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PubMed2006

Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication.

It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.

Amino Acid Sequence↗

PubMed2006

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.

We recently used computational protein design to create an extremely stable, globular protein, Top7, with a sequence and fold not observed previously in nature. Since Top7 was created in the absence of genetic selection, it provides a rare opportunity to investigate aspects of the cellular protein production and surveillance machinery that are subject to natural selection. Here we show that a portion of the Top7 protein corresponding to the final 49 C-terminal residues is efficiently mis-translated and accumulates at high levels in Escherichia coli. We used circular dichroism, size-exclusion chromatography, small-angle X-ray scattering, analytical ultra-centrifugation, and NMR spectroscopy to show that the resulting C-terminal fragment (CFr) protein adopts a compact, extremely stable, homo-dimeric structure. Based on the solution structure, we engineered an even more stable variant of CFr by disulfide-induced covalent circularisation that should be an excellent platform for design of novel functions. The accumulation of high levels of CFr exposes the high error rate of the protein translation machinery. The rarity of correspondingly stable fragments in natural proteins coupled with the observation that high quality ribosome binding sites are found to occur within E. coli protein-coding regions significantly less often than expected by random chance implies a stringent evolutionary pressure against protein sub-fragments that can independently fold into stable structures. The symmetric self-association between two identical mis-translated CFr sub-domains to generate an extremely stable structure parallels a mechanism for natural protein-fold evolution by modular recombination of protein sub-structures.

Amino Acid Sequence↗

PubMed2005

Co-evolution of X-chromosome inactivation and imprinting in mammals.

Recent studies have revealed mechanistic parallels between imprinted X-chromosome inactivation and autosomal imprinting. We suggest that neither mechanism was present in ancestral egg-laying mammals, and that both arose when the evolution of the placenta exerted selective pressure to imprint growth-related genes. We also propose that non-coding RNAs and histone modifications were adopted for the imprinting of growth suppressors on the X chromosome and on autosomes. This provides a unified hypothesis for the evolution of X-chromosome inactivation and imprinting.

Animals↗

PubMed1989

Evolution and extinction in the marine realm: some constraints imposed by phytoplankton.

The organic and mineralized remains of planktonic algae provide a rich record of microplankton evolution extending over nearly half of the preserved geological record. In general, Phanerozoic patterns of phytoplankton radiation and extinction parallel those documented for skeletonized marine invertebrates, both augmenting and constraining thought about evolution in the oceans. Rapidly increasing knowledge of Proterozoic plankton is making possible the recognition of additional episodes of diversification and extinction that antedate the Ediacaran radiation of macroscopic animals. In contrast to earlier phytoplankton history, the late Mesozoic and Cainozoic record is documented in sufficient detail to constrain theories of mass extinction in more than a general way. Broad patterns of diversity change in planktonic algae show similarities across the Cretaceous-Tertiary and Eocene-Oligocene boundaries, but detailed comparisons of origination and extinction rates in calcareous nannoplankton, as well as other algae and skeletonized protozoans, suggest that the two episodes were quite distinct. Common causation appears unlikely, casting doubt on monolithic theories of mass extinction, whether periodic or not. Studies of mass extinction highlight a broader class of insights that paleontologists can contribute to evolutionary biology: the evaluation of evolutionary change in the context of evolving Earth-surface environments.

Biological Evolution↗

PubMed2001

The natural history of protein domains.

Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus' Systema Naturae, the classification of species. With such a hierarchy in mind, we discuss the evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains. We also discuss when and how analysis of domains can be used to understand details of protein function. Unconventional features of domain evolution such as intragenomic competition, domain insertion, horizontal gene transfer, and convergent evolution are seen as analogs of organismal evolutionary events. These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology.

Animals↗

PubMed2005

How to interpret a deterioration of split function?

