An evaluation of earcons for use in auditory human-computer interfaces

An evaluation of earcons was carried out to seee whether they are an effective means of communicating information in sound. An initial experiment showed that earcons were better than unstructured bursts of sound and that musical timbres were more effective than simple tones. A second experiment was then carried out which improved upon some of the weaknesses shown up in Experiment 1 to give a significant improvement in recognition. From the results of these experiments some guidelines were drawn up for use in the creation of earcons. Earcons have been shown to be an effective method for communicating information in a human-computer interface

Parallel earcons: reducing the length of audio messages

This paper describes a method of presenting structured audio messages, earcons, in parallel so that they take less time to play and can better keep pace with interactions in a human-computer interface. The two component parts of a compound earcon are played in parallel so that the time taken is only that of a single part. An experiment was conducted to test the recall and recognition of parallel compound earcons as compared to serial compound earcons. Results showed that there are no differences in the rates of recognition between the two groups. Non-musicians are also shown to be equal in performance to musicians. Some extensions to the earcon creation guidelines of Brewster, Wright and Edwards are put forward based upon research into auditory stream segregation. Parallel earcons are shown to be an effective means of increasing the presentation rates of audio messages without compromising recognition rates

The design and evaluation of an auditory-enhanced scrollbar

A structured method is described for the analysis of interactions to identify situations where hidden information may exist and where non-speech sound might be used to overcome the associated problems. Interactions are considered in terms of events, status and modes to find any hidden information. This is then categorised in terms of the feedback needed to present it. An auditory-enhanced scrollbar, based on the method described, was then experimentally tested. Timing and error rates were used along with subjective measures of workload. Results from the experiment show a significant reduction in time to complete one task, a decrease in the mental effort required and an overall preference for the auditory-enhanced scrollbar

A systems biology approach to investigate the response of Synechocystis sp. PCC6803 to a high salt environment.

BACKGROUND: Salt overloading during agricultural processes is causing a decrease in crop productivity due to saline sensitivity. Salt tolerant cyanobacteria share many cellular characteristics with higher plants and therefore make ideal model systems for studying salinity stress. Here, the response of fully adapted Synechocystis sp. PCC6803 cells to the addition of 6% w/v NaCl was investigated using proteomics combined with targeted analysis of transcripts. RESULTS: Isobaric mass tagging of peptides led to accurate relative quantitation and identification of 378 proteins, and approximately 40% of these were differentially expressed after incubation in BG-11 media supplemented with 6% salt for 9 days. Protein abundance changes were related to essential cellular functional alterations. Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted. Temporal RT-qPCR experiments were also run to investigate protein expression changes at the transcript level, for 14 non-metabolic proteins. In 9 out of 14 cases the mRNA changes were in accordance with the proteins. CONCLUSION: Synechocystis sp. PCC6803 has the ability to regulate essential metabolic processes to enable survival in high salt environments. This adaptation strategy is assisted by further regulation of proteins involved in non-metabolic cellular processes, supported by transcriptional and post-transcriptional control. This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp. PCC6803

Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion

Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways

Simbiotics: a multi-scale integrative platform for 3D modeling of bacterial populations

Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology

The quantitative proteomic response of Synechocystis sp. PCC6803 to phosphate acclimation.

BACKGROUND: Inorganic phosphate (Pi) is a critical nutrient for all life and is periodically limiting in marine and freshwater provinces, yet little is understood how organisms acclimate to fluctuations in Pi within their environment. To investigate whole cell adaptation, we grew Synechocystis sp. PCC6803, a model freshwater cyanobacterium, in 3%, and 0.3% inorganic phosphate (Pi) media. The cells were allowed to acclimate over 60 days, and cells were harvested for quantitative high throughput mass spectrometry-based proteomics using the iTRAQ™ labelling technology. RESULTS: In total, 120 proteins were identified, and 52 proteins were considered differentially abundant compared to the control. Alkaline phosphatase (APase) activities correlated significantly (p < 0.05) with observed relative PhoA abundances. PstS1 and PstS2 were both observed, yet PstS1 was not differentially more abundant than the control. Phycobilisome protein abundances appeared to be coordinated, and are significantly less abundant in 0.3% Pi than 3% Pi cultures. Also, the central metabolic cell function appears to have shifted towards the production of (NADPH) reducing energy and nucleotide sugars. CONCLUSIONS: This acclimation response bears strong similarity to the previously reported response to nitrogen deprivation within Synechocystis sp. PCC 6803. However, it also demonstrates some characteristics of desiccation stress, such as the regulation of fatty acids and increased abundance of rehydrin in the 3% Pi culture

