A comparative analysis of karyotypes of three species of Macleaya—producers of a complex of isoquinoline alkaloids

Using a set of methods (C-banding, DAPI-staining, fluorescence hybridization in situ (FISH) with probes of 26S and 5S rDNA, and analysis of meiosis), the first comparative cytogenetic study of three species of Macleaya, producers of complex isoquinoline alkaloids, cordate Macleaya cordata (Willd.) R. Br. (2n = 20), small-fruited Macleaya microcarpa (Maxim.) Fedde (2n = 20) and Macleaya kewensis Turrill (2n = 20), was first carried out. On the basis of morphometric analysis, formulas of karyotypes were made for each species. Species ideograms for M. cordata, M. microcarpa, and M. kewensis were constructed taking into account the polymorphic variants of the C-banding patterns and indicating the location of 26S and 5S rDNA sites. A comparative study revealed that the karyotypes of M. microcarpa and M. kewensis have more in common with each other than with M. cordata. Analysis of meiotic chromosomes suggests of genetic stability of Macleaya genomes. The results of chromosome analysis were used to confirm the close relationship of Macleaya and to clarify their phylogenetic relationships.     

Effect of γ-Irradiation on Development of Lachrymator of Onion

A thermosensitive uracil requiring mutant of Bacillus subtilis Marburg 168 thy trp₂ ts42 was examined as to the colony forming ability at the permissive and nonpermissive temperatures. The viability of the mutant cells decreased rapidly at the restrictive temperature in the modified Woese’s (MW) medium. However, the cells retained viability when sodium succinate or potassium chloride was added to the medium at that temperature although uracil deficiency was unchanged. A little but significant incorporation of adenine-8-¹⁴C into RNA still continued even after the incorporation of N-acetyl-³H-d-glucosamine into acid insoluble fraction of the cells terminated in the MW medium at 48°C. Both incorporations as well as increase of absorbance were slowed down in the presence of sodium succinate at 48°C. This mutant, ts42, was more sensitive to deoxycholate (DOC) than the parent strain. The restoration of colony forming ability after the temperature shift back from 48 to 37°C was suppressed by the addition of DOC to the medium. However, the cell became resistant to DOC when uracil was added to the medium prior to the temperature shift.     

Mechanisms of action of the α-amylase of Micromonospora melanosporea

The -amylase of Micromonospora melanosporea was produced extracellularly during batch fermentation in a 5.0-1 fermentor. The absence of an organic nitrogen source in its growth medium facilitated subsequent purification of the enzyme by ammonium sulphate fractionation and two consecutive Superose-12 gel-filtration steps. The enzyme exhibited maxima for activity at pH 7.0 and 55° C and was 72% stable at pH 6.0–12.0 for 30 min at 40° C. It had a relative molecular mass of 45 000 and an isoelectric point at pH 7.6. The enzyme catalyses the conversion of starch to maltose (53%, w/w) as the predominant final end-product. Initial hydrolysis of this substrate, however, gave rise to the formation of maltooligosaccharides in the range maltotriose to maltohexaose. Maximum yields of these intermediate sugars accumulated to between 31 and 42% (w/w) as the reaction proceeded. The action of the M. melanosporea amylase on high concentrations of saccharides larger than maltotriose resulted in the formation of mainly maltose and maltotriose without concomitant glucose production. A combination of hydrolytic and transfer events is postulated to be responsible for this phenomenon and for the high maltose levels achieved. Correspondence to: C. T. Kelly     

Selection of optimal variants of Gō-like models of proteins through studies of stretching

The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales—uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching.     

