Interactions of Safranin T with nucleic acids

The interactions of Safranin T (ST) with several nucleic acids have been investigated by electrochemical, UV-visible and CD spectroscopic techniques. The form of the nucleic acid-ST complexes is sensitive to the ratio of the two species. Two electrochemically inactive complexes such as, nucleic acid-ST and nucleic acid-2ST, were formed while ST interacts with nucleic acids. Two processes were obtained from spectral experiments: (1) at the high value of R (R is defined as the ratio of the total concentration of ST to that of nucleic acid), ST is groove-binding with stacking, (2) st the low value of R, ST is groove-binding without stacking. Intrinsic binding constants were obtained by spectral methods. The experiments also show that electrostatic binding plays an important role in the interaction of ST with nucleic acids.

Long-term ecological interactions between nutrient and phytoplankton community in the Changjiang estuary

Both nitrate (NO (3) (-) ) and soluble reactive phosphate (PO (4) (3-) ) concentration in the freshwater end-member at the mouth of the Changjiang River have increased dramatically since the 1960s. Within the same period in the sea area, with surface salinity > 30, NO (3) (-) concentration has shown an obvious increase, PO (4) (3-) has not changed greatly and dissolved reactive silica (SiO (3) (2-) ) has deceased dramatically. An examination of the elemental ratio of NO (3) (-) to PO (4) (3-) at the mouth of the Changjiang River did not show a systematic trend from the 1960s to 2000s largely because both nutrients increased simultaneously. In comparison, the elemental ratio of dissolved inorganic nitrogen (DIN) to PO (4) (3-) in surface seawater, with salinity > 22, has shown a clearly increasing trend. Furthermore, an overall historical change of the SiO (3) (2-) :PO (4) (3-) ratio has undergone a reverse trend in this area. Based on the changes of SiO (3) (2-) :PO (4) (3-) and DIN:PO (4) (3-) ratios, we can conclude that an overall historical change of SiO (3) (2-) :DIN ratio has decreased in this area from the 1950-1960s to 2000s. The argument that phytoplankton productivity in the Changjiang estuary has been enhanced by increasing nutrient input from the riverine transport was supported by these results. A comparative study analyzing the shift of phytoplankton composition from the mid-1980s to 2000s was also made. The results indicated that the average yearly percentage of diatom species in the Changjiang estuary has decreased from 84.6% during 1985-1986 to 69.8% during 2004-2005. Furthermore, the average yearly percentage of diatom abundance in the Changjiang estuary decreased from 99.5% during to 75.5% over the same time period, while the abundance of dinoflagellates has increased dramatically, from 0.7% to 25.4%.

Interactions between the bloom-forming dinoflagellates Prorocentrum donghaiense and Alexandrium tamarense in laboratory cultures

Interactions between Prorocentrum donghaiense and Alexandrium tamarens, two bloom-forming dinoflagellates, were investigated using bi-algal cultures. All R donghaiense died, but A. tamarense was hardly affected by the end of the experiment when the initial cell density was set at 1.0 X 10(4) cells mL(-1) for P. donghaiense and 0.28 x 10(4) cells mL(-1) for A. tamarense. However, significant growth suppression occurred in either species when the initial cell density of P donghaiense increased to I. 0 X 105 Cells mL(-1) in the bi-algal culture, but no out-competement was observed. The simultaneous assay on the culture filtrates showed that P donghaiense filtrate prepared at a lower initial density (1.0 X 10(4) cells mL(-1)) stimulated growth of the co-cultured A. tanzarense (0.28 x 10(4) cells mL(-1)), but filtrate at a higher initial density (1.0 x 10(5) cells mL(-1)) depressed its growth. The filtrate of A. tamarense at a density of 0.28 x 10(4) cells mL(-1) killed all R donghaiense at a lower density (1.0 x 10(4) cells mL(-1)), but only exhibited an inhibitory effect on it at a higher density (1.0 x 10(5) cells mL(-1)). It is likely that these two species of microalgae interfere with each other mainly by releasing allelochemical substance(s) into the culture medium, and a direct cell-to-cell contact was not necessary for their mutual interaction. The allelopathic test further proved that A. tamarense could affect the growth of co-cultured P. donghaiense by producing allelochemical(s); moreover, A. tamarense culture filtrate at the stationary growth phase (SP) had a strongly inhibitory effect on P donghaiense compared to that at the exponential phase (EP). Results also demonstrated a dose-dependent relationship between the microalgal initial cell density and the degree of the allelopathic effect. The growth of R donghaiense and A. tamarense in the bi-algal cultures was simulated using a mathematical model to quantify the interaction. The estimated parameters from the model showed that the inhibition exerted by A. tamarense on P. donghaiense was about 17 and 8 times stronger than the inhibition P. donghaiense exerted on A. tamarense, when the initial cell density was set at 1.0 X 10(4) and 1.0 X 10(5) cells mL(-1) for P donghaiense, respectively. and 0.28 x 10(4) cells mL(-1) for A. tamarense in the bi-algal cultures. A. tamarense seems to have a survival strategy that is superior to that of P. donghaiense in bi-algal cultures under controlled laboratory conditions. (c) 2006 Elsevier B.V. All rights reserved.

