Reconstructing pre-impact vegetation cover in modified landscapes using environmental modelling, historical surveys and remnant vegetation data: a case study in the Fleurieu Peninsula, South Australia

Aim To investigate the application of environmental modelling to reconstructive mapping of pre‐impact vegetation using historical survey records and remnant vegetation data. Location The higher elevation regions of the Fleurieu Peninsula region in South Australia were selected as a case study. The Fleurieu Peninsula is an area typical of many agricultural regions in temperate Australia that have undergone massive environmental transformation since European settlement. Around 9% of the present land cover is remnant vegetation and historical survey records from the ad 1880s exist. It is a region with strong gradients in climate and topography. Methods Records of pre‐impact vegetation distribution made in surveyors’ field notebooks were transcribed into a geographical information system and the spatial and classificatory accuracy of these records was assessed. Maps of remnant vegetation distribution were obtained. Analysis was undertaken to quantify the environmental domains of historical survey record and remnant vegetation data to selected meso‐scaled climatic parameters and topo‐scaled terrain‐related indices at a 20 m resolution. An exploratory analytical procedure was used to quantify the probability of occurrence of vegetation types in environmental domains. Probability models spatially extended to geographical space produce maps of the probability of occurrence of vegetation types. Individual probability maps were combined to produce a pre‐impact vegetation map of the region. Results Surveyors’ field notebook records provide reliable information that is accurately locatable to levels of resolution such that the vegetation data can be spatially correlated with environmental variables generated on 20 m resolution environmental data sets. Historical survey records of vegetation were weakly correlated with the topo‐scaled environmental variables but were correlated with meso‐scaled climate. Remnant vegetation records similarly not only correlated to climate but also displayed stronger relationships with the topo‐scaled environmental variables, particularly slope. Main conclusions A major conclusion of this study is that multiple sources of evidence are required to reconstruct past vegetation patterns in heavily transformed region. Neither the remnant vegetation data nor historical survey records provided adequate data sets on their own to reconstruct the pre‐impact vegetation of the Fleurieu Peninsula. Multiple sources of evidence provide the only means of assessing the environmental and historical representativeness of data sets. The spatial distribution of historical survey records was more environmentally representative than remnant vegetation data, which reflect biases due to land clearance. Historical survey records were also shown to be classificatory and spatially accurate, thus are suitable for quantitative spatial analyses. Analysis of different spatial vegetation data sets in an environmental modelling framework provided a rigorous means of assessing and comparing respective data sets as well as mapping their predicted distributions based on quantitative correlations. The method could be usefully applied to other regions where predictions of pre‐impact vegetation cover are required.     

Participant understanding and recall of informed consent for induced pluripotent stem cell biobanking

The ability to generate human induced pluripotent stem cells (iPSCs) has opened new avenues for human disease modelling and therapy. The aim of our study was to determine research participants’ understanding of the information given when donating skin biopsies for the generation of patient-specific iPSCs. A customised 35-item questionnaire based on previous iPSC consent guidelines was sent to participants who had previously donated samples for iPSC research. The questionnaire asked pertinent demographic details, participants' motivation to take part in iPSC research and their attitudes towards related ethical issues. 234 participants were contacted with 141 (60.3 %) complete responses received. The median duration between recruitment and follow-up questioning was 313 days (range 10–573 days). The majority of participants (n = 129, 91.5 %) believed they understood what a stem cell was; however, only 22 (16.1 %) correctly answered questions related to basic stem cell properties. We found no statistically significant difference in responses from participants with different levels of education, or those with a health sciences background. The poor understanding amongst participants of iPSC research is unlikely to be unique to our study and may impact future research if not improved. As such, there is a need to develop an easily understood yet comprehensive consent process to ensure ongoing ethical progress of iPSC biobanking.     

Origin of bistability in the lac Operon

Multistability is an emergent dynamic property that has been invoked to explain multiple coexisting biological states. In this work, we investigate the origin of bistability in the lac operon. To do this, we develop a mathematical model for the regulatory pathway in this system and compare the model predictions with other experimental results in which a nonmetabolizable inducer was employed. We investigate the effect of lactose metabolism using this model, and show that it greatly modifies the bistable region in the external lactose (Le) versus external glucose (Ge) parameter space. The model also predicts that lactose metabolism can cause bistability to disappear for very low Ge. We have also carried out stochastic numerical simulations of the model for several values of Ge and Le. Our results indicate that bistability can help guarantee that Escherichia coli consumes glucose and lactose in the most efficient possible way. Namely, the lac operon is induced only when there is almost no glucose in the growing medium, but if Le is high, the operon induction level increases abruptly when the levels of glucose in the environment decrease to very low values. We demonstrate that this behavior could not be obtained without bistability if the stability of the induced and uninduced states is to be preserved. Finally, we point out that the present methods and results may be useful to study the emergence of multistability in biological systems other than the lac operon.     

Visualization and modelling of the thermal inactivation of bacteria in a model food.

A large number of incidents of food poisoning have been linked to undercooked meat products. The use of mathematical modelling to describe heat transfer within foods, combined with data describing bacterial thermal inactivation, may prove useful in developing safer food products while minimizing thermal overprocessing. To examine this approach, cylindrical agar blocks containing immobilized bacteria (Salmonella typhimurium and Brochothrix thermosphacta) were used as a model system in this study. The agar cylinders were subjected to external conduction heating by immersion in a water bath. They were then incubated, sliced open, and examined by image analysis techniques for regions of no bacterial growth. A finite-difference scheme was used to model thermal conduction and the consequent bacterial inactivation. Bacterial inactivation rates were modelled with values for the time required to reduce bacterial number by 90% (D) and the temperature increase required to reduce D by 90% taken from the literature. Model simulation results agreed well with experimental results for both bacteria, demonstrating the utility of the technique.     

