Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins

	Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic category. These relationships have been preserved over billions of years since the last common ancestor or sharing of protein genes between prokaryotes and eukaryotes. For each of the 21,440 members of this set of human proteins (that make significant matches to any of the 1.8 million proteins in this set of prokaryote species protein libraries) it is certain that each protein has important functions both in prokaryotes and eukaryotes and the precursor proteins have been important in the precursor species of both. That is the only explanation for the preservation of amino acid sequence similarity for the billions of years since the last common ancestor or period of sharing of proteins. Comparisons were made between the proteins of Arabidopsis thaliana and Saccharomyces cerevisiae to the proteins of the 571 prokaryote species. The results agreed with the human comparisons indicating that the conclusions apply to eukaryotes generally

Transposable element insertions have strongly affected human evolution

Comparison of a full collection of the transposable element (TE) sequences of vertebrates with genome sequences shows that the human genome makes 655 perfect full-length matches. The cause is that the human genome contains many active TEs that have caused TE inserts in relatively recent times. These TE inserts in the human genome are several types of young Alus (AluYa5, AluYb8, AluYc1, etc.). Work in many laboratories has shown that such inserts have many effects including changes in gene expression, increases in recombination, and unequal crossover. The time of these very effective changes in the human lineage genome extends back about 4 million years according to these data and very likely much earlier. Rapid human lineage-specific evolution, including brain size is known to have also occurred in the last few million years. Alu insertions likely underlie rapid human lineage evolution. They are known to have many effects. Examples are listed in which TE sequences have influenced human-specific genes. The proposed model is that the many TE insertions created many potentially effective changes and those selected were responsible for a part of the striking human lineage evolution. The combination of the results of these events that were selected during human lineage evolution was apparently effective in producing a successful and rapidly evolving species

Graviton scattering and matter distribution

In this model gravitation results from the emission and absorption of quanta (gravitons) that are scattered a few times in crossing a typical galaxy. Many features of the universe can be explained in terms of this model, although theoretical justification for the scattering of gravitons is lacking. Gravitons follow a random walk and diffuse through the outer regions of a galaxy. As a result the force of attraction follows a 1/R law, matching observed galactic rotation curves and explaining galactic dynamics without the need of dark matter. The model makes predictions regarding early stages in the expansion of the universe and the establishment of the mass distribution. It may be assumed that a nearly uniform expanding cloud of gas was present that was subject to collapse under gravitational forces. The 1/R law of attraction due to graviton diffusion is orders of magnitude more effective for initiation of collapse than the inverse square law, and it applies to blocks of gas larger than the graviton mean free path. Delay in the spread of gravitational attraction by diffusion sets a time-dependent range beyond which the attractive force is zero. In the model this causes arrays of matter to collapse locally into zones with a spacing set by the length of the range of the attractive force. An initial examination indicates that under these conditions the background radiation could have been released from a nearly uniform distribution at the time of decoupling of radiation and matter, followed by gravitational collapse into blocks of galactic mass. In the model the diffusion of gravitons continued and collapse became possible on a larger scale, initiating the formation of galactic clusters and still larger structures. The slow rate of diffusion then prevented the largest structures from attracting each other and permitted the formation of the voids on a very large scale. The model predicts that on the largest scale there is a three-dimensional repeated array of structures separated by voids. Ultimately structures larger than galactic clusters outran the diffusion of the gravitons and have since been freely expanding

Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences

The terminal regions (last 20 kb) of Saccharomyces cerevisiae chromosomes universally contain blocks of precise sequence similarity to other chromosome terminal regions. The left and right terminal regions are distinct in the sense that the sequence similarities between them are reverse complements. Direct sequence similarity occurs between the left terminal regions and also between the right terminal regions, but not between any left ends and right ends. With minor exceptions the relationships range from 80% to 100% match within blocks. The regions of similarity are composites of familiar and unfamiliar repeated sequences as well as what could be considered "single-copy" (or better "two-copy") sequences. All terminal regions were compared with all other chromosomes, forward and reverse complement, and 768 comparisons are diagrammed. It appears there has been an extensive history of sequence exchange or copying between terminal regions. The subtelomeric sequences fall into two classes. Seventeen of the chromosome ends terminate with the Y' repeat, while 15 end with the 800-nt "X2" repeats just adjacent to the telomerase simple repeats. The just-subterminal repeats are very similar to each other except that chromosome 1 right end is more divergent

Almost all human genes resulted from ancient duplication

Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins

Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation

The rate of appearance of duplex DNA renaturation, measured with single strand specific nuclease, deviates significantly from a second order reaction. Measurements reported in paper I of this series indicate an inhibition in the rate of reassociation of single strand tails on partially reassociated molecules by a factor of at least two. Equations are derived that describe the observed form of reassociation kinetics as measured with hydroxyapatite and with single strand specific nuclease. The free parameter that describes the extent of inhibition of nucleation with single strand tails in these equations has been evaluated by least squares methods and agrees with the experimentally measured value

A qualitative investigation of lay perspectives of diagnosis and self-management strategies employed by people with progressive multiple sclerosis