Chemistry of the “molecular trap” of protease-catalyzed splicing reaction of complementary segments of α-subunit of hemoglobin A

The complementary fragments of human Hb α, α_1–30, and α_31–141 are spliced together by V8 protease in the presence of 30%n-propanol to generate the full-length molecule (Hb α-semisynthetic reaction). Unlike the other protease-catalyzed protein/peptide splicing reactions of fragment complementing systems, the enzymic condensation of nonassociating segments of Hb α is facilitated by the organic cosolvent induced α-helical conformation of product acting as the “molecular trap” of the splicing reaction. The segments α_24–30 and α_31–40 are the shortest complementary segments that can be spliced by V8 protease. In the present study, the chemistry of the contiguous segment (product) α_24–40 has been manipulated by engineering the amino acid replacements to the positions α²⁷ and α³¹ to delineate the structural basis of the molecular trap. The location of Glu²⁷ and Arg³¹ residues in the contiguous segment α_24–40 (as well as in other larger segments) is ideal to generate (i, i+4) side-chain carboxylate-guanidino interaction in its α-helical conformation. The amino acid residue replacement studies have confirmed that the side chains at α²⁷ and α³¹ facilitate the semisynthetic reaction. The relative influence of the substitute at these sites on the splicing reaction depends on the chemical nature of the side chain and the location. The γ-carboxylate guanidino side-chain interaction appears to contribute up to a maximum of 85% of the thermodynamic stability of the molecular trap. The studies also demonstrate that the thermodynamic stability of the molecular trap is determined by two interdependent conformational aspects of the peptide. One is an amino acid-sequence-specific event that facilitates the induction of an α-helical conformation to the contiguous segment in the presence of organic cosolvent that imparts some amount of protease resistance to Glu³⁰-Arg³¹ peptide bond. The second structural aspect is a site-specific event, ani, i+4 side-chain interaction in the α-helical conformation of the peptide which imparts an additional thermodynamic stability to the molecular trap. The results suggest that conformationally driven “molecular traps” of protease-mediated ligation reactions of peptides could be designed into products to facilitate the modular assembly of peptides/proteins.     

Association of the subunits of the calcium-independent receptor of α-latrotoxin

CIRL-1 also called latrophilin 1 or CL belongs to the family of adhesion G protein-coupled receptors (GPCRs). As all members of adhesion GPSR family CIRL-1 consists of two heterologous subunits, extracellular hydrophilic p120 and heptahelical membrane protein p85. Both CIRL-1 subunits are encoded by one gene but as a result of intracellular proteolysis of precursor, mature receptor has two-subunit structure. It was also shown that a minor portion of the CIRL-1 receptor complexes dissociates, producing the soluble receptor ectodomain, and this dissociation is due to the second cleavage at the site between the site of primary proteolysis and the first transmembrane domain. Recently model of independent localization p120 and p85 on the cell surface was proposed. In this article we evaluated the amount of p120-p85 complex still presented on the cellular membrane and confirmed that on cell surface major amount of mature CIRL-1 presented as a p120-p85 subunit complex.     

Inhibition of colony-spreading activity of Staphylococcus aureus by secretion of δ-hemolysin

Staphylococcus aureus spreads on the surface of soft agar, a phenomenon we termed "colony spreading." Here, we found that S. aureus culture supernatant inhibited colony spreading. We purified δ-hemolysin (Hld, δ-toxin), a major protein secreted from S. aureus, as a compound that inhibits colony spreading. The culture supernatants of hld-disrupted mutants had 30-fold lower colony-spreading inhibitory activity than those of the parent strain. Furthermore, hld-disrupted mutants had higher colony-spreading ability than the parent strain. These results suggest that S. aureus negatively regulates colony spreading by secreting δ-hemolysin.     

Kinetics of renaturation and self-assembly of intermediates on the pathway of folding of the β2-subunit of Escherichia coli tryptophan-synthetase

The kinetics of renaturation of the β₂-subunit of Escherichia coli tryptophan-synthetase (l-serine hydrolyase (adding indole) E.C. 4.2.1.20) and those of its two proteolytic fragments F₁ and F₂ are studied and compared. Steps corresponding to the refolding of F₁, to the association of the folded F₁ and F₂ fragments, and to an isomerization of the associated protein are identified. These steps are ordered on the pathway of renaturation and some of their kinetic parameters are determined. This leads to a tentative kinetic model for the renaturation of nicked-β₂ starting from the denatured F₁ and F₂ fragments.The step corresponding to the refolding of the F₁ domain, as well as that corresponding to the last rate-limiting isomerization leading to the native protein, is shown to be the same in the refolding of the entire, uncleaved β₂-protein. It is concluded that the refolded F₁ fragment corresponds to a folding intermediate on the pathway of renaturation of the β₂-subunit.     

