MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record

Both the monophyly and inter-relationships of the major annelid groups have remained uncertain, despite intensive research on both morphology and molecular sequences. Morphological cladistic analyses indicate that Annelida is monophyletic and consists of two monophyletic groups, the clitellates and polychaetes, whereas molecular phylogenetic analyses suggest that polychaetes are paraphyletic and that sipunculans are crown-group annelids. Both the monophyly of polychaetes and the placement of sipunculans within annelids are in conflict with the annelid fossil record—the former because Cambrian stem taxa are similar to modern polychaetes in possessing biramous parapodia, suggesting that clitellates are derived from polychaetes; the latter because although fossil sipunculans are known from the Early Cambrian, crown-group annelids do not appear until the latest Cambrian. Here we apply a different data source, the presence versus absence of specific microRNAs—genes that encode approximately 22 nucleotide non-coding regulatory RNAs—to the problem of annelid phylogenetics. We show that annelids are monophyletic with respect to sipunculans, and polychaetes are paraphyletic with respect to the clitellate Lumbricus, conclusions that are consistent with the fossil record. Further, sipunculans resolve as the sister group of the annelids, rooting the annelid tree, and revealing the polarity of the morphological change within this diverse lineage of animals.     

Nuptial gifts fail to resolve a sexual conflict in an insect

Background  

Because of the potential benefits to individuals of saving investment for future mating opportunities, there is conflict between mates over most aspects of reproduction. Males of many species transfer compounds in the ejaculate that manipulate female reproductive physiology to increase male reproductive success. These seminal compounds are often associated with direct and/or indirect costs to females. In contrast, in some species ejaculates also contain nutrients used by females for somatic maintenance and increased reproductive output. In general, the extent to which male seminal components are detrimental or beneficial to females is poorly understood, and interactions between seminal compounds with different effects have been almost completely neglected. Here we examine the impact of male receptivity-suppressing factors and nutrient donations on female longevity and lifetime reproductive output in the bushcricket Requena verticalis.     

Managing conflict between humans and wildlife: trends in licensed operations to resolve problems with badgers Meles meles in England

• 1 Successful wildlife management needs to be underpinned by frequent evaluation of the problems arising and the management techniques used to resolve them. The aims of this review were: (i) to investigate spatial and temporal patterns in the occurrence and characteristics of badger–human conflict in England; and (ii) to determine which factors influence the success of management actions. Licences are required before interfering with badgers or setts, so we carried out analyses of records of applications received by Defra and data from follow‐up monitoring of management actions.
• 2 The number of licence applications rose significantly during the recording period (1994–2004), with an increasing proportion coming from the east of England and from urban, as opposed to rural, areas. Damage problems caused by setts were the most frequent sources of conflict in both urban and rural areas. However, the majority of rural problems related to agricultural land, whereas buildings and gardens were most affected in urban areas. A higher proportion of problems involved outlier setts in urban areas compared with rural areas.
• 3 The use of one‐way gates to exclude badgers from part or all of a problem sett was the commonest management action proposed by Defra Wildlife Advisers, with total sett closure more common in urban, compared with rural, areas. Follow‐up monitoring revealed that the success of action varied in relation to the type of sett causing a problem, the type of management action undertaken and the land use (urban or rural) at the problem location, with total closure of an urban main sett being the least successful strategy. This review provides an assessment of current trends in conflict occurrence and will help in the development of management techniques.

     

A kin-selection approach to the resolution of sex-ratio conflict between mates

We investigate an instance of conflict between mates over the sex ratio of their brood. We construct a kin-selection model for the evolution of the sex ratio assuming local resource competition (LRC) among females. We explore two basic scenarios: (a) the case where parents make simultaneous sex-ratio decisions (the simultaneous allocation model); and (b) the case where parental sex-ratio decisions occur one after the other (the sequential allocation model). In the simultaneous investment model, resolution of the conflict between mates depends on the extent to which relative paternal contribution influences the brood sex ratio. In the sequential allocation model, fathers determine primary sex-ratio through fertilization bias; then mothers modify the paternal sex-ratio decision by adjusting the level of investment of some resource that contributes to offspring survival. Under the sequential model, a compromise is always achieved; however this compromise favours one perspective or the other, depending on the extent to which maternal investment influences offspring survival.     