Experimental warming causes large and rapid species loss, dampened by simulated grazing, on the Tibetan Plateau

We investigated the independent and combined effects of experimental warming and grazing on plant species diversity on the north-eastern Tibetan Plateau, a region highly vulnerable to ongoing climate and land use changes. Experimental warming caused a 26-36% decrease in species richness, a response that was generally dampened by experimental grazing. Higher species losses occurred at the drier sites where N was less available. Moreover, we observed an indirect effect of climate change on species richness as mediated by plant-plant interactions. Heat stress and warming-induced litter accumulation are potential explanations for the species' responses to experimental warming. This is the first reported experimental evidence that climate warming could cause dramatic declines in plant species diversity in high elevation ecosystems over short time frames and supports model predictions of species losses with anthropogenic climate change.

Characterisation of bacteriophage-host interactions in Lactococcus lactis

Lactococcus lactis is used extensively world-wide for the production of fermented dairy products. Bacteriophages (phages) infecting L. lactis can result in slow or incomplete fermentations, or may even cause total fermentation failure. Therefore, bacteriophages disrupting L. lactis fermentation are of economic concern. This thesis employed a multifaceted approach to investigate various molecular aspects of phage-host interaction in L. lactis. The genome sequence of an Irish dairy starter strain, the prophage-cured L. lactis subsp. cremoris UC509.9, was studied. The 2,250,427 bp circular chromosome represents the smallest among its sequenced lactococcal equivalents. The genome displays clear genetic adaptation to the dairy niche in the form of extensive reductive evolution. Gene prediction identified 2066 protein-encoding genes, including 104 which showed significant homology to transposase-specifying genes. Over 9 % of the identified genes appear to be inactivated through stop codons or frame shift mutations. Many pseudogenes were found in genes that are assigned to carbohydrate and amino acid transport and metabolism orthologous groups, reflecting L. lactis UC509.9’s adaptation to the lactose and casein-rich dairy environment. Sequence analysis of the eight plasmids of L. lactis revealed extensive adaptation to the dairy environment. Key industrial phenotypes were mapped and novel lactococcal plasmid-associated genes highlighted. In addition to chromosomally-encoded bacteriophage resistance systems, six functional such systems were identified, including two abortive infection systems, AbiB and AbiD1, explaining the observed phage resistance of L. lactis UC509.9 Molecular analysis suggests that the constitutive expression of AbiB is not lethal to cells, suggesting the protein is expressed in an un/inactivated form. Analysis of 936 species phage sk1-escape mutants of AbiB revealed that all such mutants harbour mutations in orf6, which encodes the major capsid protein. Results suggest that the major capsid protein is required for activation of the AbiB system, although this requires furrther investigations. Temporal transcriptomes of L. lactis UC509.9 undergoing lytic infection with either one of two distinct bacteriophages, Tuc2009 and c2, was determined and compared to the transcriptome of uninfected UC509.9 cells. Whole genome microarrays performed at various time-points post-infection demonstrated a rather modest impact on host transcription. Alterations in the UC509.9 transcriptome during lytic infection appear phage-specific, with a relatively small number of differentially transcribed genes shared between infection with either Tuc2009 or c2. Transcriptional profiles of both bacteriophages during lytic infection was shown to generally correlate with previous studies and allowed the confirmation of previously predicted promoter sequences. Bioinformatic analysis of genomic regions encoding the presumed cell wall polysaccharide (CW PS) biosynthesis gene cluster of several strains of L. lactis was performed. Results demonstrate the presence of three dominant genetic types of this gene cluster, termed type A, B and C. These regions were used for the development of a multiplex PCR to identify CW PS genotype of various lactococcal strains. Analysis of 936 species phage receptor binding protein phylogeny (RBP) and CW PS genotype revealed an apparent correlation between RBP phylogeny and CW PS type, thereby providing a partial explanation for the observed narrow host range of 936 phages. Further analysis of the genetic locus encompassing the presumed CW PS biosynthesis operon of eight strains identified as belonging to the CW PS C (geno)type, revealed the presence of a variable region among the examined strains. The obtained comparative analysis allowed for the identification of five subgroups of the C type, named C1 to C5. We purified an acidic polysaccharide from the cell wall of L. lactis 3107 (C2 subtype) and confirmed that it is structurally different from the CW PS of the C1 subtype L. lactis MG1363. Combinations of genes from the variable region of C2 subtype were amplified from L. lactis 3107 and introduced into a mutant of the C1 subtype L. lactis NZ9000 (a direct derivative of MG1363) deficient in CW PS biosynthesis. The resulting recombinant mutant synthesized a CW PS with a composition characteristic for that of the C2 subtype L. lactis 3107 and not the wildtype C1 L. lactis NZ9000. The recombinant mutant exhibited a changed phage resistance/sensitivity profile consistent with that of L. lactis 3107, which unambiguously demonstrated that L. lactis 3107 CW PS is the host cell surface receptor of two bacteriophages belonging to the P335 species as well as phages that are member of the 936 species. The research presented in this thesis has significantly advanced our understanding of L. lactis bacteriophage-host interactions in several ways. Firstly, the examination of plasmidencoded bacteriophage resistance systems has allowed inferences to be made regarding the mode of action of AbiB, thereby providing a platform for further elucidation of the molecular trigger of this system. Secondly, the phage infection transcriptome data presented, in addition to previous work, has made L. lactis a model organism in terms of transcriptomic studies of bacteriophage-host interactions. And finally, the research described in this thesis has for the first time explicitly revealed the nature of a carbohydrate bacteriophage receptor in L. lactis, while also providing a logical explanation for the observed narrow host ranges exhibited by 936 and P335 phages. Future research in discerning the structures of other L. lactis CW PS, combined with the determination of the molecular interplay between receptor binding proteins of these phages and CW PS will allow an in depth understanding of the mechanism by which the most prevalent lactococcal phages identify and adsorb to their specific host.

