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This chapter gives a broad overview of the riverine ecosystem synthesis (RES) by exploring the nature and applications of all prominent riverine theories published even in the last few decades. Consequently, the focus and analysis of the review is only on those hypotheses, models, theories, and paradigms that address large-scale spatial patterns affecting the structure and function of riverine ecosystems and ecological regulation of communities at smaller spatiotemporal scales. At the larger spatial scale, this chapter concentrates the analysis on two (longitudinal and lateral) of the four recognized dimensions of rivers. It briefly covers briefly covers vertical dimension because less controversy seems to exist among stream ecologists about processes and patterns operating in this dimension. The fourth dimension, which involves temporal phenomena, is the longitudinal dimension that alludes to patterns and processes occurring along discharge and altitudinal gradients from headwaters downstream to the river mouth. And by the lateral dimension, this chapter refers to similarities and differences in communities from the main channel through slackwaters (riverscape) to the floodplains (floodscape). At smaller spatial scales, theories debating which biotic and/or abiotic factors regulate community structure and the importance of temporal phenomena are discussed. The review of selective aspects of other models is tailored to that synthesis and its specific contribution toward conceptual cohesiveness.

This chapter provides an overview of the Riverine Ecosystem Synthesis (RES), which is an integrated model derived from aspects of other aquatic and terrestrial models proposed from 1980 to 2007, combined with the perspectives on functional process zones (FPZs) and other aspects of riverine biocomplexity. The RES pertains to the entire riverine landscape, which includes both the floodscape and the riverscape. This contrasts with many lotic models whose primary emphasis or support focuses on main channel systems within headwaters. This synthesis, which incorporates the ecosystem consequences of spatiotemporal variability across mostly longitudinal and lateral dimensions, has three broad components: a fundamental, physical model describing the hierarchical patchy arrangement of riverine landscapes within longitudinal and lateral dimensions based primarily on hydrogeomorphology and emphasizing a new geomorphic division (an FPZ) between the reach and the valley scale; ecological implications of the physical model in terms of an expandable set of 17 general to specific (testable) hypotheses, or model tenets, on biocomplexity, which is applicable in some form to both pristine and altered riverine landscapes; a framework for studying, managing, and rehabilitating riverine landscapes through the use of the hierarchical physical model and aquatic applications of the terrestrially derived hierarchical patch dynamics (HPD) model. The goal is to provide a framework for the development of a cohesive theory of riverine ecosystems over time rather than to produce a finished product. This chapter draws upon three primary components of river science that contribute to the study of riverine landscapes: lotic ecology, landscape ecology, and fluvial geomorphology.

Hydrogeomorphic patches and their resultant processes play important roles in riverine landscapes. They provide physical habitat and act as ecological disturbances, among other things. River networks are complex systems that need to be interpreted within their local and historical context. Attention to identifying and characterizing FPZs within the context of river networks will improve our knowledge of riverine landscapes. At this scale, river networks are a mosaic of patches that do not simply reflect a continuum of river zones. This chapter delves into the messy business of methods—the how to's of determining the character of river networks. It cautions against a focus on seeking the single method that can be applied to any situation. The options presented in this chapter provide various approaches that can be applied to particular situations. It demonstrates that FPZs can be identified equally as well via data collected at larger or smaller scales. Characterizations that highlight specific aspects of the linkages between channel networks and resultant processes are likely to be most useful, but careless application of any characterization may prove misleading—no characterization can substitute for an alert, intelligent, and well-trained observer.

