Application of classification machine learning algorithms for characterizing nutrient transport in a clay plain agricultural watershed.

Excess nutrients in surface water and groundwater can lead to water quality deterioration in available water resources. Thus, the classification of nutrient concentrations in water resources has gained significant attention during recent decades. Machine learning (ML) algorithms are considered an efficient tool to describe nutrient loss from agricultural land to surface water and groundwater. Previous studies have applied regression and classification ML algorithms to predict nutrient concentrations in surface water and/or groundwater, or to categorize an output variable using a limited number of input variables. However, there have been no studies that examined the application of different ML classification algorithms in agricultural settings to classify various output variables using a wide range of input variables. In this study, twenty-four ML classification algorithms were implemented on a dataset from three locations within the Upper Parkhill watershed, an agricultural watershed in southern Ontario, Canada. Nutrient concentrations in surface water were classified using geochemical and physical water parameters of surface water and groundwater (e.g., pH), climate and field conditions as the input variables. The performance of these algorithms was evaluated using four evaluation metrics (e.g., classification accuracy) to identify the optimal algorithm for classifying the output variables. Ensemble bagged trees was found to be the optimal ML algorithm for classifying nitrate concentration in surface water (accuracy of 90.9%), while the weighted KNN was the most appropriate algorithm for categorizing the total phosphorus concentration (accuracy of 87%). The ensemble subspace discriminant algorithm gave the highest overall classification accuracy for the concentration of soluble reactive phosphorus and total dissolved phosphorus in surface water with an accuracy of 79.2% and 77.9%, respectively. This study exemplifies that ML algorithms can be used to signify exceedance of recommended concentrations of nutrients in surface waters in agricultural watersheds. Results are useful for decision makers to develop nutrient management strategies.

Investigating relationships between climate controls and nutrient flux in surface waters, sediments, and subsurface pathways in an agricultural clay catchment of the Great Lakes Basin.

Water quality within agricultural catchments is governed by management practices and climate conditions that control the transport, storage, and exchange of nutrients between components of the hydrologic cycle. This study aims to improve knowledge of nitrogen (N) and phosphorus (P) transport in low permeability agricultural watersheds by considering spatial and temporal trends of surface water nutrient concentrations in relation to hydroclimatic drivers, sediment quality, shallow hyporheic exchange, groundwater quality, and tile drain discharge over a 14-month field study in a clay hydrosystem of the Lake Huron basin, one of the five Great Lakes. Results found that events of varying magnitude and intensity enhanced nutrient release from overland flow and subsurface pathways. Tile drain discharge was found to be a consistent and elevated source of P and N to surface waters when flowing, mobilizing both diffuse nutrients from fertilizer application and legacy stores in the vadose zone. Surface water quality was temporally variable at the seasonal and event scale. Targeted sampling following fertilization periods, snowmelt, and moderate precipitation events revealed catchment wide elevated nutrient concentrations, emphasizing the need for targeted sampling regimes. Controls other than discharge magnitude and overland flow were found to contribute to peak nutrient concentrations, including internal nitrate loading, soil-snowmelt interaction, catchment wetness, and freeze thaw cycles. Sediments were found to store P in calcium minerals and have a high P storage capacity. Instream mechanisms such as sediment P fixation and hyporheic exchange may play a role in mediating surface water quality, but currently have no discernable benefit to year-round surface water nutrient concentrations. Best management practices need to focus on reducing sources of agricultural nutrients (e.g., field phosphorus concentrations and tile drain discharge loading) at the watershed scale to reduce nutrient concentrations and export in flashy clay catchments.

Adverse Childhood Experiences as "Upstream" Determinants of Lifestyle-Related Chronic Disease: A Scoping Perspective.

We have previously proposed a list of determinants (causes) of modern lifestyle-related chronic disorders, which provides a structure for the emerging discipline of lifestyle medicine. This consists of lifestyle factors with a common immune biomarker (metaflammation) that interact in a systems fashion linked with chronic disease outcomes. We considered this to be a work in progress and later added 3 psychosocial determinants into the causal mix: meaninglessness, alienation, and loss of culture and identity (MAL). Here, we propose adverse childhood experiences (ACEs) as deeper, or even more distal, disease drivers that may act directly or indirectly through MAL to influence later chronic disease. The links with metaflammation and the need for recognition of these embedded scars in the management of lifestyle-related health problems is discussed.

