In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL)

Background The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may lead to the design of better anti-cancer therapies. Recently, using a high resolution loss of heterozygosity (LOH) analysis, we identified a number of potential tumour suppressor genes (TSGs) within common LOH regions across cases suffering from two of the most common forms of Non-Hodgkin’s lymphoma (NHL), Follicular Lymphoma (FL) and Diffuse Large B-cell Lymphoma (DLBCL). From these studies LOH of the protein tyrosine phosphatase receptor type J (PTPRJ) gene was identified as a common event in the lymphomagenesis of these B-cell lymphomas. The present study aimed to determine the cellular pathways affected by the inactivation of these TSGs including PTPRJ in FL and DLBCL tumourigenesis. Results Pathway analytical approaches identified that candidate TSGs located within common LOH regions participate within cellular pathways, which may play a crucial role in FL and DLBCL lymphomagenesis (i.e., metabolic pathways). These analyses also identified genes within the interactome of PTPRJ (i.e. PTPN11 and B2M) that when inactivated in NHL may play an important role in tumourigenesis. We also detected genes that are differentially expressed in cases with and without LOH of PTPRJ, such as NFATC3 (nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3). Moreover, upregulation of the VEGF, MAPK and ERBB signalling pathways was also observed in NHL cases with LOH of PTPRJ, indicating that LOH-driving events causing inactivation of PTPRJ, apart from possibly inducing a constitutive activation of these pathways by reduction or abrogation of its dephosphorylation activity, may also induce upregulation of these pathways when inactivated. This finding implicates these pathways in the lymphomagenesis and progression of FL and DLBCL. Conclusions The evidence obtained in this research supports findings suggesting that FL and DLBCL share common pathogenic mechanisms. Also, it indicates that PTPRJ can play a crucial role in the pathogenesis of these B-cell tumours and suggests that activation of PTPRJ might be an interesting novel chemotherapeutic target for the treatment of these B-cell tumours.

Objective response to radiation therapy and long-term survival of patients with WHO grade II astrocytic gliomas with known LOH 1p/19q status

BACKGROUND: WHO grade II gliomas are often approached by radiation therapy (RT). However, little is known about tumor response and its potential impact on long-term survival. PATIENTS AND METHODS: Patients subjected to RT were selected from the own database of WHO grade II gliomas diagnosed between 1991 and 2000. The volumetric tumor response after RT was assessed based on magnetic resonance imaging and graded according to standard criteria as complete, partial (PR, >or= 50%), or minor (MR, 25% to <50%). RESULTS: There were 24 astrocytomas and three oligoastrocytomas. 21 patients (78%) were dead at follow-up (mean survival 74 months). None of the patients had chemotherapy. Objective response occurred in 14 patients (52%, five PR and nine MR) but was not associated with overall survival. The vast majority of the tumors had no loss of heterozygosity (LOH) 1p and/or 19q (86%). CONCLUSION: Approximately 50% of patients with astrocytic WHO grade II gliomas respond to RT despite the absence of LOH for 1p/19q. The potential predictive factors for response and the impact of response on overall survival remain unclear.

Ehren-Denkmaal : Dem Erbaren und berühmten Handwerk derer Loh- und Roth-Gerber, Sowohl im Heil. Röm. Reich, als auch andern Königl. und Fürstl. Provinzen und Ländern ... besonders gewiedmet

Ein dieser werthen Zunft mit Lieb und Neigung verbundenes Mitglied J. G. L. ; J. C. Zick fecit

Adjusting building thermostats for environmental gains : understanding the issues

There has been increasing reliance on mechanical heating, ventilation and air-conditioning (HVAC) systems to achieve thermal comfort in office buildings. The use of universal standards for thermal comfort adopted in air-conditioned spaces often results in a large disparity between mean daily external summer temperatures and temperatures experienced indoors. The extensive overuse of air-conditioning in warm climates not only isolates us from the vagaries of the external environment, but is generally dependent on non-renewable energy. A pilot study conducted at the Queensland University of Technology (QUT) involved altering the thermostat set-points to two or three degrees above the normal summer setting in two air-conditioned buildings during the subtropical summer. This paper presents the findings of the research that led to the formulation of the test study. The findings of the test study are printed in the companion paper DES 72: Adjusting Building Thermastats for Environmental Gains – a Pilot Study.