Understanding the nature of changes in biocomplexity from headwaters to a river mouth is an important path toward developing a conceptually cohesive model of riverine ecosystem structure and function. This chapter discusses another major component of model—aquatic applications of the Hierarchical patch dynamics (HPD) model.. The original, terrestrial-based HPD model integrates a general theory of spatial heterogeneity (patch dynamics) with hierarchy theory by expressing relationships among pattern, process, and scale in a landscape context. This chapter describes the meaning of patch. A patch is as a spatial unit differing from its reference background in nature and appearance, a depiction that could also be applied to temporal patches. The size of a patch is scale-, organismal-, and process-dependent and can vary greatly in temporal dimension and size (e.g., an individual rock to a river segment or a floodscape area). The HPD model is composed of five principal elements. First, ecological systems are viewed as ‘nested, discontinuous hierarchies of patch mosaics.’ Second, the dynamics of ecological systems are derived from a composite of intra- and inter-patch dynamics. Third, pattern and process are interlinked and scale-dependent. Various processes (e.g., nutrient spiraling) may create, modify, or eliminate patterns at certain spatial and temporal scales, while at the same time certain spatial and temporal patterns (e.g., differences in flow characteristics) can substantially alter ecological processes. Fourth, nonequilibrial conditions and stochastic processes play a dominant role in the so-called “ecosystem stability.” Fifth, a quasi-equilibrial, metastable state can develop at one hierarchical level through incorporation of multiple; nonequilibrial patches from the adjacent lower level.

A diverse array of physical structures may exist between and within riverine landscapes. Broad-scale patterns in the spatial arrangement of riverine landscapes are observed despite variations in the influence of independent catchment and channel variables. Rivers are continually evolving in response to longer-term natural disturbances, shorter-term pulsed or ramped human interventions, and high magnitude, low-frequency episodic events. Responses may be cyclic, nonlinear, and/or lagged, and the effects of single or multiple disturbance may overlap and interact, thereby increasing the probability of alternative states in river systems. This view of riverine landscapes moves away from notions of equilibrium and cyclic behavior as a means to explain nonlinear relationships and stochasticity. Recent views of river systems emphasize the importance of scale and their hierarchical organization, acknowledging both top-down constraints and the emergent features of bottom up influences. Contrasting views of the clinal and patch approach to the spatial arrangement and behavior of riverine landscapes reflect the differences between Darwinian and Newtonian approaches to science in some way. The former embraces the principles of complexity, contingency, and interdependence, while the latter strives for simplification, ideal systems, and predictive understanding. This chapter discusses concepts and theoretical approaches to the spatial arrangement of riverine landscapes. Following this, a review of the river characterization is presented. In particular, the results of a meta-analysis of the more commonly used river characterization schemes are presented. A characterization scheme for riverine landscapes then presented, and its application demonstrated with two case studies: the Murray–Darling Basin, Australia, and some of the rivers in the Kingdom of Lesotho, Africa.

Existing theories are used to predict responses to anthropogenic changes in riverine ecosystems, but explicit hypotheses on ecosystem behavior in altered landscapes have not been incorporated into these models. This chapter describes the types of responses expected in altered riverine ecosystems as defined by the tenets of the RES. Disturbances changing attributes in one domain will alter attributes of others through secondary or tertiary mechanisms. This chapter addresses broad changes in the nature of riverine ecosystems through direct actions on attributes and provides examples of deviations from expected patterns. The tenets of the riverine ecosystem synthesis (RES) are presented by considering how they can be used to predict changes/responses from population to landscape levels. The tenets provide a framework for applying the RES in situations encountered in altered systems and for understanding how changes in the characteristics of an FPZ influence ecosystem structure and function independent of location along a longitudinal gradient of a riverine ecosystem. A goal of this chapter is to provide key policy makers and river managers with better tools for environmental management and rehabilitation of riverine landscapes.

The importance of river classification in conservation planning and management is widely recognized. The river characterization approach presented in this chapter as part of the riverine ecosystem synthesis (RES) provides an excellent framework to classify riverine landscapes at various scales. By focusing on the scale of FPZs, scientists, river managers, and people interested in river rehabilitation will be operating at a scale that is appropriate for entire river networks. The identification and mapping of FPZs can provide a framework for conservation planning and prioritization of management activities within river networks. Interdisciplinary research in river ecosystems is a relatively young endeavor and one that is fraught with problems—linking across scales and integrating different disciplinary approaches and conceptual tools. Frameworks are useful tools for achieving this because they help define the bounds for the selection and solution of problems. They also indicate the role of empirical assumptions, carry the structural assumptions, show how facts, hypotheses, models, and expectations are linked, and indicate the scope at which a generalization or model applies. The RES provides such an integrative framework for the study of entire riverine landscapes. A framework is neither a model nor a theory because models describe how things work and theories explain phenomena. In contrast, a conceptual framework helps to order phenomena and materials, thereby revealing patterns.

