Transcriptome analyses of amoebic gill disease-affected atlantic salmon (Salmo salar) tissues reveal localized host gene suppression

The transcriptome response of Atlantic salmon (Salmo salar) displaying advanced stages of amoebic gill disease (AGD) was investigated. Naïve smolt were challenged with AGD for 19 days, at which time all fish were euthanized and their severity of infection quantified through histopathological scoring. Gene expression profiles were compared between heavily infected and naïve individuals using a 17 K Atlantic salmon cDNA microarray with real-time quantitative RT-PCR (qPCR) verification. Expression profiles were examined in the gill, anterior kidney, and liver. Twenty-seven transcripts were significantly differentially expressed within the gill; 20 of these transcripts were down-regulated in the AGD-affected individuals compared with naïve individuals. In contrast, only nine transcripts were significantly differentially expressed within the anterior kidney and five within the liver. Again the majority of these transcripts were down-regulated within the diseased individuals. A down-regulation of transcripts involved in apoptosis (procathepsin L, cathepsin H precursor, and cystatin B) was observed in AGD-affected Atlantic salmon. Four transcripts encoding genes with antioxidant properties also were down-regulated in AGD-affected gill tissue according to qPCR analysis. The most up-regulated transcript within the gill was an unknown expressed sequence tag (EST) whose expression was 218-fold (± SE 66) higher within the AGD affected gill tissue. Our results suggest that Atlantic salmon experiencing advanced stages of AGD demonstrate general down-regulation of gene expression, which is most pronounced within the gill. We propose that this general gene suppression is parasite-mediated, thus allowing the parasite to withstand or ameliorate the host response. © 2008 Springer Science+Business Media, LLC.

Resistance to amoebic gill disease (AGD) is characterised by the transcriptional dysregulation of immune and cell cycle pathways

Amoebic gill disease (AGD) is a parasite-mediated proliferative gill disease capable of affecting a range of teleost hosts. While a moderate heritability for AGD resistance in Atlantic salmon has been reported previously, the mechanisms by which individuals resist the proliferative effects remain poorly understood. To gain more knowledge of this commercially important trait, we compared gill transcriptomes of two groups of Atlantic salmon, one designated putatively resistant, and one designated putatively susceptible to AGD. Utilising a 17k Atlantic salmon cDNA microarray we identified 196 transcripts that were differentially expressed between the two groups. Expression of 11 transcripts were further examined with real-time quantitative RT-PCR (qPCR) in the AGD-resistant and AGD-susceptible animals, as well as non-infected naïve fish. Gene expression determined by qPCR was in strong agreement with the microarray analysis. A large number of differentially expressed genes were involved in immune and cell cycle responses. Resistant individuals displayed significantly higher expression of genes involved in adaptive immunity and negative regulation of the cell cycle. In contrast, AGD-susceptible individuals showed higher expression of acute phase proteins and positive regulators of the cell cycle. Combined with the gill histopathology, our results suggest AGD resistance is acquired rather than innately present, and that this resistance is for the most part associated with the dysregulation of immune and cell cycle pathways. © 2008 Elsevier Ltd. All rights reserved.

Analysis, characterisation and expression of gill-expressed carbonic anhydrase genes in the freshwater crayfish Cherax quadricarinatus

Changes in water quality parameters such as pH and salinity can have a significant effect on productivity of aquaculture species. Similarly, relative osmotic pressure influences various physiological processes and regulates expression of a number of osmoregulatory genes. Among those, carbonic anhydrase (CA) plays a key role in systemic acid–base balance and ion regulation. Redclaw crayfish (Cherax quadricarinatus) are unique in their ability to thrive in environments with naturally varied pH levels, suggesting unique adaptation to pH stress. To date, however, no studies have focused on identification and characterisation of CA or other osmoregulatory genes in C. quadricarinatus. Here, we analysed the redclaw gill transcriptome and characterized CA genes along with a number of other key osmoregulatory genes that were identified in the transcriptome. We also examined patterns of gene expression of these CA genes when exposed to three pH treatments. In total, 72,382,710 paired end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. Approximately 37% of contigs received significant BLAST hits and 22% were assigned gene ontology terms. Three full length CA isoforms; cytoplasmic CA (ChqCAc), glycosyl-phosphatidylinositol-linked CA (ChqCAg), and β-CA (ChqCA-beta) as well as two partial CA gene sequences were identified. Both partial CA genes showed high similarity to ChqCAg and appeared to be duplicated from the ChqCAg. Full length coding sequences of Na+/K+-ATPase, V-type H+-ATPase, sarcoplasmic Ca+-ATPase, arginine kinase, calreticulin and Cl− channel protein 2 were also identified. Only the ChqCAc gene showed significant differences in expression across the three pH treatments. These data provide valuable information on the gill expressed CA genes and their expression patterns in freshwater crayfish. Overall our data suggest an important role for the ChqCAc gene in response to changes in pH and in systemic acid–base balance in freshwater crayfish.

