ProFunc: a server for predicting protein function from 3D structure

ProFunc () is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally

Sotto Voce: Exploring the Interplay of Conversation and Mobile Audio Spaces

In addition to providing information to individual visitors, electronic guidebooks have the potential to facilitate social interaction between visitors and their companions. However, many systems impede visitor interaction. By contrast, our electronic guidebook, Sotto Voce, has social interaction as a primary design goal. The system enables visitors to share audio information - specifically, they can hear each other's guidebook activity using a technologically mediated audio eavesdropping mechanism. We conducted a study of visitors using Sotto Voce while touring a historic house. The results indicate that visitors are able to use the system effectively, both as a conversational resource and as an information appliance. More surprisingly, our results suggest that the technologically mediated audio often cohered the visitors' conversation and activity to a far greater degree than audio delivered through the open air.Comment: 8 page

Mapping the Constrained Coding Regions in the human genome to their corresponding proteins

Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects

Desert dust and anthropogenic aerosol interactions in the Community Climate System Model coupled-carbon-climate model

© The Authors, 2011. This article is distributed under the terms of the Creative Commons Attribution 3.0 License. The definitive version was published in Biogeosciences 8 (2011): 387-414, doi:10.5194/bg-8-387-2011.Coupled-carbon-climate simulations are an essential tool for predicting the impact of human activity onto the climate and biogeochemistry. Here we incorporate prognostic desert dust and anthropogenic aerosols into the CCSM3.1 coupled carbon-climate model and explore the resulting interactions with climate and biogeochemical dynamics through a series of transient anthropogenic simulations (20th and 21st centuries) and sensitivity studies. The inclusion of prognostic aerosols into this model has a small net global cooling effect on climate but does not significantly impact the globally averaged carbon cycle; we argue that this is likely to be because the CCSM3.1 model has a small climate feedback onto the carbon cycle. We propose a mechanism for including desert dust and anthropogenic aerosols into a simple carbon-climate feedback analysis to explain the results of our and previous studies. Inclusion of aerosols has statistically significant impacts on regional climate and biogeochemistry, in particular through the effects on the ocean nitrogen cycle and primary productivity of altered iron inputs from desert dust deposition.This work was done under the auspices of NASA NNG06G127G, NSF grants 0748369, 0932946, 0745961 and 0832782. The work of C. J. was supported by the Joint DECC/Defra Met Office Hadley Centre Climate Programme (GA01101)

Decadal changes in summertime reactive oxidized nitrogen and surface ozone over the Southeast United States

Widespread efforts to abate ozone (O3) smog have significantly reduced emissions of nitrogen oxides (NOx) over the past 2 decades in the Southeast US, a place heavily influenced by both anthropogenic and biogenic emissions. How reactive nitrogen speciation responds to the reduction in NOx emissions in this region remains to be elucidated. Here we exploit aircraft measurements from ICARTT (July–August 2004), SENEX (June–July 2013), and SEAC4RS (August–September 2013) and long-term ground measurement networks alongside a global chemistry–climate model to examine decadal changes in summertime reactive oxidized nitrogen (RON) and ozone over the Southeast US. We show that our model can reproduce the mean vertical profiles of major RON species and the total (NOy) in both 2004 and 2013. Among the major RON species, nitric acid (HNO3) is dominant (∼ 42–45%), followed by NOx (31%), total peroxy nitrates (ΣPNs; 14%), and total alkyl nitrates (ΣANs; 9–12%) on a regional scale. We find that most RON species, including NOx, ΣPNs, and HNO3, decline proportionally with decreasing NOx emissions in this region, leading to a similar decline in NOy. This linear response might be in part due to the nearly constant summertime supply of biogenic VOC emissions in this region. Our model captures the observed relative change in RON and surface ozone from 2004 to 2013. Model sensitivity tests indicate that further reductions of NOxemissions will lead to a continued decline in surface ozone and less frequent high-ozone events

Update on Prevalence of Periodontitis in Adults in the United States: NHANES 2009 to 2012

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141963/1/jper0611.pd