Independent Assessment of the 2018–19 fish deaths in the lower Darling

Three significant fish death events occurred in the Darling River near Menindee between December 2018 and January 2019. The three events took place within two adjacent weir pools in a 30 km reach of river between Texas Downs Station and Weir 32 (DPI NSW Fisheries, 2019). The main native fish species involved included Murray Cod, Silver Perch, Golden Perch, Bony Herring, with mortality estimates in the range of hundreds of thousands to over a million fish. Though post-event fish population sampling is yet to be conducted, we expect that these mortalities will impact populations in the lower Darling River, and perhaps beyond, for many years. These events constitute a serious ecological shock to the lower Darling and reverse positive ecological outcomes that had accrued from environmental watering programs. We have determined that fish deaths events were primarily caused by local hydrological and climatic conditions (Figure 1-1). The extreme hot and dry climate during 2018, extending into 2019, shaped the conditions that saw a large fish biomass, which had flourished since favourable spawning conditions in 2016, isolated in the weir pools around Menindee, with no means of escaping upstream or downstream. Those adverse climate conditions also shaped the subsequent algal bloom development and the strong and persistent thermal stratification of the weir pools, which created hypoxic conditions in the bottom waters of the pools. All that was needed for this to have a fatal impact on the fish was a trigger for the weir pool waters to become destratified and deprive the fish of oxygen. That trigger duly arrived with a series of sudden cool changes in the weather, with temperature drops and wind action initiating the turnover of the weir pool waters. This sudden depletion of oxygen, combined with the already high water and air temperatures, would have offered the large biomass of stressed fish no means of escape. For each fish death event, the weir pool in which the fish were trapped was bordered downstream by an impenetrable barrier (a weir) and upstream by a dry channel. Ultimately, it was the rapid transition from very favourable conditions to very adverse ones that resulted in such high numbers of fish deaths. We have also determined that the fish death events were shaped by a broader climatic, hydrologic and basin management context that placed the lower Darling River at risk of such fish deaths. The preceding six years (since 2012) had seen two high flow events that had delivered water into Menindee Lakes (2012 and 2016) and offered opportunities for substantial fish breeding and recruitment. Fish populations were further enhanced by the judicious use of environmental water. The end result was a considerable biomass of fish within the Menindee Lakes, post 2016. Outside of these high flow events there were minimal flows in the Darling River below Bourke. This period was preceded by the Millennium drought (2000-2010), during which time flows across the entire northern Murray– Darling Basin were reduced. All of the hydroclimatic evidence available indicates that the years since 2000 have been some of the driest on record, in terms of inflows into major upstream storages, combined with an increased number of extreme heat days, which would have had a major impact on water quality in remnant pools. Soon after the events, Basin government officials met and developed an action plan to respond to the crisis. Immediate actions underway include additional water quality monitoring in the lower Darling, the use of aerators and targeted fish relocations. These immediate actions are welcomed, however, the current situation remains critical – without significant inflows, further deaths of surviving fish may be expected. We consider that priorities and actions in the short-term should focus on anticipating a repeat of ‘worst-case scenario’ outcomes with responses focussed at the site scale. In addition, the Minister for Agriculture and Water Resources announced a Native Fish Management and Recovery Strategy to help manage and recover fish populations across the Basin. We consider that this provides a good opportunity to enhance native fish management and support native fish population recovery and should be developed and implemented through a genuine collaboration between governments, communities, and Traditional Owners. The strategy needs to build on existing and lapsed native fish programs across the Basin. Through our investigations, it became evident to us that, over the long-term, the extant water access arrangements in the northern Basin, as well as limitations in the river models used to plan water sharing, place the lower Darling River at a higher risk of conditions that can lead to fish deaths during droughts than has previously been anticipated. Given that we are witnessing an increasing frequency of low inflow sequences in the northern Basin, this presents a serious problem for safeguarding fish populations, and populations of other resident biota, during drought in the lower Darling. We have identified that changes to Barwon–Darling water access arrangements made by NSW just prior to the commencement of the Basin Plan in 2012 have enhanced the ability of irrigators to access water during low flow periods and during the first flow event immediately after a cease-to-flow period. Further, it appears that the river models used to develop water sharing arrangements have a tendency to overestimate streamflows during dry sequences, and hence underestimate the impacts of extractions during dry times

Using modelled discharge to develop satellite-based river gauging: a case study for the Amazon Basin

River discharge measurements have proven invaluable to monitor the global water cycle, assess flood risk, and guide water resource management. However, there is a delay, and ongoing decline, in the availability of gauging data and stations are highly unevenly distributed globally. While not a substitute for river discharge measurement, remote sensing is a cost-effective technology to acquire information on river dynamics in situations where ground-based measurements are unavailable. The general approach has been to relate satellite observation to discharge measured in situ, which prevents its use for ungauged rivers. Alternatively, hydrological models are now available that can be used to estimate river discharge globally. While subject to greater errors and biases than measurements, model estimates of river discharge do expand the options for applying satellite-based discharge monitoring in ungauged rivers. Our aim was to test whether satellite gauging reaches (SGRs), similar to virtual stations in satellite altimetry, can be constructed based on Moderate Resolution Imaging Spectroradiometer (MODIS) optical or Global Flood Detection System (GFDS) passive microwave-derived surface water extent fraction and simulated discharge from the World-Wide Water (W3) model version 2. We designed and tested two methods to develop SGRs across the Amazon Basin and found that the optimal grid cell selection method performed best for relating MODIS and GFDS water extent to simulated discharge. The number of potential river reaches to develop SGRs increases from upstream to downstream reaches as rivers widen. MODIS SGRs are feasible for more river reaches than GFDS SGRs due to its higher spatial resolution. However, where they could be constructed, GFDS SGRs predicted discharge more accurately as observations were less affected by cloud and vegetation. We conclude that SGRs are suitable for automated large-scale application and offer a possibility to predict river discharge variations from satellite observations alone, for both gauged and ungauged rivers.</p