Living walls - a way to green the built environment

Actions Towards Sustainable Outcomes Environmental Issues/Principal Impacts The increasing urbanisation of cities brings with it several detrimental consequences, such as: • Significant energy use for heating and cooling many more buildings has led to urban heat islands and increased greenhouse gas emissions. • Increased amount of hard surfaces, which not only contributes to higher temperatures in cities, but also to increased stormwater runoff. • Degraded air quality and noise. • Health and general well-being of people is frequently compromised, by inadequate indoor air quality. • Reduced urban biodiversity. Basic Strategies In many design situations, boundaries and constraints limit the application of cutting EDGe actions. In these circumstances, designers should at least consider the following: • Living walls are an emerging technology, and many Australian examples function more as internal feature walls. However,as understanding of the benefits and construction of living walls develops this technology could be part of an exterior facade that enhances a building’s thermal performance. • Living walls should be designed to function with an irrigation system using non-potable water. Cutting EDGe Strategies • Living walls can be part of a design strategy that effectively improves the thermal performance of a building, thereby contributing to lower energy use and greenhouse gas emissions. • Including living walls in the initial stages of design would provide greater flexibility to the design, especially of the facade, structural supports, mechanical ventilation and watering systems, thus lowering costs. • Designing a building with an early understanding of living walls can greatly reduce maintenance costs. • Including plant species and planting media that would be able to remove air impurities could contribute to improved indoor air quality, workplace productivity and well-being. Synergies and References • Living walls are a key research topic at the Centre for Subtropical Design, Queensland University of Technology: http://www.subtropicaldesign.bee.qut.edu.au • BEDP Environment Design Guide: DES 53: Roof and Facade Gardens • BEDP Environment Design Guide: GEN 4: Positive Development – Designing for Net Positive Impacts (see green scaffolding and green space frame walls). • Green Roofs Australia: www.greenroofs.wordpress.com • Green Roofs for Healthy Cities USA: www.greenroofs.org

Green a city grow a wall

As Brisbane grows, it is rapidly becoming akin to any other city in the world with its typical stark grey concrete buildings rather than being characterized by its subtropical element of abundant green vegetation. Living Walls can play a vital role in restoring the loss of this distinct local element of a subtropical city. This paper will start by giving an overview of the traditional methods of greening subtropical cities with the use of urban parks and street trees. Then, by examining a recent heat imaging map of Brisbane, the effect of green cover with the built environment will be shown. With this information from a macro level, this paper will proceed to examine a typical urban block within the Central Business District (CBD) to demonstrate urban densification in relation to greenery in the city. Then, this paper will introduce the new technology where Living Walls have the untapped potential of effectively greening a city where land is scarce and given over to high density development. Living Walls incorporated into building design does not only enhance the subtropical lifestyle that is being lost in modern cities but is also an effective means for addressing climate change. This paper will serve as a preliminary investigation into the effects of incorporating Living Walls into cities. By growing a Living Wall onto buildings, we can be part of an effective design solution for countering global warming and at the same time, Living Walls can return local character to subtropical cities, thereby greening the city as well.

A comparative study : regulatory requirements on subdivisions for increasing passive cooling

A major project in the Sustainable Built Assets core area is the Sustainable Sub-divisions – Ventilation Project that is the second stage of a planned series of research projects focusing on sustainable sub-divisions. The initial project, Sustainable Sub-divisions: Energy focused on energy efficiency and examined the link between dwelling energy efficiency and sub-divisional layout. In addition, the potential for on site electricity generation, especially in medium and high-density developments, was also examined. That project recommended that an existing lot-rating methodology be adapted for use in SEQ through the inclusion of sub divisional appropriate ventilation data. Acquiring that data is the object of this project. The Sustainable Sub-divisions; Ventilation Project will produce a series of reports. The first report (Report 2002-077-B-01) summarised the results from an industry workshop and interviews that were conducted to ascertain the current attitudes and methodologies used in contemporary sub-division design in South East Queensland. The second report (Report 2002-077-B-02) described how the project is being delivered as outlined in the Project Agreement. It included the selection of the case study dwellings and monitoring equipment and data management process. This third report (Report 2002-077-B-03) provides an analysis and review of the approaches recommended by leading experts, government bodies and professional organizations throughout Australia that aim to increase the potential for passive cooling and heating at the subdivision stage. This data will inform issues discussed on the development of the enhanced lot-rating methodology in other reports of this series. The final report, due in June 2007, will detail the analysis of data for winter 2006 and summer 2007, leading to the development and delivery of the enhanced lot-rating methodology.

