDS/PAGE. The discrepancy is due to the unusually low electrophoretic mobility of the central region of the tensin polypeptide (residues 306-981). A survey of human prostate and breast cancer cell lines by Western-blot analysis shows a lack of tensin expression in most cancer cell lines, whereas these lines express considerable amounts of focal-adhesion molecules such as talin and focal-adhesion kinase. Finally, tensin is rapidly cleaved by a focal-adhesion protease, calpain II. Incubation of cells with a calpain inhibitor, MDL, prevented tensin cleavage and induced morphological change in these cells, suggesting that cleavage of tensin and other focal-adhesion constituents by calpain disrupts maintenance of normal cell shape.

3T3 Cells↗
PubMed2026

Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.

Understanding how lineages diversify despite persistent ancestral polymorphism and recurrent gene flow remains a central challenge in evolutionary biology. Juniperus distributed across the Qinghai-Tibet Plateau provide an ideal system for addressing this question because repeated geological uplift and climatic oscillations have likely promoted cycles of lineage divergence, range shifts, and secondary contact. Here, we combined approximately 1.08 million genome-wide SNPs from 164 individuals representing thirteen Juniperus lineages with phylogenomic datasets comprising 3,381 nuclear single-copy genes and nearly complete plastomes. We detected extensive phylogenomic discordance and cytonuclear incongruence across genomic datasets. Topology weighting, coalescent simulations, quartet-based tests, and analyses of gene flow and reticulation collectively support the interpretation that these patterns were shaped by the combined effects of prolonged incomplete lineage sorting and gene flow during lineage diversification. Ecological niche analyses further provide a spatial and climatic context in which environmentally similar lineages may have had greater opportunities for secondary contact during historical range shifts. Collectively, our results reveal that the evolutionary history of Qinghai-Tibet Plateau Juniperus is characterized by reticulate diversification rather than strictly bifurcating evolution, and demonstrate how genome-wide discordance can provide biological insights into the evolutionary processes underlying lineage diversification.

Gene Flow↗
PubMed2003

On the evolution of structure in aminoacyl-tRNA synthetases.

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of the tRNA synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an RNA world to the modern world dominated by protein-enzymes. We present a structure-based phylogeny of the aminoacyl-tRNA synthetases. By using structural alignments of all of the aminoacyl-tRNA synthetases of known structure in combination with a new measure of structural homology, we have reconstructed the evolutionary history of these proteins. In order to derive unbiased statistics from the structural alignments, we introduce a multidimensional QR factorization which produces a nonredundant set of structures. Since protein structure is more highly conserved than protein sequence, this study has allowed us to glimpse the evolution of protein structure that predates the root of the universal phylogenetic tree. The extensive sequence-based phylogenetic analysis of the tRNA synthetases (Woese et al., Microbiol. Mol. Biol. Rev. 64:202-236, 2000) has further enabled us to reconstruct the complete evolutionary profile of these proteins and to make connections between major evolutionary events and the resulting changes in protein shape. We also discuss the effect of functional specificity on protein shape over the complex evolutionary course of the tRNA synthetases.

Amino Acid Sequence↗
PubMed2026

Experimental evolution reveals genetic routes for adaptive loss of the antibacterial type VI secretion system.

The type VI secretion system (T6SS) is a contractile nanomachine used by Gram-negative bacteria to deliver effector proteins into target cells, contributing to both interbacterial competition and pathogenesis. Although T6SS gene clusters are present in recently isolated commensal and pathogenic Escherichia coli strains, they are absent from classical laboratory strains that have been propagated for decades in pure cultures, suggesting that T6SS can be lost in the absence of competition. Here, we combined experimental evolution with whole-genome sequencing to track the fate of the enteroaggregative Escherichia coli (EAEC) Sci1 T6SS during competition with either T6SS-susceptible or T6SS-immune bacteria. After ∼640 generations, T6SS activity was largely maintained during competition with T6SS-susceptible bacteria, whereas ∼90% of clones evolved with T6SS-immune bacteria lost or attenuated T6SS activity through diverse mutations within the sci1 promoter, essential T6SS structural genes, or the rfaH transcriptional antiterminator. We identified two RfaH-binding ops elements within the sci1 cluster, revealing antitermination as a regulatory element of EAEC T6SS transcription, which is conserved among Enterobacteriaceae. Our findings highlight how experimental evolution can reveal the selective forces shaping T6SS maintenance and identify new regulatory components controlling its activity.

Journal Article↗
PubMed1978

Quasi-elastic light scattering from migrating chemotactic bands of Escherichia coli.