Assessment of the causes and solutions to the significant 2018-19 fish deaths in the Lower Darling River, New South Wales, Australia

In late 2018 to early 2019, three significant fish death events occurred in the Lower Darling River, Australia, with mortality estimates of millions of fish. We examined the proximate and ultimate causes of these events. We determined that not only were the conditions existing at the time a significant contributing factor, but that antecedent conditions, particularly during the period 2010-17, also contributed. The extreme hot and dry climate during 2018, extending into 2019, shaped the conditions that saw a large fish biomass, which had flourished in the Darling River and Menindee Lakes since favourable spawning conditions in 2016, isolated in weir pools, with no means of escaping upstream or downstream. Strong and persistent weir pool stratification created hypoxic conditions in the hypolimnion. A series of sudden cool changes subsequently initiated rapid and sudden mixing of the stratified waters, causing depletion of oxygen throughout the water column and resulting in the fish deaths. The events were also shaped by broader climatic, hydrological and basin management contexts that placed the Lower Darling River at risk of such fish deaths. Our observations have implications for future river management, and we make several suggestions how policy makers and river operators can minimise fish death risks into the future

Two-dimensional NMR lineshape analysis

NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions

Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells.

Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system.We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing. In vitro small-molecule inhibitor sensitivity profiling was used to identify candidate therapeutic vulnerabilities.Although APOBEC3B expression increased the incorporation of genomic uracil, invoked DDR biomarkers and caused cell cycle arrest, inactivation of p53 circumvented APOBEC3B-induced cell cycle arrest without reversing the increase in genomic uracil or DDR biomarkers. The continued expression of APOBEC3B in p53-defective cells not only caused a kataegic mutational signature but also caused hypersensitivity to small-molecule DDR inhibitors (ATR, CHEK1, CHEK2, PARP, WEE1 inhibitors) as well as cisplatin/ATR inhibitor and ATR/PARP inhibitor combinations.Although loss of p53 might allow tumour cells to tolerate elevated APOBEC3B expression, continued expression of this enzyme might impart a number of therapeutic vulnerabilities upon tumour cells

The dUTPase Enzyme Is Essential in Mycobacterium smegmatis

Thymidine biosynthesis is essential in all cells. Inhibitors of the enzymes involved in this pathway (e.g. methotrexate) are thus frequently used as cytostatics. Due to its pivotal role in mycobacterial thymidylate synthesis dUTPase, which hydrolyzes dUTP into the dTTP precursor dUMP, has been suggested as a target for new antitubercular agents. All mycobacterial genomes encode dUTPase with a mycobacteria-specific surface loop absent in the human dUTPase. Using Mycobacterium smegmatis as a fast growing model for Mycobacterium tuberculosis, we demonstrate that dUTPase knock-out results in lethality that can be reverted by complementation with wild-type dUTPase. Interestingly, a mutant dUTPase gene lacking the genus-specific loop was unable to complement the knock-out phenotype. We also show that deletion of the mycobacteria-specific loop has no major effect on dUTPase enzymatic properties in vitro and thus a yet to be identified loop-specific function seems to be essential within the bacterial cell context. In addition, here we demonstrated that Mycobacterium tuberculosis dUTPase is fully functional in Mycobacterium smegmatis as it rescues the lethal knock-out phenotype. Our results indicate the potential of dUTPase as a target for antitubercular drugs and identify a genus-specific surface loop on the enzyme as a selective target

Vegetation‐hydrology dynamics in complex terrain of semiarid areas: 2. Energy‐water controls of vegetation spatiotemporal dynamics and topographic niches of favorability

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95632/1/wrcr11124.pd

Structure-Function Studies of DNA Binding Domain of Response Regulator KdpE Reveals Equal Affinity Interactions at DNA Half-Sites

Expression of KdpFABC, a K+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABCBS) via the winged helix-turn-helix type DNA binding domain (KdpEDBD). Exploration of E. coli KdpEDBD and kdpFABCBS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpEDBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpEDBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpEDBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins

Hsmar1 transposition is sensitive to the topology of the transposon donor and the target

Hsmar1 is a member of the Tc1-mariner superfamily of DNA transposons. These elements mobilize within the genome of their host by a cut-and-paste mechanism. We have exploited the in vitro reaction provided by Hsmar1 to investigate the effect of DNA supercoiling on transposon integration. We found that the topology of both the transposon and the target affect integration. Relaxed transposons have an integration defect that can be partially restored in the presence of elevated levels of negatively supercoiled target DNA. Negatively supercoiled DNA is a better target than nicked or positively supercoiled DNA, suggesting that underwinding of the DNA helix promotes target interactions. Like other Tc1-mariner elements, Hsmar1 integrates into 5′-TA dinucleotides. The direct vicinity of the target TA provides little sequence specificity for target interactions. However, transposition within a plasmid substrate was not random and some TA dinucleotides were targeted preferentially. The distribution of intramolecular target sites was not affected by DNA topology