Mapping Reaction-Diffusion Networks at the Plant Wound Site With Pathogens.

The rich collection of microbes colonizing the plant root making up the rhizosphere function as a multigenomic organ for nutrient distribution. The extent to which its dynamic mutualistic cellular order depends on morphogenic signaling, while likely, remains unknown. We have shown that reaction-diffusion chemical networks constructed with model plant and bacterial metabolites can mimic processes ranging from oxidative burst kinetics to traveling waves and extracellular stationary state reaction-diffusion networks for spatiotemporal ordering of the rhizosphere. Plant parasites and pathogens can be limited by host attachment require dynamic informational networks and continue to provide insight into what controls the rhizosphere. Here we take advantage of Agrobacterium tumefaciens, a plant pathogen with a gated receptor that requires simultaneous perception of two plant metabolites. Genetic manipulations have created receptors allowing each metabolite concentration to be correlated with pathogen behavior. The development of the florescent strains used here provide initial maps of the reaction-diffusion dynamics existing in the rhizosphere, revealing significant differences in the signaling landscape of host and non-host plants before and after wounding, specifically highlighting networks that may inform rhizosphere organization.

Lifestyle Medicine in Australia: A Potted History-So Far.

Lifestyle medicine commenced in Australia in response to the rise in chronic diseases following the epidemiological transition that began in the 1980s. Today, it is flourishing with an annual conference, a variety of multidisciplinary members, and a developed pedagogy for the "art-science."

The MexE/MexF/AmeC Efflux Pump of Agrobacterium tumefaciens and Its Role in Ti Plasmid Virulence Gene Expression.

Expression of the tumor-inducing (Ti) plasmid virulence genes of Agrobacterium tumefaciens is required for the transfer of DNA from the bacterium into plant cells, ultimately resulting in the initiation of plant tumors. The vir genes are induced as a result of exposure to certain phenol derivatives, monosaccharides, and low pH in the extracellular milieu. The soil, as well as wound sites on a plant-the usual site of the virulence activity of this bacterium-can contain these signals, but vir gene expression in the soil would be a wasteful utilization of energy. This suggests that mechanisms may exist to ensure that vir gene expression occurs only at the higher concentrations of inducers typically found at a plant wound site. In a search for transposon-mediated mutations that affect sensitivity for the virulence gene-inducing activity of the phenol, 3,5-dimethoxy-4-hydroxyacetophenone (acetosyringone [AS]), an RND-type efflux pump homologous to the MexE/MexF/OprN pump of Pseudomonas aeruginosa was identified. Phenotypes of mutants carrying an insertion or deletion of pump components included hypersensitivity to the vir-inducing effects of AS, hypervirulence in the tobacco leaf explant virulence assay, and hypersensitivity to the toxic effects of chloramphenicol. Furthermore, the methoxy substituents on the phenol ring of AS appear to be critical for recognition as a pump substrate. These results support the hypothesis that the regulation of virulence gene expression is integrated with cellular activities that elevate the level of plant-derived inducers required for induction so that this occurs preferentially, if not exclusively, in a plant environment.IMPORTANCE Expression of genes controlling the virulence activities of a bacterial pathogen is expected to occur preferentially at host sites vulnerable to that pathogen. Host-derived molecules that induce such activities in the plant pathogen Agrobacterium tumefaciens are found in the soil, as well as in the plant. Here, we tested the hypothesis that mechanisms exist to suppress the sensitivity of Agrobacterium species to a virulence gene-inducing molecule by selecting for mutant bacteria that are hypersensitive to its inducing activity. The mutant genes identified encode an efflux pump whose proposed activity increases the concentration of the inducer necessary for vir gene expression; this pump is also involved in antibiotic resistance, demonstrating a relationship between cellular defense activities and the control of virulence in Agrobacterium.

