A Hybrid Sequencing Approach Completes the Genome Sequence of Thermoanaerobacter ethanolicus JW 200

Thermoanaerobacter ethanolicus JW 200 has been identified as a potential sustainable biofuel producer due to its ability to readily ferment carbohydrates to ethanol. A hybrid sequencing approach, combining Oxford Nanopore and Illumina DNA sequence reads, was applied to produce a single contiguous genome sequence of 2,911,280 bp

A Low-cost Novel Optical Sensor for In Situ Water Quality Monitoring

With increasing environmental pressure due to global climate change, increases in global population and the need for sustainable obtained resources, water resources management is critical. In-situ sensors are fundamental to the management of water systems by providing early warning, forecasting and baseline data to stakeholders. To be fit-for-purpose, monitoring using in-situ sensors has to be carried out in a cost effective way and allow implementation at larger spatial scales. If networks of sensors are to become not only a reality but common place, it is necessary to produce reliable, inexpensive, rugged sensors integrated with data analytics. In this context, the aim of this project was to design and develop a low cost, robust and reliable optical sensor which capable of continuous measurement of chemical and physical parameters in aquatic environments. An iterative engineering design method cycling between sensor design, prototyping and testing was used for the realisation and optimisation of the sensor. The sensor can provide absorption, scatter, and fluorescence readings over a broad spectral range (280nm to 850nm) and temperature readings in real-time using a suite of optical sensors (CMOS Spectrometers and photodiode detector), custom designed LED array light source and a digital temperature probe. Custom electronics and firmware were developed to control the sensor and facilitate data transmission to an external network. Sensor electronics are housed in a marine grade watertight housing; the optical components are mounted inside a custom designed 3D-printed optical head which joins with the sensor housing. The sensor is capable of measuring a range of optical parameters and temperature in a single measurement cycle. Sensor analytical performance was demonstrated in the laboratory, for detection and quantification of turbidity using analytical standards and in the field by comparison with a commercially available multi- parameter probe (YSI, EXO 2). The laboratory and field trials demonstrate that the sensor is fit-for-purpose and an excellent tool for early warning monitoring by providing high frequency time-series data, operate unattended in-situ for extended periods of times and capture pollution events

Links between the three-dimensional movements of whale sharks (Rhincodon typus) and the bio-physical environment off a coral reef

Funding: This research was supported by funding from Santos Ltd and The Australian Institute of Marine Science (AIMS).Background Measuring coastal-pelagic prey fields at scales relevant to the movements of marine predators is challenging due to the dynamic and ephemeral nature of these environments. Whale sharks (Rhincodon typus) are thought to aggregate in nearshore tropical waters due to seasonally enhanced foraging opportunities. This implies that the three-dimensional movements of these animals may be associated with bio-physical properties that enhance prey availability. To date, few studies have tested this hypothesis. Methods Here, we conducted ship-based acoustic surveys, net tows and water column profiling (salinity, temperature, chlorophyll fluorescence) to determine the volumetric density, distribution and community composition of mesozooplankton (predominantly euphausiids and copepods) and oceanographic properties of the water column in the vicinity of whale sharks that were tracked simultaneously using satellite-linked tags at Ningaloo Reef, Western Australia. Generalised linear mixed effect models were used to explore relationships between the 3-dimensional movement behaviours of tracked sharks and surrounding prey fields at a spatial scale of ~ 1 km. Results We identified prey density as a significant driver of horizontal space use, with sharks occupying areas along the reef edge where densities were highest. These areas were characterised by complex bathymetry such as reef gutters and pinnacles. Temperature and salinity profiles revealed a well-mixed water column above the height of the bathymetry (top 40 m of the water column). Regions of stronger stratification were associated with reef gutters and pinnacles that concentrated prey near the seabed, and entrained productivity at local scales (~ 1 km). We found no quantitative relationship between the depth use of sharks and vertical distributions of horizontally averaged prey density. Whale sharks repeatedly dove to depths where spatially averaged prey concentration was highest but did not extend the time spent at these depth layers. Conclusions Our work reveals previously unrecognized complexity in interactions between whale sharks and their zooplankton prey.Publisher PDFPeer reviewe

