Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

‘Supersize me’ : on equine obesity

There’s nothing like travel to broaden the mind. As a young man living in Britain during the 1980s I thought I knew about human obesity, but it took a visit to the US to show me what an epidemic looks like. Nowadays I live in Australia, where human obesity is rife. We have plenty of fat horses too (Sillence et al., 2006), but they are noticeable. In fact, it was only recently during a return visit to Britain, that I was finally sold on the concept of an equine obesity epidemic. It seems that in the UK, the fat horse or pony is now so commonplace that it has come to represent the norm in the eyes of many owners. I met clinicians who claim to have forgotten what a fit horse looks like, and heard anecdotes of a responsible owner who kept their animals in a healthy body condition, only to be reported to the RSPCA for ‘cruelty’. Round and shiny have become the order of the day and, as we have learned from the tsunami of human obesity, once a problem reaches a certain scale it can seem unstoppable, despite the attendant risks, costs and consequences.

Nitrous oxide emissions from subtropical horticultural soils : a time series analysis

Time series regression models were used to examine the influence of environmental factors (soil water content and soil temperature) on the emissions of nitrous oxide (N2O) from subtropical soils, by taking into account temporal lagged environmental factors, autoregressive processes, and seasonality for three horticultural crops in a subtropical region of Australia. Fluxes of N2O, soil water content, and soil temperature were determined simultaneously on a weekly basis over a 12-month period in South East Queensland. Annual N2O emissions for soils under mango, pineapple, and custard apple were 1590, 1156, and 2038 g N2O-N/ha, respectively, with most emissions attributed to nitrification. The N2O-N emitted from the pineapple and custard apple crops was equivalent to 0.26 and 2.22%, respectively, of the applied mineral N. The change in soil water content was the key variable for describing N2O emissions at the weekly time-scale, with soil temperature at a lag of 1 month having a significant influence on average N2O emissions (averaged) at the monthly time-scale across the three crops. After accounting for soil temperature and soil water content, both the weekly and monthly time series regression models exhibited significant autocorrelation at lags of 1–2 weeks and 1–2 months, and significant seasonality for weekly N2O emissions for mango crop and for monthly N2O emissions for mango and custard apple crops in this location over this time-frame. Time series regression models can explain a higher percentage of the temporal variation of N2O emission compared with simple regression models using soil temperature and soil water content as drivers. Taking into account seasonal variability and temporal persistence in N2O emissions associated with soil water content and soil temperature may lead to a reduction in the uncertainty surrounding estimates of N2O emissions based on limited sampling effort.

Bioreactor for blood product production

The feasibility of ex vivo blood production is limited by both biological and engineering challenges. From an engineering perspective, these challenges include the significant volumes required to generate even a single unit of a blood product, as well as the correspondingly high protein consumption required for such large volume cultures. Membrane bioreactors, such as hollow fiber bioreactors (HFBRs), enable cell densities approximately 100-fold greater than traditional culture systems and therefore may enable a significant reduction in culture working volumes. As cultured cells, and larger molecules, are retained within a fraction of the system volume, via a semipermeable membrane it may be possible to reduce protein consumption by limiting supplementation to only this fraction. Typically, HFBRs are complex perfusion systems having total volumes incompatible with bench scale screening and optimization of stem cell-based cultures. In this article we describe the use of a simplified HFBR system to assess the feasibility of this technology to produce blood products from umbilical cord blood-derived CD34+ hematopoietic stem progenitor cells (HSPCs). Unlike conventional HFBR systems used for protein manufacture, where cells are cultured in the extracapillary space, we have cultured cells in the intracapillary space, which is likely more compatible with the large-scale production of blood cell suspension cultures. Using this platform we direct HSPCs down the myeloid lineage, while targeting a 100-fold increase in cell density and the use of protein-free bulk medium. Our results demonstrate the potential of this system to deliver high cell densities, even in the absence of protein supplementation of the bulk medium.

An exploration of the professional competencies required in engineering asset management

Engineering asset management (EAM) is a rapidly growing and developing field. However, efforts to select and develop engineers in this area are complicated by our lack of understanding of the full range of competencies required to perform. This exploratory study sought to clarify and categorise the professional competencies required of individuals at different hierarchical levels within EAM. Data from 14 interviews and 61 on-line survey participants has informed the development of an initial Professional Competency Framework. The nine competency categories indicate that Engineers working in this field need to be able to collaborate and influence others, complete objectives within organizational guidelines and be able to manage themselves effectively. Limitations and potential uses in practice and research for this framework are discussed.

