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1.
Israel A. Ramírez-Alanis Justin B. Renaud Silverio García-Lara Rima Menassa Guy A. Cardineau 《Plant methods》2018,14(1):98
Background
Expression of economically relevant proteins in alternative expression platforms, especially plant expression platforms, has gained significant interest in recent years. A special interest in working with plants as bioreactors for the production of pharmaceutical proteins is related to low production costs, product safety and quality. Among the different properties that plants can also offer for the production of recombinant proteins, protein glycosylation is crucial since it may have an impact on pharmaceutical functionality and/or stability.Results
The pharmaceutical glycoprotein human Granulocyte-Colony Stimulating Factor was transiently expressed in Nicotiana benthamiana plants and subjected to mammalian-specific mucin-type O-glycosylation by co-expressing the pharmaceutical protein together with the glycosylation machinery responsible for such post-translational modification.Conclusions
The pharmaceutical glycoprotein human Granulocyte-Colony Stimulating Factor can be expressed in N. benthamiana plants via agroinfiltration with its native mammalian-specific mucin-type O-glycosylation.2.
Wiebke Kämper Patrizia K. Werner Andrea Hilpert Catrin Westphal Nico Blüthgen Thomas Eltz Sara Diana Leonhardt 《Landscape Ecology》2016,31(10):2245-2258
Context
Abundance and diversity of bumblebees have been declining over the past decades. To successfully conserve bumblebee populations, we need to understand how landscape characteristics affect the quantity and quality of floral resources collected by colonies and subsequently colony performance.Objectives
We therefore investigated how amount and composition of pollen collected by buff-tailed bumblebee Bombus terrestris colonies was affected by the surrounding landscape (i.e. the proportion of forest, urban, semi-natural habitats) and how they were related to colony growth.Methods
Thirty B. terrestris colonies were placed at grassland sites differing in surrounding landscape. Colonies were established in spring when availability of flowering plants was highest, and their weight gain was monitored for 1 month. We additionally recorded the quantity and compared plant taxonomic composition and nutritional quality (i.e. amino acid composition) of pollen stored.Results
Bumblebee colonies varied little in the pollen spectra collected despite differences in surrounding landscape composition. They collected on average 80 % of pollen from woody plants, with 34 % belonging to the genus Acer. Early colony growth positively correlated with total amount of woody pollen and protein collected and decreased with increasing proportions of semi-natural habitats and total amino acid concentrations.Conclusions
Our results suggest that woody plant species represent highly important pollen sources for the generalist forager B. terrestris early in the season. We further show that colony growth of B. terrestris is predominantly affected by the quantity, not quality, of forage, indicating that several abundant plant species flowering throughout the bumblebees’ foraging season may cover the colonies’ nutritional needs.3.
Hayley R. Tumas Brian M. Shamblin Mark Woodrey Nathan P. Nibbelink Richard Chandler Campbell Nairn 《Landscape Ecology》2018,33(9):1585-1601
Context
Common species important for ecosystem restoration stand to lose as much genetic diversity from anthropogenic habitat fragmentation and climate change as rare species, but are rarely studied. Salt marshes, valuable ecosystems in widespread decline due to human development, are dominated by the foundational plant species black needlerush (Juncus roemerianus Scheele) in the northeastern Gulf of Mexico.Objectives
We assessed genetic patterns in J. roemerianus by measuring genetic and genotypic diversity, and characterizing population structure. We examined population connectivity by delineating possible dispersal corridors, and identified landscape factors influencing population connectivity.Methods
A panel of 19 microsatellite markers was used to genotype 576 samples from ten sites across the northeastern Gulf of Mexico from the Grand Bay National Estuarine Research Reserve (NERR) to the Apalachicola NERR. Genetic distances (FST and Dch) were used in a least cost transect analysis (LCTA) within a hierarchical model selection framework.Results
Genetic and genotypic diversity results were higher than expected based on life history literature, and samples structured into two large, admixed genetic clusters across the study area, indicating sexual reproduction may not be as rare as predicted in this clonal macrophyte. Digitized coastal transects buffered by 500 m may represent possible dispersal corridors, and developed land may significantly impede population connectivity in J. roemerianus.Conclusions
Results have important implications for coastal restoration and management that seek to preserve adaptive potential by sustaining natural levels of genetic diversity and conserving population connectivity. Our methodology could be applied to other common, widespread and understudied species.4.