A novel dynamic passive sampling approach for the marine monitoring of emerging contaminants

Anthropogenic contaminants enter the marine environment directly from land-based sources, however they can also be emitted or re-mobilised in the marine environment. The EU Marine Strategy Framework Directive (MSFD) is responsible for providing provisions against the pollution of marine waters by chemical substances. These contaminants are of great concern due to their known toxicological effects (i.e., endocrine disruption, immunotoxicity), with some known to accumulative in organisms and food webs. However, it is impossible to capture all contaminants that may be present in this dynamic marine environment. As a result, many of these chemicals and chemical mixtures have been characterised as ‘contaminants of emerging concern’ (CECs). Passive samplers can accumulate pollutants and concentrate sufficient amounts of pollutants from water for chemical analysis where spot sampling methods often fail. This study evaluates the use of a novel dynamic passive sampling approach for the determination of CECs in seawater

Biofouling studies on marine rated materials and coatings

Materials immersed in water experience a series of biological and chemical processes, resulting in the formation of complex layers with attached organism, known as biofouling. Biofouling In the aquatic environment shortens the life-time of immersed structures increases fuel consumption of ships and affects the functioning and data quality of water Instrumentation. All immersed instrumentation, including operational components (membranes, optical windows and electrodes), housings and mooring components are subject to biofouling and prone to irreversible damage. In marine environments biofouling has long been considered a limiting factor and is recognised as one of the main obstacles for long term in-situ monitoring. For a large percentage of deployed instrumentation, biofouling is the single biggest factor affecting the operation, maintenance, and data quality and responsible for high ownership costs to the point where it becomes prohibitively expensive to maintain operational networks and infrastructure. The selection of materials, and coatings with anti-fouling properties has become an increasingly difficult challenge but one that must be constantly reviewed and updated to advance the development of materials, composites and coatings that can be widely used in aquatic ecosystems and allow devices and structures submerged or in contact with water to last longer and reduce maintenance costs. In this scoping study, a range of materials commonly used in the construction of marine sensors and 2 anti-fouling paints were deployed for 1 year to test their robustness and anti-fouling performance in the estuarine brackish water ecosystem in Dublin. Exposed panels were assessed using eDNA (16S rRNA, 18S rRNA) and image analysis with microscope techniques, to characterise the biodiversity of both the microbiofouling (i.e., microscopic bacteria and algae) and the macrobiofouling organisms (i.e., barnacles and mussels). Results presented will discuss the biofouling progression on different materials and the role they have in the design of antifouling strategies. In addition, the work demonstrates the benefits of environmental testing in rapid screening of antifouling materials for the marine environment

"Surviving discrimination by pulling together" : LGBTQI cancer patient and carer experiences of minority stress and social support

Background: Lesbian, gay, bisexual, transgender, queer and/or intersex (LGBTQI) people with cancer and their carers report poorer psychological outcomes than the general non-LGBTQI cancer population. There is growing acknowledgement that these health inequities can be explained by minority stress, which can be buffered by social support. Study Aim: To examine subjective experiences of minority stress and social support for LGBTQI people with cancer and their carers, drawing on qualitative findings from the Out with Cancer study. Method: An online survey including open ended items was completed by 430 LGBTQI cancer patients and 132 partners and other carers, representing a range of tumor types, sexual and gender identities, age and intersex status. A sub-sample of 104 patients and 31 carers completed an interview, with a follow-up photovoice activity and second interview completed by 45 patients and 10 carers. Data was thematically analysed using an intersectional theoretical framework. Results: Historical and present-day experiences of discrimination, violence, family rejection and exclusion created a legacy of distress and fear. This impacted on trust of healthcare professionals and contributed to distress and unmet needs in cancer survivorship and care. Social support, often provided by partners and other chosen family, including intimate partners and other LGBTQI people, buffered the negative impacts of minority stress, helping LGBTQI patients deal with cancer. However, some participants lacked support due to not having a partner, rejection from family of origin and lack of support within LGBTQI communities, increasing vulnerability to poor psychological wellbeing. Despite the chronic, cumulative impacts of minority stress, LGBTQI patients and carers were not passive recipients of discriminatory and exclusion in cancer care, demonstrating agency and resistance through collective action and advocacy. Conclusion: LGBTQI people have unique socio-political histories and present-day psycho-social experiences that contribute to distress during cancer. Social support serves to buffer and ameliorate this distress. There is a need for cancer healthcare professionals and support services to be aware of and responsive to these potential vulnerabilities, including the intersectional differences in experiences of minority stress and social support. There is also a need for recognition and facilitation of social support among LGBTQI people with cancer and their carers

LGBTQI cancer patients' quality of life and distress : a comparison by gender, sexuality, age, cancer type and geographical remoteness

Background: There is growing acknowledgement of the psycho-social vulnerability of lesbian, gay, bisexual, transgender, queer and/or intersex (LGBTQI) people with cancer. The majority of research to date has focused on cisgender adults with breast or prostate cancer. Study Aim: This study examined psycho-social factors associated with distress and quality of life for LGBTQI cancer patients and survivors, across a range of sexualities and gender identities, intersex status, tumor types, ages and urban/ rural/remote location using an intersectional theoretical framework. Method: 430 LGBTQI people with cancer completed an online survey, measuring distress, quality of life (QOL), and a range of psycho-social variables. Participants included 216 (50.2%) cisgender women, 145 (33.7%) cisgender men, and 63 (14.7%) transgender and gender diverse (TGD) people. Thirty-one (7.2%) participants reported intersex variation and 90 (20%) were adolescents or young adults (AYA), aged 15-39. The majority lived in urban areas (54.4%) and identified as lesbian, gay or bisexual (73.7%), with 10.9% identifying as bisexual, and 10.5% as queer, including reproductive (32.4%) and non-reproductive (67.6%) cancers. Results: Forty-one percent of participants reported high or very high distress levels, 3-6 times higher than previous non-LGBTQI cancer studies. Higher rates of distress and lower QOL were identified in TGD compared to cisgender people, AYAs compared to older people, those who identify as bisexual or queer, compared to those who identify as lesbian, gay or homosexual, and those who live in rural or regional areas, compared to urban areas. Elevated distress and lower QOL was associated with greater minority stress (discrimination in life and in cancer care, discomfort being LGBTQI, lower outness) and lower social support, in these subgroups. There were no differences between reproductive and non-reproductive cancers. For the whole sample, distress and poor QOL were associated with physical and sexual concerns, the impact of cancer on gender and LGBTQI identities, minority stress, and lack of social support. Conclusion: LGBTQI people with cancer are at high risk of distress and impaired QOL. Research and oncology healthcare practice needs to recognize the diversity of LGBTQI communities, and the ways in which minority stress and lack of social support may affect wellbeing

Attitudes, knowledge and practice behaviours of oncology health care professionals towards lesbian, gay, bisexual, transgender, queer and intersex (LGBTQI) patients and their carers : a mixed-methods study

Objective: There is growing recognition that health care professionals (HCPs) and policy makers are insufficiently equipped to provide culturally competent care to lesbian, gay, bisexual, transgender, queer and intersex (LGBTQI) cancer patients and their families. We examined HCP attitudes, knowledge, and practices regarding LGBTQI cancer care using a mixed-methods research design. Method: Surveys were completed by 357 oncology HCPs in nursing (40%), medical (24%), allied health (19%), and clinical leadership roles (11%); 48 of the surveyed HCPs were interviewed. Results: Most HCPs reported being comfortable treating LGBTQI patients, but reported low levels of confidence and knowledge and systemic barriers to LGBTQI cancer care. Most wanted more education and training, particularly on trans and gender-diverse people (TGD) and those born with intersex variations. Conclusion: Education of HCPs and health system changes are required to overcome barriers to the provision of culturally competent cancer care for LGBTQI patients. Practice implications: These findings reinforce the need for inclusion of LGBTQI content in HCP education and professional training curricula, and institutional support for LGBTQI-inclusive practice behaviours. This includes administrative and visual cues to signal safety of LGBTQI patients within cancer care, facilitating inclusive environments, and the provision of tailored patient-centred care