Optimizing resiliency of reserve networks to climate change: multispecies conservation planning in the Pacific Northwest,USA

The effectiveness of a system of reserves may be compromised under climate change as species' habitat shifts to nonreserved areas, a problem that may be compounded when well‐studied vertebrate species are used as conservation umbrellas for other taxa. The Northwest Forest Plan was among the first efforts to integrate conservation of wide‐ranging focal species and localized endemics into regional conservation planning. We evaluated how effectively the plan's focal species, the Northern Spotted Owl, acts as an umbrella for localized species under current and projected future climates and how the regional system of reserves can be made more resilient to climate change. We used the program maxent to develop distribution models integrating climate data with vegetation variables for the owl and 130 localized species. We used the program zonation to identify a system of areas that efficiently captures habitat for both the owl and localized species and prioritizes refugial areas of climatic and topographic heterogeneity where current and future habitat for dispersal‐limited species is in proximity. We projected future species' distributions based on an ensemble of contrasting climate models, and incorporating uncertainty between alternate climate projections into the prioritization process. Reserve solutions based on the owl overlap areas of high localized‐species richness but poorly capture core areas of localized species' distribution. Congruence between priority areas across taxa increases when refugial areas are prioritized. Although core‐area selection strategies can potentially increase the conservation value and resilience of regional reserve systems, they accentuate contrasts in priority areas between species and over time and should be combined with a broadened taxonomic scope and increased attention to potential effects of climate change. Our results suggest that systems of fixed reserves designed for resilience can increase the likelihood of retaining the biological diversity of forest ecosystems under climate change.     

Climate warming and the decline of amphibians and reptiles in Europe

Aim We explore the relationship between current European distributions of amphibian and reptile species and observed climate, and project species potential distributions into the future. Potential impacts of climate warming are assessed by quantifying the magnitude and direction of modelled distributional shifts for every species. In particular we ask, first, what proportion of amphibian and reptile species are projected to lose and gain suitable climate space in the future? Secondly, do species projections vary according to taxonomic, spatial or environmental properties? And thirdly, what climate factors might be driving projections of loss or gain in suitable environments for species? Location Europe. Methods Distributions of species are modelled with four species–climate envelope techniques (artificial neural networks, generalized linear models, generalized additive models, and classification tree analyses) and distributions are projected into the future using five climate‐change scenarios for 2050. Future projections are made considering two extreme assumptions: species have unlimited dispersal ability and species have no dispersal ability. A novel hybrid approach for combining ensembles of forecasts is then used to group linearly covarying projections into clusters with reduced inter‐model variability. Results We show that a great proportion of amphibian and reptile species are projected to expand distributions if dispersal is unlimited. This is because warming in the cooler northern ranges of species creates new opportunities for colonization. If species are unable to disperse, then most species are projected to lose range. Loss of suitable climate space for species is projected to occur mainly in the south‐west of Europe, including the Iberian Peninsula, whilst species in the south‐east are projected to gain suitable climate. This is because dry conditions in the south‐west are projected to increase, approaching the levels found in North Africa, where few amphibian species are able to persist. Main conclusions The impact of increasing temperatures on amphibian and reptile species may be less deleterious than previously postulated; indeed, climate cooling would be more deleterious for the persistence of amphibian and reptile species than warming. The ability of species to cope with climate warming may, however, be offset by projected decreases in the availability of water. This should be particularly true for amphibians. Limited dispersal ability may further increase the vulnerability of amphibians and reptiles to changes in climate.     