5.
Background
Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here.Results
To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues.Conclusions
This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.6.
Xenia K. Volk Johannes P. Gattringer Annette Otte Sarah Harvolk-Schöning 《Landscape Ecology》2018,33(3):371-387
Context
Methods for measuring restoration success that include functional connectivity between species’ populations are rare in landscape ecology and restoration practices. We developed an approach that analyzes connectivity between populations of target species and their dispersal probabilities to assess restoration success based on easily accessible input data. Applying this method to landscape development scenarios can help optimize restoration planning.Objectives
We developed an assessment for restoration success and restoration planning based on functional connectivity between species’ populations and spatially explicit scenarios. The method was used in a case study to test its applicability.Methods
Based on data on available habitat, species’ occurrence and dispersal ranges, connectivity metrics and dispersal probabilities for target species are calculated using the software Conefor Sensinode. The metrics are calculated for scenarios that reflect possible changes in the landscape to provide a basis for future restoration planning. We applied this approach to floodplain meadows along the Upper Rhine for four plant species and three future scenarios.Results
In the case study, habitats of the target species were poorly connected. Peucedanum officinale and Sanguisorba officinalis were more successful in recolonizing new habitats than Iris spuria and Serratula tinctoria. The scenarios showed that restoration of species-rich grassland was beneficial for dispersal of the target species. As expected in the agriculturally dominated study area, restoration of former arable land significantly increased dispersal probabilities.Conclusions
In the case study, the developed approach was easily applicable and provided reasonable results. Its implementation will be helpful in decision-making for future restoration planning.7.
8.
Context
Submersed aquatic vegetation (SAV) performs water quality enhancing functions that are critical to the overall health of estuaries such as the Chesapeake Bay. However, eutrophication and sedimentation have decimated the Bay’s SAV population to a fraction of its historical coverage. Understanding the spatial distribution of and connectedness among patches is important for assessing the dynamics and health of the remaining SAV population.Objectives
We seek to explore the distribution of SAV patches and patterns of potential connectivity in the Chesapeake Bay through time.Methods
We assess critical distances, from complete patch isolation to connection of all patches, in a merged composite coverage map that represents the sum of all probable Vallisneria americana containing patches between 1984 and 2010 and in coverage maps for individual years within that timeframe for which complete survey data are available.Results
We have three key findings: First, the amount of SAV coverage in any given year is much smaller than the total recently occupied acreage. Second, the vast majority of patches of SAV that are within the tolerances of V. americana are ephemeral, being observed in only 1 or 2 years out of 26 years. Third, this high patch turnover results in highly variable connectivity from year to year, dependent on dispersal distance and patch arrangement.Conclusions
Most of the connectivity thresholds are beyond reasonable dispersal distances for V. americana. If the high turnover in habitat occupancy is due to marginal water quality, relatively small improvements could greatly increase V. americana growth and persistence.9.
Context
In deserts, many plant species exhibit a patchy spatial distribution within a harsh habitat matrix, where the likelihood of propagule dispersal among patches is uncertain, but may be promoted by landscape corridors or dispersal vectors.Objectives
We examine the connectivity of a representative desert plant species (Acacia (Senegalia) greggii), and the ability of three major factors (animal dispersal agents, water flow along dry-washes, and climate) to facilitate dispersal within four watersheds in the Mojave National Preserve.Methods
We genotyped 323 individuals sampled across 22 one-hectare sites using ten nuclear microsatellite markers.Results
A hierarchical AMOVA revealed no significant differentiation among watersheds (F RT = 0.00, P > 0.10), and very little genetic structure among all sites (F ST = 0.03, P < 0.001), indicating regional connectivity. Mantel tests indicated distance along dry-washes best explained genetic distance between sites (r = 0.47, P < 0.05) when compared to Euclidean distance (P > 0.05), a distance measure based on rodent dispersal (P > 0.05), and a distance measure avoiding inhospitable climate (P > 0.05). An AIC comparison of generalized linear models found that within site genetic diversity (H E and allelic richness) and average relatedness were best explained by slope (which increases seed dispersal potential via water flow) and area of the upstream watershed (which determines the number of potential seed donors), rather than plant density or habitat suitability.Conclusions
Together, these findings indicate that dry-washes are key landscape features that enhance dispersal and regional connectivity in this patchy desert plant.10.