Direct writing of chitosan scaffolds using a robotic system

Purpose – This paper aims to present a novel rapid prototyping (RP) fabrication methods and preliminary characterization for chitosan scaffolds. Design – A desktop rapid prototyping robot dispensing (RPBOD) system has been developed to fabricate scaffolds for tissue engineering (TE) applications. The system is a computer-controlled four-axis machine with a multiple-dispenser head. Neutralization of the acetic acid by the sodium hydroxide results in a precipitate to form a gel-like chitosan strand. The scaffold properties were characterized by scanning electron microscopy, porosity calculation and compression test. An example of fabrication of a freeform hydrogel scaffold is demonstrated. The required geometric data for the freeform scaffold were obtained from CT-scan images and the dispensing path control data were converted form its volume model. The applications of the scaffolds are discussed based on its potential for TE. Findings – It is shown that the RPBOD system can be interfaced with imaging techniques and computational modeling to produce scaffolds which can be customized in overall size and shape allowing tissue-engineered grafts to be tailored to specific applications or even for individual patients. Research limitations/implications – Important challenges for further research are the incorporation of growth factors, as well as cell seeding into the 3D dispensing plotting materials. Improvements regarding the mechanical properties of the scaffolds are also necessary. Originality/value – One of the important aspects of TE is the design scaffolds. For customized TE, it is essential to be able to fabricate 3D scaffolds of various geometric shapes, in order to repair tissue defects. RP or solid free-form fabrication techniques hold great promise for designing 3D customized scaffolds; yet traditional cell-seeding techniques may not provide enough cell mass for larger constructs. This paper presents a novel attempt to fabricate 3D scaffolds, using hydrogels which in the future can be combined with cells.

Green roofs : understanding their benefits for Australia

Summary of Actions Towards Sustainable Outcomes Environmental Issues / Principal Impacts The increased growth of cities is intensifying its impact on people and the environment through: • increased use of energy for the heating and cooling of more buildings, leading to urban heat islands and more greenhouse gas emissions • increased amount of hard surfaces contributing to higher temperatures in cities and more stormwater runoff • degraded air quality and noise impact • reduced urban biodiversity • compromised health and general well-being of people Basic Strategies In many design situations boundaries and constraints limit the application of cutting EDGe actions. In these circumstances designers should at least consider the following: • Consider green roofs early in the design process in consultation with all stakeholders to enable maximised integration with building systems and to mitigate building cost (avoid constructing as a retrofit). • Design of the green roof as part of a building’s structural, mechanical and hydraulic systems could lead to structural efficiency, the ability to optimise cooling benefits and better integrated water recycling systems. • Inform the selection of the type of green roof by considering its function, for example designing for social activity, required maintenance/access regime, recycling of water or habitat regeneration or a combination of uses. • Evaluate existing surroundings to determine possible links to the natural environment and choice of vegetation for the green roof with availability of local plant supply and expertise. Cutting EDGe Strategies • Create green roofs to contribute positively to the environment through reduced urban heat island effect and building temperatures, to improved stormwater quality, increased natural habitats, provision of social spaces and opportunity for increased local food supply. • Maximise solar panel efficiency by incorporating with design of green roof. • Integrate multiple functions for a single green roof such as grey water recycling, food production, more bio-diverse plantings, air quality improvement and provision of delightful spaces for social interaction. Synergies & references • BEDP Environment Design Guide DES 53: Roof and Facade Gardens GEN 4: Positive Development – designing for Net Positive Impacts TEC 26: Living Walls - a way to green the built environment • Green Roofs Australia: www.greenroofs.wordpress.com • International Green Roof Association: www.igra-world.com • Green Roofs for Healthy Cities (USA): www.greenroofs.org • Centre for Urban Greenery and Ecology (Singapore): http://research.cuge.com.sg

Accommodating serendipity in the active studio

This paper presents a series of ongoing experiments to facilitate serendipity in the design studio through a diversity of delivery modes. These experiments are conducted in a second year architectural design studio, and include physical, dramatic and musical performance. The act of designing is always exploratory, always seeking an unknown resolution, and the ability to see and capture the value in the unexpected is a critical aspect of such creative design practice. Engaging with the unexpected is however a difficult ability to develop in students. Just how can a student be schooled in such abilities when the challenge and the context are unforeseeable? How can students be offered meaningful feedback about an issue that cannot be predicted, when feedback comes in the form of extrinsic assessment from a tutor? This project establishes a number of student activities that seek to provide intrinsic feedback from the activity itself. Further to this, the project seeks to heighten student engagement with the project through physical expression and performance: utilising more of the students’ senses than just vision and hearing. Diana Laurillard’s theories of conversational frameworks (2002) are used to interrogate the act of dramatic performance as an act of learning, with particular reference to the serendipitous activities of design. Such interrogation highlights the feedback mechanisms that facilitate intrinsic feedback and fast, if not instantaneous, cycles of learning. The physical act of performance itself provides a learning experience that is not replicable in other modes of delivery. Student feedback data and independent assessment of project outcomes are used to assess the success of this studio model.