OBJECTIVE: A drop of split renal function often constitutes a criterion for pyeloplasty in hydronephrosis since it is considered as representing deterioration of the affected kidney. The aim of this work was to determine, in a selected population of patients with a drop of split function of at least 5%, if the evolution of single kidney glomerular filtration rate (SKGFR) was parallel to the one of split renal function. METHODS: From a large data basis, we found retrospectively only 29 children (10 below and 19 above two years of age at first examination) having had at least two Tc-99m mertiatide (Tc-99m MAG3) renographic explorations for various urological diseases, with a decrease of split function of at least 5% between the two examinations. Evolution of split function was compared to evolution of SKGFR obtained by means of the combination of Tc-99m MAG3 split function and overall glomerular filtration rate as given by the chromium Cr 51 ethylenediamine tetraacetic acid (EDTA) clearance. RESULTS: For the group above two years of age, SKGFR increased or remained stable in 63% of the cases, while in the children less than 2 years of age, a decrease of SKGFR was never observed, according to the maturation of overall GFR in this age group. Thus, the decrease of split function was not necessarily associated with a similar decrease of SKGFR. CONCLUSION: In patients with unilateral or bilateral urological disorders, deterioration of split renal function does not necessary correspond to a loss of function of the affected kidney. SKGFR often modifies the interpretation of split function.

Chelating Agents↗

PubMed1997

Fragmented and scrambled mitochondrial ribosomal RNA coding regions among green algae: a model for their origin and evolution.

Mitochondrial ribosomal RNA coding regions in the only three green algal taxa investigated to date are fundamentally different in that they are continuous in Prototheca wickerhamii, but highly fragmented and scrambled in Chlamydomonas reinhardtii and Chlamydomonas eugametos. To gain more insight into the mode of evolution of fragmented and scrambled mitochondrial ribosomal RNA (rRNA) genes within the green algal group, this work (1) provides additional information on fragmentation patterns of mitochondrial small- and large-subunit (SSU and LSU) rRNAs that strongly supports the concept of a gradual increase in the extent of discontinuity of mitochondrial rRNAs among chlorophycean green algae and (2) reports the first example of fragmented and scrambled mitochondrial LSU rRNA coding regions in a green algal taxon outside the Chlamydomonas group. The present study (1) suggests that the scrambling of the mitochondrial rRNA coding regions may have occurred early in the evolution of fragmented and scrambled mitochondrial rRNA genes within the chlorophycean green algal group, most likely in parallel with the fragmentation events, (2) proposes recombination as a possible mechanism involved in the evolution of these mitochondrial rRNA genes, and (3) presents a hypothetical pathway for converting continuous mitochondrial rRNA genes into the highly fragmented and scrambled rRNA coding regions of Chlamydomonas through a series of recombinatorial events between short repeated sequences.

Animals↗

PubMed1999

Alcohol consumption and gender in the 20th century: the case of Switzerland.

Given the changes of gender roles in this century it is hardly justified to assume constant proportions of alcohol consumption for males and females. The purpose of the study was to reconstruct the consumption trends of males and females in Switzerland since the beginning of the 20th century. Cirrhosis mortality and survey data were used to disaggregate by sex the per capita alcohol consumption derived from sales data. The disaggregation of the per capita alcohol consumption based on liver cirrhosis mortality suggests that the evolution of alcohol consumption in Switzerland followed a parallel course for both sexes only until the 1930s. The low consumption during World War II and the evident increase until the beginning of the '60s seem to have resulted above all from the variations in consumption of beer by men. The decrease in total alcohol consumption observed since the '70s is also most probably due only to men; there is no indication of a decreasing consumption by women. The tendency of male and female consumption patterns to become more similar should be taken into account in the prevention of alcohol misuse.

Adult↗

PubMed1981

Light and immunoelectronmicroscopic study of Hodgkin's disease: evidence of immunoglobulin synthesis by tumor cells.