Using social media to facilitate knowledge transfer in complex engineering environments : a primer for educators

While highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Consequently, an essential challenge for engineering organisations wishing to overcome informational silos is to implement mechanisms that facilitate, encourage and sustain interactions between otherwise disconnected groups. This paper acts as a primer for those seeking to gain an understanding of the design, functionality and utility of a suite of software tools generically termed social media technologies in the context of optimising the management of tacit engineering knowledge. Underpinned by knowledge management theory and using detailed case examples, this paper explores how social media technologies achieve such goals, allowing for the transfer of knowledge by tapping into the tacit and explicit knowledge of disparate groups in complex engineering environments.

Bone tissue engineering : from bench to bedside - Review article

The drive to develop bone grafts for the filling of major gaps in the skeletal structure has led to a major research thrust towards developing biomaterials for bone engineering. Unfortunately, from a clinical perspective, the promise of bone tissue engineering which was so vibrant a decade ago has so far failed to deliver the anticipated results of becoming a routine therapeutic application in reconstructive surgery. Here we describe the analysis of long-term bone regeneration studies in preclinical animal models, exploiting methods of micro- and nano analysis of biodegradable composite scaffolds.

Direct fabrication as a patient-targeted therapeutic in a clinical environment

A paradigm shift is taking place in orthopaedic and reconstructive surgery. This transition from using medical devices and tissue grafts towards the utilization of a tissue engineering approach combines biodegradable scaffolds with cells and/or biological molecules in order to repair and/or regenerate tissues. One of the potential benefits offered by solid freeform fabrication (SFF) technologies is the ability to create such biodegradable scaffolds with highly reproducible architecture and compositional variation across the entire scaffold due to their tightly controlled computer-driven fabrication. Many of these biologically activated materials can induce bone formation at ectopic and orthotopic sites, but they have not yet gained widespread use due to several continuing limitations, including poor mechanical properties, difficulties in intraoperative handling, lack of porosity suitable for cellular and vascular infiltration, and suboptimal degradation characteristics. In this chapter, we define scaffold properties and attempt to provide some broad criteria and constraints for scaffold design and fabrication in combination with growth factors for bone engineering applications. Lastly, we comment on the current and future developments in the field, such as the functionalization of novel composite scaffolds with combinations of growth factors designed to promote cell attachment, cell survival, vascular ingrowth, and osteoinduction.

Effects of oxygen and culture system on in vitro propagation and redifferentiation of osteoarthritic human articular chondrocytes

Regenerative medicine-based approaches for the repair of damaged cartilage rely on the ability to propagate cells while promoting their chondrogenic potential. Thus, conditions for cell expansion should be optimized through careful environmental control. Appropriate oxygen tension and cell expansion substrates and controllable bioreactor systems are probably critical for expansion and subsequent tissue formation during chondrogenic differentiation. We therefore evaluated the effects of oxygen and microcarrier culture on the expansion and subsequent differentiation of human osteoarthritic chondrocytes. Freshly isolated chondrocytes were expanded on tissue culture plastic or CultiSpher-G microcarriers under hypoxic or normoxic conditions (5% or 20% oxygen partial pressure, respectively) followed by cell phenotype analysis with flow cytometry. Cells were redifferentiated in micromass pellet cultures over 4 weeks, under either hypoxia or normoxia. Chondrocytes cultured on tissue culture plastic proliferated faster, expressed higher levels of cell surface markers CD44 and CD105 and demonstrated stronger staining for proteoglycans and collagen type II in pellet cultures compared with microcarrier-cultivated cells. Pellet wet weight, glycosaminoglycan content and expression of chondrogenic genes were significantly increased in cells differentiated under hypoxia. Hypoxia-inducible factor-3alpha mRNA was up-regulated in these cultures in response to low oxygen tension. These data confirm the beneficial influence of reduced oxygen on ex vivo chondrogenesis. However, hypoxia during cell expansion and microcarrier bioreactor culture does not enhance intrinsic chondrogenic potential. Further improvements in cell culture conditions are therefore required before chondrocytes from osteoarthritic and aged patients can become a useful cell source for cartilage regeneration.

Bone tissue engineering

Currently, well-established clinical therapeutic approaches for bone reconstruction are restricted to the transplantation of autografts and allografts, and the implantation of metal devices or ceramic-based implants to assist bone regeneration. These standard techniques face significant disadvantages. As a result, research has focused on the development of alternative therapeutic concepts aiming to design and engineer unparalleled structural and functional bone grafts. Substantial academic and commercial interest has been sparked in bone engineering methods to stimulate, control and eventually replicate key events of bone regeneration ex vivo. Over the years, this interest has further increased and bone tissue engineering has now become a well-recognized research discipline in the area of regenerative medicine. The following chapter gives an overview of bone tissue engineering principles. It focuses on research related to the combination of scaffolds with multipotent precursor cells, such as bone marrow-derived mesenchymal stem cells or human umbilical cord perivascular cells, and the clinical applications of these tissue engineered bone constructs.