CDKN2A is not the principal target of deletions on the short arm of chromosome 9 in neuroendocrine (Merkel cell) carcinoma of the skin

The majority of small-cell lung cancers (SCLCs) express p16 but not pRb. Given our previous study showing loss of pRb in Merkel cell carcinoma (MCC)/neuroendocrine carcinoma of the skin and the clinicopathological similarities between SCLC and MCC, we wished to determine if this was also the case in MCC. Twenty-nine MCC specimens from 23 patients were examined for deletions at 10 loci on 9p and 1 on 9q. No loss of heterozygosity (LOH) was seen in 9 patients including 2 for which tumour and cell line DNAs were examined. Four patients had LOH for all informative loci on 9p. Ten tumours showed more limited regions of loss on 9p, and from these 2 common regions of deletion were determined. Half of all informative cases had LOH at D9S168, the most telomeric marker examined, and 3 specimens showed loss of only D9S168. A second region (IFNA-D9S126) showed LOH in 10 (44%) cases, and case MCC26 showed LOH for only D9S126, implicating genes centromeric of the CDKN2A locus. No mutations in the coding regions of p16 were seen in 7 cell lines tested, and reactivity to anti-p16 antibody was seen in all 11 tumour specimens examined and in 6 of 7 cell lines from 6 patients. Furthermore, all cell lines examined reacted with anti-p14(ARF) antibody. These results suggest that neither transcript of the CDKN2A locus is the target of deletions on 9p in MCC and imply the existence of tumour-suppressor genes mapping both centromeric and telomeric of this locus.

Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development

Cytogenetic and loss of heterozygosity (LOH) studies have long indicated the presence of a tumor suppressor gene (TSG) on 9p involved in the development of melanoma. Although LOH at 9p has been reported in approximately 60% of melanoma tumors, only 5-10% of these tumors have been shown to carry CDKN2A mutations, raising the possibility that another TSG involved in melanoma maps to chromosome 9p. To investigate this possibility, a panel of 37 melanomas derived from 35 individuals was analyzed for CDKN2A mutations by single-strand conformation polymorphism analysis and sequencing. The melanoma samples were then typed for 15 markers that map to 9p13-24 to investigate LOH trends in this region. In those tumors demonstrating retention of heterozygosity at markers flanking CDKN2A and LOH on one or both sides of the gene, multiplex microsatellite PCR was performed to rule out homozygous deletion of the region encompassing CDKN2A. CDKN2A mutations were found in tumors from 5 patients [5 (14%) of 35], 4 of which demonstrated LOH across the entire region examined. The remaining tumor with no observed LOH carried two point mutations, one on each allele. Although LOH was identified at one or more markers in 22 (59%) of 37 melanoma tumors corresponding to 20 (57%) of 35 individuals, only 11 tumors from 9 individuals [9 (26%) of 35] demonstrated LOH at D9S942 and D9S1748 the markers closest to CDKN2A. Of the remaining 11 tumors with LOH 9 demonstrated LOH at two or more contiguous markers either centromeric and/or telomeric to CDKN2A while retaining heterozygosity at several markers adjacent to CDKN2A. Multiplex PCR revealed one tumor carried a homozygous deletion extending from D9S1748 to the IFN-alpha locus. In the remaining eight tumors, multiplex PCR demonstrated that the observed heterozygosity was not attributable to homozygous deletion and stromal contamination at D9S1748, D9S942, or D9S974, as measured by comparative amplification strengths, which indicates that retention of heterozygosity with flanking LOH does not always indicate a homozygous deletion. This report supports the conclusions of previous studies that a least two TSGs involved in melanoma development in addition to CDKN2A may reside on chromosome 9p.

PTEN inactivation is rare in melanoma tumours but occurs frequently in melanoma cell lines

Deletions detected in cytogenetic and loss of heterozygosity (LOH) studies indicate that at least one tumour suppressor gene maps to the long arm of chromosome 10. Previous deletion mapping studies have observed LOH on 10q in about 30% of melanomas analysed. The PTEN gene, mapping to chromosome band 10q23.3, encodes a protein with both lipid and protein phosphatase activity. Somatic mutations and deletions in have been detected in a variety of cell lines and tumours, including melanoma samples. We performed mutation analyses and extensive allelic loss studies to investigate the role this gene plays in melanoma pathogenesis. We found that a total of 34 out of 57 (60%) melanoma cell lines carried hemizygous deletions of chromosome 10q encompassing the PTEN locus. A further three cell lines carried smaller deletions excluding PTEN. Inactivation of both PTEN alleles by exon-specific homozygous deletion or mutation was observed in 13 out of 57 (23%) melanoma cell lines. The mutation spectrum observed does not indicate an important role for ultraviolet radiation in the genesis of these mutations, and evidence from three cell lines supports the acquisition of PTEN aberrations in culture. Ten out of 49 (20%) matched melanoma tumour/normal samples harboured hemizygous deletions of either the whole chromosome or most of the long arm. Mutations within were detected in only one of the 10 tumours demonstrating LOH at 10q23 that were analysed. These results suggest that PTEN inactivation may be important for the propagation of melanoma cells in culture, and that another chromosome 10 tumour suppressor gene may be important for melanoma pathogenesis.