Roadmap Analysis of Protein-Protein Interactions. Master\u27s Thesis, August 2007

The ability to effectively model the interaction between proteins is an important and open problem. In molecular biology it is well accepted that from sequence arises form and from form arises function but relating structure to function remains a challenge. The function of a given protein is defined by its interactions. Likewise a malfunction or a change in protein-protein interactions is a hallmark of many diseases. Many researchers are studying the mechanisms of protein-protein interactions and one of the overarching goals of the community is to predict whether two proteins will bind, and if so what the final conformation will be. Attention is seldom paid to the association pathways that allow two proteins to bind. Evidence has shown that the information in the association pathways can play a vital role in understanding the interaction itself. This thesis presents a novel and scalable approach to computing association pathways between two proteins using the Probabilistic Roadmap (PRM) framework. We will discuss the challenges in extending PRM to the domain of protein-protein interactions such as performing structural mappings in a reduced space of flexibility, and sampling high dimensional conformation spaces. We will present analysis of individual association pathways as well as methods for estimating collective properties of the energy landscape. Our results indicate that these methods can discriminate between true and false protein binding interfaces. Finally, we will present condensing methods such as pathway clustering and visualization using dimensionality reduction that can be be applied to create compact representations of the interaction space

A Modified Evidence-Based Practice- Knowledge, Attitudes, Behaviour and Decisions/Outcomes Questionnaire is Valid Across Multiple Professions Involved in Pain Management

BACKGROUND: A validated and reliable instrument was developed to knowledge, attitudes and behaviours with respect to evidence-based practice (EBB-KABQ) in medical trainees but requires further adaptation and validation to be applied across different health professionals. METHODS: A modified 33-item evidence-based practice scale (EBP-KABQ) was developed to evaluate EBP perceptions and behaviors in clinicians. An international sample of 673 clinicians interested in treatment of pain (mean age = 45 years, 48% occupational therapists/physical therapists, 25% had more than 5 years of clinical training) completed an online English version of the questionnaire and demographics. Scaling properties (internal consistency, floor/ceiling effects) and construct validity (association with EBP activities, comparator constructs) were examined. A confirmatory factor analysis was used to assess the 4-domain structure EBP knowledge, attitudes, behavior, outcomes/decisions). RESULTS: The EBP-KABQ scale demonstrated high internal consistency (Cronbach\u27s alpha = 0.85), no evident floor/ceiling effects, and support for a priori construct validation hypotheses. A 4-factor structure provided the best fit statistics (CFI =0.89, TLI =0.86, and RMSEA = 0.06). CONCLUSIONS: The EBP-KABQ scale demonstrates promising psychometric properties in this sample. Areas for improvement are described

A Catalog of Very Isolated Galaxies from the SDSS Data Release 1

We present a new catalog of isolated galaxies obtained through an automated systematic search. These 2980 isolated galaxies were found in approximately 2099 sq deg of sky in the Sloan Digital Sky Survey Data Release 1 (SDSS DR1) photometry. The selection algorithm, implementing a variation on the criteria developed by Karachentseva in 1973, proved to be very efficient and fast. This catalog will be useful for studies of the general galaxy characteristics. Here we report on our results.Comment: 67 pages, which includes 14 figures. Accepted for publication by A

Mapping functional transcription factor networks from gene expression data

A critical step in understanding how a genome functions is determining which transcription factors (TFs) regulate each gene. Accordingly, extensive effort has been devoted to mapping TF networks. In Saccharomyces cerevisiae, protein–DNA interactions have been identified for most TFs by ChIP-chip, and expression profiling has been done on strains deleted for most TFs. These studies revealed that there is little overlap between the genes whose promoters are bound by a TF and those whose expression changes when the TF is deleted, leaving us without a definitive TF network for any eukaryote and without an efficient method for mapping functional TF networks. This paper describes NetProphet, a novel algorithm that improves the efficiency of network mapping from gene expression data. NetProphet exploits a fundamental observation about the nature of TF networks: The response to disrupting or overexpressing a TF is strongest on its direct targets and dissipates rapidly as it propagates through the network. Using S. cerevisiae data, we show that NetProphet can predict thousands of direct, functional regulatory interactions, using only gene expression data. The targets that NetProphet predicts for a TF are at least as likely to have sites matching the TF's binding specificity as the targets implicated by ChIP. Unlike most ChIP targets, the NetProphet targets also show evidence of functional regulation. This suggests a surprising conclusion: The best way to begin mapping direct, functional TF-promoter interactions may not be by measuring binding. We also show that NetProphet yields new insights into the functions of several yeast TFs, including a well-studied TF, Cbf1, and a completely unstudied TF, Eds1