Contextualizing a university-school STEM education collaboration : distributed and self-activated leadership for project outcomes

Implementing educational reform requires partnerships, and university-school collaborations in the form of investigative and experimental projects can aim to determine the practicalities of reform. However, there are funded projects that do not achieve intended outcomes. In the context of a new reform initiative in education, namely, science, technology, engineering and mathematics (STEM) education, this article explores the management of a government-funded project. In a university school partnership for STEM education, how can leadership be distributed for achieving project outcomes? Participants included university personnel from different STEM areas, school teachers and school executives. Data collected included observations, interviews, resource materials, and video and photographic images. Findings indicated that leadership roles were distributed and selfactivated by project partners according to their areas of expertise and proximal activeness to the project phases, that is: (1) establishing partnerships; (2) planning and collaboration; (3) project implementation; and (4) project evaluation and further initiatives. Leadership can be intentional and unintentional within project phases, and understanding how leadership can be distributed and selfactivated more purposefully may aid in generating more expedient project outcomes.

Protein monoubiquitination and polyubiquitination generate structural diversity to control distinct biological processes

Ubiquitination involves the attachment of ubiquitin (Ub) to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Polyubiquitination through different lysines (seven) or the N-terminus of Ub can generate different protein-Ub structures. These include monoubiquitinated proteins, polyubiqutinated proteins with homotypic chains through a particular lysine on Ub or mixed polyubiquitin chains generated by polymerization through different Ub lysines. The ability of the ubiquitination pathway to generate different protein-Ub structures provides versatility of this pathway to target proteins to different fates. Protein ubiquitination is catalyzed by Ub-conjugating and Ub-ligase enzymes, with different combinations of these enzymes specifying the type of Ub modification on protein substrates. How Ub-conjugating and Ub-ligase enzymes generate this structural diversity is not clearly understood. In the current review, we discuss mechanisms utilized by the Ub-conjugating and Ub-ligase enzymes to generate structural diversity during protein ubiquitination, with a focus on recent mechanistic insights into protein monoubiquitination and polyubiquitination.

From tiers to tables – enhancing student experience through collaborative learning spaces

BACKGROUND Collaborative and active learning have been clearly identified as ways students can engage in learning with each other and the academic staff. Traditional tier based lecture theatres and the didactic style they engender are not popular with students today as evidenced by the low attendance rates for lectures. Many universities are installing spaces designed with tables for group interaction with evolutions on spaces such as the TEAL (Technology Enabled Active Learning) (Massachusetts Institute of Technology, n.d.) and SCALE-UP (Student-Centred Activities for Large-Enrolment Undergraduate Programs) (North Carolina State University, n.d.) models. Technology advances in large screen computers and applications have also aided the move to these collaborative spaces. How well have universities structured learning using these spaces and how have students engaged with the content, technology, space and each other? This paper investigates the application of collaborative learning in such spaces for a cohort of 800+ first year engineers in the context of learning about and developing professional skills representative of engineering practice. PURPOSE To determine whether moving from tiers to tables enhances the student experience. Does utilising technology rich, activity based, collaborative learning spaces lead to positive experiences and active engagement of first year undergraduate engineering students? In developing learning methodology and approach in new learning spaces, what needs to change from a more traditional lecture and tutorial configuration? DESIGN/METHOD A post delivery review and analysis of outcomes was undertaken to determine how well students and tutors engaged with learning in new collaborative learning spaces. Data was gathered via focus group and survey of tutors, students survey and attendance observations. The authors considered the unit delivery approach along with observed and surveyed outcomes then conducted further review to produce the reported results. RESULTS Results indicate high participation in the collaborative sessions while the accompanying lectures were poorly attended. Students reported a high degree of satisfaction with the learning experience; however more investigation is required to determine the degree of improvement in retained learning outcomes. Survey feedback from tutors found that students engaged well in the activities during tutorials and there was an observed improvement in the quality of professional practice modelled by students during sessions. Student feedback confirmed the positive experiences in these collaborative learning spaces with 30% improvement in satisfaction ratings from previous years. CONCLUSIONS It is concluded that the right mix of space, technology and appropriate activities does engage students, improve participation and create a rich experience to facilitate potential for improved learning outcomes. The new Collaborative Teaching Spaces, together with integrated technology and tailored activities, has transformed the delivery of this unit and improved student satisfaction in tutorials significantly.