Application of the broadband collision-induced dissociation (bbCID) mass spectrometry approach for protein glycosylation and phosphorylation analysis

Rationale Analysis of post‐translationally modified peptides by mass spectrometry (MS) remains incomplete, in part due to incomplete sampling of all peptides which is inherent to traditional data‐dependent acquisition (DDA). An alternative MS approach, data‐independent acquisition (DIA), enables comprehensive recording of all detectable precursor and product ions, independent of precursor intensity. The use of broadband collision‐induced dissociation (bbCID), a DIA method, was evaluated for the identification of protein glycosylation and phosphorylation. Methods bbCID was applied to identify glycopeptides and phosphopeptides generated from standard proteins using a high‐resolution Bruker maXis 3G mass spectrometer. In bbCID, precursor and product ion spectra were obtained by alternating low and high collision energy. Precursor ions were assigned manually based on the detection of diagnostic ions specific to either glycosylation or phosphorylation. The composition of the glycan modification was resolved in the positive ion mode, while the level of phosphorylation was investigated in the negative ion mode. Results The results demonstrate for the first time that the use of a bbCID approach is suitable for the identification of glycopeptides and phosphopeptides based on the detection of specific diagnostic and associated precursor ions. The novel use of bbCID in negative ion mode allowed the discrimination of singly and multiply phosphorylated peptides based on the detection of phosphate diagnostic ions. The results also demonstrate the ability of this approach to allow the identification of glycan composition in N‐ and O‐linked glycopeptides, in positive ion mode. Conclusions We contend that bbCID is a valuable addition to the existing toolkit for PTM discovery. Moreover, this technique could be employed to direct targeted proteomics methods, particularly where there is no a priori information on glycosylation or phosphorylation status. This technique is immediately relevant to the characterisation of individual proteins or biological samples of low complexity, as demonstrated for the analysis of the glycosylation status of a therapeutic protein

Generation of Recombinant N-Linked Glycoproteins in E. coli

The production of N-linked recombinant glycoproteins is possible in a variety of biotechnology host cells, and more recently in the bacterial workhorse, Escherichia coli. This methods chapter will outline the components and procedures needed to produce N-linked glycoproteins in E. coli, utilizing Campylobacter jejuni glycosylation machinery, although other related genes can be used with minimal tweaks to this methodology. To ensure a successful outcome, various methods will be highlighted that can confirm glycoprotein production to a high degree of confidence, including the gold standard of mass spectrometry analysis

Resources for situated actions

In recent years, advances in software tools have made it easier to analyze interactive system specifications, and the range of their possible behaviors. However, the effort involved in producing the specifications of the system is still substantial, and a difficulty exists regarding the specification of plausible behaviors on the part of the user. Recent trends in technology towards more mobile and distributed systems further exacerbates the issue, as contextual factors come in to play, and less structured, more opportunistic behavior on the part of the user makes purely task-based analysis difficult. In this paper we consider a resourced action approach to specification and analysis. In pursuing this approach we have two aims - firstly, to facilitate a resource-based analysis of user activity, allowing resources to be distributed across a number of artifacts, and secondly to consider within the analysis a wider range of plausible and opportunistic user behaviors without a heavy specification overhead, or requiring commitment to detailed user models.We acknowledge with thanks EPSRC grant EP/F01404X/1 and FCT/FEDER grant POSC/EIA/56646/2004. Michael Harrison is grateful to colleagues in the ReSIST NoE (www.resit-noe.org)