Transgenerational soil‐mediated differences between plants experienced or naïve to a grass invasion

Invasive species may undergo rapid change as they invade. Native species persisting in invaded areas may also experience rapid change over this short timescale relative to native populations in uninvaded areas. We investigated the response of the native Achillea millefolium to soil from Holcus lanatus‐invaded and uninvaded areas, and we sought to determine whether differential responses between A. millefolium from invaded (invader experienced) and uninvaded (invader naïve) areas were mediated by soil community changes. Plants grown from seed from experienced and naïve areas responded differently to invaded and uninvaded soil with respect to germination time, biomass, and height. Overall, experienced plants grew faster and taller than their naïve counterparts. Naïve native plants showed negative feedbacks with their home soil and positive feedbacks with invaded soil; experienced plants were less responsive to soil differences. Our results suggest that native plants naïve to invasion may be more sensitive to soil communities than experienced plants, consistent with recent studies. While differences between naïve and experienced plants are transgenerational, our design cannot differentiate between differences that are genetically based, plastic, or both. Regardless, our results highlight the importance of seed source and population history in restoration, emphasizing the restoration potential of experienced seed sources.     

A simple landscape-scale test of a spatially explicit population model: patch occupancy in fragmented south-eastern Australian forests

The results of a landscape‐scale test of ALEX, a widely used metapopulation model for Population Viability Analysis (PVA), are described. ALEX was used to predict patch occupancy by the laughing kookkaburra and the sacred kingfisher in patches of eucalypt forest in south‐eastern Australia. These predictions were compared to field surveys to determine the accuracy of the model. Predictions also were compared to a “naïve” null model assuming no fragmentation effects.
The naïve null model significantly over‐predicted the number of eucalypt patches occupied by the sacred kingfisher, but the observed patch occupancy was not significantly different from that predicted using ALEX. ALEX produced a better fit to the field data than the naïve null model for the number of patches occupied by the laughing kookaburra. Nevertheless, ALEX still significantly over‐predicted the number of occupied patches, particularly remnants dominated by certain forest types – ribbon gum and narrow‐leaved peppermint. The predictions remained significantly different from observations, even when the habitat quality of these patches was reduced to zero. Changing the rate of dispersal improved overall predicted patch occupancy, but occupancy rates for the different forest types remained significantly different from the field observations. The lack of congruence between field data and model predictions could have arisen because the laughing kookaburra may move between an array of patches to access spatially separated food and nesting resources in response to fragmentation. Alternatively, inter‐specific competition may be heightened in a fragmented habitat. These types of responses to fragmentation are not incorporated as part of traditionally applied metapopulation models. Assessments of predictions from PVA models are rare but important because they can reveal the types of species for which forecasts are accurate and those for which they are not. This can assist the collection of additional empirical data to identify important factors affecting population dynamics.     

Quantifying the impacts of bushfire on populations of wild koalas (Phascolarctos cinereus): Insights from the 2019/20 fire season

The impact of bushfire events on wild Koala (Phascolarctos cinereus) populations is poorly understood. Following the 2019/2020 bushfire season in eastern Australia, we resurveyed 123 field sites for which contemporaneous (current koala generation) pre‐fire survey data were available. Field sites were distributed across six fire grounds between Foster and Ballina on the north coast of New South Wales. At these sites, pre‐fire naïve occupancy levels by koalas ranged from 25% to 71% of the sampled habitat, while post‐fire naïve occupancy levels ranged from 0% to 47%. The median reduction in the naïve occupancy rate by koalas when considered across all six fire grounds was 71% when standardized against pre‐fire occupancy levels. Field data provided strong corroboration between site‐based, post‐fire foliage canopy cover estimates and modelled Google Earth Engine Burnt Area Map (GEEBAM) fire‐severity categories. In terms of GEEBAM fire‐severity categories, koala survival was five times more likely in areas where forest canopies were modelled as Unburnt or Partially burnt, compared to areas where forest canopies were Fully burnt. The capacity of bushfire‐affected koala populations to recover from the 2019/20 fire season will be conditional upon size of the original population in each fire‐affected area, the enactment and implementation of supportive, recovery‐themed management regimes, future inter‐fire intervals and associated intensities. Management actions necessary to assist recovery actions are discussed.     