Spatiotemporal variations of nitrogen and phosphorus in a clay plain hydrological system in the Great Lakes Basin.

Nutrient imbalance in groundwater and surface water resources can have severe implications on human and aquatic life, including contamination of drinking water sources and the degradation of ecosystems. A field-based watershed-scale study was completed to investigate nutrient dynamics and hydrologic processes in an agriculturally-dominant clay plain system within the Great Lakes Basin. Spatial and temporal variations of nitrogen and phosphorus were examined by sampling groundwater and surface water regularly over a period of one year (June 2017 to July 2018) for nutrients including nitrate, soluble reactive phosphorus, total dissolved phosphorus and total reactive phosphorus. Nitrate transport from surrounding agricultural land to surface water was intensified with an increase in precipitation events in spring and early winter and phosphorus transport to surface water was increased during freeze-thaw cycles in the winter. The results are pertinent to the improvement of current nutrient and water management policies in clay plain systems where nutrient imbalances in surface water are a concern.

Psychosocial Determinants of Chronic Disease: Implications for Lifestyle Medicine.

We have previously identified a number of "determinants" of chronic disease, using the acronym NASTIE ODOURS. These have been given the collective term "anthropogens," in this journal and other publications, to help direct the management of modern chronic ailments to a monocausal focus, akin to that afforded infectious diseases by the "germ theory." We suggested the acronym NASTIE ODOURS as a starting point for a taxonomy of lifestyle medicine determinants. In the current article, we add 3, less quantifiable, but currently increasingly more important psychosocial experiences to these: Lack of Meaning, Alienation, and Loss of culture, changing the previous acronym to NASTIE MAL ODOURS. As with other determinants, all have accumulating evidence of an underlying low-grade, systemic, inflammatory physiological base ("metaflammation"), but with the need for further research to solidify these findings.

Shared medical appointments for Aboriginal and Torres Strait Islander men.

BACKGROUND: Aboriginal and Torres Strait Islander health is generally the worst of any population group in Australia. Inaccessibility to health services is one possible cause of this. Shared medical appointments (SMAs) appear to be a culturally competent and appropriate way of improving access to, and the quality of, primary healthcare services for Aboriginal and Torres Strait Islander peoples. OBJECTIVE: The objective of this article is to assess the acceptability and appropriateness of SMAs as an adjunct process in primary care for Aboriginal and Torres Strait Islander men. METHODS: As part of a broader study on SMAs, three SMA sessions were delivered at an Aboriginal men's health centre in northern New South Wales. One-day training sessions in SMA facilitation were also provided to two groups of 12-14 Aboriginal health workers (AHWs). Mixed methods were used to assess patient and provider satisfaction, subjective outcomes, and operational procedures in the SMA groups, as well as interest in the SMA process by AHWs. RESULTS: Satisfaction with SMAs among Aboriginal men was unanimously positive, with the numbers in the group increasing over time. Patients most enjoyed the 'yarn up' nature of SMAs with peer support, which reduced the 'scary' and culturally 'unnatural' nature of one-on-one consultations with a general practitioner (GP). AHWs who were trained to a level to conduct SMAs saw this as an effective way of improving cultural competence in, and accessibility of, their various Aboriginal health services. DISCUSSION: The results, though not generalisable, suggest that SMAs may offer a culturally safe and appropriate tool to enhance Aboriginal and Torres Strait Islander peoples' access to primary care.

Involvement of Agrobacterium tumefaciens Galacturonate Tripartite ATP-Independent Periplasmic (TRAP) Transporter GaaPQM in Virulence Gene Expression.