Simulating climate change impacts on forests and associated vascular epiphytes in a subtropical island of East Asia

Aim This study aims to assess the impact of climate change on forests and vascular epiphytes, using species distribution models (SDMs). Location Island of Taiwan, subtropical East Asia. Methods A hierarchical modelling approach incorporating forest migration velocity and forest type–epiphyte interactions with classical SDMs was used to model the responses of eight forest types and 237 vascular epiphytes for the year 2100 under two climate change scenarios. Forest distributions were modelled and modified by dominant tree species’ dispersal limitations and hypothesized persistence under unfavourable climate conditions (20 years for broad‐leaved trees and 50 years for conifers). The modelled forest projections together with 16 environmental variables were used as predictors in models of epiphyte distributions. A null method was applied to validate the significance of epiphyte SDMs, and potential vulnerable species were identified by calculating range turnover rates. Results For the year 2100, the model predicted a reduction in the range of most forest types, especially for Picea and cypress forests, which shifted to altitudes c. 400 and 300 m higher, respectively. The models indicated that epiphyte distributions are highly correlated with forest types, and the majority (77–78%) of epiphyte species were also projected to lose 45–58% of their current range, shifting on average to altitudes c. 400 m higher than currently. Range turnover rates suggested that insensitive epiphytes were generally lowland or widespread species, whereas sensitive species were more geographically restricted, showing a higher correlation with temperature‐related factors in their distributions. Main conclusions The hierarchical modelling approach successfully produced interpretable results, suggesting the importance of considering biotic interactions and the inclusion of terrain‐related factors when developing SDMs for dependant species at a local scale. Long‐term monitoring of potentially vulnerable sites is advised, especially of those sites that fall outside current conservation reserves where additional human disturbance is likely to exacerbate the effect of climate change.     

Spatial scale affects bioclimate model projections of climate change impacts on mountain plants

Plant species have responded to recent increases in global temperatures by shifting their geographical ranges poleward and to higher altitudes. Bioclimate models project future range contractions of montane species as suitable climate space shifts uphill. The species–climate relationships underlying such models are calibrated using data at either ‘macro’ scales (coarse resolution, e.g. 50 km × 50 km, and large spatial extent) or ‘local’ scales (fine resolution, e.g. 50 m × 50 m, and small spatial extent), but the two approaches have not been compared. This study projected macro (European) and local models for vascular plants at a mountain range in Scotland, UK, under low (+1.7 °C) and high (+3.3 °C) climate change scenarios for the 2080s. Depending on scenario, the local models projected that seven or eight out of 10 focal montane species would lose all suitable climate space at the site. However, the European models projected such a loss for only one species. The cause of this divergence was investigated by cross‐scale comparisons of estimated temperatures at montane species' warm range edges. The results indicate that European models overestimated species' thermal tolerances because the input coarse resolution climate data were biased against the cold, high‐altitude habitats of montane plants. Although tests at other mountain ranges are required, these results indicate that recent large‐scale modelling studies may have overestimated montane species' ability to cope with increasing temperatures, thereby underestimating the potential impacts of climate change. Furthermore, the results suggest that montane species persistence in microclimatic refugia might not be as widespread as previously speculated.     

Marine reserve design theory for species with ontogenetic migration

Models for marine reserve design have been developed primarily with ‘reef fish’ life histories in mind: sedentary adults in patches connected by larval dispersal. However, many fished species undertake ontogenetic migrations, such as from nursery grounds to adult spawning habitats, and current theory does not fully address the range of reserve options posed by that situation. I modelled a generic species with ontogenetic migration to investigate the possible benefits of reserves under three alternative scenarios. First, the fishery targets adult habitat, and reserves can sustain yields under high exploitation, unless habitat patches are well connected. Second, the fishery targets the nursery, and reserves are highly effective, regardless of connectivity patterns. Third, the fishery targets both habitats, and reserves only succeed if paired on adjacent, well-connected nursery and adult patches. In all cases, reserves can buffer populations against overexploitation but would not enhance fishery yield beyond that achievable by management without reserves. These results summarize the general situations in which management using reserves could be useful for ontogenetically migrating species, and the type of connectivity data needed to inform reserve design.     

