The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations

The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease, requires both Mn(2+) and ATP for efficient cleavage of the inteinless recA allele. In this study, we show that Mg(2+) alone was sufficient to stimulate PI-MtuI to cleave double-stranded DNA at ectopic sites. In the absence of Mg(2+), PI-MtuI formed complexes with topologically different forms of DNA containing ectopic recognition sequences with equal affinity but failed to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly within the ectopic recognition sequence to generate either a blunt end or 1-2-nucleotide 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal ion-binding ligands (Asp(122), Asp(222), and Glu(220)) together with immunoprecipitation assays provided compelling evidence to link both the Mg(2+)- and Mn(2+) and ATP-dependent endonuclease activities to PI-MtuI. The kinetic mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential mechanism with transient accumulation of nicked circular duplex DNA as an intermediate. Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA transposition and hence its lateral transfer in natural populations.

The chemical ecology of seed dispersal in monoecious and dioecious figs

In the nursery pollination system of figs (Ficus, Moraceae), flower-bearing receptacles called syconia breed pollinating wasps and are units of both pollination and seed dispersal. Pollinators and mammalian seed dispersers are attracted to syconia by volatile organic compounds (VOCs). In monoecious figs, syconia produce both wasps and seeds, while in (gyno)dioecious figs, male (gall) fig trees produce wasps and female (seed) fig trees produce seeds. VOCs were collected using dynamic headspace adsorption methods on freshly collected figs from different trees using Super Q® collection traps. VOC profiles were determined using gas chromatography–mass spectrometry (GC–MS).The VOC profile of receptive and dispersal phase figs were clearly different only in the dioecious mammal-dispersed Ficus hispida but not in dioecious bird-dispersed F. exasperata and monoecious bird-dispersed F. tsjahela. The VOC profile of dispersal phase female figs was clearly different from that of male figs only in F. hispida but not in F. exasperata, as predicted from the phenology of syconium production which only in F. hispida overlaps between male and female trees. Greater difference in VOC profile in F. hispida might ensure preferential removal of seed figs by dispersal agents when gall figs are simultaneously available.The VOC profile of only mammal-dispersed female figs of F. hispida had high levels of fatty acid derivatives such as amyl-acetates and 2-heptanone, while monoterpenes, sesquiterpenes and shikimic acid derivatives were predominant in the other syconial types. A bird- and mammal-repellent compound methyl anthranilate occurred only in gall figs of both dioecious species, as expected, since gall figs containing wasp pollinators should not be consumed by dispersal agents.

Pollinator limitation and the effect of breeding systems on plant reproduction in forest fragments

Reproduction of plants in fragmented habitats may be limited because of lower diversity or abundance of pollinators, and/or variation in local plant density. We assessed natural fruit set and pollinator limitation in ten species of woody plants in natural and restored fragments in the Pondicherry region of southern India, to see whether breeding system of plants (self-compatible and self-incompatible) affected fruit set. We tested whether the number of flowering individuals in the fragments affected the fruit set and further examined the adult and sapling densities of self-compatible (SC) and self-incompatible (SI) species. We measured the natural level of fruit set and pollinator limitation (calculated as the difference in fruit set between hand cross-pollinated and naturally pollinated flowers). Our results demonstrate that there was a higher level of pollinator limitation and hence lower levels of natural fruit set in self-incompatible species as compared to self-compatible species. However, the hand cross-pollinated flowers in SC and SI species produced similar levels of fruit set,further indicating that lower fruit set was due to pollinator limitation and not due to lack of cross-compatible individuals in the fragments. There was no significant relation between number of flowering individuals and the levels of natural fruit set, except for two species Derris ovalifolia, Ixora pavetta. In these species the natural fruit set decreased with increasing population size, again indicating pollinator limitation. The adult and sapling densities in self-compatible species were significantly higher than inself-incompatible species. These findings indicate that the low reproductive output in self-incompatible species may eventually lead to lower population sizes. Restoration of pollinator services along with plant species in fragmented habitats is important for the long-term conservation of biodiversity. (C) 2009 Elsevier Masson SAS. All rights reserved.