Monosaccharides capable of serving as nutrients for the soil bacterium Agrobacterium tumefaciens are also inducers of the vir regulon present in the tumor-inducing (Ti) plasmid of this plant pathogen. One such monosaccharide is galacturonate, the predominant monomer of pectin found in plant cell walls. This ligand is recognized by the periplasmic sugar binding protein ChvE, which interacts with the VirA histidine kinase that controls vir gene expression. Although ChvE is also a member of the ChvE-MmsAB ABC transporter involved in the utilization of many neutral sugars, it is not involved in galacturonate utilization. In this study, a putative tripartite ATP-independent periplasmic (TRAP) transporter, GaaPQM, is shown to be essential for the utilization of galacturonic acid; we show that residue R169 in the predicted sugar binding site of the GaaP is required for activity. The gene upstream of gaaPQM (gaaR) encodes a member of the GntR family of regulators. GaaR is shown to repress the expression of gaaPQM, and the repression is relieved in the presence of the substrate for GaaPQM. Moreover, GaaR is shown to bind putative promoter regions in the sequences required for galacturonic acid utilization. Finally, A. tumefaciens strains carrying a deletion of gaaPQM are more sensitive to galacturonate as an inducer of vir gene expression, while the overexpression of gaaPQM results in strains being less sensitive to this vir inducer. This supports a model in which transporter activity is crucial in ensuring that vir gene expression occurs only at sites of high ligand concentration, such as those at a plant wound site.

Patients' and providers' satisfaction with shared medical appointments.

BACKGROUND: Shared medical appointments (SMAs) are comprehensive medical visits conducted with groups of patients. We have previously discussed the potential and assessed likely support for SMAs in Australia. In this paper, we report on patient and provider satisfaction, and some subjective outcomes. OBJECTIVE: To measure patients' and providers' attitude and satisfaction with SMAs after attending at least two, and consider the most appropriate form of SMA suited to Australian conditions. METHODS: A total of 24 SMAs were conducted in eight medical centres in New South Wales, South Australia and Queensland. Satisfaction and subjective outcomes from these sessions were tested in a mixed method analysis after more than 200 attendances. RESULTS: Satisfaction with SMAs was high among patients and providers. Almost all of the patients involved said they would continue using SMAs, if these were available. All providers wished to continue being involved as an alternative form of clinical management. DISCUSSION: The results of this pilot study, and our previously reported studies, suggest that SMAs could be a valuable process tool in chronic disease management in Australia.

The Receiver of the Agrobacterium tumefaciens VirA Histidine Kinase Forms a Stable Interaction with VirG to Activate Virulence Gene Expression.

The plant pathogen Agrobacterium tumefaciens carries a virulence gene system that is required for the initiation of crown gall tumors on susceptible plants. Expression of the vir genes is activated by the VirA/VirG two component regulatory system. VirA is a histidine kinase which signals the presence of certain chemicals found at the site of a plant wound. The receiver domain located at its carboxyl terminus defines VirA as a hybrid histidine kinase. Here, we show that the VirA receiver interacts with the DNA-binding domain of VirG. This finding supports the hypothesis that the receiver acts as a recruiting factor for VirG. In addition, we show that removal of the VirA receiver allowed vir gene expression in response to glucose in a dose dependent manner, indicating that the receiver controls VirG activation and suggesting that the supplementary ChvE-sugar signal increases this activity.

A user assessment of the potential for shared medical appointments in Australia.

BACKGROUND: In some countries, shared medical appointments (SMAs) have been shown to be more effective than single consultations for managing chronic diseases. Our study was designed as the first stage of a Royal Australian College of General Practitioners (RACGP) funded project to assess potential patient and provider support for SMAs if they were to become available in Australia. METHODS: We conducted focus groups with healthcare providers and patients with diabetes in four large regional health centres in NSW. The data were analysed using rigorous qualitative processes. RESULTS: Healthcare provider participants appeared overwhelmingly in favour of SMAs, while patients were divided on the process. Where opposed, patients cited concerns about confidentiality and their satisfaction with the status quo. DISCUSSION: There appears to be a groundswell of interest in SMAs that warrants further investigation in the Australian healthcare system. Issues of reimbursement, homogeneity of groups and training need further consideration.

GxySBA ABC transporter of Agrobacterium tumefaciens and its role in sugar utilization and vir gene expression.

