Water stress vulnerability of four Banksia species in contrasting Ecohydrological habitats on the Gnangara Mound, Western Australia

The distribution of obligate and facultative phreatophytic vegetation reflects the gradient of ecohydrological habitats in a landscape. Preliminary investigations of Banksia vulnerability to xylem embolism have reported that obligate phreatophytes are more susceptible to water stress than facultative phreatophytes (Froend & Drake 2006). A quantitative measure of plant susceptibility to water stress is vital when establishing environmental water requirements. This study investigated interspecific differences in vulnerability to water stress for two facultative phreatophytes (B. attenuata and B. menziesii) and two obligate pln·eatophytes (B. ilicifolia and B. littoralis) at the same position along an ecohydrological gradient on the Gnangara Groundwater Mound, Westem Australia. In addition, intraspecific differences to water stress between populations that occupy contrasting ecohydrological habitats were also determined. Plant susceptibility to water stress was established using vulnerability curves, which demonstrate the xylem potentials at which vessels become embolised. Stem-specific and leaf-specific hydraulic conductivity, as well as Huber values (ratio of stem to leaf area), were also determined to support these findings. It was found that ecohydrological habitats are a primary detennining factor of plant hydraulic architecture, particularly vulnerability to xylem embolism. At the same ecohydrological habitat, where water is readily accessible there were no interspecific differences in vulnerability to water stress. In contrast, the facultative phreatophytes, B. attenuata and B. menziesii, appeared to be plastic in vulnerability to embolism in response to developing in a more xeric environment. Both facultative phreatophyte species were found to be more resistant to xylem embolism at the more xeric dune crest site in contrast to the bottom slope site. B. ilicifolia did not differ in vulnerability to embolism, supporting its classification as an obligate phreatophyte. This study highlights the importance of understanding site hydrological attributes when determining environmental water allocation for obligate and facultative phreatophytes

The response of Banksia roots to change in water table level in a Mediterranean-type environment

For phreatophytic plants to persist in a given habitat they need to maintain a functional connection to the water table, and the capacity for roots to respond to changes in the water table is a key aspect of this. If root growth is limited by season, plants may not be able to grow roots to adjust to changes in the water table at a particular time of the year. The redistribution of roots, particularly the capacity for roots to follow the water table down in summer and autumn months, is vital for phreatophytic plants to maintain a functional connection with the water table. Root activity by phreatophytic Banksia in south-west Western Australia was assessed using root in-growth bags, with above-ground plant phenological processes observed simultaneously. The root in-growth bag technique that was used showed that Banksia roots are able to grow, provided soil conditions are conducive and there are no endogenous limitations to root growth at different times of the year, such as a dormancy period. The ability to grow at any time in response to soil conditions might be an essential prerequisite for phreatophytes if they are to survive fluctuating water table conditions in seasonally water-limited environments

Rapid root elongation by phreatophyte seedlings does not imply tolerance of water table decline

Key message Despite high rates of root elongation during phreatophyte establishment once connection to groundwater has occurred and leaf area develops, seedlings demonstrate limited capacity for root elongation in response to groundwater decline. Abstract In a water-limited environment, rapid root elongation immediately after germination can be critical for a plant to reach deeper water sources such as a water table to avoid water deficit stress. However, once plants have accessed a water table, their continued survival may depend on their ability to adapt their root distribution to changes in the depth to a water table. In glasshouse experiments using two Banksia species with contrasting water requirements, we investigated (1) the rate of root elongation by young seedlings in the presence of a shallow water table, and (2) whole plant response to rapid water table decline using older seedlings that had established root contact with a water table. The results of the first experiment agree with the hypothesis that the facultative phreatophyte, B. attenuata, has a faster rate of root elongation than the obligate phreatophyte, B. littoralis. These differences are likely related to the contrasting habitat preferences of the two species. Older seedlings in the second experiment demonstrated a water-saving response to a declining water table, rapidly closing stomata to limit water loss. Additionally, roots did not elongate to follow the water table and plants were quickly disconnected from the saturated zone. For the two phreatophytic Banksia species, the capacity for rapid growth by young seedlings did not translate to an ability for established seedlings to adapt their root distribution to survive rapid water table decline

Transdisciplinary environmental research: trial and evaluation. Final report

A group of four NESP Northern Australia Environmental Resources Hub projects operating in the Fitzroy River catchment (Western Australia) used a transdisciplinary (participatory, interdisciplinary and outcomes-focused) approach by having water resource management as a common theme. The projects partly integrated their research processes and outputs and developed strong links with research users. The transdisciplinary project team included researchers from four projects, who integrated their research processes and outputs in pairs: 1.3.3 (Environmental water requirements) and 1.5 (Indigenous water requirements); 1.6 (Multi-objective planning) and 5.4 (Showing and sharing knowledge). Project 6.2 (this research) aimed to support the development of a transdisciplinary research (TDR) approach in the Fitzroy catchment and contribute to the emerging body of knowledge on transdisciplinarity more broadly. We achieved that aim by conducting a formative evaluation (i.e. during project implementation) of the collaboration between the four projects above. This involved: (1) the development of the Theory of Change of this collaboration, (2) a literature review, (3) interviews of research users, and (4) researchers’ reflection on the previous steps. The team identified different research impacts occurring because of people’s participation in, or access to the outputs of research. Research impacts, on both researchers and research users, included: • learning and increased understanding of scientific information • development of new skills or social learning (i.e. learning from working together with other stakeholders) • empowerment (e.g. meeting and deliberating with peers regarding collective action because of the projects) • enhancing communication with other groups and a better understanding of their perspectives • creating new contacts (e.g. meeting new people) and strengthening existing relationships. Two projects (Environmental water requirements and Indigenous water requirements) have directly contributed to the Fitzroy catchment water allocation plan and to stakeholders’ submissions on the draft water plan consultation (i.e. Western Australian Department of Water and Environmental Regulation [DWER] Discussion Paper). The Multi-objective planning and Showing and sharing knowledge projects contributed with less tangible outcomes such as enhancing communication, and strengthening relationships and Indigenous institutions. Researchers identified processes or outputs that contributed positively to knowledge uptake by research users, for example, the use of videos and interactive maps, which can help users such as Traditional Owners to assimilate and use project information. They also identified things that hindered the use of project outcomes, such as confusion between the roles of research and government planning, and the limited capacity of some organisations to use research outputs