Differences in parasite susceptibility and costs of resistance between naturally exposed and unexposed host populations

It is generally assumed that resistance to parasitism entails costs. Consequently, hosts evolving in the absence of parasites are predicted to invest less in costly resistance mechanisms than hosts consistently exposed to parasites. This prediction has, however, rarely been tested in natural populations. We studied the susceptibility of three naïve, three parasitized and one recently isolated Asellus aquaticus isopod populations to an acanthocephalan parasite. We found that parasitized populations, with the exception of the isopod population sympatric with the parasite strain used, were less susceptible to the parasite than the naïve populations. Exposed but uninfected (resistant) isopods from naïve populations, but not from parasitized populations, exhibited greater mortality than controls, implying that resistance entails survival costs primarily for naïve isopods. These results suggest that parasites can drive the evolution of host resistance in the wild, and that co‐existence with parasites may increase the cost‐effectiveness of defence mechanisms.     

Controlled cortical impact injury affects dopaminergic transmission in the rat striatum

The therapeutic benefits of dopamine (DA) agonists after traumatic brain injury (TBI) imply a role for DA systems in mediating functional deficits post‐TBI. We investigated how experimental TBI affects striatal dopamine systems using fast scan cyclic voltammetry (FSCV), western blot, and d‐amphetamine‐induced rotational behavior. Adult male Sprague–Dawley rats were injured by a controlled cortical impact (CCI) delivered unilaterally to the parietal cortex, or were naïve controls. Amphetamine‐induced rotational behavior was assessed 10 days post‐CCI. Fourteen days post‐CCI, animals were anesthetized and underwent FSCV with bilateral striatal carbon fiber microelectrode placement and stimulating electrode placement in the medial forebrain bundle (MFB). Evoked DA overflow was assessed in the striatum as the MFB was electrically stimulated at 60 Hz for 10 s. In 23% of injured animals, but no naïve animals, rotation was observed with amphetamine administration. Compared with naïves, striatal evoked DA overflow was lower for injured animals in the striatum ipsilateral to injury (p < 0.05). Injured animals exhibited a decrease in V_max (52% of naïve, p < 0.05) for DA clearance in the hemisphere ipsilateral to injury compared with naïves. Dopamine transporter (DAT) expression was proportionally decreased in the striatum ipsilateral to injury compared with naïve animals (60% of naïve, p < 0.05), despite no injury‐related changes in vesicular monoamine transporter or D₂ receptor expression (DRD₂) in this region. Collectively, these data appear to confirm that the clinical efficacy of dopamine agonists in the treatment of TBI may be related to disruptions in the activity of subcortical dopamine systems.     

Orientation behavior of Propylaea japonica toward visual and olfactory cues from its prey–host plant combination

The lady beetle Propylaea japonica (Thunberg) (Coleoptera: Coccinellidae) is an important predator of aphids in agroecosystems. The inundative release of coccinellid beetles can be an effective biological control strategy. An understanding of how biological control agents perceive and use stimuli from host plants is the key to successfully implement commercially produced predators. Here, we studied the relative role of visual and volatile cues. Dual‐choice assays using foraging‐naïve and foraging‐experienced P. japonica adults were conducted using cotton plants [Gossypium hirsutum L. (Malvaceae)] with or without infestation by the cotton aphid, Aphis gossypii (Glover) (Hemiptera: Aphididae). Overall, experienced beetles were more attracted than naïve beetles toward cues associated with aphid‐infested plants. Experienced beetles were also more responsive to olfactory cues compared with naïve beetles. Both foraging‐naïve and ‐experienced lady beetles integrate olfactory and visual cues from plants infested with aphids, with an apparently greater reliance on olfactory cues. The results suggest that foraging experience may increase prey location in P. japonica.     

Assessing the effectiveness of long-term monitoring of the Broad-toothed Rat in the Barrington Tops National Park,Australia