Child sexual abuse and access to justice for civil claims: Time to reform the Limitation of Actions Act 1974 (Qld)

In 2015, Victoria passed laws removing the time limit in which a survivor of child sexual abuse can commence a civil claim for personal injury. The law applies also to physical abuse, and to psychological injury arising from those forms of abuse. In 2016, New South Wales made almost identical legal reforms. These reforms were partly motivated by the recommendations of inquiries into institutional child abuse. Of particular relevance is that the Australian Royal Commission Into Institutional Responses to Child Sexual Abuse recommended in 2015 that all States and Territories remove their time limits for civil claims. This presentation explores the problems with standard time limits when applied to child sexual abuse cases (whether occurring within or beyond institutions), the scientific, ethical and legal justifications for lifting the time limits, and solutions for future law reform.

Models of Dispersal and Diversification

Ecology and evolutionary biology is the study of life on this planet. One of the many methods applied to answering the great diversity of questions regarding the lives and characteristics of individual organisms, is the utilization of mathematical models. Such models are used in a wide variety of ways. Some help us to reason, functioning as aids to, or substitutes for, our own fallible logic, thus making argumentation and thinking clearer. Models which help our reasoning can lead to conceptual clarification; by expressing ideas in algebraic terms, the relationship between different concepts become clearer. Other mathematical models are used to better understand yet more complicated models, or to develop mathematical tools for their analysis. Though helping us to reason and being used as tools in the craftmanship of science, many models do not tell us much about the real biological phenomena we are, at least initially, interested in. The main reason for this is that any mathematical model is a simplification of the real world, reducing the complexity and variety of interactions and idiosynchracies of individual organisms. What such models can tell us, however, both is and has been very valuable throughout the history of ecology and evolution. Minimally, a model simplifying the complex world can tell us that in principle, the patterns produced in a model could also be produced in the real world. We can never know how different a simplified mathematical representation is from the real world, but the similarity models do strive for, gives us confidence that their results could apply. This thesis deals with a variety of different models, used for different purposes. One model deals with how one can measure and analyse invasions; the expanding phase of invasive species. Earlier analyses claims to have shown that such invasions can be a regulated phenomena, that higher invasion speeds at a given point in time will lead to a reduction in speed. Two simple mathematical models show that analysis on this particular measure of invasion speed need not be evidence of regulation. In the context of dispersal evolution, two models acting as proof-of-principle are presented. Parent-offspring conflict emerges when there are different evolutionary optima for adaptive behavior for parents and offspring. We show that the evolution of dispersal distances can entail such a conflict, and that under parental control of dispersal (as, for example, in higher plants) wider dispersal kernels are optimal. We also show that dispersal homeostasis can be optimal; in a setting where dispersal decisions (to leave or stay in a natal patch) are made, strategies that divide their seeds or eggs into fractions that disperse or not, as opposed to randomized for each seed, can prevail. We also present a model of the evolution of bet-hedging strategies; evolutionary adaptations that occur despite their fitness, on average, being lower than a competing strategy. Such strategies can win in the long run because they have a reduced variance in fitness coupled with a reduction in mean fitness, and fitness is of a multiplicative nature across generations, and therefore sensitive to variability. This model is used for conceptual clarification; by developing a population genetical model with uncertain fitness and expressing genotypic variance in fitness as a product between individual level variance and correlations between individuals of a genotype. We arrive at expressions that intuitively reflect two of the main categorizations of bet-hedging strategies; conservative vs diversifying and within- vs between-generation bet hedging. In addition, this model shows that these divisions in fact are false dichotomies.

Evaluation of relative growth limitation due to depletion of glucose and oxygen during fungal growth on a spherical solid particle

A mathematical model for glucose and oxygen consumption, and cell growth during fungal growth on a single solid particle is developed. A moving biofilm is assumed to be present on the surface of the solid particle. Initially only glucose is assumed to be growth limiting and later oxygen transferred from the gas phase on to the biofilm is also assumed to be growth limiting. Glucose is found to be severely growth limiting when assumed to be the only growth limiting factor and its limiting levels far less severe when oxygen limitation is also included. The objective of the model is to gain a better understanding of the mass transfer and relative growth limiting characteristics of glucose and oxygen in fungal growth systems. The results obtained from the model proposed here will be the subject of future work.