This is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this record.This article explores how people with progressive multiple sclerosis give meaning to their experiences. It builds upon the self-management literature, which has captured the tension between the desire for retaining normalcy and the increasing burden of self-management associated with chronic disease progression. This repeat interview study is empirically grounded in 28 interviews with 14 people with progressive multiple sclerosis. We identified gender differences in diagnosis-seeking which impacted subsequent sense-making. Male respondents found a diagnosis of multiple sclerosis difficult to come to terms with, and an enduring sense of loss or anger could inhibit further sense-making. A diagnosis of multiple sclerosis was more difficult to obtain for women respondents, and any sense of certainty that diagnosis provided framed their subsequent sense-making strategies. The complex sequelae of multiple sclerosis require that self-management strategies are both contextual and timely, although even the most accomplished self-managers can lose their sense of self with neurodegeneration. Disease progression can be associated with suicidal ideation, suggesting the need for greater dialogue to ensure that people with multiple sclerosis are adequately supported to fulfil their quality of life at all stages of neurodegeneration. These lay perspectives emphasise the articulation of affect rather than the rendering of a medical diagnosis, although diagnosis may provide a degree of certainty in the short term. The ethos of self-management ensures people attempt to retain their sense of ‘normality’ and existent social roles for as long as possible, but this ethos can negate both one’s ability to self-manage and the management of self.The author(s) disclosed receipt of the following financial support for the research, authorship, and/ or publication of this article: This research was funded by the MS Society (Grant No. 908)

Macromere cell fates during sea urchin development

This paper examines the cell lineage relationships and cell fates in embryos of the sea urchin Strongylocentrotus purpuratus leading to the various cell types derived from the definitive vegetal plate territory or the veg_2 tier of cells. These cell types are gut, pigment cells, basal cells and coelomic pouches. They are cell types that constitute embryonic structures through cellular migration or rearrangement unlike the relatively non-motile ectoderm cell types. For this analysis, we use previous knowledge of lineage to assign macromeres to one of four types: VOM, the oral macromere; VAM, the aboral macromere, right and left VLM, the lateral macromeres. Each of the four macromeres contributes progeny to all of the cell types that descend from the definitive vegetal plate. Thus in the gut each macromere contributes to the esophagus, stomach and intestine, and the stripe of labeled cells descendant from a macromere reflects the re-arrangement of cells that occurs during archenteron elongation. Pigment cell contributions exhibit no consistent pattern among the four macromeres, and are haphazardly distributed throughout the ectoderm. Gut and pigment cell contributions are thus radially symmetrical. In contrast, the VOM blastomere contributes to both of the coelomic pouches while the other three macromeres contribute to only one or the other pouch. The total of the macromere contribution amounts to 60% of the cells constituting the coelomic pouches

A feasibility study: California Department of Forestry and Fire Protection utilization of infrared technologies for wildland fire suppression and management

NASA's JPL has completed a feasibility study using infrared technologies for wildland fire suppression and management. The study surveyed user needs, examined available technologies, matched the user needs with technologies, and defined an integrated infrared wildland fire mapping concept system configuration. System component trade-offs were presented for evaluation in the concept system configuration. The economic benefits of using infrared technologies in fire suppression and management were examined. Follow-on concept system configuration development and implementation were proposed

Direct introduction of cloned DNA into the sea urchin zygote nucleus, and fate of injected DNA

A method is described for microinjection of cloned DNA into the zygote nucleus of Lytechinus variegatus. Eggs of this species are unusually transparent, facilitating visual monitoring of the injection process. The initial fate of injected DNA fragments appears similar to that observed earlier for exogenous DNA injected into unfertilized egg cytoplasm. Thus after end-to-end ligation, it is replicated after a lag of several hours to an extent indicating that it probably participates in most of the later rounds of DNA synthesis undergone by the host cell genomes during cleavage. The different consequences of nuclear versus cytoplasmic injection are evident at advanced larval stages. Larvae descendant from eggs in which exogenous DNA was injected into the nuclei are four times more likely (32% versus 8%) to retain this DNA in cell lineages that replicate very extensively during larval growth, i.e. the lineages contributing to the imaginal rudiment, and thus to display greatly enhanced contents of the exogenous DNA. Similarly, 36% of postmetamorphic juveniles from a nuclear injection sample retained the exogenous DNA sequences, compared to 12% of juveniles from a cytoplasmic injection sample. However, the number of copies of the exogenous DNA sequences retained per average genome in postmetamorphic juveniles was usually less than 0.1 (range 0.05-50), and genome blot hybridizations indicate that these sequences are organized as integrated, randomly oriented, end-to-end molecular concatenates. It follows that only a small fraction of the cells of the average juvenile usually retains the exogenous sequences. Thus, even when introduced by nuclear microinjection, the stable incorporation of exogenous DNA in the embryo occurs in a mosaic fashion, although in many recipients the DNA enters a wider range of cell lineages than is typical after cytoplasmic injection. Nuclear injection would probably be the route of choice for studies of exogenous DNA function in the postembryonic larval rudiment