We report the observation of migrating chemotactic bands of Escherichia coli in a buffer solution. The temporal development of the bacterial density profile is observed by the scattered light intensity as the band migrates through a stationary laser beam. We have made a preliminary analysis of the observed band profile with help of the Keller-Segel theory. The model accounts for only some aspects of the observed time evolution of the density profile. The microscopic motility characteristics of the E. coli in the band are simultaneously studied by photon correlation. The measured correlation functions are analyzed to obtain the spatial dependence of the half-width within the band. A simple analytical model is proposed to account for the contribution of the twiddle motion to the correlation function. By analyzing the correlation function as a superposition of straight-line and twiddle motions, we obtain a satisfactory agreement between the theory and the measured angular dependence of the line shape. As a consequence we are able to extract a parameter beta, which measures the average fraction of twiddling bacteria in the center of the band at a given time.

Cell Movement↗
PubMed2006

Signal dynamics in Sonic hedgehog tissue patterning.

During development, secreted signaling factors, called morphogens, instruct cells to adopt specific mature phenotypes. However, the mechanisms that morphogen systems employ to establish a precise concentration gradient for patterning tissue architecture are highly complex and are typically analyzed only at long times after secretion (i.e. steady state). We have developed a theoretical model that analyzes dynamically how the intricate transport and signal transduction mechanisms of a model morphogen, Sonic hedgehog (Shh), cooperate in modular fashion to regulate tissue patterning in the neural tube. Consistent with numerous recent studies, the model elucidates how the dynamics of gradient formation can be a key determinant of cell response. In addition, this work yields several novel insights into how different transport mechanisms or ;modules' control pattern formation. The model predicts that slowing the transport of a morphogen, such as by lipid modification of the ligand Shh, by ligand binding to proteoglycans, or by the moderate upregulation of dedicated transport molecules like Dispatched, can actually increase the signaling range of the morphogen by concentrating it near the secretion source. Furthermore, several transcriptional targets of Shh, such as Patched and Hedgehog-interacting protein, significantly limit its signaling range by slowing transport and promoting ligand degradation. This modeling approach elucidates how individual modular elements that operate dynamically at various times during patterning can shape a tissue pattern.

Animals↗
PubMed1984

The cell in the field of gravity and the centrifugal field.

It appears that the literature and logic that the earth's gravity has been one factor in the limitation of cell size, as well as being an important influence on the diversity of cell types and sizes throughout biological evolution. Analysis of the literature reveals an inverse relationship between the centrifugal force needed for intracellular stratification and cell size. The cells studied ranged in size from approximately 1 mm (amphibian eggs, Pelomyxa) to 0.01 mm (erythrocyte, lymphocyte), and g-forces ranged from about 100 g to 100 000 g respectively. Stratification within cell nuclei and organelles requires even greater forces, presumably because of their smaller size. Extrapolation from centrifugal forces to the force of gravity, and from the full stratification to the initial sedimentation of cell parts suggests a hypothesis for the evolutionary survival and existence of cells in the field of gravity. Average cell size results, in part, from the physical equilibrium between the destructive influence of the force of gravity and the protective role of diffusion and the cytoskeleton. At increased forces of gravity the cell size would thus be decreased, whereas at lower gravitational forces and weightlessness cell size would be expected to increase. Mechanisms of protection of giant cells against internal sedimentation are based on protoplasmic motion, thin and elongated shape of the cell body, increased cytoplasmic viscosity, and a reduced range of specific gravity of cell components, relative to the ground-plasm. The nucleolus, due to its higher density, is considered as a possible trigger of mitosis.

Animals↗
PubMed2006

Population bottlenecks in quasispecies dynamics.

The characteristics of natural populations result from different stochastic and deterministic processes that include reproduction with error, selection, and genetic drift. In particular, population fluctuations constitute a stochastic process that may play a very relevant role in shaping the structure of populations. For example, it is expected that small asexual populations will accumulate mutations at a higher rate than larger ones. As a consequence, in any population the fixation of mutations is accelerated when environmental conditions cause population bottlenecks. Bottlenecks have been relatively frequent in the history of life and it is generally accepted that they are highly relevant for speciation. Although population bottlenecks can occur in any species, their effects are more noticeable in organisms that form large and heterogeneous populations, such as RNA viral quasispecies. Bottlenecks can also positively select and isolate particles that still keep the ability to infect cells from a disorganized population created by crossing the error threshold.

Base Sequence↗
PubMed2003

Detecting adaptive molecular evolution: additional tools for the parasitologist.