The direct immunoperoxidase technique with peroxidase-conjugated F(ab')2 fragments was used at the light and electron microscopic levels to identify intracytoplasmic immunoglobulin (CIg) components in malignant cells of Hodgkin's disease. In each of the 27 cases studied, Hodgkin and Reed-Sternberg cells contained either IgG or IgM, with both light chains often present simultaneously. The number of IgG-positive malignant cells was inversely related to changes in the lymphoid compartment, as defined by the Rye grading system. The evolution from lymphocytic predominance to lymphocytic depletion was paralleled by a decrease of IgM-positive cells and by a substantial increase (to exclusiveness) of IgG-containing cells. These immunoelectronmicroscopic studies disclosed definite morphologic evidence of CIg synthesis by Hodgkin, Reed-Sternberg and lacunar cells. The immunoglobulin components were also synthesized by lymphoid B cells at different levels of modulation. Immunoglobulin synthesis by malignant cells was localized in perinuclear zone, on free cytoplasmic ribosomes and profiles of rough endoplasmic reticulum. The results of this joint light and electron microscopic study support the view that Hodgkin, Reed-Sternberg and lacunar cells belong to the B-cell compartment within Hodgkin's disease.

B-Lymphocytes↗

PubMed1987

Modification of the properties of S2 state in photosynthetic O2-evolving center by replacement of chloride with other anions.

Properties of the S2 state formed in photosystem II membranes in which Cl- had been replaced by various anions were investigated by means of thermoluminescence measurements and low temperature EPR spectroscopy. The Br--substituted membranes showed the normal thermoluminescence B-band arising from S2Q-B charge recombination, whereas the SO2-4-, F--, CH3COO--, and NO-3-substituted membranes showed modified B-bands with variously upshifted peak temperatures. The extent of the peak temperature upshift varied in parallel with the extent of inhibition of O2 evolution depending on the anion species. A normal EPR S2 multiline signal was induced in Br--substituted membranes, but its amplitude was reduced to less than 10% in F--, NO-3-, CH3COO--, and SO2-4-substituted membranes, In contrast, the g = 4.1 signal from S2 was markedly enhanced in F-- and NO-3-substituted membranes, not much affected in CH3COO-- and SO2-4-substituted membranes, and decreased to 70% in Br--substituted membranes. Based on these data, the effect of various types of S2 modification on the O2-evolving activity was discussed. It was suggested that anions have an important role in regulating the interaction between the Mn atoms, and thereby adjust the redox properties of the S2 state to enable further transitions beyond S2.

Anions↗

PubMed2005

Dynamics of parietal neural activity during spatial cognitive processing.

Dynamic neural processing unrelated to changes in sensory input or motor output is likely to be a hallmark of cognitive operations. Here we show that neural representations of space in parietal cortex are dynamic while monkeys perform a spatial cognitive operation on a static visual stimulus. We recorded neural activity in area 7a during a visual maze task in which monkeys mentally followed a path without moving their eyes. We found that the direction of the followed path could be recovered from neuronal population activity. When the monkeys covertly processed a path that turned, the population representation of path direction shifted in the direction of the turn. This neural population dynamic took place during a period of unchanging visual input and showed characteristics of both serial and parallel processing. The data suggest that the dynamic evolution of parietal neuronal activity is associated with the progression of spatial cognitive operations.

Action Potentials↗

PubMed2000

Adaptive amplification: an inducible chromosomal instability mechanism.

Adaptive mutation is an induced response to environmental stress in which mutation rates rise, producing permanent genetic changes that can adapt cells to stress. This contrasts with neo-Darwinian views of genetic change rates blind to environmental conditions. DNA amplification is a flexible, reversible genomic change that has long been postulated to be adaptive. We report the discovery of adaptive amplification at the lac operon in Escherichia coli. Additionally, we find that adaptive amplification is separate from, and does not lead to, adaptive point mutation. This contradicts a prevailing alternative hypothesis whereby adaptive mutation is normal mutability in amplified DNA. Instead, adaptive mutation and amplification are parallel routes of inducible genetic instability allowing rapid evolution under stress, and escape from growth inhibition.

Base Pair Mismatch↗

PubMed1997

New CRRT systems: impact on dose delivery.