Deficiencies in individual DNA repair systems are involved in both de novo and therapy-related acute myeloid leukaemia (t-AML), as indicated by genetic markers involving nucleotide excision repair (NER gene polymorphisms), double-strand-break (DSB) or mismatch repair (microsatellite instability (MSI)). We modified a host cell reactivation (HCR) assay for functional DNA repair system analysis of living primary haematopoietic cells; 2 x 10(5) normal peripheral blood lymphocytes (PBLs) and cord blood CD34+ progenitor cells were cryopreserved, thawed and transfected with 75-250 ng luciferase reporter plasmid (pCMVLuc) using DEAE-dextran (0.1 mg/mL) in a transfection volume of 250 microL. We obtained luciferase activities of approximately 300-fold above background in CD34+ progenitor cells and approximately 2000-fold in PBLs, thus rendering these cells applicable for DNA repair analysis. We then evaluated the NER (UV-irradiated pCMVLuc) and DSB repair capacity (linearized pCMVLuc) of normal lymphocytes and several leukaemic cell lineages. Kasumi-1 and HL-60 AML cells exhibited a reduced NER capacity compared to normal GM03715 lymphocytes, PBLs and CD34+ progenitor cells (6.2 +/- 0.9%, 6.5 +/- 0.9% vs. 12.3 +/- 1.8%, 13.5 +/- 0.7% and 13.5 +/- 2.0%, respectively). Kasumi-1 AML tells exhibited a reduced DSB repair capacity compared to AG10107 and GM03715 normal lymphocytes as well as CEM acute T-cell lymphoblastic leukaemia cells (6.4 +/- 0.8% vs. 10.8 +/- 0.7%, 27.3 +/- 1.1% and 20.5 +/- 1.6%, respectively). The modified HCR assay can be used for functional DNA repair analysis in living cells of patients with pre- and post-leukaemic conditions as well as in leukaemic blasts to elucidate the role of DNA repair in de novo and t-AML leukaemogenesis and to determine the individual susceptibility to t-AML prior to chemotherapy.

Murray-Darling Freshwater Research CentreMDFRC item.Soil seed banks are an important component of plant community diversity in ephemeral wetlands, allowing many species to persist through unpredictable periods of flood and drought. Spatial variation of extant vegetation in such habitats commonly reflects patterns of flood history and often varies predictably between broadly differing hydro-geomorphic habitat types. Here we investigate whether spatial variation of soil seed banks is similarly controlled by fluvial processes at this scale. Results are presented from a seedling emergence trial using samples collected from a range of habitat types, and at different scales within these, in the ephemeral Narran Lakes system in semi-arid Australia. Composition and structure of soil seed banks varied significantly between habitat types reflecting broad differences in flood frequency. As predicted, germinable seed abundance was found to be highest in intermediately flooded habitats. Variability in soil seed bank composition at a local scale was also found to be influenced by hydrology with greater spatial heterogeneity evident in the river channel as well as amongst the least frequently inundated riparian and floodplain habitats.

Genomic instability is the driving force behind cancer development. Human syndromes with DNA repair deficiencies comprise unique opportunities to study the clinical consequences of faulty genome maintenance leading to premature aging and premature cancer development. These syndromes include chromosomal breakage syndromes with defects in DNA damage signal transduction and double-strand break repair, mismatch repair defective syndromes as well as nucleotide excision repair defective syndromes. The same genes that are severely affected in these model diseases may harbour more subtle variations in the 'healthy' normal population leading to genomic instability, cancer development, and accelerated aging at later stages of life. Thus, studying those syndromes and the molecular mechanisms behind can significantly contribute to our understanding of (skin) cancerogenesis as well as to the development of novel individualized preventive and therapeutic anticancer strategies. The establishment of centers of excellence for studying rare genetic model diseases may be helpful in this direction.

A trend in river science over the last 15 years has been the increased emphasis on larger systems. This has been refl ected in an expanding literature base describing the physical character and processes of large rivers. The 1989 special issue of Canadian Journal of Fisheries and Aquatic Sciences was one of the fi rst publications to deal specifi - cally with large river systems. Although papers from this symposium (Dodge, 1989) had a multidisciplinary focus, 11 of the 49 papers dealt with the form and process of large fl oodplain rivers. The geomorphological character of large lowland rivers was presented in Lowland Floodplain Rivers: Geomorphological Perspectives (Carling and Petts, 1992).

UNLABELLED: The objective of this study was to analyze different types of nodal basin recurrence after sentinel lymph node biopsy (SLNB) for melanoma. PATIENTS AND METHODS: Kaplan-Meier estimates and the Cox proportional hazards model were used to study 2653 patients from 3 German melanoma centers retrospectively.The estimated 5-year negative predictive value of SLNB was 96.4%. The estimated false-negative (FN) rates after 1, 2, 3, 5, and 10 years were 2.5%, 4.6%, 6.4%, 8.7%, and 12.6%, respectively. Independent factors associated with false negativity were older age, fewer SLNs excised, and head or neck location of the primary tumor. Compared with SLN-positive patients, the FNs had a significantly lower survival. In SLN-positive patients undergoing completion lymphadenectomy (CLND), the 5-year nodal basin recurrence rate was 18.3%. The recurrence rates for axilla, groin, and neck were 17.2%, 15.5%, and 44.1%, respectively. Significant factors predicting local relapse after CLND were older age, head, or neck location of the primary tumor, ulceration, deeper penetration of the metastasis into the SLN, tumor-positive CLND, and >2 lymph node metastases. All kinds of nodal relapse were associated with a higher prevalence of in-transit metastases.The FN rate after SLNB steadily increases over the observation period and should, therefore, be estimated by the Kaplan-Meier method. False-negativity is associated with fewer SLNs excised. The beneficial effect of CLND on nodal basin disease control varies considerably across different risk groups. This should be kept in mind about SLN-positive patients when individual decisions on prophylactic CLND are taken. peerReviewed

In-transit metastasis is an important morbidity factor after sentinel lymphonodectomy (SLNE). So far, factors posing an increased risk after SLNE have not been adequately analyzed. Using Kaplan-Meier estimations and the Cox proportional hazards model, we analyzed the risk of developing in-transit metastases after SLNE for 328 consecutive patients (median tumor thickness, 2.0 mm; median follow-up period, 40 months). The 5-year probability of developing in-transit metastases as a first recurrence was 11.2%. After negative and positive SLNE, the probabilities were 6.3% and 24%, respectively. Patients in whom satellite metastases were excised concurrently with the primary tumor had a probability of recurrence with in-transit metastases of 41%. In sentinel lymph node (SLN)-negative patients with primary tumors having a thickness of more than 4 mm, the probability was 22.1%. Among the group of SLN-positive patients, significantly increased in-transit probabilities were observed in those with primary tumors that were thicker than 4 mm (41.8%), with tumors located on the distal extremities (42.1%), and with penetration of the nodal metastasis of >1 mm into the SLN (36%) and in patients with capsular breakthrough (63.3%). By using multifactorial analysis, the SLN status (P = .005), Breslow thickness (P = .0009), and extremity location of the primary melanoma (P = .005) significantly predicted the risk of in-transit recurrence. Satellite metastasis (P < .089), Clark level, and ulceration did not reach significance. Subgroups of patients can be identified who seem to have an increased risk of developing in-transit metastases as a first recurrence after SLNE. Individualized therapeutic strategies should be developed for these patients.

Compared with intraoperative sentinel lymph node identification using blue dye only, the introduction of a hand-held gamma probe has improved the identification rates. In this retrospective study, further aspects related to the introduction of gamma-guided preparation are analysed in detail.81 patients who underwent sentinel biopsy using the blue dye technique were compared to 247 patients whose operations were guided by blue dye and gamma probe.After the introduction of radio-guided surgery, the sentinel node identification rate increased from 87.7 % to 99.2 % (P0.00001). The number of harvested sentinel lymph nodes increased from 1.4 +/- 0.9 to 1.8 +/- 0.09 (P0.00001). The "clinical false-negative rate" decreased from 15.8 % to 9.6 %. The percentage of positive completion lymphadenectomy decreased from 50 % to 24.6 %. The risk of postoperative seroma decreased as a consequence of gamma guided preparation (5.1 % versus 15 %, P = 0.01). Regarding overall survival and recurrence-free survival, there were no significant differences between both groups. The 5-year-probability of nodal basin failure was 7.9 % after negative sentinel biopsy and 25.3 % after positive sentinel lymphonodectomy plus consecutive completion lymphadenectomy.Combined application of blue dye and gamma-probe improved sensitivity and decreased the risk of postoperative seroma. The probability of recurrence and survival was not influenced by the technique of intraoperative sentinel node identification.

Individuals with the rare DNA repair deficiency syndrome xeroderma pigmentosum (XP) are sensitive to the sun and exhibit a 1000-fold increased risk for developing skin cancers, including cutaneous melanoma. Inherited polymorphisms of XP genes may contribute to subtle variations in DNA repair capacity and genetic susceptibility to melanoma. We investigated the role of three polymorphic alleles of the DNA repair gene XPC in a hospital-based case-control study of 294 Caucasian patients from Germany who had cutaneous melanoma and 375 healthy cancer-free sex-matched Caucasian control subjects from the same area. We confirmed that the XPC intron 9 PAT+, intron 11 -6A, and the exon 15 2920C polymorphisms are in a linkage disequilibrium. Only 1.6% of the 669 donors genotyped were discordant for these three polymorphisms. The allele frequencies (cases: controls) were for intron 9 PAT+ 41.7%:36.9%, for intron 11 -6A 41.8%:37.0% and for exon 15 2920C 41.3%:37.3%. Using multivariate logistic regression analyses to control for age, skin type and number of nevi, the three polymorphisms were significantly associated with increased risks of melanoma: OR 1.87 (95% CI: 1.10-3.19; P = 0.022), OR 1.83 (95% CI: 1.07-3.11; P = 0.026), and OR 1.82 (95% CI: 1.07-3.08; P = 0.026), respectively. Exploratory multivariate analyses of distinct subgroups revealed that these polymorphisms were associated with increased risks for the development of multiple primary melanomas (n = 28). The results of our case-control study support the hypothesis that the intron 9 PAT+, intron 11 -6A and exon 15 2920C haplotype may contribute to the risk of developing cutaneous melanoma by increasing the rate of an alternatively spliced XPC mRNA isoform that skips exon 12 and leads to reduced DNA repair. Our results should be validated in independent samples in order to guard against false positive findings.

Despite the demonstrated utility of the Australian River Assessment Scheme (AUSRIVAS) to provide national-scale information on the biological condition of rivers, there is no commensurate scheme that can provide standardised information on physical habitat. Existing habitat assessment methods are not suitable for implementation on a national scale, so we present a new habitat assessment protocol that incorporates favorable elements of existing methods. Habitat Predictive Modelling forms the basis for the protocol because it can predict the occurrence of local-scale features from large-scale data, uses the reference condition concept, can be modified to incorporate a range of biologically and geomorphologically relevant variables, and employs a rapid survey approach. However, the protocol has been augmented with geomorphological variables and incorporates principles of hierarchy and geomorphological river zonation. There are four sequential components to the implementation of the protocol: reference site selection, data collection, predictive model construction and assessment of test sites using the predictive models. Once implemented, the habitat assessment protocol will provide a standardised tool for the assessment of river habitat condition at a variety of governance levels.

With regard to malignant melanoma, the impact of lymph node surgery on the development of loco-regional cutaneous metastases (LCM) has not yet been adequately addressed. However, this aspect is of interest, since sentinel lymphonodectomy (SLNE) has been suspected of causing LCM by inducing entrapment of melanoma cells. We analysed 244 patients with SLNE and compared the data with 199 patients treated with delayed lymph node dissection (DLND) for clinically palpable metastases. Analysis of both groups commenced at the time of excision of the primary tumour, using the Kaplan-Meier method. LCM that appeared as a first recurrence, as well as the overall probability of developing LCM, were recorded. For sentinel-negative patients with a primary melanoma >1mm thick, the 5-year probability of developing LCM as a first recurrence was 6.9 +/- 0.02% (+/-standard error of the mean (SEM)). The probability was 17.6 +/- 0.03% in the DLND group. Comparing the two node-positive subgroups, the probability of developing LCM as a first recurrence was significantly higher in patients with positive SLNE (27.3 +/- 0.05%, P = 0.03). However, the 5-year overall probability of developing LCM did not differ significantly in the node-positive groups (33.3% in the DLND group vs. 33.7% in patients with positive sentinel lymph nodes (SLNs)). Since early excision of lymphatic metastases by SLNE avoids nodal recurrences, thereby prolonging the recurrence-free interval, the chance of LCM to manifest as a first recurrence should inevitably increase. However, the overall in-transit probability is not increased after SLNE.

Many rivers experience intermittent flows naturally or as a consequence of water abstraction. Climate change is likely to exacerbate flow variability such that dry spells may become more common. It is important to understand the ecological consequences of flow intermittency and habitat fragmentation in rivers, and to identify and protect habitat patches that provide refugia for aquatic biota. This paper explores environmental factors influencing dry season fish losses from isolated waterbodies in Cooper Creek, an unregulated arid-zone river in the Lake Eyre Basin, Australia. Multivariate ordination techniques and classification and regression trees (CART) were used to decompose species–environment relationships into a hierarchically structured data set, and to determine factors explaining changes in fish assemblage structure and species losses over a single dry season. Canonical correspondence analysis (CCA) explained 74% of fish assemblage change in terms of waterhole morphology (wetted perimeter, depth), habitat structure (bench development, off-take channels), waterhole quality (eroded banks, gross primary production), the size of surrounding floodplains and the relative isolation of waterholes. Classification trees for endemic and restricted species reaffirmed the importance of these waterhole and floodplain variables as drivers of fish losses. The CCA and CART models offer valuable tools for identification of refugia in Cooper Creek and, possibly, other dryland rivers.

Freshwater ecosystems are a foundation of our social, cultural, spiritual and economic well being. The degraded condition of many of Australia’s river ecosystems is testament to our failure to manage these resources wisely. Ecosystem science involves the holistic study of complex biophysical systems to understand the drivers that influence ecological pattern and process. Ecosystem science should underpin both water management and policy. Our understanding of aquatic ecosystems lags behind the increasing problems caused by past land and water management. Current post-graduate training programmes will not provide the aquatic ecosystem scientists needed by government and management agencies to prevent further degradation. We advocate new initiatives to capture the skills, knowledge and innovation of our research community by engaging scientists and managers in large-scale, long-term ecosystem science programmes across Australia and to integrate these programmes with community aspirations, policy, planning and management. We call on management agencies to increase their support for and uptake and use of ecosystem science. We also advocate establishment of national archives for long-term ecologically-relevant data and samples, and clear custodial arrangements to protect, update and facilitate knowledge-transfer. These initiatives need to be supported by more extensive, better-funded post-graduate and post-doctoral programmes in ecosystem science and management.

Waterholes within the dryland Cooper Creek, Lake Eyre Basin, Australia, are connected only during floods and are typically isolated for long periods. Spatial changes in the macroinvertebrate assemblages of 15 of these waterholes belonging to four regions were explored and these changes were related to environmental aspects of the waterholes measured at four spatial scales: floodplain, waterhole, within waterhole and sample habitat. To explore temporal patterns, one region was sampled on four occasions differing in time since connection. Spatial patterns were characterised by ‘differentiation by distance’ whereby samples collected closer to each other in the landscape were more similar in assemblage composition than those collected further apart. Thus, there were significant differences between the assemblages of the four regions. Although there was a correlation between macroinvertebrate spatial patterns and a combination of local habitat, geomorphology and water chemistry attributes, it appears unlikely that these variables were responsible for the faunal differentiation by distance. Temporal variability was larger than spatial variability and temporal assemblage patterns were best explained by the ‘connectivity potential’ of waterholes, reflecting the position of individual waterholes within the broader channel network and long-term connectivity relationships, rather than the actual time since hydrological connection.