Comparative analysis of gill transcriptomes of two freshwater crayfish, Cherax cainii and C. destructor

We undertook deep sequencing of gill transcriptomes from two freshwater crayfish, Cherax cainii and Cherax destructor, in order to generate genomic resources for future genomics research. Over 83 and 100 million high quality (quality score (Q) ≥ 30) paired-end Illumina reads (150 bp) were assembled into 147,101 and 136,622 contigs in C. cainii and C. destructor, respectively. A total of 24,630 and 23,623 contigs received significant BLASTx hits and allowed the identification of multiple gill expressed candidate genes associated with pH and salinity balance. These functionally annotated transcripts will provide a resource to facilitate comparative genomic research in the genus Cherax, and in particular allow insights into respiratory and osmoregulatory physiology of this group of animals.

Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus

The pH and salinity balance mechanisms of crayfish are controlled by a set of transport-related genes. We identified a set of the genes from the gill transcriptome from a freshwater crayfish Cherax quadricarinatus using the Illumina NGS-sequencing technology. We identified and characterized carbonic anhydrase (CA) genes and some other key genes involved in systematic acid-base balance and osmotic/ionic regulation. We also examined expression patterns of some of these genes across different sublethal pH levels [1]. A total of 72,382,710 paired-end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. About 37% of the contigs received significant BLAST hits and 22% were assigned gene ontology terms. These data will assist in further physiological-genomic studies in crayfish.

Experiences in Passively Detecting Session Hijacking Attacks in IEEE 802.11 Networks

Current IEEE 802.11 wireless networks are vulnerable to session hijacking attacks as the existing standards fail to address the lack of authentication of management frames and network card addresses, and rely on loosely coupled state machines. Even the new WLAN security standard - IEEE 802.11i does not address these issues. In our previous work, we proposed two new techniques for improving detection of session hijacking attacks that are passive, computationally inexpensive, reliable, and have minimal impact on network performance. These techniques utilise unspoofable characteristics from the MAC protocol and the physical layer to enhance confidence in the intrusion detection process. This paper extends our earlier work and explores usability, robustness and accuracy of these intrusion detection techniques by applying them to eight distinct test scenarios. A correlation engine has also been introduced to maintain the false positives and false negatives at a manageable level. We also explore the process of selecting optimum thresholds for both detection techniques. For the purposes of our experiments, Snort-Wireless open source wireless intrusion detection system was extended to implement these new techniques and the correlation engine. Absence of any false negatives and low number of false positives in all eight test scenarios successfully demonstrated the effectiveness of the correlation engine and the accuracy of the detection techniques.

Intrusion detection techniques in wireless local area networks

This research investigates wireless intrusion detection techniques for detecting attacks on IEEE 802.11i Robust Secure Networks (RSNs). Despite using a variety of comprehensive preventative security measures, the RSNs remain vulnerable to a number of attacks. Failure of preventative measures to address all RSN vulnerabilities dictates the need for a comprehensive monitoring capability to detect all attacks on RSNs and also to proactively address potential security vulnerabilities by detecting security policy violations in the WLAN. This research proposes novel wireless intrusion detection techniques to address these monitoring requirements and also studies correlation of the generated alarms across wireless intrusion detection system (WIDS) sensors and the detection techniques themselves for greater reliability and robustness. The specific outcomes of this research are: A comprehensive review of the outstanding vulnerabilities and attacks in IEEE 802.11i RSNs. A comprehensive review of the wireless intrusion detection techniques currently available for detecting attacks on RSNs. Identification of the drawbacks and limitations of the currently available wireless intrusion detection techniques in detecting attacks on RSNs. Development of three novel wireless intrusion detection techniques for detecting RSN attacks and security policy violations in RSNs. Development of algorithms for each novel intrusion detection technique to correlate alarms across distributed sensors of a WIDS. Development of an algorithm for automatic attack scenario detection using cross detection technique correlation. Development of an algorithm to automatically assign priority to the detected attack scenario using cross detection technique correlation.