It is likely that infectious diseases have shaped the evolution of many vertebrates, including humans. The etiological agents of disease continuously strive to evade the immune response and the immune response, in turn, seeks to change in order to keep pace with the invaders. This 'arms race' may be characterized by the selection for new variant hosts and new variant parasites. Here we discuss the utility of phylogenetics in detecting adaptive evolution at the molecular level and, for illustration, we concentrate on a family of surface-exposed proteins (the rifins) found in the recently sequenced genome of Plasmodium falciparum. We employed phylogeny-based methods in order to characterize adaptive evolution in these proteins. We found evidence for adaptive evolution in many of the amino acid residues in at least one lineage. These results indicate that there has been selection for those strains of P. falciparum that contain the new genotypes. These proteins are likely to be of great importance for the survival of the parasite. Studies of the interaction of these proteins with the antigen-presenting cells of the immune system should lead to a better understanding of malarial infection.

Adaptation, Physiological↗
PubMed1985

[Metabolism of phosphate-limited Streptomyces cultures. III. The ambivalent effect of phosphates in nourseothricin-producing cultures of Streptomyces noursei JA 3890b].

A common condition in the evolution of organisms and their metabolism seems to be a latent lack of available phosphate in the natural environment. Accordingly, the phosphate dependent metabolisms of the soil-living streptomycetes should be stamped by lack of phosphate, too. The biosynthesis of the streptothricin antibiotic nourseothricin by Streptomyces noursei 3890b is initiated by limitation of soluble phosphate in the fermentation medium. At the other side is shown that a certain rate of feeding of phosphate during the fermentation increases the nourseothricin biosynthesis. An ambivalente role of phosphate on the secondary metabolite biosynthesis is stated. The limitation of phosphate leads to a special physiological state of the producer, characterized by secondary product formation and dephosphorylating activities in cells. This state is temporally stabilized by the presence of a sufficient phosphate supply, realized by enzymatic hydrolysis of complex phosphate-containing substrates or by a direct feeding of inorganic phosphate to the fermentations. The occurrence of different physiological states in respect to the phosphate-dependent metabolism is described by S-shaped functions of the relationship between specific growth rate and the phosphate concentration in the medium. The special behaviour of Streptomyces noursei cells at phosphate limitation is discussed to be the result of the dephosphorylating activities in cells, hydrolyzing phosphoester-bonds of regulatory metabolites as well as energy-rich compounds.

Anti-Bacterial Agents↗
PubMed2006

To be or not to be B7.

The activation of lymphocytes and development of adaptive immune responses is initiated by the engagement of TCRs by antigenic peptide-MHC complexes and shaped at the clonal level by both positive and negative costimulatory signals. The B7 family members are involved at several stages in this process. In this issue of the JCI, Vogt et al. show that the B7 family-related protein V-set and Ig domain-containing 4 (VSIG4) can act as an inhibitor of T cell activation (see the related article beginning on page 2817). Intriguingly, the same molecule was recently independently identified as a complement receptor of the Ig superfamily (CRIg) and was convincingly demonstrated to be a receptor for complement component 3 fragments. These findings raise interesting questions regarding the physiological roles and mechanisms of action of this molecule. Identification of dual functions of this molecule provides an additional level of complexity in T cell costimulation.

Animals↗
PubMed2026

Methylation profiling of normal tissue adjacent to breast tumors reveals two distinct groups with divergent tumor microenvironment features.

We previously identified diverse genetic evolutionary patterns in whole-genome sequencing of paired normal tissue adjacent to tumor (NAT) and tumor tissues from Hong Kong breast cancer (HKBC) patients. Here, we investigated whether DNA methylation (DNAm) contributes to NAT heterogeneity and shapes the tumor microenvironment (TME). Genome-wide DNAm profiling was performed on paired NAT and tumor tissues from 188 HKBC patients using the Infinium 850 K array. RNA-seq data were available for 76 NATs and 177 tumors. Cellular composition was inferred using MethylCIBERSORT, CIBERSORTx, and EpiDISH, and histopathologic features were assessed on 115 H&E-stained sections. Unsupervised clustering identified two distinct NAT subtypes with divergent TME characteristics. Cluster 1 (N = 139) showed higher epithelial and fibroblast content and enrichment of estrogen response pathways. Cluster 2 (N = 49) exhibited an immune-metabolic phenotype characterized by increased fat and immune cells, stromal disruption, inflammatory pathway activation, and greater macrophage infiltration. Cluster 2 patients also demonstrated significantly younger epigenetic age estimated using multiple epigenetic clocks. These DNAm-defined NAT subtypes and associated TME features were validated in 97 NAT samples from TCGA breast cancer patients. Overall, our findings identify DNAm-driven NAT heterogeneity with distinct TME landscapes, providing new insights into field cancerization and tumor evolution in breast cancer.

Journal Article↗