Patrick?C.?Boyle Simon?Schwizer Sarah?R.?Hind Christine?M.?Kraus Susana?De la?Torre Diaz Bin?He Gregory?B.?Martin
Background
The plant plasma membrane is a key battleground in the war between plants and their pathogens. Plants detect the presence of pathogens at the plasma membrane using sensor proteins, many of which are targeted to this lipophilic locale by way of fatty acid modifications. Pathogens secrete effector proteins into the plant cell to suppress the plant’s defense mechanisms. These effectors are able to access and interfere with the surveillance machinery at the plant plasma membrane by hijacking the host’s fatty acylation apparatus. Despite the important involvement of protein fatty acylation in both plant immunity and pathogen virulence mechanisms, relatively little is known about the role of this modification during plant-pathogen interactions. This dearth in our understanding is due largely to the lack of methods to monitor protein fatty acid modifications in the plant cell.Results
We describe a rapid method to detect two major forms of fatty acylation, N-myristoylation and S-acylation, of candidate proteins using alkyne fatty acid analogs coupled with click chemistry. We applied our approach to confirm and decisively demonstrate that the archetypal pattern recognition receptor FLS2, the well-characterized pathogen effector AvrPto, and one of the best-studied intracellular resistance proteins, Pto, all undergo plant-mediated fatty acylation. In addition to providing a means to readily determine fatty acylation, particularly myristoylation, of candidate proteins, this method is amenable to a variety of expression systems. We demonstrate this using both Arabidopsis protoplasts and stable transgenic Arabidopsis plants and we leverage Agrobacterium-mediated transient expression in Nicotiana benthamiana leaves as a means for high-throughput evaluation of candidate proteins.Conclusions
Protein fatty acylation is a targeting tactic employed by both plants and their pathogens. The metabolic labeling approach leveraging alkyne fatty acid analogs and click chemistry described here has the potential to provide mechanistic details of the molecular tactics used at the host plasma membrane in the battle between plants and pathogens.11.
Jason J. Kolbe Paul VanMiddlesworth Andrew C. Battles James T. Stroud Bill Buffum Richard T. T. Forman Jonathan B. Losos 《Landscape Ecology》2016,31(8):1795-1813
Context
Urban landscapes are a mixture of built structures, human-altered vegetation, and remnant semi-natural areas. The spatial arrangement of abiotic and biotic conditions resulting from urbanization doubtless influences the establishment and spread of non-native species in a city.Objectives
We investigated the effects of habitat structure, thermal microclimates, and species coexistence on the spread of a non-native lizard (Anolis cristatellus) in the Miami metropolitan area of South Florida (USA).Methods
We used transect surveys to estimate lizard occurrence and abundance on trees and to measure vegetation characteristics, and we assessed forest cover and impervious surface using GIS. We sampled lizard body temperatures, habitat use, and relative abundance at multiple sites.Results
At least one of five Anolis species occupied 79 % of the 1035 trees surveyed in primarily residential areas, and non-native A. cristatellus occupied 25 % of trees. Presence and abundance of A. cristatellus were strongly associated with forest patches, dense vegetation, and high canopy cover, which produced cooler microclimates suitable for this species. Presence of A. cristatellus was negatively associated with the ecologically similar non-native A. sagrei, resulting in reduced abundance and a shift in perch use of A. cristatellus.Conclusions
The limited spread of A. cristatellus in Miami over 35 years is due to the patchy, low-density distribution of wooded habitat, which limits dispersal by diffusion. The presence of congeners may also limit spread. Open habitats—some parks, yards and roadsides—contain few if any A. cristatellus, and colonization of isolated forest habitat appears to depend on human-mediated dispersal.12.
