110,925 research outputs found
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast).
Results: In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable.
Conclusions: Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70% to 95% of total phosphoproteins, but only 40% to 60% of total p-sites
Catching and displaying memory cues for a mobile augmented memory system
This report goes over and details the progress of the 2013 COMP477 project “Augmenting Memory: The Digital Parrot on Mobile Devices” undertaken by Jake Bellamy and supervised by Annika Hinze at the University of Waikato.
The report begins with an overview on the problem with remembering events in people’s lives and details the background information on the Digital Parrot system. It also describes the previous project that preceded this one, which began to conceptualize the Digital Parrot on mobile devices. It analyses problems with the current design of the system and addresses them.
The report then goes on to conduct an in depth user study with the functioning version of the software. The user study finds design flaws and incorrect functionality in the application that would not have otherwise been apparent.
Finally, the report concludes with a proposed user interface concept that addresses all of the issues found in the user study and describes how the system would work. It describes the initial implementation that has begun in building this system
Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody
Background
G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens.
Methods
SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures.
Results
The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability.
Conclusions
Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells.
General significance
The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface
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Use of 3D body motion to freeform surface design
This paper presents a novel surface modelling approach by utilising a 3D motion capture system. For designing a large-sized surface, a network of splines is initially set up. Artists or designers wearing motion markers on their hands can then change shapes of the splines with their hands. Literarily they can move their bodies freely to any positions to perform their tasks. They can also move their hands in 3D free space to detail surface characteristics by their gestures. All their design motions are recorded in the motion capturing system and transferred into 3D curves and surfaces correspondingly. This paper reports this novel surface design method and some case studies
Modeling the scaling properties of human mobility
While the fat tailed jump size and the waiting time distributions
characterizing individual human trajectories strongly suggest the relevance of
the continuous time random walk (CTRW) models of human mobility, no one
seriously believes that human traces are truly random. Given the importance of
human mobility, from epidemic modeling to traffic prediction and urban
planning, we need quantitative models that can account for the statistical
characteristics of individual human trajectories. Here we use empirical data on
human mobility, captured by mobile phone traces, to show that the predictions
of the CTRW models are in systematic conflict with the empirical results. We
introduce two principles that govern human trajectories, allowing us to build a
statistically self-consistent microscopic model for individual human mobility.
The model not only accounts for the empirically observed scaling laws but also
allows us to analytically predict most of the pertinent scaling exponents
The origin of bursts and heavy tails in human dynamics
The dynamics of many social, technological and economic phenomena are driven
by individual human actions, turning the quantitative understanding of human
behavior into a central question of modern science. Current models of human
dynamics, used from risk assessment to communications, assume that human
actions are randomly distributed in time and thus well approximated by Poisson
processes. In contrast, there is increasing evidence that the timing of many
human activities, ranging from communication to entertainment and work
patterns, follow non-Poisson statistics, characterized by bursts of rapidly
occurring events separated by long periods of inactivity. Here we show that the
bursty nature of human behavior is a consequence of a decision based queuing
process: when individuals execute tasks based on some perceived priority, the
timing of the tasks will be heavy tailed, most tasks being rapidly executed,
while a few experience very long waiting times. In contrast, priority blind
execution is well approximated by uniform interevent statistics. These findings
have important implications from resource management to service allocation in
both communications and retail.Comment: Supplementary Material available at http://www.nd.edu/~network
A monoclonal antibody-based immunoassay to measure the antibody response against the repeat region of the circumsporozoite protein of Plasmodium falciparum
Background: The malaria vaccine candidate RTS, S/AS01 (GSK Vaccines) induces high IgG concentration against the circumsporozoite protein (CSP) of Plasmodium falciparum. In human vaccine recipients circulating anti-CSP antibody concentrations are associated with protection against infection but appear not to be the correlate of protection. However, in a humanized mouse model of malaria infection prophylactic administration of a human monoclonal antibody (MAL1C), derived from a RTS, S/AS01-immunized volunteer, directed against the CSP repeat region, conveyed full protection in a dose-dependent manner suggesting that antibodies alone are able to prevent P. falciparum infection when present in sufficiently high concentrations. A competition ELISA was developed to measure the presence of MAL1C-like antibodies in polyclonal sera from RTS, S/AS01 vaccine recipients and study their possible contribution to protection against infection.
Results: MAL1C-like antibodies present in polyclonal vaccine-induced sera were evaluated for their ability to compete with biotinylated monoclonal antibody MAL1C for binding sites on the capture antigen consisting of the recombinant protein encompassing 32 NANP repeats of CSP (R32LR). Serum samples were taken at different time points from participants in two RTS, S/AS01 vaccine studies (NCT01366534 and NCT01857869). Vaccine-induced protection status of the study participants was determined based on the outcome of experimental challenge with infected mosquito bites after vaccination. Optimal conditions were established to reliably detect MAL1C-like antibodies in polyclonal sera. Polyclonal anti-CSP antibodies and MAL1C-like antibody content were measured in 276 serum samples from RTS, S/AS01 vaccine recipients using the standard ELISA and MAL-1C competition ELISA, respectively. A strong correlation was observed between the results from these assays. However, no correlation was found between the results of either assay and protection against infection.
Conclusions: The competition ELISA to measure MAL1C-like antibodies in polyclonal sera from RTS, S/AS01 vaccine recipients was robust and reliable but did not reveal the elusive correlate of protection
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