Infant-nonmother interactions of free-ranging mantled howlers (Alouatta palliata) in Costa Rica

Proximate and ultimate explanations of interactions between infants and nonmothers vary depending upon the relatedness of the interactors. We investigated interactions of infants and nonmothers from a 22-month continuous study and from the long-term monitoring of the mantled howler population of La Pacifica, Guanacaste Province, Costa Rica. Relatedness is low or absent in these mantled howler groups. Juvenile females appeared to practice care skills with older infants, but as most first infants died, they failed to benefit. Infant positive interactions with adults occurred with the mother and probable father. Other adult females behaved aggressively toward the youngest infants. Mothers were retentive of infants and responded negatively to these interactions, suggesting that they perceived them as threatening. Interactions with infants appear to reflect competition in groups of unrelated adults. A review of other populations of Alouatta palliata and other species of howlers indicate variability in social group size and suggest variability in intragroup relatedness. We suggest that further study will confirm that social behavior (including interactions with infants) will vary by resource availability (group size) and associated demographic patterns (male and female migration) that affect relatedness in howler social groups.

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play.

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer-algae chemostats; alewife-zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife-zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.

Maternal rank influences the outcome of aggressive interactions between immature chimpanzees

© 2014 The Association for the Study of Animal Behaviour.For many long-lived mammalian species, extended maternal investment has a profound effect on offspring integration in complex social environments. One component of this investment may be aiding young in aggressive interactions, which can set the stage for offspring social position later in life. Here we examined maternal effects on dyadic aggressive interactions between immature (<12 years) chimpanzees. Specifically, we tested whether relative maternal rank predicted the probability of winning an aggressive interaction. We also examined maternal responses to aggressive interactions to determine whether maternal interventions explain interaction outcomes. Using a 12-year behavioural data set (2000-2011) from Gombe National Park, Tanzania, we found that relative maternal rank predicted the probability of winning aggressive interactions in male-male and male-female aggressive interactions: offspring were more likely to win if their mother outranked their opponent's mother. Female-female aggressive interactions occurred infrequently (two interactions), so could not be analysed. The probability of winning was also higher for relatively older individuals in male-male interactions, and for males in male-female interactions. Maternal interventions were rare (7.3% of 137 interactions), suggesting that direct involvement does not explain the outcome for the vast majority of aggressive interactions. These findings provide important insight into the ontogeny of aggressive behaviour and early dominance relationships in wild apes and highlight a potential social advantage for offspring of higher-ranking mothers. This advantage may be particularly pronounced for sons, given male philopatry in chimpanzees and the potential for social status early in life to translate more directly to adult rank.