Challenging endoscopy reprocessing guidelines: a prospective study investigating the safe shelf life of flexible endoscopes in a tertiary gastroenterology unit.

Professional prac− tice guidelines for endoscope reprocessing re− commend reprocessing endoscopes between each case and proper storage following repro− cessing after the last case of the list. There is lim− ited empirical evidence to support the efficacy of endoscope reprocessing prior to use in the first case of the day; however, internationally, many guidelines continue to recommend this practice. The aim of this study is to estimate a safe shelf life for flexible endoscopes in a high−turnover gastroenterology unit. Materials and methods: In a prospective obser− vational study, all flexible endoscopes in active service during the 3−week study period were mi− crobiologically sampled prior to reprocessing be− fore the first case of the day (n = 200). The main outcome variables were culture status, organism cultured, and shelf life. Results: Among the total number of useable samples (n = 194), the overall contamination rate was 15.5 %, with a pathogenic contamination rate of 0.5 %. Mean time between last case one day and reprocessing before the first case on the next day (that is, shelf life) was 37.62 h (SD 36.47). Median shelf life was 18.8 h (range 5.27± 165.35 h). The most frequently identified organ− ism was coagulase−negative Staphylococcus, an environmental nonpathogenic organism. Conclusions: When processed according to es− tablished guidelines, flexible endoscopes remain free from pathogenic organisms between last case and next day first case use. Significant re− ductions in the expenditure of time and resources on reprocessing endoscopes have the potential to reduce the restraints experienced by high−turnover endoscopy units and improve ser− vice delivery.

Sex on premises venue (SOPV) health promotion project in response to sustained increases in HIV notifications

Background: Due to increases in HIV notifications in Queensland, a health promotion outreach project was developed with sex on premises venues (SOPV) in Brisbane. Methods: A health promotion officer (HPO) promoted safer sex behaviours among SOPV patrons over 14 months, including providing information, counselling and skills to enhance safer sexual behaviours and providing referrals. Surveys were introduced to facilitate discussions regarding HIV/sexually transmissible infections, testing and safer sex practices. Results: The project demonstrated feasibility within this highly sexualised environment, and was enhanced by careful monitoring and revising the procedure to improve patron/staff responses to the project. The introduction of a survey instrument was a significant contributor to the project’s effectiveness, providing opportunities for patrons to discuss a variety of key sexual health issues. Conclusions: This initiative reflected effective partnering between the Health Department, a community HIV/lesbian, gay, bisexual and transgender organisation and private industry. Despite initial difficulties, the presence of a health worker within an SOPV was acceptable to patrons and allowed for brief interventions to be conducted. This project was deemed effective for a limited time period and within certain constraints.

Water sensitive urban design : landscape planning and design to improve water quality in Shijiazhaung and Yueyang

Water quality issues are heavily dependent on land development and management decisions within river and lake catchments or watersheds. Economic benefits of urbanisation may be short‐ lived without cleaner environmental outcomes. However, whole‐of‐catchment thinking is not, as yet, as frequent a consideration in urban planning and development in China as it is in many other countries. Water is predominantly seen as a resource to be ‘owned’ by different jurisdictions and allocated to numerous users, both within a catchment and between catchments. An alternative to this approach is to think of water in the same way as other commodities that must be kept moving through a complex transport system. Water must ultimately arrive at particular destinations in the biosphere, although it travels across a broad landscape and may be held up temporarily at certain places along the way. While water extraction can be heavily controlled, water pollution is far more difficult to regulate. Both have significant impacts on water availability and flows both now and in the future. As Chinese cities strive to improve economic conditions for their citizens, new centres are being rebuilt and environmental valued

Gilding the lily : Ephraim Island

Gilding the Lily, a Gold Coast version of Ephraim, the biblical 'great kingdom to the north', is a $545 million development that will have 385 residences when it is finished in 2007. EDAW Australia's Brisbane office was responsible for the reclaimed island's landscape architecture.