Identification of the galactosyltransferase of Cryptococcus neoformans involved in the biosynthesis of basidiomycete-type glycosylinositolphosphoceramide

The pathogenic fungus Cryptococcus neoformans synthesizes a complex family of glycosylinositolphosphoceramide (GIPC) structures. These glycosphingolipids (GSLs) consist of mannosylinositolphosphoceramide (MIPC) extended by β1-6-linked galactose, a unique structure that has to date only been identified in basidiomycetes. Further extension by up to five mannose residues and a branching xylose has been described. In this study, we identified and determined the gene structure of the enzyme Ggt1, which catalyzes the transfer of a galactose residue to MIPC. Deletion of the gene in C. neoformans resulted in complete loss of GIPCs containing galactose, a phenotype that could be restored by the episomal expression of Ggt1 in the deletion mutant. The entire annotated open reading frame, encoding a C-terminal GT31 galactosyltransferase domain and a large N-terminal domain of unknown function, was required for complementation. Notably, this gene does not encode a predicted signal sequence or transmembrane domain. The demonstration that Ggt1 is responsible for the transfer of a galactose residue to a GSL thus raises questions regarding the topology of this biosynthetic pathway and the function of the N-terminal domain. Phylogenetic analysis of the GGT1 gene shows conservation in hetero- and homobasidiomycetes but no homologs in ascomycetes or outside of the fungal kingdo

A Systematic Review of Medication Adherence Thresholds Dependent of Clinical Outcomes

Background: In pharmacotherapy, the achievement of a target clinical outcome requires a certain level of medication intake or adherence. Based on Haynes's early empirical definition of sufficient adherence to antihypertensive medications as taking ≥80% of medication, many researchers used this threshold to distinguish adherent from non-adherent patients. However, we propose that different diseases, medications and patient's characteristics influence the cut-off point of the adherence rate above which the clinical outcome is satisfactory (thereafter medication adherence threshold). Moreover, the assessment of adherence and clinical outcomes may differ greatly and should be taken into consideration. To our knowledge, very few studies have defined adherence rates linked to clinical outcomes. We aimed at investigating medication adherence thresholds in relation to clinical outcomes.Method: We searched for studies that determined the relationship between adherence rates and clinical outcomes in the databases PubMed, EmbaseⓇ and Web of Science™ until December 2017, limited to English-language. Our outcome measure was any threshold value of adherence. The inclusion criteria of the retrieved studies were (1) any measurement of medication adherence, (2) any assessment of clinical outcomes, and (3) any method to define medication adherence thresholds in relation to clinical outcomes. We excluded articles considered as a tutorial. Two authors (PB and IA) independently screened titles and abstracts for relevance, reviewed full-texts, and extracted items. The results of the included studies are presented qualitatively.Result: We analyzed 6 articles that assessed clinical outcomes linked to adherence rates in 7 chronic disease states. Medication adherence was measured with Medication Possession Ratio (MPR, n = 3), Proportion of Days Covered (PDC, n = 1), both (n = 1), or Medication Event Monitoring System (MEMS). Clinical outcomes were event free episodes, hospitalization, cortisone use, reported symptoms and reduction of lipid levels. To find the relationship between the targeted clinical outcome and adherence rates, three studies applied logistic regression and three used survival analysis. Five studies defined adherence thresholds between 46 and 92%. One study confirmed the 80% threshold as valid to distinguish adherent from non-adherent patients.Conclusion: The analyzed studies were highly heterogeneous, predominantly concerning methods of calculating adherence. We could not compare studies quantitatively, mostly because adherence rates could not be standardized. Therefore, we cannot reject or confirm the validity of the historical 80% threshold. Nevertheless, the 80% threshold was clearly questioned as a general standard

