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At least 19 recordsLinked to original sources
PubMed2005

The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).

Archaea↗
PubMed1998

Conserved linkage groups associated with large-scale chromosomal rearrangements between Old World and New World Leishmania genomes.

The genus Leishmania can be taxonomically separated into three main groups: the Old World subgenus L. (Leishmania), the New World subgenus L. (Leishmania) and the New World subgenus L. (Viannia). The haploid genome of Old World Leishmania species has been shown to contain 36 chromosomes defined as physical linkage groups; the latter were found entirely conserved across species. In the present study, we tried to verify whether this conservation of the genome structure extends to the New World species of Leishmania. 300 loci were explored by hybridization on optimized pulsed field gel electrophoresis separations of the chromosomes of polymorphic strains of the six main pathogenic Leishmania species of the New World. When comparing these New World karyotypes with their Old World counterparts, 32 out of 36 linkage groups were found conserved among all species. Four chromosomal rearrangements were found. All species belonging to the L. (Viannia) subgenus were characterized by the presence (i) of a short sequence exchange between chromosomes 26 and 35, and (ii) more importantly, of a fused version of chromosomes 20 and 34 which are separated in all Old World species. 69 additional markers were isolated from a plasmid library specifically constructed from the rearranged chromosomes 20+34 in an attempt to detect mechanisms other than a fusion or breakage: only two markers out of 40 did not belong to the linkage groups 20 and 34. On the other hand, all strains belonging to the New World subgenus L. (Leishmania) were characterized by two different chromosomal rearrangements of the same type (fusion/breakage) as above as compared with Old World species: chromosomes 8+29 and 20+36. Consequently, these two groups of species have 35 and 34 heterologous chromosomes, respectively. Overall, these results show that large-scale chromosomal rearrangements occurred during the evolution of the genus Leishmania, and that the three main groups of pathogenic species are characterized by different chromosome numbers. Nevertheless, translocations seem particularly rare, and the conservation of the major linkage groups should be an essential feature for the compared genetics between species of this parasite.

Animals↗
PubMed2004

A congested football calendar and the wellbeing of players: correlation between match exposure of European footballers before the World Cup 2002 and their injuries and performances during that World Cup.

OBJECTIVES: To investigate the correlation between exposure of footballers in European clubs to match play in the months before the World Cup 2002 and their injuries and performances during that World Cup. METHODS: The team doctors at 11 of the best football clubs in Europe prospectively recorded players' exposure and injuries during the 2001-2002 season (July 2001-May 2002). Sixty five players participated in the World Cup in Korea/Japan (June 2002). During the World Cup, the clubs reported injuries sustained by these players, and their performance was evaluated by three international experts. RESULTS: The number of team matches during the season varied between 40 and 76 for the different countries involved. The individual player had a mean of 36 matches during the season. Top players played more matches, especially during the final period of the season. Players who participated in the World Cup played more matches during the season than those who did not (46 v 33 matches). World Cup players did not show any increased risk of injury during the season. About 29% incurred injuries during the World Cup, and 32% performed below their normal standard. The players who underperformed had played more matches during the 10 weeks before the World Cup than those who performed better than expected (12.5 v 9, p<0.05). Twenty three (60%) of the 38 players who had played more than one match a week before the World Cup incurred injuries or underperformed during the World Cup. CONCLUSIONS: There is considerable variation in the number of matches played per season in European professional football leagues. Top level players are obliged to play many matches especially during the final period of the season.

Adult↗
PubMed1995

HERV-H endogenous retroviruses: presence in the New World branch but amplification in the Old World primate lineage.