Retention Time Variability as a Mechanism for Animal Mediated Long-Distance Dispersal

Long-distance dispersal (LDD) events, although rare for most plant species, can strongly influence population and community dynamics. Animals function as a key biotic vector of seeds and thus, a mechanistic and quantitative understanding of how individual animal behaviors scale to dispersal patterns at different spatial scales is a question of critical importance from both basic and applied perspectives. Using a diffusion-theory based analytical approach for a wide range of animal movement and seed transportation patterns, we show that the scale (a measure of local dispersal) of the seed dispersal kernel increases with the organisms' rate of movement and mean seed retention time. We reveal that variations in seed retention time is a key determinant of various measures of LDD such as kurtosis (or shape) of the kernel, thinkness of tails and the absolute number of seeds falling beyond a threshold distance. Using empirical data sets of frugivores, we illustrate the importance of variability in retention times for predicting the key disperser species that influence LDD. Our study makes testable predictions linking animal movement behaviors and gut retention times to dispersal patterns and, more generally, highlights the potential importance of animal behavioral variability for the LDD of seeds.

A meta-analysis of the traits affecting dispersal ability in butterflies: can wingspan be used as a proxy?

1. Dispersal ability of a species is a key ecological characteristic, affecting a range of processes from adaptation, community dynamics and genetic structure, to distribution and range size. It is determined by both intrinsic species traits and extrinsic landscape-related properties. 2. Using butterflies as a model system, the following questions were addressed: (i) given similar extrinsic factors, which intrinsic species trait(s) explain dispersal ability? (ii) can one of these traits be used as a proxy for dispersal ability? (iii) the effect of interactions between the traits, and phylogenetic relatedness, on dispersal ability. 3. Four data sets, using different measures of dispersal, were compiled from published literature. The first data set uses mean dispersal distances from capture-mark-recapture studies, and the other three use mobility indices. Data for six traits that can potentially affect dispersal ability were collected: wingspan, larval host plant specificity, adult habitat specificity, mate location strategy, voltinism and flight period duration. Each data set was subjected to both unifactorial, and multifactorial, phylogenetically controlled analyses. 4. Among the factors considered, wingspan was the most important determinant of dispersal ability, although the predictive powers of regression models were low. Voltinism and flight period duration also affect dispersal ability, especially in case of temperate species. Interactions between the factors did not affect dispersal ability, and phylogenetic relatedness was significant in one data set. 5. While using wingspan as the only proxy for dispersal ability maybe problematic, it is usually the only easily accessible species-specific trait for a large number of species. It can thus be a satisfactory proxy when carefully interpreted, especially for analyses involving many species from all across the world.

Seed dispersal in changing landscapes

A growing understanding of the ecology of seed dispersal has so far had little influence on conservation practice, while the needs of conservation practice have had little influence on seed dispersal research. Yet seed dispersal interacts decisively with the major drivers of biodiversity change in the 21st century: habitat fragmentation, overharvesting, biological invasions, and climate change. We synthesize current knowledge of the effects these drivers have on seed dispersal to identify research gaps and to show how this information can be used to improve conservation management. The drivers, either individually, or in combination, have changed the quantity, species composition, and spatial pattern of dispersed seeds in the majority of ecosystems worldwide, with inevitable consequences for species survival in a rapidly changing world. The natural history of seed dispersal is now well-understood in a range of landscapes worldwide. Only a few generalizations that have emerged are directly applicable to conservation management, however, because they are frequently confounded by site-specific and species-specific variation. Potentially synergistic interactions between disturbances are likely to exacerbate the negative impacts, but these are rarely investigated. We recommend that the conservation status of functionally unique dispersers be revised and that the conservation target for key seed dispersers should be a population size that maintains their ecological function, rather than merely the minimum viable population. Based on our analysis of conservation needs, seed dispersal research should be carried out at larger spatial scales in heterogenous landscapes, examining the simultaneous impacts of multiple drivers on community-wide seed dispersal networks. (C) 2011 Elsevier Ltd. All rights reserved.

Influence limitation in multi-campaign social networks: A Shapley value based approach

We investigate the problem of influence limitation in the presence of competing campaigns in a social network. Given a negative campaign which starts propagating from a specified source and a positive/counter campaign that is initiated, after a certain time delay, to limit the the influence or spread of misinformation by the negative campaign, we are interested in finding the top k influential nodes at which the positive campaign may be triggered. This problem has numerous applications in situations such as limiting the propagation of rumor, arresting the spread of virus through inoculation, initiating a counter-campaign against malicious propaganda, etc. The influence function for the generic influence limitation problem is non-submodular. Restricted versions of the influence limitation problem, reported in the literature, assume submodularity of the influence function and do not capture the problem in a realistic setting. In this paper, we propose a novel computational approach for the influence limitation problem based on Shapley value, a solution concept in cooperative game theory. Our approach works equally effectively for both submodular and non-submodular influence functions. Experiments on standard real world social network datasets reveal that the proposed approach outperforms existing heuristics in the literature. As a non-trivial extension, we also address the problem of influence limitation in the presence of multiple competing campaigns.