A range-wide experiment to investigate nutrient and soil moisture interactions in loblolly pine plantations

© 2015 by the authors.The future climate of the southeastern USA is predicted to be warmer, drier and more variable in rainfall, which may increase drought frequency and intensity. Loblolly pine (Pinus taeda) is the most important commercial tree species in the world and is planted on ~11 million ha within its native range in the southeastern USA. A regional study was installed to evaluate effects of decreased rainfall and nutrient additions on loblolly pine plantation productivity and physiology. Four locations were established to capture the range-wide variability of soil and climate. Treatments were initiated in 2012 and consisted of a factorial combination of throughfall reduction (approximate 30% reduction) and fertilization (complete suite of nutrients). Tree and stand growth were measured at each site. Results after two growing seasons indicate a positive but variable response of fertilization on stand volume increment at all four sites and a negative effect of throughfall reduction at two sites. Data will be used to produce robust process model parameterizations useful for simulating loblolly pine growth and function under future, novel climate and management scenarios. The resulting improved models will provide support for developing management strategies to increase pine plantation productivity and carbon sequestration under a changing climate.

Quantifying ecosystem-level consequences of ocean acidification and warming by scaling up individual level responses of a predator snail and its trophic interactions

Understanding long‐term, ecosystem‐level impacts of climate change is challenging because experimental research frequently focuses on short‐term, individual‐level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14‐month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual‐level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual‐level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large‐scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local‐environmental conditions and resource availability. Such changes in macro‐scale distributions cannot be predicted by investigating individual‐level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long‐term, multiscale responses to multiple stressors, in an ecosystem context.

Horizon scanning for invasive alien species with the potential to threaten biodiversity in Great Britain

Invasive alien species (IAS) are considered one of the greatest threats to biodiversity, particularly through their interactions with other drivers of change. Horizon scanning, the systematic examination of future potential threats and opportunities, leading to prioritization of IAS threats is seen as an essential component of IAS management. Our aim was to consider IAS that were likely to impact on native biodiversity but were not yet established in the wild in Great Britain. To achieve this, we developed an approach which coupled consensus methods (which have previously been used for collaboratively identifying priorities in other contexts) with rapid risk assessment. The process involved two distinct phases: 1. Preliminary consultation with experts within five groups (plants, terrestrial invertebrates, freshwater invertebrates, vertebrates and marine species) to derive ranked lists of potential IAS. 2. Consensus-building across expert groups to compile and rank the entire list of potential IAS. Five hundred and ninety-one species not native to Great Britain were considered. Ninety-three of these species were agreed to constitute at least a medium risk (based on score and consensus) with respect to them arriving, establishing and posing a threat to native biodiversity. The quagga mussel, Dreissena rostriformis bugensis, received maximum scores for risk of arrival, establishment and impact; following discussions the unanimous consensus was to rank it in the top position. A further 29 species were considered to constitute a high risk and were grouped according to their ranked risk. The remaining 63 species were considered as medium risk, and included in an unranked long list. The information collated through this novel extension of the consensus method for horizon scanning provides evidence for underpinning and prioritizing management both for the species and, perhaps more importantly, their pathways of arrival. Although our study focused on Great Britain, we suggest that the methods adopted are applicable globally.