When to Use Transdisciplinary Approaches for Environmental Research

Transdisciplinary research (TDR) can help generate solutions to environmental challenges and enhance the uptake of research outputs, thus contributing to advance sustainability in social-ecological systems. Our aim is to support investment decisions in TDR; more specifically, to help funders, researchers, and research users to decide when and why it is most likely to be worth investing in TDR approaches. To achieve our aim, we: 1) define TDR and use a decision tree comparing it with alternative modes of research (i.e., basic, applied, disciplinary, multi-disciplinary, and interdisciplinary research) to help researchers and funders distinguish TDR from other research modes; 2) identify features of the research problem and context (complexity, diverse knowledge systems, contestation, power imbalance, and disagreement on the need for transformative change) where a TDR approach could be more appropriate than the alternative research modes; and 3) explore the idea that the intensity of the contextual features in (2), together with the problem at hand, will help determine where a research project stands in a continuum from low- to high-TDR. We present five studies exemplifying lower- to higher-TDR approaches that are distinguished by: 1) the number and variety of research participants engaged; 2) the strength of involvement of non-academic actors; and 3) the number and variety of disciplines and knowledge systems involved in the research

Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency

Purpose Lamb-Shaffer syndrome (LAMSHF) is a neurodevelopmental disorder described in just over two dozen patients with heterozygous genetic alterations involving SOX5, a gene encoding a transcription factor regulating cell fate and differentiation in neurogenesis and other discrete developmental processes. The genetic alterations described so far are mainly microdeletions. The present study was aimed at increasing our understanding of LAMSHF, its clinical and genetic spectrum, and the pathophysiological mechanisms involved. Methods Clinical and genetic data were collected through GeneMatcher and clinical or genetic networks for 41 novel patients harboring various types ofSOX5 alterations. Functional consequences of selected substitutions were investigated. Results Microdeletions and truncating variants occurred throughout SOX5. In contrast, most missense variants clustered in the pivotal SOX-specific high-mobility-group domain. The latter variants prevented SOX5 from binding DNA and promoting transactivation in vitro, whereas missense variants located outside the high-mobility-group domain did not. Clinical manifestations and severity varied among patients. No clear genotype-phenotype correlations were found, except that missense variants outside the high-mobility-group domain were generally better tolerated. Conclusions This study extends the clinical and genetic spectrum associated with LAMSHF and consolidates evidence that SOX5 haploinsufficiency leads to variable degrees of intellectual disability, language delay, and other clinical features

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year

Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands

Significant benefits of AIP testing and clinical screening in familial isolated and young-onset pituitary tumors

Context Germline mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are responsible for a subset of familial isolated pituitary adenoma (FIPA) cases and sporadic pituitary neuroendocrine tumors (PitNETs). Objective To compare prospectively diagnosed AIP mutation-positive (AIPmut) PitNET patients with clinically presenting patients and to compare the clinical characteristics of AIPmut and AIPneg PitNET patients. Design 12-year prospective, observational study. Participants & Setting We studied probands and family members of FIPA kindreds and sporadic patients with disease onset ≤18 years or macroadenomas with onset ≤30 years (n = 1477). This was a collaborative study conducted at referral centers for pituitary diseases. Interventions & Outcome AIP testing and clinical screening for pituitary disease. Comparison of characteristics of prospectively diagnosed (n = 22) vs clinically presenting AIPmut PitNET patients (n = 145), and AIPmut (n = 167) vs AIPneg PitNET patients (n = 1310). Results Prospectively diagnosed AIPmut PitNET patients had smaller lesions with less suprasellar extension or cavernous sinus invasion and required fewer treatments with fewer operations and no radiotherapy compared with clinically presenting cases; there were fewer cases with active disease and hypopituitarism at last follow-up. When comparing AIPmut and AIPneg cases, AIPmut patients were more often males, younger, more often had GH excess, pituitary apoplexy, suprasellar extension, and more patients required multimodal therapy, including radiotherapy. AIPmut patients (n = 136) with GH excess were taller than AIPneg counterparts (n = 650). Conclusions Prospectively diagnosed AIPmut patients show better outcomes than clinically presenting cases, demonstrating the benefits of genetic and clinical screening. AIP-related pituitary disease has a wide spectrum ranging from aggressively growing lesions to stable or indolent disease course

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe