What’s really damaging the Reef?: Tracing the origin and fate of the ecologically detrimental sediment and associated bioavailable nutrients

This report addresses six key systematic questions to help inform the debate on the influence of anthropogenic sediment and associated particulate nutrients delivered to the Great Barrier Reef (GBR) lagoon. They are: 1. What is the influence of the newly-delivered sediment (i.e. from flood plumes) on turbidity regimes at coral reef and seagrass locations of the inshore GBR? 2. What is the contribution of the anthropogenic component of this sediment on turbidity regimes? 3. What are the characteristics of the suspended particulate matter (and associated particulate nutrients) that influence light and turbidity regimes and how do these change over the estuarine mixing gradient of flood plumes? 4. How does the particulate organic component of the suspended particulate matter and associated microbial community composition change from the catchment to reef? 5. How bioavailable is the suspended particulate matter along the estuarine mixing gradient 6. Where does the sediment (and associated particulate nutrients) that influence light and turbidity regimes in the GBR come from in the Burdekin catchment so that management efforts can be prioritised? This final project report is divided into eight separate stand-alone research chapters which collectively address these six key questions

Sediment tracing from the catchment to reef 2016 to 2018: Flood plume, marine sediment trap and logger data time series

The sediment dynamics at marine sites in the inshore GBRL region likely fall into three separate categories including sites where: 1. input of new terrigenous sediments have by far the greatest influence on sediment exposure and subsequent resuspension (e.g. Dunk Island, Orpheus Island, Havannah Island, Cleveland Bay?); 2. input of new terrigenous sediments are at least equivalent to resuspension events which likely increases upon larger river discharge events (e.g. Cleveland Bay?, Orchard Rocks). 3. input of new terrigenous sediments are less than or equal to common resuspension events (e.g. Middle Reef, Geoffrey Bay). This provides some of the first empirical data to support the findings of the satellite photic depth modelling of Fabricius et al. (2014, 2016) where the delivery of new terrigenous sediment considerably influences water clarity on the inshore Great Barrier Reef

Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection

Anticancer Gene Transfer for Cancer Gene Therapy

Gene therapy vectors are among the treatments currently used to treat malignant tumors. Gene therapy vectors use a specific therapeutic transgene that causes death in cancer cells. In early attempts at gene therapy, therapeutic transgenes were driven by non-specific vectors which induced toxicity to normal cells in addition to the cancer cells. Recently, novel cancer specific viral vectors have been developed that target cancer cells leaving normal cells unharmed. Here we review such cancer specific gene therapy systems currently used in the treatment of cancer and discuss the major challenges and future directions in this field

Super-resolution for upper abdominal MRI: Acquisition and post-processing protocol optimization using brain MRI control data and expert reader validation

Purpose Magnetic resonance (MR) cholangiopancreatography (MRCP) is an established specialist method for imaging the upper abdomen and biliary/pancreatic ducts. Due to limitations of either MR image contrast or low through‐plane resolution, patients may require further evaluation with contrast‐enhanced computed tomography (CT) images. However, CT fails to offer the high tissue‐ductal‐vessel contrast‐to‐noise ratio available on T2‐weighted MR imaging. Methods MR super‐resolution reconstruction (SRR) frameworks have the potential to provide high‐resolution visualizations from multiple low through‐plane resolution single‐shot T2‐weighted (SST2W) images as currently used during MRCP studies. Here, we (i) optimize the source image acquisition protocols by establishing the ideal number and orientation of SST2W series for MRCP SRR generation, (ii) optimize post‐processing protocols for two motion correction candidate frameworks for MRCP SRR, and (iii) perform an extensive validation of the overall potential of upper abdominal SRR, using four expert readers with subspeciality interest in hepato‐pancreatico‐biliary imaging. Results Obtained SRRs show demonstrable advantages over traditional SST2W MRCP data in terms of anatomical clarity and subjective radiologists’ preference scores for a range of anatomical regions that are especially critical for the management of cancer patients. Conclusions Our results underline the potential of using SRR alongside traditional MRCP data for improved clinical diagnosis

Conformational adaptation of Asian macaque TRIMCyp directs lineage specific antiviral activity

TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates. All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5α but they have distinct lentiviral specificities, conferring HIV-1 restriction in New World owl monkeys and HIV-2 restriction in Old World rhesus macaques. Here we provide evidence that Asian macaque TRIMCyps have acquired changes that switch restriction specificity between different lentiviral lineages, resulting in species-specific alleles that target different viruses. Structural, thermodynamic and viral restriction analysis suggests that a single mutation in the Cyp domain, R69H, occurred early in macaque TRIMCyp evolution, expanding restriction specificity to the lentiviral lineages found in African green monkeys, sooty mangabeys and chimpanzees. Subsequent mutations have enhanced restriction to particular viruses but at the cost of broad specificity. We reveal how specificity is altered by a scaffold mutation, E143K, that modifies surface electrostatics and propagates conformational changes into the active site. Our results suggest that lentiviruses may have been important pathogens in Asian macaques despite the fact that there are no reported lentiviral infections in current macaque populations

A Novel Adeno-Associated Viral Variant for Efficient and Selective Intravitreal Transduction of Rat Müller Cells

BACKGROUND:The pathologies of numerous retinal degenerative diseases can be attributed to a multitude of genetic factors, and individualized treatment options for afflicted patients are limited and cost-inefficient. In light of the shared neurodegenerative phenotype among these disorders, a safe and broad-based neuroprotective approach would be desirable to overcome these obstacles. As a result, gene delivery of secretable-neuroprotective factors to Müller cells, a type of retinal glia that contacts all classes of retinal neurons, represents an ideal approach to mediate protection of the entire retina through a simple and innocuous intraocular, or intravitreal, injection of an efficient vehicle such as an adeno-associated viral vector (AAV). Although several naturally occurring AAV variants have been isolated with a variety of tropisms, or cellular specificities, these vectors inefficiently infect Müller cells via intravitreal injection. METHODOLOGY/PRINCIPAL FINDINGS:We have previously applied directed evolution to create several novel AAV variants capable of efficient infection of both rat and human astrocytes through iterative selection of a panel of highly diverse AAV libraries. Here, in vivo and in vitro characterization of these isolated variants identifies a previously unreported AAV variant ShH10, closely related to AAV serotype 6 (AAV6), capable of efficient, selective Müller cell infection through intravitreal injection. Importantly, this new variant shows significantly improved transduction relative to AAV2 (>60%) and AAV6. CONCLUSIONS/SIGNIFICANCE:Our findings demonstrate that AAV is a highly versatile vector capable of powerful shifts in tropism from minor sequence changes. This isolated variant represents a new therapeutic vector to treat retinal degenerative diseases through secretion of neuroprotective factors from Müller cells as well as provides new opportunities to study their biological functions in the retina