Loss of frugivore seed dispersal services under climate change

The capacity of species to track shifting climates into the future will strongly influence outcomes for biodiversity under a rapidly changing climate. However, we know remarkably little about the dispersal abilities of most species and how these may be influenced by climate change. Here we show that climate change is projected to substantially reduce the seed dispersal services provided by frugivorous vertebrates in rainforests across the Australian Wet Tropics. Our model projections show reductions in both median and long-distance seed dispersal, which may markedly reduce the capacity of many rainforest plant species to track shifts in suitable habitat under climate change. However, our analyses suggest that active management to maintain the abundances of a small set of important frugivores under climate change could markedly reduce the projected loss of seed dispersal services and facilitate shifting distributions of rainforest plant species.

Mammalian Frugivores With Different Foraging Behavior Can Show Similar Seed Dispersal Effectiveness

Frugivores with disparate foraging behavior are considered to vary in their seed dispersal effectiveness (SDE). Measured SDEs for gibbons and macaques for a primate-fruit' were comparable despite the different foraging and movement behavior of the primates. This could help facilitate fruit trait convergence in diverse fruit-frugivore networks.

Impacts of climate change and management responses in tropical forests depend on complex frugivore-mediated seed dispersal

AimBiodiversity outcomes under global change will be influenced by a range of ecological processes, and these processes are increasingly being considered in models of biodiversity change. However, the level of model complexity required to adequately account for important ecological processes often remains unclear. Here we assess how considering realistically complex frugivore-mediated seed dispersal influences the projected climate change outcomes for plant diversity in the Australian Wet Tropics (all 4313 species). LocationThe Australian Wet Tropics, Queensland, Australia. MethodsWe applied a metacommunity model (M-SET) to project biodiversity outcomes using seed dispersal models that varied in complexity, combined with alternative climate change scenarios and habitat restoration scenarios. ResultsWe found that the complexity of the dispersal model had a larger effect on projected biodiversity outcomes than did dramatically different climate change scenarios. Applying a simple dispersal model that ignored spatial, temporal and taxonomic variation due to frugivore-mediated seed dispersal underestimated the reduction in the area of occurrence of plant species under climate change and overestimated the loss of diversity in fragmented tropical forest remnants. The complexity of the dispersal model also changed the habitat restoration approach identified as the best for promoting persistence of biodiversity under climate change. Main conclusionsThe consideration of complex processes such as frugivore-mediated seed dispersal can make an important difference in how we understand and respond to the influence of climate change on biodiversity.

Fruit Trait Preference in Rhesus Macaques (Macaca mulatta) and its Implications for Seed Dispersal

Primates constitute 25-40 % of the frugivore biomass of tropical forests. Primate fruit preference, as a determinant of seed dispersal, can therefore have a significant impact on these ecosystems. Although the traits of fruits included in primate diets have been described, fruit trait preference has been less studied with respect to fruit availability. We examined fruit trait preference and its implications for seed dispersal in the rhesus macaque (Macaca mulatta), a dietarily flexible species and important seed disperser, at the Buxa Tiger Reserve, India. Over a year, we monitored the phenology of selected trees in the study area, observed the feeding behavior of rhesus macaques using scans and focal animal sampling, and documented morphological traits of the fruits/seeds consumed. Using generalized linear modeling, we found that the kind of edible tissue was the chief determinant of fruit consumption, with M. mulatta feeding primarily on fruits with juicy-soft pulp and acting as seed predators for those with no discernible pulp. Overall, the preferred traits were external covers that could be easily pierced by a fingernail, medium to large seeds, true stone-like seeds, and juicy-soft edible tissue, thereby implying that fruit taxa with these traits had a higher probability of being dispersed. Macaques were more selective during the high fruit availability period than the low fruit availability period, preferentially feeding on soft-skinned fruits with juicy-soft pulp. We suggest that further studies be conducted across habitats and time to understand the consistency of interactions between primates and fruits with specific traits to determine the degree of selective pressure (if any) that is exerted by primates on fruit traits.