The evolution of technology and biomaterials has permitted a parallel development of renal replacement therapies in the acute, critically ill patient. From the original description of continuous arteriovenous hemofiltration, new techniques such as continuous venovenous hemofiltration, hemodiafiltration, and high flux dialysis have been developed and clinically used. A parallel improvement in efficiency has been achieved with urea daily clearances as high as 50 L or more. The use of special highly permeable dialyzers has also permitted an increase in the clearances of larger solutes, thus leading to significant removals of chemical substances involved in acute inflammation and sepsis. In this field, recent observations have suggested using hemofiltration with high volumes of fluid exchange. The hardware and software of the newer CRRT systems are key in achieving these results and in safely performing such challenging techniques.

Hemofiltration↗

PubMed1982

Ammonium ions enhance the flow through the pyruvate dehydrogenase in Ehrlich ascites tumor cells.

The flow through pyruvate dehydrogenase was assayed in glycolysing cells by the evolution of 14CO2 from [1-14C] pyruvate. Parallel incubations were carried out in high bicarbonate buffer (25 mM) and in bicarbonate-free buffer. The activation of the complex by NH+4 was only observed in high bicarbonate buffer, because the dilution of labelled CO2 in the presence of an excess of bicarbonate enables the quantitative determination of labelled CO2 evolved from pyruvate in the decarboxylase step. In the bicarbonate-free buffer the activation of the complex was not observed, because the 14CO2 evolved from pyruvate was consumed by biosynthetic processes inside the cell. On the contrary in isolated hepatocytes the NH+4 activation of the pyruvate dehydrogenase was observed in both buffers. In Ehrlich ascites cells, in common with other mammalian tissues, pyruvate dehydrogenase activity was found to be inversely correlated to the intramitochondrial ATP/ADP ratio.

Adenine Nucleotides↗

PubMed1999

Developmental expression and localization of glycogen synthase kinase-3beta in rat brain.

Glycogen synthase kinase (GSK)-3beta is a protein kinase in the wingless/wnt pathway and as such is involved in the regulation of growth and development of the neural tissue in Drosophila and in vertebrates. This enzyme is also abundantly expressed in the mammal adult brain, where it might play a role in the regulation of several substrates. The expression and the neuroanatomical distribution of GSK-3beta immunoreactivity in the rat brain from embryonic up to adult stages has been studied. GSK-3beta was expressed in the developing brain with the highest expression observed from 18 days of embryonic life up to 10 days of postnatal life. Its expression decreased thereafter and was lowest in the adult. GSK-3beta was strongly expressed in developing neurons but only weakly expressed in layers containing neuroblasts. In the adult and during development, GSK-3beta was detected in the pericarya and proximal part of dendrites. In the embryo, an intense GSK-3beta immunoreactivity was also observed in axonal tracts. This axonal immunoreactivity had markedly decreased by 10 days of postnatal life and was absent at 20 days of postnatal life and in the adult. No GSK-3beta immunoreactivity was detected in astrocytes. The GSK-3beta immunoreactivity was found in most brain regions, although significant local variations of GSK-3beta expression were observed. The developmental evolution of GSK-3beta compartmentalization in neurons parallels that of phosphorylated tau, a protein considered to be a physiological substrate for the kinase.

Animals↗

PubMed2005

Discovery and high-throughput screening of heteroleptic iridium complexes for photoinduced hydrogen production.

The catalytic process of photoinduced hydrogen generation via the reduction of water has been investigated. The use of parallel synthetic techniques has facilitated the synthesis of a 32 member library of heteroleptic iridium complexes that was screened, using high-throughput photophysical techniques, to identify six potential photosensitizers for use in catalytic photoinduced hydrogen production. A Pd/Ni thin film hydrogen selective sensor allowed for rapid quantification of hydrogen produced via illumination of aqueous systems of the photosensitizer, tris(2,2'-dipyridyl)dichlorocobalt ([Co(bpy)(3)]Cl(2)), and triethanolamine (a sacrificial reductant) with ultra-bright light emitting diodes (LEDs). The use of an 8-well parallel photoreactor expedited the investigation of the hydrogen evolution process and facilitated mechanistic studies. All six compounds investigated produced considerably more hydrogen than commonly utilized photosensitizers and had relative quantum efficiencies of hydrogen production up to 37 times greater than that of Ru(bpy)(3)(2+).