The scale at which algal biodiversity is partitioned across the landscape, and the biophysical processes and biotic interactions which shape these communities in dryland river refugia was studied on two occasions from 30 sites in two Australian dryland rivers. Despite the waterholes studied having characteristically high levels of abiogenic turbidity, a total of 186 planktonic microalgae, 253 benthic diatom and 62 macroalgal species were recorded. The phytoplankton communities were dominated by flagellated cryptophytes, euglenophytes and chlorophytes, the diatom communities by cosmopolitan taxa known to tolerate wide environmental conditions, and the macroalgal communities by filamentous cyanobacteria. All algal communities showed significant differences between catchments and sampling times, with a suite of between 5 and 12 taxa responsible for ~50% of the observed change. In general, algal assemblage patterns were poorly correlated with the measured environmental variables. Phytoplankton and diatom assemblage patterns were weakly correlated with several waterhole geomorphic measures, whereas macroalgal assemblage patterns showed some association with variability in ionic concentration.

Published in Rivers Research and Applications, 2005; 21 (2-3):91-91 at www.interscience.wiley.com

Spatial and temporal variation in fish-assemblage structure within isolated waterholes on the floodplains of Cooper Creek, Australia, was studied during the 2001 dry season, a period of natural drought in this arid-zone river. Spatial variation in fish-assemblage structure and the abundance of five species in disconnected waterholes early in the dry season (April 2001) were related to the extent of floodplain inundation 14 months previously, and to the interconnectedness of waterholes and waterhole habitat structure. As the dry season progressed, waterhole volumes decreased owing to evaporative water loss and structural habitat elements (anabranches, bars, boulders) became exposed. Marked changes in fish assemblage structure between the early (April) and late (September) dry season were related to habitat loss but not to water chemistry. Interactions between flow and habitat across a nested hierarchy of spatial scales (the floodplain, the waterhole and habitat patches within waterholes) were crucial to the persistence of fish assemblages through the 2001 dry season. We conclude that the magnitude, timing and frequency of floodplain inundation and natural variations in waterhole volume must be maintained if we wish to sustain the distinctive habitats and fish assemblages of this arid-zone floodplain river.

Therapy related acute myelogenous leukemia (t-AML) is frequently observed among patients who undergo a high dose chemotherapy and its incidence varies between 5 to 15% in non-myeloablative and myeloablative treatment protocols. Deficiencies in individual DNA-repair systems seem to be involved in t-AML leukemogenesis since indirect genetic markers of impaired DNA repair, e.g. microsatellite instability (mismatch repair) and polymorphisms of XRCC genes (base/nucleotide excision repair), are frequent in these patients. To directly determine the activity of different DNA repair systems we developed a modified host cell reactivation (HCR) assay which is applicable for the analysis of primary hematopoietic cells of clinical samples. This assay determines the ability of transfected host cells to repair damaged plasmid DNA as reflected in the recovery of luciferase activity. Depending on the type of DNA damage introduced to the plasmid prior to transfection, different DNA repair systems can be analysed, e.g. nucleotide excision repair (NER) or double strand break repair. We performed the HCR assay using 75 to 250 ng luciferase reporter gene plasmid (pCMV-Luc). Lymphocytes and cord blood CD34+-progenitor cells from healthy donors were collected according to the convention of Helsinki. 200,000 to 2,000,000 cells were cryopreserved, thawed and transfected using DEAE-dextran at a concentration of 0,1 mg/ml in a transfection volume of 250 μl. We obtained luciferase activities of 350-fold above background in CD34+ progenitor cells (1000-fold in lymphocytes) rendering these cells applicable for DNA repair analysis. In addition, we evaluated the normalized NER capacity (1000 J/m2 UVC irradiated plasmid vs. unirradiated control) of lymphocytes and two AML cell lineages, Kasumi-1 and HL60. Kasumi-1 and HL60 cells exhibited a significantly reduced NER capacity compared to lymphocytes (6.15% +/− 1.57% and 6.5% +/− 1.59% vs. 12.3% +/− 3.2%). Clinical AML samples are currently been investigated. Our modified HCR can be used for functional DNA repair analysis in fresh and cryopreserved patient samples of pre- and post-leukemic conditions as well as in leukemic blasts to elucidate the role of defective DNA repair during t-AML leukemogenesis. Furthermore, the modified HCR may also be used to determine the individual susceptibility for therapy related myeloid leukemia prior to chemotherapy.

