28 research outputs found
Abstracting the Familiar
The ideas presented in this Artist\u27s Statement give some insights into the background and early development of the painted and drawn works illustrated by the accompanying slides
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
<p>Abstract</p> <p>Background</p> <p>Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible functional modules. The value of such modules for gaining insight into the underlying biological processes depends on their functional coherence. The challenges that we wish to address are to define and quantify the functional coherence of modules in relationship networks, so that they can be used to infer function of as yet unannotated proteins, to discover previously unknown roles of proteins in diseases as well as for better understanding of the regulation and interrelationship between different elements of complex biological systems.</p> <p>Results</p> <p>We have defined the functional coherence of modules with respect to the Gene Ontology (GO) by considering two complementary aspects: (i) the fragmentation of the GO functional categories into the different modules and (ii) the most representative functions of the modules. We have proposed a set of metrics to evaluate these two aspects and demonstrated their utility in <it>Arabidopsis thaliana</it>. We selected 2355 proteins for which experimentally established protein-protein interaction (PPI) data were available. From these we have constructed five relationship networks, four based on single types of data: PPI, co-expression, co-occurrence of protein names in scientific literature abstracts and sequence similarity and a fifth one combining these four evidence types. The ability of these networks to suggest biologically meaningful grouping of proteins was explored by applying Markov clustering and then by measuring the functional coherence of the clusters.</p> <p>Conclusions</p> <p>Relationship networks integrating multiple evidence-types are biologically informative and allow more proteins to be assigned to a putative functional module. Using additional evidence types concentrates the functional annotations in a smaller number of modules without unduly compromising their consistency. These results indicate that integration of more data sources improves the ability to uncover functional association between proteins, both by allowing more proteins to be linked and producing a network where modular structure more closely reflects the hierarchy in the gene ontology.</p
Resistance to Mucosal Lysozyme Compensates for the Fitness Deficit of Peptidoglycan Modifications by Streptococcus pneumoniae
The abundance of lysozyme on mucosal surfaces suggests that successful colonizers must be able to evade its antimicrobial effects. Lysozyme has a muramidase activity that hydrolyzes bacterial peptidoglycan and a non-muramidase activity attributable to its function as a cationic antimicrobial peptide. Two enzymes (PgdA, a N-acetylglucosamine deacetylase, and Adr, an O-acetyl transferase) that modify different sites on the peptidoglycan of Streptococcus pneumoniae have been implicated in its resistance to lysozyme in vitro. Here we show that the antimicrobial effect of human lysozyme is due to its muramidase activity and that both peptidoglycan modifications are required for full resistance by pneumococci. To examine the contribution of lysozyme and peptidoglycan modifications during colonization of the upper respiratory tract, competition experiments were performed with wild-type and pgdAadr mutant pneumococci in lysozyme M-sufficient (LysM+/+) and -deficient (LysMâ/â) mice. The wild-type strain out-competed the double mutant in LysM+/+, but not LysMâ/â mice, indicating the importance of resistance to the muramidase activity of lysozyme during mucosal colonization. In contrast, strains containing single mutations in either pgdA or adr prevailed over the wild-type strain in both LysM+/+ and LysMâ/â mice. Our findings demonstrate that individual peptidoglycan modifications diminish fitness during colonization. The competitive advantage of wild-type pneumococci in LysM+/+ but not LysMâ/â mice suggests that the combination of peptidoglycan modifications reduces overall fitness, but that this is outweighed by the benefits of resistance to the peptidoglycan degrading activity of lysozyme
Multi-messenger observations of a binary neutron star merger
On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transientâs position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta
Multi-messenger Observations of a Binary Neutron Star Merger
On 2017 August 17 a binary neutron star coalescence candidate (later
designated GW170817) with merger time 12:41:04 UTC was observed through
gravitational waves by the Advanced LIGO and Advanced Virgo detectors.
The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray
burst (GRB 170817A) with a time delay of ⌠1.7 {{s}} with respect to
the merger time. From the gravitational-wave signal, the source was
initially localized to a sky region of 31 deg2 at a
luminosity distance of {40}-8+8 Mpc and with
component masses consistent with neutron stars. The component masses
were later measured to be in the range 0.86 to 2.26 {M}ÈŻ
. An extensive observing campaign was launched across the
electromagnetic spectrum leading to the discovery of a bright optical
transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC
4993 (at ⌠40 {{Mpc}}) less than 11 hours after the merger by the
One-Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The
optical transient was independently detected by multiple teams within an
hour. Subsequent observations targeted the object and its environment.