Monosaccharides available in the extracellular milieu of Agrobacterium tumefaciens can be transported into the cytoplasm, or via the periplasmic sugar binding protein, ChvE, play a critical role in controlling virulence gene expression. The ChvE-MmsAB ABC transporter is involved in the utilization of a wide range of monosaccharide substrates but redundant transporters are likely given the ability of a chvE-mmsAB deletion strain to grow, albeit more slowly, in the presence of particular monosaccharides. In this study, a putative ABC transporter encoded by the gxySBA operon is identified and shown to be involved in the utilization of glucose, xylose, fucose, and arabinose, which are also substrates for the ChvE-MmsAB ABC transporter. Significantly, GxySBA is also shown to be the first characterized glucosamine ABC transporter. The divergently transcribed gene gxyR encodes a repressor of the gxySBA operon, the function of which can be relieved by a subset of the transported sugars, including glucose, xylose, and glucosamine, and this substrate-induced expression can be repressed by glycerol. Furthermore, deletion of the transporter can increase the sensitivity of the virulence gene expression system to certain sugars that regulate it. Collectively, the results reveal a remarkably diverse set of substrates for the GxySBA transporter and its contribution to the repression of sugar sensitivity by the virulence-controlling system, thereby facilitating the capacity of the bacterium to distinguish between the soil and plant environments.

Role of the VirA histidine autokinase of Agrobacterium tumefaciens in the initial steps of pathogenesis.

Histidine kinases serve as critical environmental sensing modules, and despite their designation as simple two-component modules, their functional roles are remarkably diverse. In Agrobacterium tumefaciens pathogenesis, VirA serves with VirG as the initiating sensor/transcriptional activator for inter-kingdom gene transfer and transformation of higher plants. Through responses to three separate signal inputs, low pH, sugars, and phenols, A. tumefaciens commits to pathogenesis in virtually all flowering plants. However, how these three signals are integrated to regulate the response and why these signals might be diagnostic for susceptible cells across such a broad host-range remains poorly understood. Using a homology model of the VirA linker region, we provide evidence for coordinated long-range transmission of inputs perceived both outside and inside the cell through the creation of targeted VirA truncations. Further, our evidence is consistent with signal inputs weakening associations between VirA domains to position the active site histidine for phosphate transfer. This mechanism requires long-range regulation of inter-domain stability and the transmission of input signals through a common integrating domain for VirA signal transduction.

Shared medical appointments - an adjunct for chronic disease management in Australia?

BACKGROUND: The incidence of chronic disease continues largely unabated in modern western societies. While the content (physiology, determinants) of these diseases is well studied, processes of dealing with them at the clinical level have been less well considered. Shared medical appointments (SMAs) or group consultations (also often referred to as group visits) are 'a series of individual office visits sequentially attending to each patient's unique medical needs individually, but in a supportive group setting where all can listen, interact and learn'. OBJECTIVE: To examine the potential acceptability of SMAs for the management of chronic diseases in the Australian context. DISCUSSION: SMAs were developed in the US to improve access to care, utilise peer support, reduce costs and improve patient and provider satisfaction in the management of chronic disease. An SMA is a comprehensive medical visit, not just a group education session, where a significant part of the added value comes from the facilitated peer interaction, particularly around aspects of self-management and empowerment. While more studies are required to compare outcomes with conventional one-on-one consultations, the reported gains in time efficiency, patient numbers managed, and patient as well as provider satisfaction, are sufficient to justify further consideration of a trial of SMAs in Australia.

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals.

Agrobacterium tumefaciens is a broad host range plant pathogen that combinatorially recognizes diverse host molecules including phenolics, low pH, and aldose monosaccharides to activate its pathogenic pathways. Chromosomal virulence gene E (chvE) encodes a periplasmic-binding protein that binds several neutral sugars and sugar acids, and subsequently interacts with the VirA/VirG regulatory system to stimulate virulence (vir) gene expression. Here, a combination of genetics, X-ray crystallography, and isothermal calorimetry reveals how ChvE binds the different monosaccharides and also shows that binding of sugar acids is pH dependent. Moreover, the potency of a sugar for vir gene expression is modulated by a transport system that also relies on ChvE. These two circuits tune the overall system to respond to sugar concentrations encountered in vivo. Finally, using chvE mutants with restricted sugar specificities, we show that there is host variation in regard to the types of sugars that are limiting for vir induction.