The evolutionary origin and age of the HERV-H family of human endogenous retrovirus-like sequences was investigated in this study. HERV-H elements exist in approximately 900 partially deleted copies and 50-100 more intact forms in humans and Old World monkeys. However, their possible presence in more divergent species is unknown. We have isolated a 1.6-kb genomic DNA segment from the New World monkey marmoset that had been PCR amplified using human HERV-H primers. DNA and protein comparisons and database searches indicate that this marmoset clone is more closely related to human HERV-H elements than to any other sequence, indicating that HERV-H-related sequences do exist in New World monkeys. In contrast to the high copy numbers of deleted elements in Old World primates. Southern blot analysis shows that such elements are present in less than 50 copies in two different species of New World monkey. To estimate evolutionary ages of the common deleted form of the element, a selected DNA segment from the pol region was compared from multiple human HERV-H elements. This comparison suggests that many HERV-H elements of the abundant deleted subfamily integrated approximately 30-35 million years ago. Very similar percentage divergence values between 5' and 3' long terminal repeats of individual elements of the deleted subfamily also suggest that these elements are close in age. These results indicate that HERV-H elements first appeared in the germline prior to the New World/Old World divergence over 40 million years ago. Interestingly, they remained in low numbers in the New World branch while a subfamily underwent a major amplification in Old World primates before the time of divergence of hominoids from Old World monkeys.

Animals↗
PubMed1991

Poverty crisis in the Third World: the contradictions of World Bank policy.

Politicians, the mainstream media, and orthodox social science have all been telling us of a final victory of capitalism over socialism, suggesting that capitalism is the only viable option for solving the world's problems. Yet, the global capitalist system is itself entering the third decade of a profound structural crisis, the costs of which have been borne largely by the exploited and oppressed peoples of the underdeveloped periphery. While the World Bank's latest World Development Report recognizes the current poverty crisis in the third world, its "two-part strategy" for alleviating poverty is based on an inadequate analysis of how peripheral capitalist development marginalizes the basic needs of the third world poor. Hence, the World Bank's assertion that free-market policies are consistent with effective antipoverty programs does not confront the class structures and global capitalist interests bound up with the reproduction of mass poverty in the third world. The World Bank's subordination of the basic needs of the poor to free-market adjustments and reforms in fact suggests that the real purpose of its "two-part strategy" is to ensure continued extraction of surplus from third world countries by maintaining the basic structure of imperialist underdevelopment.

Developing Countries↗
PubMed1999

Shared vector-borne zoonoses of the Old World and New World: home grown or translocated?

Humans inhabiting the Old World and New World share a wide variety of pathogens. Processes that result in the disjunct biogeographic distribution of pathogens with common vertebrate reservoirs or vectors are more difficult to unravel than those influencing the distribution of infections spread only through human-to-human transmission. The origins of species and complexes of tick-borne bacteria are unclear. The agent of Lyme borreliosis may have speciated in the New World following geographical isolation of ticks harboring ancestral spirochetes; the subsequent spread to Europe of B. burgdorferi sensu stricto may have occurred within historical times. Other tick-borne agents, such as the ehrlichiae causing human granulocytic ehrlichiosis, are genetically very similar in the Old World and New World. As the taxonomic distinctions among these related agents of human and veterinary importance appear increasingly blurred, the processes leading to the current discontinuous geographic distributions will also become the source of continuing speculation. Accumulating data suggest an Old World origin for a group of bacteria that include B. elizabethae, a human pathogen first identified from the New World. The potential public health significance of these newly described organisms is undefined, but of international interest as their vertebrate reservoir has been introduced throughout the world.

Animals↗
PubMed1995

Solution structure of an Old World-like neurotoxin from the venom of the New World scorpion Centruroides sculpturatus Ewing.

We have determined the solution structure of an alpha-toxin, CsE-V, isolated from the venom of the New World scorpion Centruroides sculpturatus Ewing (CsE). This toxin causes spontaneous rhythmic contractions in muscle. Unlike other New World toxins from CsE, this protein exhibits amino acid insertions and deletions at locations similar to Old World toxins and may thus represent a transition protein between the New World and Old World scorpion alpha-toxins. Sequence-specific assignments were made using 600 MHz 1H two-dimensional NMR data. NOESY, PH-COSY and amide-exchange data were used to deduce constraints for molecular modeling calculations. Distance geometry and dynamical simulated annealing calculations were performed to generate a family of 70 structures free of constraint violations. With respect to this family of structures, the energy-minimized average structure had root-mean-square deviations of 0.74 and 1.32 A for backbone and all atoms, respectively (excluding the C-terminal dipeptide, which is disordered). As with other scorpion toxins, the secondary structure of CsE-V consists of an alpha-helix, a three-strand anti-parallel beta-sheet, four beta-turns, and a hydrophobic patch that includes tyrosine residues in herringbone configuration. Unlike the CsE-v3 and -v1 proteins from C. sculpturatus, all of the proline residues were found to be in the trans configuration. The alpha-helix is slightly longer in CsE-V. The overall structure is more similar to the Old World alpha-toxin AaH-II from Androctonus australis Hector (r.m.s.d 1.59 A for backbone atoms of matching residues) than to the New World alpha-toxin CsE-v3 (r.m.s.d. 1.91 A). These structural data on CsE-V add further to our knowledge of the conformational repertoire exhibited by these sodium channel-binding neurotoxins.