Biodiversity monitoring is crucial for effective conservation efforts. Effective monitoring allows managers to determine the status and trends of biodiversity, as well as the success of conservation actions. The population of the Broad-toothed Rats (Mastacomys fuscus) in the Barrington Tops National Park New South Wales, Australia has been monitored since 1999 via scat and live-trapping surveys. We reviewed the methods used and analysed the data produced with the aim of describing patterns of population change over time using a range of outcome variables and identifying different climate correlates. A secondary aim was to explore the use of population statistics that account for imperfect detection by comparing naïve occupancy, with an index of relative abundance based on trap effort, the latency to find scats during scat surveys and an occupancy model based on trapping surveys. Neither of these three methods accounts for detectability variation. Naïve occupancy decreased slightly over time, while the relative abundance based on trap effort revealed no evidence of change. Additionally, naïve occupancy decreased with increasing temperature while temperature had no clear impact on relative abundance. Finally, precipitation had no impact on either naïve occupancy or relative abundance. We found no evidence of a relationship between the latency to find scats and the index of relative abundance, suggesting that one or neither is related to actual abundance. Finally, a multi-season occupancy model found occupancy probability to be 0.78 ± 0.23 (standard error); detection probability as 0.51 ± 0.06; seasonal colonisation rate as 0.36 ± 0.13 and seasonal extinction rate at 0.44 ± 0.13. We conclude that despite significant investment in monitoring, this historical data set does not allow managers to ascertain whether population change has occurred and to identify potential drivers of change. Careful consideration of future methods, in particular, whether there is imperfect detection in scat surveys, will help to inform future monitoring.     

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores

For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore‐associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response.     

First Documentation of Cultural Transmission of Predator Recognition by Larval Amphibians

Predation is a pervasive selective agent shaping a prey's behaviour, morphology and life history. To survive, prey animals have to respond adaptively to predation threats and this can be achieved through learned predator recognition. Cultural transmission of predator recognition is likely a widespread means of learning in social animals, including mammals, birds and fishes. However, no studies have investigated the cultural transmission of predator recognition in amphibians. In our study, we examined whether naïve woodfrog (Rana sylvatica) tadpoles can acquire the recognition of the odour of a predatory tiger salamander (Ambystoma tigrinum) from experienced conspecifics. After conditioning some tutors to recognize salamander odour, we paired naïve observer tadpoles with either a salamander‐naïve or salamander‐experienced tutor and exposed the pairs to either salamander odour or a water control. Observers were subsequently tested alone for a response to salamander odour. We found that when given salamander odour, observer tadpoles that were paired with a salamander‐experienced tutor successfully learned to recognize the salamander odour as a threat, whereas the observers paired with salamander‐naïve tutors did not. Likewise, tadpoles exposed to the water control did not learn to recognize the salamander regardless of whether they were paired with a naïve or experienced tutor. This is the first study demonstrating cultural transmission of predator recognition in an amphibian species.     

Peripheral residence of naïve CD4 T cells induces MHC class II-dependent alterations in phenotype and function

Background

As individual naïve CD4 T lymphocytes circulate in the body after emerging from the thymus, they are likely to have individually varying microenvironmental interactions even in the absence of stimulation via specific target recognition. It is not clear if these interactions result in alterations in their activation, survival and effector programming. Naïve CD4 T cells show unimodal distribution for many phenotypic properties, suggesting that the variation is caused by intrinsic stochasticity, although underlying variation due to subsets created by different histories of microenvironmental interactions remains possible. To explore this possibility, we began examining the phenotype and functionality of naïve CD4 T cells differing in a basic unimodally distributed property, the CD4 levels, as well as the causal origin of these differences.

Results

We examined separated CD4hi and CD4lo subsets of mouse naïve CD4 cells. CD4lo cells were smaller with higher CD5 levels and lower levels of the dual-specific phosphatase (DUSP)6-suppressing micro-RNA miR181a, and responded poorly with more Th2-skewed outcomes. Human naïve CD4lo and CD4hi cells showed similar differences. Naïve CD4lo and CD4hi subsets of thymic single-positive CD4 T cells did not show differences whereas peripheral naïve CD4lo and CD4hi subsets of T cell receptor (TCR)-transgenic T cells did. Adoptive transfer-mediated parking of naïve CD4 cells in vivo lowered CD4 levels, increased CD5 and reactive oxygen species (ROS) levels and induced hyporesponsiveness in them, dependent, at least in part, on availability of major histocompatibility complex class II (MHCII) molecules. ROS scavenging or DUSP inhibition ameliorated hyporesponsiveness. Naïve CD4 cells from aged mice showed lower CD4 levels and cell sizes, higher CD5 levels, and hyporesponsiveness and Th2-skewing reversed by DUSP inhibition.

Conclusions

Our data show that, underlying a unimodally distributed property, the CD4 level, there are subsets of naïve CD4 cells that vary in the time spent in the periphery receiving MHCII-mediated signals and show resultant alteration of phenotype and functionality via ROS and DUSP activity. Our findings also suggest the feasibility of potential pharmacological interventions for improved CD4 T cell responses during vaccination of older people via either anti-oxidant or DUSP inhibitor small molecules.

     

Genome‐wide profiling of humoral immune response to Coxiella burnetii infection by protein microarray

Comprehensive evaluation of the humoral immune response to Coxiella burnetii may identify highly needed diagnostic antigens and potential subunit vaccine candidates. Here we report the construction of a protein microarray containing 1901 C. burnetii ORFs (84% of the entire proteome). This array was probed with Q‐fever patient sera and naïve controls in order to discover C. burnetii‐specific seroreactive antigens. Among the 21 seroreactive antigens identified, 13 were significantly more reactive in Q‐fever cases than naïve controls. The remaining eight antigens were cross‐reactive in both C. burnetii infected and naïve patient sera. An additional 64 antigens displayed variable seroreactivity in Q‐fever patients, and underscore the diversity of the humoral immune response to C. burnetii. Nine of the differentially reactive antigens were validated on an alternative immunostrip platform, demonstrating proof‐of‐concept development of a consistent, safe, and inexpensive diagnostic assay alternative. Furthermore, we report here the identification of several new diagnostic antigens and potential subunit vaccine candidates for the highly infectious category B alphaproteobacteria, C. burnetii.     

Sharp simultaneous confidence intervals for the means of selected populations with application to microarray data analysis

Summary Simultaneous inference for a large number, N, of parameters is a challenge. In some situations, such as microarray experiments, researchers are only interested in making inference for the K parameters corresponding to the K most extreme estimates. Hence it seems important to construct simultaneous confidence intervals for these K parameters. The naïve simultaneous confidence intervals for the K means (applied directly without taking into account the selection) have low coverage probabilities. We take an empirical Bayes approach (or an approach based on the random effect model) to construct simultaneous confidence intervals with good coverage probabilities. For N= 10,000 and K= 100, typical for microarray data, our confidence intervals could be 77% shorter than the naïve K‐dimensional simultaneous intervals.     

Autologous versus allogeneic peptide-pulsed dendritic cells for anti-tumour vaccination: expression of allogeneic MHC supports activation of antigen specific T cells,but impairs early naïve cytotoxic priming and anti-tumour therapy

Background

Dendritic cells (DC) pulsed with MHC class I-restricted tumour associated antigen (TAA) peptides have been widely tested in pre-clinical models and early clinical studies for their ability to prime cytotoxic T cell (CTL) responses. The effect of co-expression of allogeneic MHC antigens on DC immunogenicity has not been addressed, and has implications for the feasibility of clinical applications.

Objective

This study compared DC from autologous H-2^b or semi-allogeneic F1 H-2^bxk mice pulsed with the H-2^b-restricted model ovalbumin (OVA) peptide SIINFEKL, and compared in vitro and in vivo their ability to (i) activate specific OT1 cells, (ii) prime naïve CTL, and (iii) protect against B16.OVA challenge. Peptide-pulsed autologous and allogeneic DC were also tested in naïve human CTL priming assays.

Results

Semi-allogeneic DC expressed higher levels of co-stimulatory molecules. On pulsing with SIINFEKL they triggered greater proliferation of OT1 cells in vitro and in vivo, but were less effective at naïve CTL priming and tumour protection. Autologous human DC were similarly more potent at naïve CTL priming against the melanoma-associated TAA MART-1 in vitro.

Conclusion

The expression of allogeneic MHC antigens on peptide-pulsed DC impairs naïve CTL priming and anti-tumour effects, despite effective TAA presentation both in vitro and in vivo.

     

After the crash: How do predators adjust following the invasion of a novel toxic prey type?

The ability of a native predator to adjust to a dangerously toxic invasive species is key to avoiding an ongoing suppression of the predator's population and the trophic cascade of effects that can result. Many species of anurophagous predators have suffered population declines due to the cane toad's (Rhinella marina: Bufonidae) invasion of Australia; these predators can be fatally poisoned from attempting to consume the toxic toad. We studied one such toad‐vulnerable predator, the yellow‐spotted monitor (Varanus panoptes: Varanidae), testing whether changes to the predator's feeding behaviour could explain how the species persists following toad invasion. Wild, free‐roaming lizards from (1) toad‐naïve and (2) toad‐exposed populations were offered non‐toxic native frogs and slightly toxic cane toads (with parotoid glands removed) in standardized feeding trials. Toad‐naïve lizards readily consumed both frogs and toads, with some lizards displaying overt signs of illness after consuming toads. In contrast, lizards from toad‐exposed populations consumed frogs but avoided toads. Repeated encounters with toads did not modify feeding responses by lizards from the toad‐naïve populations, suggesting that aversion learning is limited (but may nonetheless occur). Our results suggest that this vulnerable predator can adjust to toad invasion by developing an aversion to feeding on the toxic invader, but it remains unclear as to whether the lizard's toad‐aversion arises via adaptation or learning.     

Reconstitution of the cellular response to DNA damage in vitro using damage-activated extracts from mammalian cells

In proliferating mammalian cells, DNA damage is detected by sensors that elicit a cellular response which arrests the cell cycle and repairs the damage. As part of the DNA damage response, DNA replication is inhibited and, within seconds, histone H2AX is phosphorylated. Here we describe a cell-free system that reconstitutes the cellular response to DNA double strand breaks using damage-activated cell extracts and naïve nuclei. Using this system the effect of damage signalling on nuclei that do not contain DNA lesions can be studied, thereby uncoupling signalling and repair. Soluble extracts from G1/S phase cells that were treated with etoposide before isolation, or pre-incubated with nuclei from etoposide-treated cells during an in vitro activation reaction, restrain both initiation and elongation of DNA replication in naïve nuclei. At the same time, H2AX is phosphorylated in naïve nuclei in a manner that is dependent upon the phosphatidylinositol 3-kinase-like protein kinases. Notably, phosphorylated H2AX is not focal in naïve nuclei, but is evident throughout the nucleus suggesting that in the absence of DNA lesions the signal is not amplified such that discrete foci can be detected. This system offers a novel screening approach for inhibitors of DNA damage response kinases, which we demonstrate using the inhibitors wortmannin and LY294002.     

Population dynamics of brown trout (Salmo trutta) in Spruce Creek Pennsylvania: A quarter‐century perspective

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Density dependence and population dynamics of black rhinos (Diceros bicornis michaeli) in Kenya’s rhino sanctuaries

Density‐dependent feedback mechanisms provide insights into the population dynamics and interactions of large herbivores with their ecosystem. Sex ratio also has particularly important implications for growth rates of many large mammal populations through its influence on reproductive potential. Therefore, the interrelationships between density‐dependent factors, comprising density, sex ratio and underlying growth rates (r) were examined for the Eastern black rhino (Diceros bicornis michaeli) living in three rhino sanctuaries in Kenya using four population models. The exponential and logistic models gave similar results and the former were accepted because they better portrayed the actual situation on the ground. Sex ratios in all sanctuary populations were positively correlated with r but interpreted with realization of other factors also affecting r. We caution that the results of population models should be interpreted alongside ground‐truthed observations. We recommend that future translocation strategies should take into account sex and age structures of the donor population, while future studies of density dependence should take into account both biotic and abiotic factors.     

Statistical analysis of personal radiofrequency electromagnetic field measurements with nondetects

Exposimeters are increasingly applied in bioelectromagnetic research to determine personal radiofrequency electromagnetic field (RF‐EMF) exposure. The main advantages of exposimeter measurements are their convenient handling for study participants and the large amount of personal exposure data, which can be obtained for several RF‐EMF sources. However, the large proportion of measurements below the detection limit is a challenge for data analysis. With the robust ROS (regression on order statistics) method, summary statistics can be calculated by fitting an assumed distribution to the observed data. We used a preliminary sample of 109 weekly exposimeter measurements from the QUALIFEX study to compare summary statistics computed by robust ROS with a naïve approach, where values below the detection limit were replaced by the value of the detection limit. For the total RF‐EMF exposure, differences between the naïve approach and the robust ROS were moderate for the 90th percentile and the arithmetic mean. However, exposure contributions from minor RF‐EMF sources were considerably overestimated with the naïve approach. This results in an underestimation of the exposure range in the population, which may bias the evaluation of potential exposure‐response associations. We conclude from our analyses that summary statistics of exposimeter data calculated by robust ROS are more reliable and more informative than estimates based on a naïve approach. Nevertheless, estimates of source‐specific medians or even lower percentiles depend on the assumed data distribution and should be considered with caution. Bioelectromagnetics. Bioelectromagnetics 29:471–478, 2008. © 2008 Wiley‐Liss, Inc.