Ocean acidification has different effects on the production of DMS and DMSP measured in cultures of Emiliania huxleyi and a mesocosm study: a comparison of laboratory monocultures and community interactions

The human-induced rise in atmospheric carbon dioxide since the industrial revolution has led to increasing oceanic carbon uptake and changes in seawater carbonate chemistry, resulting in lowering of surface water pH. In this study we investigated the effect of increasing CO2 partial pressure (pCO2) on concentrations of volatile biogenic dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP), through monoculture studies and community pCO2 perturbation. DMS is a climatically important gas produced by many marine algae: it transfers sulfur into the atmosphere and is a major influence on biogeochemical climate regulation through breakdown to sulfate and formation of subsequent cloud condensation nuclei (CCN). Overall, production of DMS and DMSP by the coccolithophore Emiliania huxleyi strain RCC1229 was unaffected by growth at 900 matm pCO2, but DMSP production normalised to cell volume was 12% lower at the higher pCO2 treatment. These cultures were compared with community DMS and DMSP production during an elevated pCO2 mesocosm experiment with the aim of studying E. huxleyi in the natural environment. Results contrasted with the culture experiments and showed reductions in community DMS and DMSP concentrations of up to 60 and 32% respectively at pCO2 up to 3000 matm, with changes attributed to poorer growth of DMSP-producing nanophytoplankton species, including E. huxleyi, and potentially increased microbial consumption of DMSand dissolvedDMSPat higher pCO2.DMSandDMSPproduction differences between culture and community likely arise from pH affecting the inter-species responses between microbial producers and consumers.

Grassland-herbivore interactions: How do grazers coexist?

We develop a new approach to modeling grazing systems that links foraging characteristics (intake and digestive constraints) with resource dynamics via the probability of encounter with different grass heights. Three complementary models are presented: the generation of a grass height structure through selective grazing; investigating the conditions for consumer coexistence; and, using a simplified resource structure, the consequences for consumer abundance. The main finding is that coexistence between grazers differing in body size is possible if a single-resource type becomes differentiated in its height structure. Large grazers can facilitate food availability for smaller species but with the latter being competitively dominant. The relative preference given to different resource partitions is important in determining the nature of population interactions. Large-body and small-body grazer populations can interact through competitive, parasitic, commensalist, or amensalist relationships, depending on the way they partition the resource as well as their relative populations and the dynamics of resource renewal. The models provide new concepts of multispecies carrying capacity (stock equilibrium) in grazed systems with implications for conservation and management. We conclude that consumer species are not substitutable; therefore, the use of rangeland management concepts such as "livestock units" may be inappropriate.

“Islands” in Holocene forests: implications for forest openness, landscape clearance and “culture-steppe” species

Human activity has undoubtedly had a major impact on Holocene forested ecosystems, with the concurrent expansion of plants and animals associated with cleared landscapes and pasture, also known as 'culture-steppe'. However, this anthropogenic perspective may have underestimated the contribution of autogenic disturbance (e.g. wind-throw, fire), or a mixture of autogenic and anthropogenic processes, within early Holocene forests. Entomologists have long argued that the north European primary forest was probably similar in structure to pasture woodland. This idea has received support from the conservation biologist Frans Vera, who has recently strongly argued that the role of large herbivores in maintaining open forests in the primeval landscapes of Europe has been seriously underestimated. This paper reviews this debate from a fossil invertebrate perspective and looks at several early Holocene insect assemblages. Although wood taxa are indeed important during this period, species typical of open areas and grassland and dung beetles, usually associated with the dung of grazing animals, are persistent presences in many early woodland faunas. We also suggest that fire and other natural disturbance agents appear to have played an important ecological role in some of these forests, maintaining open areas and creating open vegetation islands within these systems. More work, however, is required to ascertain the role of grazing animals, but we conclude that fossil insects have a significant contribution to make to this debate. This evidence has fundamental implications in terms of how the palaeoecological record is interpreted, particularly by environmental archaeologists and palaeoecologists who may be more interested in identifying human-environment interactions rather than the ecological processes which may be preserved within palaeoecological records.

Measurement of charge exchange and X-ray emission cross sections for solar wind-comet interactions

X-ray emission from a comet was observed for the first time in 1996. One of the mechanisms believed to be contributing to this surprisingly strong emission is the interaction of highly charged solar wind ions with cometary gases. Reported herein are total absolute charge-exchange and normalized line-emission (X-ray) cross sections for collisions of high-charge state (+3 to +10) C, N, O, and Ne ions with the cometary species H2O and CO2. It is found that in several cases the double charge-exchange cross sections can be large, and in the case of C3+ they are equal to those for single charge exchange. Present results are compared to cross section values used in recent comet models. The importance of applying accurate cross sections, including double charge exchange, to obtain absolute line-emission intensities is emphasized.