New Research Evaluating Similarities Between Human and Chimpanzee DNA

A preliminary study was performed by Tomkins comparing 40,000 chimpanzee genomic sequences against the human genome which indicated that reported levels of human-chimp DNA similarity were significantly lower than commonly reported. The present, follow-up study was then completed in which chimp chromosomes were sliced into new individual query files of varying string lengths and queried against their human chromosome homolog. This allowed for comparisons to be optimized irrespective of the linear order of genes and sequence features. The definition of similarity was the amount (percent) of optimally aligned chimp DNA. For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76 percent, depending on the chromosome. Only 69 percent of the chimpanzee X chromosome was similar to human and only 43 percent of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal alignment conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary time-scales and dogmatic presuppositions about a common ancestor

The Chasm Between the Human and Chimpanzee Genomes: A Review of the Evolutionary Literature

Data has been extracted from secular literature that is contrary to the common claim that very few genetic differences exist between chimpanzees and humans. We found that significant reported differences exist in genomic similarity and gene regulation between chimpanzees and humans. The DNA sequence differences and genetic mechanisms reported in the literature support the conclusion that significant and unbridgeable genetic differences exist between humans and chimpanzees that defy evolutionary claims of a common ancestor

Judicial Review, Irrationality, and the Legitimacy of Merits-Review

The definition of the irrationality ground of judicial review recognises the constitutional principle of the separation of powers, in allowing for judicial control of the executive only very rarely. The author in a previous article in this study found that the courts, on occasions, had intervened in circumstances where administrative decisions arguably were not irrational. To this end, the purpose of this article is to assess the constitutionality of these seemingly low standards of irrationality. The author does so by reference either to the manner of review employed—the use of the proportionality principle, for example—or the context of the administrative decision under scrutiny, such as the infringement of the applicant’s fundamental rights. The author finds that the cases from the previous article where low standards of irrationality were arguably adopted were, in fact, legitimate according to these chosen methods of evaluation. However, this is an interim conclusion because, for reasons of word length, the author is unable to complete a full assessment here. It is therefore proposed that a subsequent article will continue to examine the constitutionality of these cases. Furthermore, the author will also try and establish a zone of executive decision-making, for reasons of democracy, where the courts are excluded from irrationality review. If the author is unsuccessful in this regard, the final conclusion of this study will inevitably be that low standards of judicial intervention exist without limit—a clear assault on the constitutional principle stated above

Phylogenetic Analyses of Vitis (Vitaceae) Based on Complete Chloroplast Genome Sequences: Effects of Taxon Sampling and Phylogenetic Methods on Resolving Relationships Among Rosids

Background The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place Cucumis as sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade. Conclusion Phylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19-37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Background: Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.Results: Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.Conclusions: When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution

Straw blood cell count, growth, inhibition and comparison to apoptotic bodies

<p>Abstract</p> <p>Background</p> <p>Mammalian cells transform into individual tubular straw cells naturally in tissues and in response to desiccation related stress <it>in vitro</it>. The transformation event is characterized by a dramatic cellular deformation process which includes: condensation of certain cellular materials into a much smaller tubular structure, synthesis of a tubular wall and growth of filamentous extensions. This study continues the characterization of straw cells in blood, as well as the mechanisms of tubular transformation in response to stress; with specific emphasis placed on investigating whether tubular transformation shares the same signaling pathway as apoptosis.</p> <p>Results</p> <p>There are approximately 100 billion, unconventional, tubular straw cells in human blood at any given time. The straw blood cell count (SBC) is 45 million/ml, which accounts for 6.9% of the bloods dry weight. Straw cells originating from the lungs, liver and lymphocytes have varying nodules, hairiness and dimensions. Lipid profiling reveals severe disruption of the plasma membrane in CACO cells during transformation. The growth rates for the elongation of filaments and enlargement of rabbit straw cells is 0.6~1.1 (μm/hr) and 3.8 (μm³/hr), respectively. Studies using apoptosis inhibitors and a tubular transformation inhibitor in CACO2 cells and in mice suggested apoptosis produced apoptotic bodies are mediated differently than tubular transformation produced straw cells. A single dose of 0.01 mg/kg/day of p38 MAPK inhibitor in wild type mice results in a 30% reduction in the SBC. In 9 domestic animals SBC appears to correlate inversely with an animal's average lifespan (R²= 0.7).</p> <p>Conclusion</p> <p>Straw cells are observed residing in the mammalian blood with large quantities. Production of SBC appears to be constant for a given animal and may involve a stress-inducible protein kinase (P38 MAPK). Tubular transformation is a programmed cell survival process that diverges from apoptosis. SBCs may be an important indicator of intrinsic aging-related stress.</p

Quantifying local rainfall dynamics and uncertain boundary conditions into a nested regional-local flood modeling system

[Abstract:] Inflow discharge and outflow stage estimates for hydraulic flood models are generally derived from river gauge data. Uncertainties in the measured inflow data and the neglect of rainfall-runoff contributions to the modeled domain downstream of the gauging locations can have a significant impact on these estimated “whole reach” inflows and consequently on flood predictions. In this study, a method to incorporate rating curve uncertainty and local rainfall-runoff dynamics into the predictions of a reach-scale flood model is proposed. The methodology is applied to the July 2007 floods of the River Severn in UK. Discharge uncertainty bounds are generated applying a nonparametric local weighted regression approach to stage-discharge measurements for two gauging stations. Measured rainfall downstream from these locations is used as input to a series of subcatchment regional hydrological model to quantify additional local inflows along the main channel. A regional simplified-physics hydraulic model is then applied to combine these contributions and generate an ensemble of discharge and water elevation time series at the boundaries of a local-scale high complexity hydraulic model. Finally, the effect of these rainfall dynamics and uncertain boundary conditions are evaluated on the local-scale model. Accurate prediction of the flood peak was obtained with the proposed method, which was only possible by resolving the additional complexity of the extreme rainfall contributions over the modeled area. The findings highlight the importance of estimating boundary condition uncertainty and local rainfall contributions for accurate prediction of river flows and inundation at regional scales.María Bermúdez gratefully acknowledges financial support from the Spanish Regional Government of Galicia (postdoctoral grant reference ED481B 2014/156-0). Gemma Coxon was supported by NERC MaRIUS: Managing the Risks, Impacts and Uncertainties of droughts and water Scarcity, grant NE/L010399/1. Jim Freer and Paul Bates by NERC Susceptibility of catchments to INTense RAinfall and flooding, grant NE/K00882X/1. A free version of the model LISFLOOD-FP is available for download at www.bristol.ac.uk/geography/research/hydrology/models/lisflood/. A free version of the model Iber is available for download at www.iberaula.es. The river cross-section data, the LiDAR digital elevation model and the gauging station rainfall, stage, flow and rating curve data of the presented case study are freely available from the Environment Agency ([email protected])Xunta de Galicia; ED481B 2014/156-0Inglaterra. University of Bristol; NE/L010399/1Inglaterra. University of Bristol; NE/K00882X/