LGBTQI inclusive cancer care : a discourse analytic study of health care professional, patient and carer perspectives

Background: Awareness of the specific needs of LGBTQI cancer patients has led to calls for inclusivity, cultural competence, cultural safety and cultural humility in cancer care. Examination of oncology healthcare professionals’ (HCP) perspectives is central to identifying barriers and facilitators to inclusive LGBTQI cancer care. Study Aim: This study examined oncology HCPs perspectives in relation to LGBTQI cancer care, and the implications of HCP perspectives and practices for LGBTQI patients and their caregivers. Method: 357 oncology HCPs in nursing (40%), medical (24%), allied health (19%) and leadership (11%) positions took part in a survey; 48 HCPs completed an interview. 430 LGBTQI patients, representing a range of tumor types, sexual and gender identities, age and intersex status, and 132 carers completed a survey, and 104 LGBTQI patients and 31 carers undertook an interview. Data were analysed using thematic discourse analysis. Results: Three HCP subject positions – ways of thinking and behaving in relation to the self and LGBTQI patients – were identified:’Inclusive and reflective’ practitioners characterized LGBTQI patients as potentially vulnerable and offered inclusive care, drawing on an affirmative construction of LGBTQI health. This resulted in LGBTQI patients and their carers feeling safe and respected, willing to disclose sexual orientation and gender identity (SOGI) status, and satisfied with cancer care. ‘Egalitarian practitioners’ drew on discourses of ethical responsibility, positioning themselves as treating all patients the same, not seeing the relevance of SOGI information. This was associated with absence of LGBTQI-specific information, patient and carer anxiety about disclosure of SOGI, feelings of invisibility, and dissatisfaction with healthcare. ‘Anti-inclusive’ practitioners’ expressed open hostility and prejudice towards LGBTQI patients, reflecting a cultural discourse of homophobia and transphobia. This was associated with patient and carer distress, feelings of negative judgement, and exclusion of same-gender partners. Conclusion: Derogatory views and descriptions of LGBTQI patients, and cis-normative practices need to be challenged, to ensure that HCPs offer inclusive and affirmative care. Building HCP’s communicative competence to work with LGBTQI patients needs to become an essential part of basic training and ongoing professional development. Visible indicators of LGBTQI inclusivity are essential, alongside targeted resources and information for LGBTQI people

Almost invisible : a review of inclusion of LGBTQI people with cancer in online patient information resources

Objective: This review assessed the inclusion of lesbian, gay, bisexual, trans, queer and/or intersex (LGBTQI) people in online cancer information. Methods: The websites of Australian cancer organizations were reviewed to identify if they included LGBTQI people and the extent and nature of this inclusion. Websites that did not include LGBTQI people were then reviewed to identify if information was implicitly LGBTQI inclusive. International LGBTQI cancer information resources were reviewed to identify key content. Results: Of sixty-one Australian cancer organization websites reviewed, eight (13%) mentioned LGBTQI people, including 13 information resources targeted to LGBTQI people and 19 general cancer information resources that mentioned LGBTQI people. For Australian cancer websites that did not mention LGBTQI people, 88% used gender neutral language to refer to partners, 69% included a range of sexual behaviours, 13% used gender neutral language when referring to hormones or reproductive anatomy but none acknowledged diverse relationship types. Internationally, 38 LGBTQI-specific cancer information resources were identified. Conclusions: Cancer patient information resources need to be LGBTQI inclusive. LGBTQI-targeted resources are required to address this population's unique needs and improve cultural safety and cancer outcomes. Practice implications: Recommendations are provided for LGBTQI inclusive cancer patient information resources