Journal Article↗

PubMed2001

Neurofibrillary tangles and tau phosphorylation.

Neurofibrillary tangles (NFTs) are a characteristic neuropathological lesion of Alzheimer's disease (AD). They are composed of a highly-phosphorylated form of the microtubule-associated protein tau. We are investigating the relationship between NFTs and microtubule stability and how tau phosphorylation and function is affected in transgenic models and by co-expression with beta-amyloid precursor protein and presenilins. In most NFT-bearing neurons, we observed a strong reduction in acetylated alpha-tubulin immunoreactivity (a marker of stable microtubules) and a reduction of the in situ hybridization signal for tubulin mRNA. In transfected cells, mutated tau forms (corresponding to tau mutations identified in familial forms of frontotemporal dementias linked to chromosome 17) were less efficient in their ability to sustain microtubule growth. These observations are consistent with the hypothesis that destabilization of the microtubule network is an important mechanism of cell dysfunction in Alzheimer's disease. The glycogen synthase kinase-3 beta (GSK-3 beta) generates many phosphorylated sites on tau. We performed a neuroanatomical study of GSK-3 beta distribution showing that developmental evolution of GSK-3 beta compartmentalization in neurons paralleled that of phosphorylated tau. Studies on transfected cells and on cultured neurons showed that GSK-3 beta activity controls tau phosphorylation and tau functional interaction with microtubules. Tau phosphorylation was not affected in neurons overexpressing beta-amyloid precursor protein. Transgenic mice expressing a human tau isoform and double transgenic animals for tau and mutated presenilin 1 have been generated; a somatodendritic accumulation of phosphorylated transgenic tau proteins, as observed in the pretangle stage in AD, has been observed but NFTs were not found, suggesting that additional factors might be necessary to induce their formation.

Alzheimer Disease↗

PubMed2002

Tuberous sclerosis complex tumor suppressor-mediated S6 kinase inhibition by phosphatidylinositide-3-OH kinase is mTOR independent.

The evolution of mitogenic pathways has led to the parallel requirement for negative control mechanisms, which prevent aberrant growth and the development of cancer. Principally, such negative control mechanisms are represented by tumor suppressor genes, which normally act to constrain cell proliferation (Macleod, K. 2000. Curr. Opin. Genet. Dev. 10:81-93). Tuberous sclerosis complex (TSC) is an autosomal-dominant genetic disorder, characterized by mutations in either TSC1 or TSC2, whose gene products hamartin (TSC1) and tuberin (TSC2) constitute a putative tumor suppressor complex (TSC1-2; van Slegtenhorst, M., M. Nellist, B. Nagelkerken, J. Cheadle, R. Snell, A. van den Ouweland, A. Reuser, J. Sampson, D. Halley, and P. van der Sluijs. 1998. Hum. Mol. Genet. 7:1053-1057). Little is known with regard to the oncogenic target of TSC1-2, however recent genetic studies in Drosophila have shown that S6 kinase (S6K) is epistatically dominant to TSC1-2 (Tapon, N., N. Ito, B.J. Dickson, J.E. Treisman, and I.K. Hariharan. 2001. Cell. 105:345-355; Potter, C.J., H. Huang, and T. Xu. 2001. Cell. 105:357-368). Here we show that loss of TSC2 function in mammalian cells leads to constitutive S6K1 activation, whereas ectopic expression of TSC1-2 blocks this response. Although activation of wild-type S6K1 and cell proliferation in TSC2-deficient cells is dependent on the mammalian target of rapamycin (mTOR), by using an S6K1 variant (GST-DeltaC-S6K1), which is uncoupled from mTOR signaling, we demonstrate that TSC1-2 does not inhibit S6K1 via mTOR. Instead, we show by using wortmannin and dominant interfering alleles of phosphatidylinositide-3-OH kinase (PI3K) that increased S6K1 activation is contingent upon the suppression of TSC2 function by PI3K in normal cells and is PI3K independent in TSC2-deficient cells.

Adaptor Proteins, Signal Transducing↗