From China with love

Like the Montagues and the Capulets, the East and West have had a great many affairs that have stirred suspicions of one another. But for those of us fortunate enough to cross the cultural divide, Gillian Lawson says there is much about which to be curious, excited and anxious.

Rhetoric of landscape architecture and interior design discourses : preparation for cross-disciplinary practice

The rhetoric of the pedagogic discourses of landscape architectural students and interior design students is described as part of a doctoral study undertaken to document practices and orientations prior to cross-disciplinary collaboration. We draw on the theoretical framework of Basil Bernstein, an educational sociologist, and the rhetorical method of Kenneth Burke, a literary dramatist, to study the grammars of ‘landscape’ representation employed within these disciplinary examples. We investigate how prepared final year students are for working in a cross-disciplinary manner. The discursive interactions of their work, as illustrated by four examples of drawn images and written text, are described. Our findings suggest that we need to concern ourselves aspects of our pedagogic discourse that brings uniqueness and value to our disciplines ,as well as that shared discourses between disciplines.

Rethinking regional green space networks in China

Ecological networks are often represented as utopian webs of green meandering through cities, across states, through regions and even across a country (Erickson, 2006, p.28; Fabos, 2004, p.326; Walmsley, 2006). While this may be an inspiring goal for some in developed countries, the reality may be somewhat different in developing countries. China, in its shift to urbanisation and suburbanisation, is also being persuaded to adjust its planning schemes according to these aspirational representations of green spaces (Yu et al, 2006, p.237; Zhang and Wang, 2006, p.455). The failure of other countries to achieve regional goals of natural and cultural heritage protection on the ground in this way (Peterson et al, 2007; Ryan et al, 2006; von Haaren and Reich, 2006) suggests that there may be flaws in the underpinning concepts that are widely circulated in North American and Western European literature (Jongman et al, 2004; Walmsley, 2006). In China, regional open space networks, regional green infrastructure or regional ecological corridors as we know them in the West, are also likely to be problematic, at least in the foreseeable future. Reasons supporting this view can be drawn from lessons learned from project experience in landscape planning and related fields of study in China and overseas. Implementation of valuable regional green space networks is problematic because: • the concept of region as a spatial unit for planning green space networks is ambiguous and undefinable for practical purposes; • regional green space networks traditionally require top down inter-governmental cooperation and coordination which are generally hampered by inequalities of influence between and within government agencies; • no coordinating body with funding powers exists for regional green space development and infrastructure authorities are still in transition from engineering authorities; • like other infrastructure projects, green space is likely to become a competitive rather than a complementary resource for city governments; • stable long-term management, maintenance and uses of green space networks must fit into a ‘family’ social structure rather than a ‘public good’ social structure, particularly as rural and urban property rights are being re-negotiated with city governments; and • green space provision is a performance indicator of urban improvement in cities within the city hierarchy and remains quantitatively-based (land area, tree number and per capita share) rather than qualitatively-based with local people as the focus.

Meeting and greeting : activities in public outdoor spaces outside high-density urban residential communities

This paper examines the opportunities for social activities in public outdoor spaces associated with high-density residential living. This study surveyed activities in outdoor spaces outside three high-density residential communities in Brisbane. Results indicated that activity patterns in public outdoor space outside residential communities are different to general urban public outdoor space. This broadly but not fully supports current theories concerning activities in public space. That is some environmental factors have impacts on the level of social interaction. The relationship between outdoor space and a residential building may have a significant impact on the level of social activities. As a consequence, a new classification of activities in public space is suggested. In improving the level of social contact in public outdoor space outside a residential community, the challenge is how to encourage people to leave their comfortable homes and spend a short time in these public spaces. For residential buildings and public space to be treated as an integrated whole, the outdoor open spaces close to and surrounding these buildings must have a more welcoming design.