Early ultraviolet observations revealed a blue transient that faded
within 48 hours. Optical and infrared observations showed a redward
evolution over âŒ10 days. Following early non-detections, X-ray and
radio emission were discovered at the transientâs position ⌠9
and ⌠16 days, respectively, after the merger. Both the X-ray and
radio emission likely arise from a physical process that is distinct
from the one that generates the UV/optical/near-infrared emission. No
ultra-high-energy gamma-rays and no neutrino candidates consistent with
the source were found in follow-up searches. These observations support
the hypothesis that GW170817 was produced by the merger of two neutron
stars in NGC 4993 followed by a short gamma-ray burst (GRB 170817A) and
a kilonova/macronova powered by the radioactive decay of r-process
nuclei synthesized in the ejecta.</p
The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts
Biodiversity continues to decline in the face of increasing anthropogenic pressures
such as habitat destruction, exploitation, pollution and introduction of
alien species. Existing global databases of speciesâ threat status or population
time series are dominated by charismatic species. The collation of datasets with
broad taxonomic and biogeographic extents, and that support computation of
a range of biodiversity indicators, is necessary to enable better understanding of
historical declines and to project â and avert â future declines. We describe and
assess a new database of more than 1.6 million samples from 78 countries representing
over 28,000 species, collated from existing spatial comparisons of
local-scale biodiversity exposed to different intensities and types of anthropogenic
pressures, from terrestrial sites around the world. The database contains
measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35)
biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains
more than 1% of the total number of all species described, and more than
1% of the described species within many taxonomic groups â including flowering
plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans
and hymenopterans. The dataset, which is still being added to, is
therefore already considerably larger and more representative than those used
by previous quantitative models of biodiversity trends and responses. The database
is being assembled as part of the PREDICTS project (Projecting Responses
of Ecological Diversity In Changing Terrestrial Systems â www.predicts.org.uk).
We make site-level summary data available alongside this article. The full database
will be publicly available in 2015
sPlotOpen - An environmentally balanced, open-access, global dataset of vegetation plots
Motivation Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co-occurring within delimited local areas. This allows species absences to be inferred, information seldom provided by existing global plant datasets. Although many vegetation plots have been recorded, most are not available to the global research community. A recent initiative, called 'sPlot', compiled the first global vegetation plot database, and continues to grow and curate it. The sPlot database, however, is extremely unbalanced spatially and environmentally, and is not open-access. Here, we address both these issues by (a) resampling the vegetation plots using several environmental variables as sampling strata and (b) securing permission from data holders of 105 local-to-regional datasets to openly release data. We thus present sPlotOpen, the largest open-access dataset of vegetation plots ever released. sPlotOpen can be used to explore global diversity at the plant community level, as ground truth data in remote sensing applications, or as a baseline for biodiversity monitoring. Main types of variable contained Vegetation plots (n = 95,104) recording cover or abundance of naturally co-occurring vascular plant species within delimited areas. sPlotOpen contains three partially overlapping resampled datasets (c. 50,000 plots each), to be used as replicates in global analyses. Besides geographical location, date, plot size, biome, elevation, slope, aspect, vegetation type, naturalness, coverage of various vegetation layers, and source dataset, plot-level data also include community-weighted means and variances of 18 plant functional traits from the TRY Plant Trait Database. Spatial location and grain Global, 0.01-40,000 m(2). Time period and grain 1888-2015, recording dates. Major taxa and level of measurement 42,677 vascular plant taxa, plot-level records. Software format Three main matrices (.csv), relationally linked
Dual Pili Post-translational modifications synergize to mediate meningococcal adherence to platelet activating factor receptor on human airway cells
Pili of pathogenic Neisseria are major virulence factors associated with adhesion, twitching motility, auto-aggregation, and DNA transformation. Pili of N. meningitidis are subject to several different post-translational modifications. Among these pilin modifications, the presence of phosphorylcholine (ChoP) and a glycan on the pilin protein are phase-variable (subject to high frequency, reversible on/off switching of expression). In this study we report the location of two ChoP modifications on the C-terminus of N. meningitidis pilin. We show that the surface accessibility of ChoP on pili is affected by phase variable changes to the structure of the pilin-linked glycan. We identify for the first time that the platelet activating factor receptor (PAFr) is a key, early event receptor for meningococcal adherence to human bronchial epithelial cells and tissue, and that synergy between the pilin-linked glycan and ChoP post-translational modifications is required for pili to optimally engage PAFr to mediate adherence to human airway cells