Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Can houseplants improve indoor air quality by removing CO2 and increasing relative humidity?

High indoor CO2 concentrations and low relative humidity (RH) create an array of well-documented human health issues. Therefore, assessing houseplants’ potential as a low-cost approach to CO2 removal and increasing RH is important. We investigated how environmental factors such as ’dry’ ( 0.30 m3 m-3) growing substrates, and indoor light levels (‘low’ 10 µmol m-2 s-1, ‘high’ 50 µmol m-2 s-1 and ‘very high’ 300 µmol m-2 s-1), influence the plants’ net CO2 assimilation (‘A’) and water-vapour loss. Seven common houseplant taxa – representing a variety of leaf types, metabolisms and sizes – were studied for their ability to assimilate CO2 across a range of indoor light levels. Additionally, to assess the plants’ potential contribution to RH increase, the plants’ evapo-transpiration (ET) was measured. At typical ‘low’ indoor light levels ‘A’ rates were generally low (< 3.9 mg hr-1). Differences between ‘dry’ and ’wet’ plants at typical indoor light levels were negligible in terms of room-level impact. Light compensation points (i.e. light levels at which plants have positive ‘A’) were in the typical indoor light range (1-50 µmol m-2 s-1) only for two studied Spathiphyllum wallisii cultivars and Hedera helix; these plants would thus provide the best CO2 removal indoors. Additionally, increasing indoor light levels to 300 µmol m-2 s-1 would, in most species, significantly increase their potential to assimilate CO2. Species which assimilated the most CO2 also contributed most to increasing RH

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

<p>Abstract</p> <p>Background</p> <p>Chromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. The aim of this study was to investigate the extent and characteristics of sites of ASHM in human embryonic stem cells (hESCs).</p> <p>Results</p> <p>Using a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. We found that, although they were rare, sites of ASHM were substantially enriched at loci displaying ASE. Many were also found at known imprinted regions, hence sites of ASHM are likely to be better markers of imprinted regions than sites of ASM. We also found that sites of ASHM and ASE in hESCs colocalize at risk loci for developmental syndromes mediated by deletions, providing insights into the etiology of these disorders.</p> <p>Conclusion</p> <p>These results demonstrate the potential importance of ASHM patterns in the interpretation of disease loci, and the protocol described provides a basis for similar studies of ASHM in other cell types to further our understanding of human disease susceptibility.</p

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%–63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with “overprediction” of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation

Interaction between plant species and substrate type in the removal of CO2 indoors

Elevated indoor concentrations of carbon dioxide [CO2] cause health issues, increase workplace absenteeism and reduce cognitive performance. Plants can be part of the solution, reducing indoor [CO2] and acting as a low-cost supplement to building ventilation systems. Our earlier work on a selection of structurally and functionally different indoor plants identified a range of leaf-level CO2 removal rates, when plants were grown in one type of substrate. The work presented here brings the research much closer to real indoor environments by investigating CO2 removal at a whole-plant level and in different substrates. Specifically, we measured how the change of growing substrate affects plants’ capacity to reduce CO2 concentrations. Spathiphyllum wallisii 'Verdi', Dracaena fragrans 'Golden Coast' and Hedera helix, representing a range of leaf types and sizes and potted in two different substrates, were tested. Potted plants were studied in a 0.15 m3 chamber under ‘very high’ (22000 lux), ‘low’ (~ 500 lux) and ‘no’ light (0 lux) in ‘wet’ (> 30 %) and ‘dry’ (< 20 %) substrate. At ‘no’ and ‘low’ indoor light, houseplants increased the CO2 concentration in both substrates; respiration rates, however, were deemed negligible in terms of the contribution to a room-level concentration, as they added ~ 0.6% of a human’s contribution. In ‘very high’ light D. fragrans, in substrate 2, showed potential to reduce [CO2] to a near-ambient (600 ppm) concentration in a shorter timeframe (12 hrs, e.g. overnight) and S. wallisii over a longer period (36 hrs, e.g. weekend)

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Suppression in Pb-Pb Collisions at the LHC.

The production of the ψ(2S) charmonium state was measured with ALICE in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV, in the dimuon decay channel. A significant signal was observed for the first time at LHC energies down to zero transverse momentum, at forward rapidity (2.5<y<4). The measurement of the ratio of the inclusive production cross sections of the ψ(2S) and J/ψ resonances is reported as a function of the centrality of the collisions and of transverse momentum, in the region p_{T}<12  GeV/c. The results are compared with the corresponding measurements in pp collisions, by forming the double ratio [σ^{ψ(2S)}/σ^{J/ψ}]_{Pb-Pb}/[σ^{ψ(2S)}/σ^{J/ψ}]_{pp}. It is found that in Pb-Pb collisions the ψ(2S) is suppressed by a factor of ∼2 with respect to the J/ψ. The ψ(2S) nuclear modification factor R_{AA} was also obtained as a function of both centrality and p_{T}. The results show that the ψ(2S) resonance yield is strongly suppressed in Pb-Pb collisions, by a factor of up to ∼3 with respect to pp. Comparisons of cross section ratios with previous Super Proton Synchrotron findings by the NA50 experiment and of R_{AA} with higher-p_{T} results at LHC energy are also reported. These results and the corresponding comparisons with calculations of transport and statistical models address questions on the presence and properties of charmonium states in the quark-gluon plasma formed in nuclear collisions at the LHC