Toward an Integrated Model of Capsule Regulation in Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen that causes serious human disease in immunocompromised populations. Its polysaccharide capsule is a key virulence factor which is regulated in response to growth conditions, becoming enlarged in the context of infection. We used microarray analysis of cells stimulated to form capsule over a range of growth conditions to identify a transcriptional signature associated with capsule enlargement. The signature contains 880 genes, is enriched for genes encoding known capsule regulators, and includes many uncharacterized sequences. One uncharacterized sequence encodes a novel regulator of capsule and of fungal virulence. This factor is a homolog of the yeast protein Ada2, a member of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex that regulates transcription of stress response genes via histone acetylation. Consistent with this homology, the C. neoformans null mutant exhibits reduced histone H3 lysine 9 acetylation. It is also defective in response to a variety of stress conditions, demonstrating phenotypes that overlap with, but are not identical to, those of other fungi with altered SAGA complexes. The mutant also exhibits significant defects in sexual development and virulence. To establish the role of Ada2 in the broader network of capsule regulation we performed RNA-Seq on strains lacking either Ada2 or one of two other capsule regulators: Cir1 and Nrg1. Analysis of the results suggested that Ada2 functions downstream of both Cir1 and Nrg1 via components of the high osmolarity glycerol (HOG) pathway. To identify direct targets of Ada2, we performed ChIP-Seq analysis of histone acetylation in the Ada2 null mutant. These studies supported the role of Ada2 in the direct regulation of capsule and mating responses and suggested that it may also play a direct role in regulating capsule-independent antiphagocytic virulence factors. These results validate our experimental approach to dissecting capsule regulation and provide multiple targets for future investigation

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying transcription factors (TFs) involved in a specific process and used it to map regulation of the key virulence factor of a deadly fungus—its capsule. The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, midlevel, and “foreman” TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to laboratories focused on specific physiological processes

GNOSIS: the first instrument to use fibre Bragg gratings for OH suppression

GNOSIS is a prototype astrophotonic instrument that utilizes OH suppression fibres consisting of fibre Bragg gratings and photonic lanterns to suppress the 103 brightest atmospheric emission doublets between 1.47-1.7 microns. GNOSIS was commissioned at the 3.9-meter Anglo-Australian Telescope with the IRIS2 spectrograph to demonstrate the potential of OH suppression fibres, but may be potentially used with any telescope and spectrograph combination. Unlike previous atmospheric suppression techniques GNOSIS suppresses the lines before dispersion and in a manner that depends purely on wavelength. We present the instrument design and report the results of laboratory and on-sky tests from commissioning. While these tests demonstrated high throughput and excellent suppression of the skylines by the OH suppression fibres, surprisingly GNOSIS produced no significant reduction in the interline background and the sensitivity of GNOSIS and IRIS2 is about the same as IRIS2. It is unclear whether the lack of reduction in the interline background is due to physical sources or systematic errors as the observations are detector noise-dominated. OH suppression fibres could potentially impact ground-based astronomy at the level of adaptive optics or greater. However, until a clear reduction in the interline background and the corresponding increasing in sensitivity is demonstrated optimized OH suppression fibres paired with a fibre-fed spectrograph will at least provide a real benefits at low resolving powers.Comment: 15 pages, 13 figures, accepted to A

Effects of an evidence service on community-based AIDS service organizations' use of research evidence: A protocol for a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>To support the use of research evidence by community-based organizations (CBOs) we have developed 'Synthesized HIV/AIDS Research Evidence' (SHARE), which is an evidence service for those working in the HIV sector. SHARE consists of several components: an online searchable database of HIV-relevant systematic reviews (retrievable based on a taxonomy of topics related to HIV/AIDS and open text search); periodic email updates; access to user-friendly summaries; and peer relevance assessments. Our objective is to evaluate whether this 'full serve' evidence service increases the use of research evidence by CBOs as compared to a 'self-serve' evidence service.</p> <p>Methods/design</p> <p>We will conduct a two-arm randomized controlled trial (RCT), along with a follow-up qualitative process study to explore the findings in greater depth. All CBOs affiliated with Canadian AIDS Society (n = 120) will be invited to participate and will be randomized to receive either the 'full-serve' version of SHARE or the 'self-serve' version (a listing of relevant systematic reviews with links to records on PubMed and worksheets that help CBOs find and use research evidence) using a simple randomized design. All management and staff from each organization will be provided access to the version of SHARE that their organization is allocated to. The trial duration will be 10 months (two-month baseline period, six-month intervention period, and two month crossover period), the primary outcome measure will be the mean number of logins/month/organization (averaged across the number of users from each organization) between baseline and the end of the intervention period. The secondary outcome will be intention to use research evidence as measured by a survey administered to one key decision maker from each organization. For the qualitative study, one key organizational decision maker from 15 organizations in each trial arm (n = 30) will be purposively sampled. One-on-one semi-structured interviews will be conducted by telephone on their views about and their experiences with the evidence service they received, how helpful it was in their work, why it was helpful (or not helpful), what aspects were most and least helpful and why, and recommendations for next steps.</p> <p>Discussion</p> <p>To our knowledge, this will be the first RCT to evaluate the effects of an evidence service specifically designed to support CBOs in finding and using research evidence.</p> <p>Trial registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT01257724">NCT01257724</a></p