Insect Diversity in Phytoremediation and Bioaccumulation of Se

A variety of plant species are being considered for the phytoremediation of selenium (Se) contaminated soils in agricultural regions of central California. Use of this plant-based technology may also attract a wide range of insects to these Se-accumulating plants. The first field study surveyed the diversity of insects attracted to tall fescue, birdsfoot trefoil, kenaf, and Indian mustard. Over 7500 specimens were collected by a sweep net collection technique for one complete growing season. Most of the 84 families identified were associated with beneficial insects, although pestiferous insects, for example, thrips, aphids, lygus, and leafhoppers, were also found. In the second study the bioaccumulation of Se in the cabbage looper [Trichoplusia ni (Hübner)] was investigated on Indian mustard grown in Se-rich water culture solution. Neonate larvae were transferred to plants and fed on Se-treated and no Se treated plants (controls) for 14 days, respectively. Pupae were collected from each treatment and incubated until adult insects emerged. Almost 50% fewer pupae were collected from Se-treated plants compared with “controls”, resulting in fewer adult insects. Selenium concentrations were as high as 3173 μg Se kg^-1 DW in adult insects hatched from Se-treated plants compared with <5 μg Se kg^-1 DW in insects from “controls”. Based on both studies, we concluded that insect diversity should be determined and insects monitored for bioaccumulation of Se on phytoremediation sites in agricultural regions.     

Novel mutations involving βI-, βIIA-, or βIVB-tubulin isotypes with functional resemblance to βIII-tubulin in breast cancer

Tubulin is the target for very widely used anti-tumor drugs, including Vinca alkaloids, taxanes, and epothilones, which are an important component of chemotherapy in breast cancer and other malignancies. Paclitaxel and other tubulin-targeting drugs bind to the β subunit of tubulin, which is a heterodimer of α and β subunits. β-Tubulin exists in the form of multiple isotypes, which are differentially expressed in normal and neoplastic cells and differ in their ability to bind to drugs. Among them, the βIII isotype is overexpressed in many aggressive and metastatic cancers and may serve as a prognostic marker in certain types of cancer. The underpinning mechanisms accounting for the overexpression of this isotype in cancer cells are unclear. To better understand the role of β-tubulin isotypes in cancer, we analyzed over 1000 clones from 90 breast cancer patients, sequencing their β-tubulin isotypes, in search of novel mutations. We have elucidated two putative emerging molecular subgroups of invasive breast cancer, each of which involve mutations in the βI-, βIIA-, or βIVB isotypes of tubulin that increase their structural, and possibly functional, resemblance to the βIII isotype. A unifying feature of the first of the two subgroups is the mutation of the highly reactive C239 residue of βI- or βIVB-tubulin to L239, R239, Y239, or P239, culminating in probable conversion of these isotypes from ROS-sensitive to ROS-resistant species. In the second subgroup, βI, βIIA, and βIVB have up to seven mutations to the corresponding residues in βIII-tubulin. Given that βIII-tubulin has emerged as a pro-survival factor, overexpression of this isotype may confer survival advantages to certain cancer cell types. In this mini-review, we bring attention to a novel mechanism by which cancer cells may undergo adaptive mutational changes involving alternate β-tubulin isotypes to make them acquire some of the pro-survival properties of βIII-tubulin. These “hybrid” tubulins, combining the sequences and/or properties of two wild-type tubulins (βIII and either βI, βIIA, or βIVB), are novel isotypes expressed solely in cancer cells and may contribute to the molecular understanding and stratification of invasive breast cancer and provide novel molecular targets for rational drug development.     

The transcriptome of Toxoplasma gondii

Background  

Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown.     

The Pseudomonas syringae type III effector AvrRpm1 induces significant defenses by activating the Arabidopsis nucleotide-binding leucine-rich repeat protein RPS2

Plant disease resistance (R) proteins recognize potential pathogens expressing corresponding avirulence (Avr) proteins through 'gene-for-gene' interactions. RPM1 is an Arabidopsis R-protein that triggers a robust defense response upon recognizing the Pseudomonas syringae effector AvrRpm1. Avr-proteins of phytopathogenic bacteria include type III effector proteins that are often capable of enhancing virulence when not recognized by an R-protein. In rpm1 plants, AvrRpm1 suppresses basal defenses induced by microbe-associated molecular patterns. Here, we show that expression of AvrRpm1 in rpm1 plants induced PR-1, a classical defense marker, and symptoms including chlorosis and necrosis. PR-1 expression and symptoms were reduced in plants with mutations in defense signaling genes ( pad4 , sid2 , npr1 , rar1 , and ndr1 ) and were strongly reduced in rpm1 rps2 plants, indicating that AvrRpm1 elicits defense signaling through the Arabidopsis R-protein, RPS2. Bacteria expressing AvrRpm1 grew more on rpm1 rps2 than on rpm1 plants. Thus, independent of its classical 'gene-for-gene' activation of RPM1, AvrRpm1 also induces functionally relevant defenses that are dependent on RPS2. Finally, AvrRpm1 suppressed host defenses and promoted the growth of type III secretion mutant bacteria equally well in rps2 and RPS2 plants, indicating that virulence activity of over-expressed AvrRpm1 predominates over defenses induced by weak activation of RPS2.