Characterization of the mmsAB-araD1 (gguABC) genes of Agrobacterium tumefaciens.

The chvE-gguABC operon plays a critical role in both virulence and sugar utilization through the activities of the periplasmic ChvE protein, which binds to a variety of sugars. The roles of the GguA, GguB, and GguC are not known. While GguA and GguB are homologous to bacterial ABC transporters, earlier genetic analysis indicated that they were not necessary for utilization of sugars as the sole carbon source. To further examine this issue, in-frame deletions were constructed separately for each of the three genes. Our growth analysis clearly indicated that GguA and GguB play a role in sugar utilization and strongly suggests that GguAB constitute an ABC transporter with a wide range of substrates, including L-arabinose, D-fucose, D-galactose, D-glucose, and D-xylose. Site-directed mutagenesis showed that a Walker A motif was vital to the function of GguA. We therefore propose renaming gguAB as mmsAB, for multiple monosaccharide transport. A gguC deletion affected growth only on L-arabinose medium, suggesting that gguC encodes an enzyme specific to L-arabinose metabolism, and this gene was renamed araD1. Results from bioinformatics and experimental analyses indicate that Agrobacterium tumefaciens uses a pathway involving nonphosphorylated intermediates to catabolize L-arabinose via an L-arabinose dehydrogenase, AraA(At), encoded at the Atu1113 locus.

The integrity of the periplasmic domain of the VirA sensor kinase is critical for optimal coordination of the virulence signal response in Agrobacterium tumefaciens.

The plant pathogen Agrobacterium tumefaciens responds to three main signals at the plant-bacterium interface: phenolics, such as acetosyringone (AS), monosaccharides, and acidic pH (∼5.5). These signals are transduced via the chromosomally encoded sugar binding protein ChvE and the Ti plasmid-encoded VirA/VirG two-component regulatory system, resulting in the transcriptional activation of the Ti plasmid virulence genes. Here, we present genetic and physical evidence that the periplasmic domain of VirA dimerizes independently of other parts of the protein, and we examine the effects of several engineered mutations in the periplasmic and transmembrane regions of VirA on vir-inducing capacity as indicated by AS sensitivity and maximal level of vir-inducing activity at saturating AS levels. The data indicate that helix-breaking mutations throughout the periplasmic domain of VirA or mutations that reposition the second transmembrane domain (TM2) of VirA relieve the periplasmic domain's repressive effects on the maximal activity of this kinase in response to phenolics, effects normally relieved only when ChvE, sugars, and low pH are also present. Such relief, however, does not sensitize VirA to low concentrations of phenolics, the other major effect of the ChvE-sugar and low pH signals. We further demonstrate that amino acid residues in a small Trg-like motif in the periplasmic domain of VirA are crucial for transmission of the ChvE-sugar signal to the cytoplasmic domain. These experiments provide evidence that small perturbations in the periplasmic domain of VirA can uncouple sugar-mediated changes in AS sensitivity from the sugar-mediated effects on maximal activity.

The receiver domain of hybrid histidine kinase VirA: an enhancing factor for vir gene expression in Agrobacterium tumefaciens.

The plant pathogen Agrobacterium tumefaciens expresses virulence (vir) genes in response to chemical signals found at the site of a plant wound. VirA, a hybrid histidine kinase, and its cognate response regulator, VirG, regulate vir gene expression. The receiver domain at the carboxyl end of VirA has been described as an inhibitory element because its removal increased vir gene expression relative to that of full-length VirA. However, experiments that characterized the receiver region as an inhibitory element were performed in the presence of constitutively expressed virG. We show here that VirA's receiver domain is an activating factor if virG is expressed from its native promoter on the Ti plasmid. When virADeltaR was expressed from a multicopy plasmid, both sugar and the phenolic inducer were essential for vir gene expression. Replacement of wild-type virA on pTi with virADeltaR precluded vir gene induction, and the cells did not accumulate VirG or induce transcription of a virG-lacZ fusion in response to acetosyringone. These phenotypes were corrected if the virG copy number was increased. In addition, we show that the VirA receiver domain can interact with the VirG DNA-binding domain.