Amino Acid Sequence↗
PubMed1991

Auditory perception is not special: we see the world, we feel the world, we hear the world.

The literature on "contrast" provides no evidence that durational contrast should occur in the speech and nonsence signals used in research cited by Diehl et al. [J. Acoust. Soc. Am. 89, 2905-2909 (1991)]. Moreover, there is evidence that, in comparable signals, it does not occur. Accordingly, their own account of the collection of findings on rate normalization is not viable. Their comments on my research do not imperil my interpretation of it or challenge my criticism that classification judgments of acoustically analogous speech and nonsense signals do not permit interpretation, by themselves, in terms of underlying auditory-system mechanisms. Their arguments that in auditory perception, uniquely, we hear proximal stimulation, not its physical causal sources, is implausible. Their theoretical perspective generally, I argue, is unrealistic.

Auditory Perception↗
PubMed1978

The neuroanatomical organization of pathways between the dorsal lateral geniculate nucleus and visual cortex in Old World and New World primates.

Pathways between the dorsal lateral geniculate nucleus (dLGN) and visual cortex in Old World (Macaca, Papio, Erythrocebus, Cercopithecus) and New World (Saimiri, Cebus) primates were studied after injections of horseradish peroxidase and H3 or S35 amino acids into the dLGN or visual cortex. Trans-synaptic autoradiography was also used to study these pathways after an injection of H3 proline-fucose into one eye. The subsequent autoradiographs of visual cortex showed that Old World primates have separate eye inputs (ocular dominance columns) in the striate cortex, whereas New World monkeys have overlapping or non-separated eye inputs. In both primate groups the geniculocortical input to layer IVA formed a pattern which resembled a honeycomb in tangential sections, unlike the solidly labeled layer IVC. Also common to the two primate groups was a projection from dLGN to layer VI. There was no dLGN projection to any prestriate area in any of the primates. However, after an injection limited to the prestriate cortex of Macaca, light autoradiographic labeling was seen in the interlaminar zones and the magnocellular and S laminae, demonstrating a prestriate-dLGN pathway. Our results indicate that the primate visual system differs significantly from the cat in having no dLGN projection to area 18. There are also signficant differences between primates in the level at which the possibility of binocularity (of an excitatory nature) first occurs in the striate cortex because in the species studied thus far with neuroanatomical methods, Old World primates have ocular dominance columns in layer IV but most New World monkeys lack them.

Animals↗
PubMed2004

Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster.

Drosophila melanogaster originated in Africa, spread to Europe and Asia, and is believed to have colonized the New World in the past few hundred years. Levels of genetic variation are typically reduced in New World populations, consistent with a founder event following range expansion out of Africa and the Old World. We describe the patterns of mtDNA length variation within and among several populations of Drosophila melanogaster from the Old and New World. MtDNA length variation is due to insertion and deletion of tandem repeats in the control region (D-loop) of D. melanogaster mitochondrial genome. The distinct mutational dynamics of this system provide an opportunity to compare the patterns of variation in this marker to those of other markers with different mutational pressures and linkage relationships. The data show significantly more length variation in African and Asian samples than in New World samples. New World samples also show more pronounced skew of the length distribution. Our results are distinct from an earlier study that showed significantly higher levels of length variation and heteroplasmy. The level of heteroplasmy is highly correlated with the number of years that samples have been maintained in laboratory culture, suggesting that relaxed selection in small populations permits the accumulation of mtDNA length variation and heteroplasmy. Together, the data indicate that mtDNA length variants retain a signature of founder events and selection, and suggest that further investigation into the mutation-selection dynamics of the D-loop region of mtDNA would provide a distinct and informative marker for analysis of the recent history of populations.

Animals↗
PubMed2001

Old World sources of the first New World human inhabitants: a comparative craniofacial view.

Human craniofacial data were used to assess the similarities and differences between recent and prehistoric Old World samples, and between these samples and a similar representation of samples from the New World. The data were analyzed by the neighbor-joining clustering procedure, assisted by bootstrapping and by canonical discriminant analysis score plots. The first entrants to the Western Hemisphere of maybe 15,000 years ago gave rise to the continuing native inhabitants south of the U.S.-Canadian border. These show no close association with any known mainland Asian population. Instead they show ties to the Ainu of Hokkaido and their Jomon predecessors in prehistoric Japan and to the Polynesians of remote Oceania. All of these also have ties to the Pleistocene and recent inhabitants of Europe and may represent an extension from a Late Pleistocene continuum of people across the northern fringe of the Old World. With roots in both the northwest and the northeast, these people can be described as Eurasian. The route of entry to the New World was at the northwestern edge. In contrast, the Inuit (Eskimo), the Aleut, and the Na-Dene speakers who had penetrated as far as the American Southwest within the last 1,000 years show more similarities to the mainland populations of East Asia. Although both the earlier and later arrivals in the New World show a mixture of traits characteristic of the northern edge of Old World occupation and the Chinese core of mainland Asia, the proportion of the latter is greater for the more recent entrants.

Americas↗
PubMed1967

The world outlook for conventional agriculture. More emphasis is needed on farm price policy and plant research if future world food needs are to be met.

1) The worldwide demand for food will continue to be strong in the coming decades. Two forces-rapidly growing population and, in much of the world, rapidly rising incomes-are expected to result in increases in the demand for food even more rapid than those that have occurred during the past. 2) Conventional agriculture has assured an adequate food supply for the economically advanced one-third of the world. The challenge now is to assure an adequate food supply for the remaining two-thirds, where population is now increasing at the rate of 1 million people per week and where malnutrition is already widespread. 3) Economically feasible prospects for significantly expanding the world's area of cultivated land in the 1960's and 1970's are limited and largely confined to sub-Saharan Africa and the Amazon Basin. Even here, agronomic problems will limit the rate of expansion. When the cost of desalting seawater is substantially reduced-probably not before the late 1970's or early 1980's at best-it may become feasible to irrigate large areas of desert. 4) Given the limited possibilities for expanding the area of land under cultivation, most of the increases in world food needs must be met, for the foreseeable future, by raising the productivity of land already under cultivation. Food output per acre, rather static throughout most of history, has begun to increase rapidly in some of the more advanced countries in recent decades. All of the increases in food production over the past quarter century in North America, western Europe, and Japan have come from increasing the productivity of land already under cultivation. The area under cultivation has actually declined. 5) Achieving dramatic gains in land productivity requires a massive investment of capital and the widespread adoption of new technology. A similar effort must now be made in the less-developed nations if these nations are to feed their people. The most important single factor influencing this rate of investment is food prices, more particularly the relationship between the price farmers receive for their food products and the cost of modern inputs such as fertilizer. 6) In some of the more-developed countries where per-acre yields have been rising for a long time, there is now evidence that the rate of yield increase may be slowing. Nonrecurring inputs may have made their maximum contribution to output in the case of some crops, pushing yield levels past the middle of the S-shaped logistic curve. Although this cannot be determined with any certainty, the possibility that the middle of the curve has been passed in some instances should be taken into account in viewing the long-term future. 7) If the rate of increase in yield per acre does in fact begin to slow in some of the agriculturally advanced countries, additional pressure will be put on the less-developed countries-which have much of the world's unrealized food-production potential-to meet the continuing future increases in world food needs. 8) Man has not yet been able to bypass the process of photosynthesis in the production of food. This dependence on photosynthesis plays a significant role in determining the upper levels of the S-shaped yield curve. Additional research is urgently needed to increase the photosynthetic efficiency of crops and to raise the upper levels of economically feasible yields.

Agriculture↗