Does dispersal capacity matter for freshwater biodiversity under climate change?

1. Freshwater ecosystems appear to be sensitive to even minor climatic shifts, and the dendritic nature of rivers as well as patchy distribution of habitats within the terrestrial landscape could limit the ability of species to track suitable climate conditions. Although the importance of dispersal is recognised in theory, there is great uncertainty when quantifying the capacity of species to shift their distributions in response to climate change.
2. The influence of dispersal capacity on species’ vulnerability to climate change was assessed, using the modelled projections of 527 freshwater species in New South Wales (NSW), Australia. Species’ future ranges were calculated by iteratively identifying colonisation of accessible habitats and loss of suitable habitats within network models. The accessibility of new habitats was based on a given dispersal mode (aquatic, semi‐terrestrial and aerial). The relative impact of dispersal parameters on projected range were evaluated alongside other known sources of uncertainty (climate and emissions scenarios, modelling algorithm and biological group), analysed collectively in a generalised additive mixed‐model, and spatially to locate regions of NSW where projections are associated with the most uncertainty.
3. Our simulations (1.4 million scenario combinations) suggest at least a third of species will lose more than half their range under climate change. Nevertheless, we emphasise the broad uncertainty that any average encapsulates. Dispersal capacity only had a minor impact on projected range shifts relative to other modelling assumptions but the network‐pathways and maps of uncertainty have value for conservation planning at large scales. Projected range losses initially decreased rapidly as dispersal rates increased but the benefits are reduced above 2–3 km year^?1. Taxa restricted to dispersal within the stream network (aquatic) were more vulnerable to climate change than taxa with semi‐terrestrial or aerial dispersal and maps of variation due to dispersal mode and rate indicate where habitat connectivity would be most beneficial.
4. This study demonstrates the breadth of uncertainties that challenge plans for improving ecosystem adaptation under climate change and highlights where in the landscape those differences were consistent. We emphasise the need for freshwater conservation studies to be ecologically representative, to focus on broad‐scale connectivity for taxa that can move between catchments, and an accessible network of refugia for taxa with more limited dispersal.

     

Modelling distribution in European stream macroinvertebrates under future climates

Climate change is predicted to have profound effects on freshwater organisms due to rising temperatures and altered precipitation regimes. Using an ensemble of bioclimatic envelope models (BEMs), we modelled the climatic suitability of 191 stream macroinvertebrate species from 12 orders across Europe under two climate change scenarios for 2080 on a spatial resolution of 5 arc minutes. Analyses included assessments of relative changes in species’ climatically suitable areas as well as their potential shifts in latitude and longitude with respect to species’ thermal preferences. Climate‐change effects were also analysed regarding species’ ecological and biological groupings, namely (1) endemicity and (2) rarity within European ecoregions, (3) life cycle, (4) stream zonation preference and (5) current preference. The BEMs projected that suitable climate conditions would persist in Europe in the year 2080 for nearly 99% of the modelled species regardless of the climate scenario. Nevertheless, a decrease in the amount of climatically suitable areas was projected for 57–59% of the species. Depending on the scenario, losses could be of 38–44% on average. The suitable areas for species were projected to shift, on average, 4.7–6.6° north and 3.9–5.4° east. Cold‐adapted species were projected to lose climatically suitable areas, while gains were expected for warm‐adapted species. When projections were analysed for different species groupings, only endemics stood out as a particular group. That is, endemics were projected to lose significantly larger amounts of suitable climatic areas than nonendemic species. Despite the uncertainties involved in modelling exercises such as this, the extent of projected distributional changes reveals further the vulnerability of freshwater organisms to climate change and implies a need to understand the consequences for ecological function and biodiversity conservation.     

A framework integrating physiology,dispersal and land‐use to project species ranges under climate change

To study the potential effects of climate change on species, one of the most popular approaches are species distribution models (SDMs). However, they usually fail to consider important species‐specific biological traits, such as species’ physiological capacities or dispersal ability. Furthermore, there is consensus that climate change does not influence species distributions in isolation, but together with other anthropogenic impacts such as land‐use change, even though studies investigating the relative impacts of different threats on species and their geographic ranges are still rare. Here we propose a novel integrative approach which produces refined future range projections by combining SDMs based on distribution, climate, and physiological tolerance data with empirical data on dispersal ability as well as current and future land‐use. Range projections based on different combinations of these factors show strong variation in projected range size for our study species Emberiza hortulana. Using climate and physiological data alone, strong range gains are projected. However, when we account for land‐use change and dispersal ability, future range‐gain may even turn into a future range loss. Our study highlights the importance of accounting for biological traits and processes in species distribution models and of considering the additive effects of climate and land‐use change to achieve more reliable range projections. Furthermore, with our approach we present a new tool to assess species’ vulnerability to climate change which can be easily applied to multiple species.     

Projected changes in distributions of Australian tropical savanna birds under climate change using three dispersal scenarios

Identifying the species most vulnerable to extinction as a result of climate change is a necessary first step in mitigating biodiversity decline. Species distribution modeling (SDM) is a commonly used tool to assess potential climate change impacts on distributions of species. We use SDMs to predict geographic ranges for 243 birds of Australian tropical savannas, and to project changes in species richness and ranges under a future climate scenario between 1990 and 2080. Realistic predictions require recognition of the variability in species capacity to track climatically suitable environments. Here we assess the effect of dispersal on model results by using three approaches: full dispersal, no dispersal and a partial-dispersal scenario permitting species to track climate change at a rate of 30 km per decade. As expected, the projected distributions and richness patterns are highly sensitive to the dispersal scenario. Projected future range sizes decreased for 66% of species if full dispersal was assumed, but for 89% of species when no dispersal was assumed. However, realistic future predictions should not assume a single dispersal scenario for all species and as such, we assigned each species to the most appropriate dispersal category based on individual mobility and habitat specificity; this permitted the best estimates of where species will be in the future. Under this "realistic" dispersal scenario, projected ranges sizes decreased for 67% of species but showed that migratory and tropical-endemic birds are predicted to benefit from climate change with increasing distributional area. Richness hotspots of tropical savanna birds are expected to move, increasing in southern savannas and southward along the east coast of Australia, but decreasing in the arid zone. Understanding the complexity of effects of climate change on species' range sizes by incorporating dispersal capacities is a crucial step toward developing adaptation policies for the conservation of vulnerable species.     

Modeling plant species distributions under future climates: how fine scale do climate projections need to be?

Recent studies suggest that species distribution models (SDMs) based on fine‐scale climate data may provide markedly different estimates of climate‐change impacts than coarse‐scale models. However, these studies disagree in their conclusions of how scale influences projected species distributions. In rugged terrain, coarse‐scale climate grids may not capture topographically controlled climate variation at the scale that constitutes microhabitat or refugia for some species. Although finer scale data are therefore considered to better reflect climatic conditions experienced by species, there have been few formal analyses of how modeled distributions differ with scale. We modeled distributions for 52 plant species endemic to the California Floristic Province of different life forms and range sizes under recent and future climate across a 2000‐fold range of spatial scales (0.008–16 km²). We produced unique current and future climate datasets by separately downscaling 4 km climate models to three finer resolutions based on 800, 270, and 90 m digital elevation models and deriving bioclimatic predictors from them. As climate‐data resolution became coarser, SDMs predicted larger habitat area with diminishing spatial congruence between fine‐ and coarse‐scale predictions. These trends were most pronounced at the coarsest resolutions and depended on climate scenario and species' range size. On average, SDMs projected onto 4 km climate data predicted 42% more stable habitat (the amount of spatial overlap between predicted current and future climatically suitable habitat) compared with 800 m data. We found only modest agreement between areas predicted to be stable by 90 m models generalized to 4 km grids compared with areas classified as stable based on 4 km models, suggesting that some climate refugia captured at finer scales may be missed using coarser scale data. These differences in projected locations of habitat change may have more serious implications than net habitat area when predictive maps form the basis of conservation decision making.