The impact of channel morphology and flow on physical habitat availability for the two-spined blackfish (Gadopsis bispinosus) was assessed in the Cotter River, ACT, Australia. Physical habitat requirements for three life stages were identified based on previous field sampling in the Cotter River. Two sites were selected with contrasting channel morphology: Spur Hole, with a moderate gradient and runs and glides, and Vanity’s Crossing, with a steeper gradient, rapids, and fast-flowing pools. Physical Habitat Simulation System (PHABSIM) was used to simulate the flow v. physical habitat availability relationship for each life stage at both sites. Clear differences were apparent between sites, with Spur Hole characterised by increasing habitat with increasing flow and Vanity’s Crossing showing the opposite relationship. The nature of the channel morphology determined this difference, with Spur Hole characterised by marginal zones becoming inundated at higher flows and providing additional suitable physical habitat as discharge increases. Vanity’s Crossing does not contain similar marginal zones. Further analysis demonstrated that high water velocity was the most important factor limiting physical habitat availability at both sites. This approach demonstrates the importance of channel morphology in determining physical habitat availability and an alternative use of PHABSIM to highlight limiting factors for target species.

The form and structure of a tributary confluence bar in a regulated channel are analysed and related to channel adjustment to the imposed flow regime. The bar is characterized by a tripartite structure with two facies, and by marked lateral coarsening, characteristics which relate to the changing hydraulic conditions within the narrowing channel form.

Variations of channel substrate composition are described for a regulated river which has experienced channel change since dam completion. Sediment samples were obtained using bulk (grab) sampling and freeze-coring. Data derived from the two methods are shown to differ. Bulk-sample data describe the bed surface layer; its grain-size variations are related to bedform. Freeze-core data describe the sub-surface structure and the fine size-grades. The gravel framework-supported substrate of the control reaches constrasts with the sand-dominated substrate of the aggraded reach, although in both cases the substrate coarsens upwards. In the former this relates to the development of a sand matrix within the gravel-framework substrate, and in the latter, sand-bed channel, to the progressive addition of a gravel component towards the surface which is related to the process of channel change. At the local-scale, bedform is shown to exert an important control on the character of substrate change induced by flow regulation.

This study examines the distribution and composition of fine sediment within the gravel-bed substrate of the channelized River Tame, within and below the Birmingham conurbation, United Kingdom. A freeze coring technique was employed to collect undistributed volumetric samples, to a depth of 30-40 cm, providing information not only on the gross deposit but also on the vertical structure of the river bed in terms of textural and geochemical properties. The urbanized substrate differs from that of the natural river, both in terms of the volume of matrix sediment present, which is less than ‚expected’, and in the size characteristics of the coarse framework and finer matrix components. Moreover heavy metal concentrations within the urbanized matrix sediment are up to 3000 times greater than background levels and maximum concentrations are shown to occur at a depth of more than 15 cm within the substrate.

The spatial and temporal dynamics of physical habitat in rivers is driven by the interaction between channel morphology and discharge. However, little is known about how altered discharge affects the dynamics of habitat patches such as slackwaters. This study investigated the influence of discharge on the availability, stability, quality, and diversity of slackwaters in a southeastern Australian lowland river. The area, spatial configuration, permanence, and within-patch characteristics of slackwaters of two reaches in a regulated section and two reaches in a largely unregulated section of the river were compared. There was less slackwater area and it was less permanent at higher discharges and in the two regulated reaches than at lower discharges and in the largely unregulated reaches. Individual slackwaters were more homogenous in relation to within-patch characteristics in the regulated than in the largely unregulated reaches. However, variability in the spatial configuration of slackwaters and within-patch characteristics and diversity at the reach scale were not related to discharge. We suggest that channel morphology, rather than discharge, is the main driver of these characteristics.