Amy E. Frazier 《Landscape Ecology》2016,31(2):351-363
Context
Considerable research has examined scale effects for patch-based metrics with the ultimate goal of predicting values at finer resolutions (i.e., downscaling), but results have been inconsistent. Surface metrics have been suggested as an alternative to patch-based metrics, although far less is known about their scaling relationships and downscaling potential. If successful, downscaling would enable integration of disparate datasets and comparison of landscapes using different resolution datasets.Objectives
(1) Determine how surface metrics scale as resolution changes and how consistent those scaling relationships are across landscapes. (2) Test whether these scaling relationships can be accurately downscaled to predict metric values for finer resolutions.Methods
Various scaling functions were fit to 16 surface metrics computed for multiple resolutions for a set of landscapes. Best-fitting functions were then extrapolated to test downscaling behavior (i.e., predict metric value for a finer resolution) for an independent set of validation landscapes. Relative error was assessed between the predicted and true values to determine downscaling robustness.Results
Seven surface metrics (Sa, Sq, S10z, Sdq, Sds, Sdr, Srwi) fit consistently well (R2 > 0.99) with a 3rd order polynomial or power law. Of those, the scaling functions for Sa, Sq, and S10z were able to predict metric values at a finer resolution within 5 %. Three metrics, (Ssk, Sku, Sfd) were also notable in terms of fit and downscaling.Conclusions
Many metrics exhibit consistent scaling relations across resolution, and several are able to accurately predict values at finer resolutions. However, prediction accuracy is likely related to the amount of information lost during aggregation.13.
Kevin McGarigal Bradley W. Compton Ethan B. Plunkett William V. DeLuca Joanna Grand Eduard Ene Scott D. Jackson 《Landscape Ecology》2018,33(7):1029-1048
Context
Conservation planning is increasingly using “coarse filters” based on the idea of conserving “nature’s stage”. One such approach is based on ecosystems and the concept of ecological integrity, although myriad ways exist to measure ecological integrity.Objectives
To describe our ecosystem-based index of ecological integrity (IEI) and its derivative index of ecological impact (ecoImpact), and illustrate their applications for conservation assessment and planning in the northeastern United States.Methods
We characterized the biophysical setting of the landscape at the 30 m cell resolution using a parsimonious suite of settings variables. Based on these settings variables and mapped ecosystems, we computed a suite of anthropogenic stressor metrics reflecting intactness (i.e., freedom from anthropogenic stressors) and resiliency metrics (i.e., connectivity to similar neighboring ecological settings), quantile-rescaled them by ecosystem and geographic extent, and combined them in a weighted linear model to create IEI. We used the change in IEI over time under a land use scenario to compute ecoImpact.Results
We illustrated the calculation of IEI and ecoImpact to compare the ecological integrity consequences of a 70-year projection of urban growth to an alternative scenario involving securing a network of conservation core areas (reserves) from future development.Conclusions
IEI and ecoImpact offer an effective way to assess ecological integrity across the landscape and examine the potential ecological consequences of alternative land use and land cover scenarios to inform conservation decision making.14.
Context
Although small isolated habitat patches may not be able to maintain a minimum viable population, small patches that are structurally isolated may be functionally connected if individuals can cross the gaps between them, in which case, their areas could be added to form a larger habitat patch, eventually surpassing the size threshold for holding a viable population.Objectives
We studied whether models based on the size and isolation of habitat patches could be used to predict the distribution of the Chestnut-throated Huet-Huet (Pteroptochos castaneus) in fragmented landscapes of the coastal range of the Maule region, central Chile.Methods
We selected seven 10,000-ha landscapes (8.4–70.7% forest cover). For each habitat patch we made 18 predictions of the presence of the species based on the combination of two thresholds: three critical patch sizes for maintaining a viable population (62.5, 125 and 250 ha) and six critical isolation distances between patches (0, 10, 50, 100, 150 and 200 m). We used playbacks in 59 sampling points to estimate the species’ presence/absence. We used logistic regressions to test whether the output of the patch-matrix models could explain part of the variation in the presence of Pteroptochos castaneus.Results
The best predictions for the presence of P. castaneus were obtained with the most conservative scenarios (125–250 ha to 0–10 m), including a positive effect of the understory cover and a lack of effect of the forest type (native or exotic).Conclusions
Our findings suggest that the long term persistence of P. castaneus may depend on the existence of large and/or very connected forest tracts.15.
16.
Clémentine Azam Isabelle Le Viol Jean-François Julien Yves Bas Christian Kerbiriou 《Landscape Ecology》2016,31(10):2471-2483
Context
Light pollution is a global change affecting a major proportion of global land surface. Although the impacts of Artificial Light At Night (ALAN) have been documented locally for many taxa, the extent of effect of ALAN at a landscape scale on biodiversity is unknown.Objectives
We characterized the landscape-scale impacts of ALAN on 4 insectivorous bat species Pipistrellus pipistrellus, Pipistrellus kuhlii, Eptesicus serotinus, Nyctalus leisleri, and compared the extent of their effects to other major land-use pressures.Methods
We used a French national-scale monitoring program recording bat activity among 2-km car transect surveys, and extracted landscape characteristics around transects with satellite and land cover layers. For each species, we performed multi-model averaging at 4 landscape scales (from 200 to 1000 m buffers around transects) to compare the relative effects of the average radiance, the proportion of impervious surface and the proportion of intensive agriculture.Results
For all species, ALAN had a stronger negative effect than impervious surface at the 4 landscape scales tested. This effect was weaker than the effect of intensive agriculture. The negative effect of ALAN was significant for P. pipistrellus, P. kuhlii and E. serotinus, but not for N. leisleri. The effect of impervious surface varied among species while intensive agriculture had a significant negative effect on the 4 species.Conclusion
Our results highlight the need to consider the impacts of ALAN on biodiversity in land-use planning and suggest that using only impervious surface as a proxy for urbanization may lead to underestimated impacts on biodiversity.17.
Yoshitaka Kanaoka Daichi Kuniyoshi Eri Inada Yohei Koide Yoshihiro Okamoto Hideshi Yasui Yuji Kishima 《Plant methods》2018,14(1):102
Background
To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice (Oryza sativa) and African rice (O. glaberrima). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed HS loci, but this complicated genetic system remains poorly understood.Results
Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Application of the anther culture (AC) method caused these immature microspores to induce callus. The segregation distortion of 11 among 13 known HS loci was assessed in the callus population. Using many individual calli, fine mapping of the HS loci was attempted based on heterozygotes produced from chromosome segment substitution lines (CSSLs). Transmission ratio distortion (TRD) from microspores was detected at 6 of 11 HS loci in the callus population. The fine mapping of S1 and S19 loci using CSSLs revealed precise distances of markers from the positions of HS loci exhibiting excessive TRD.Conclusions
We demonstrated that AC to generate callus populations derived from immature microspores is a useful methodology for genetic study. The callus population facilitated detection of TRD at multiple HS loci and dramatically shortened the process for mapping hybrid sterility genes.18.
Patrick D. Culbert Ine Dorresteijn Jacqueline Loos Murray K. Clayton Joern Fischer Tobias Kuemmerle 《Landscape Ecology》2017,32(2):429-444
Context
Ecological impacts of past land use can persist for centuries. While present-day land use is relatively easy to quantify, characterizing historical land uses and their legacies on biodiversity remains challenging. Southern Transylvania in Romania is a biodiversity-rich area which has undergone major political and socio-economic changes, from the Austro-Hungarian Empire to two World Wars, communist dictatorship, capitalist democracy, and EU accession—all leading to widespread land-use changes.Objectives
We investigated whether present-day community composition of birds, plants, and butterflies was associated with historical land use.Methods
We surveyed birds, plants, and butterflies at 150 sites and classified those sites as forest, arable land, or managed grassland for six epochs using historical maps from the 1870s, 1930s, and 1970s, satellite imagery from 1985 to 2000, and field visits in 2012. Sites were labelled permanent if they had the same land use at all epochs and non-permanent otherwise. We used clustering and PERMANOVA based on community similarity to test for associations between community composition and land-use history.Results
We found significant differences (p = 0.030) in bird communities between permanent and non-permanent forest sites, and permanent and non-permanent grassland sites (p = 0.051). No significant associations were found among plants or butterflies and land-use history.Conclusions
Bird communities were associated with historical land use, though plants and butterflies were not. Historical land-use change in our study area was likely not sufficiently intense to cross relevant ecological thresholds that would lead to legacy effects in present-day plant and butterfly communities.19.
20.
Ronan Marrec Gaël Caro Paul Miguet Isabelle Badenhausser Manuel Plantegenest Aude Vialatte Vincent Bretagnolle Bertrand Gauffre 《Landscape Ecology》2017,32(12):2383-2398