Towards a scientific concept of free will as a biological trait: spontaneous actions and decision-making in invertebrates

Until the advent of modern neuroscience, free will used to be a theological and a metaphysical concept, debated with little reference to brain function. Today, with ever increasing understanding of neurons, circuits and cognition, this concept has become outdated and any metaphysical account of free will is rightfully rejected. The consequence is not, however, that we become mindless automata responding predictably to external stimuli. On the contrary, accumulating evidence also from brains much smaller than ours points towards a general organization of brain function that incorporates flexible decision-making on the basis of complex computations negotiating internal and external processing. The adaptive value of such an organization consists of being unpredictable for competitors, prey or predators, as well as being able to explore the hidden resource deterministic automats would never find. At the same time, this organization allows all animals to respond efficiently with tried-and-tested behaviours to predictable and reliable stimuli. As has been the case so many times in the history of neuroscience, invertebrate model systems are spearheading these research efforts. This comparatively recent evidence indicates that one common ability of most if not all brains is to choose among different behavioural options even in the absence of differences in the environment and perform genuinely novel acts. Therefore, it seems a reasonable effort for any neurobiologist to join and support a rather illustrious list of scholars who are trying to wrestle the term 'free will' from its metaphysical ancestry. The goal is to arrive at a scientific concept of free will, starting from these recently discovered processes with a strong emphasis on the neurobiological mechanisms underlying them.     

Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose.     

Towards a systematic approach to the dynamic adaptation of structured parallel computations using model predictive control

Adaptiveness is an essential feature for distributed parallel applications executed on dynamic environments like Grids and Clouds. Being adaptive means that parallel components can change their configuration at run-time (by modifying their parallelism degree or switching to a different parallel variant) to face irregular workload or to react to uncontrollable changes of the execution platform. A critical problem consists in the definition of adaptation strategies able to select optimal reconfigurations (minimizing operating costs and reconfiguration overhead) and achieve the stability of control decisions (avoiding unnecessary reconfigurations). This paper presents an approach to apply Model Predictive Control (a form of optimal control studied in Control Theory) to adaptive parallel computations expressed according to the Structured Parallel Programming methodology. We show that predictive control is amenable to achieve stability and optimality by relying on the predictability of structured parallelism patterns and the possibility to express analytical cost models of their QoS metrics. The approach has been exemplified on two case-studies, providing a first assessment of its potential and feasibility.     

Towards a unifying approach to diversity measures: bridging the gap between the Shannon entropy and Rao's quadratic index

The diversity of a species assemblage has been studied extensively for many decades in relation to its possible connection with ecosystem functioning and organization. In this view most diversity measures, such as Shannon's entropy, rely upon information theory as a basis for the quantification of diversity. Also, traditional diversity measures are computed using species relative abundances and cannot account for the ecological differences between species. Rao first proposed a diversity index, termed quadratic diversity (Q) that incorporates both species relative abundances and pairwise distances between species. Quadratic diversity is traditionally defined as the expected distance between two randomly selected individuals. In this paper, we show that quadratic diversity can be interpreted as the expected conflict among the species of a given assemblage. From this unusual interpretation, it naturally follows that Rao's Q can be related to the Shannon entropy through a generalized version of the Tsallis parametric entropy.     

Some remarks on the compatibility between determinism and unpredictability

Determinism and unpredictability are compatible since deterministic flows can produce, if sensitive to initial conditions, unpredictable behaviors. Within this perspective, the notion of scenario to chaos transition offers a new form of predictability for the behavior of sensitive to initial condition systems under the variation of a control parameter. In this paper I first shed light on the genesis of this notion, based on a dynamical systems approach and on considerations of structural stability. I then suggest a link to the figure of epigenetic landscape, partially inspired by a dynamical systems perspective, and offering a theoretical framework to apprehend developmental noise.     

Minimum conflict: a divide-and-conquer approach to phylogeny estimation.

MOTIVATION: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other. RESULTS: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called "minimum conflict phylogeny estimation" (MCOPE), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small "undisputed" trees on the basis of alignments considering structural homology. AVAILABILITY: MCOPEis available via http://bibiserv.techfak.uni-bielefeld.de/mcope/. CONTACT: fuellen@alum.mit.edu     

Using clones and copper to resolve the genetic architecture of metal tolerance in a marine invader

The global spread of invasive species may be facilitated by adaptation to the practices that humans use to manage those species. For example, marine invertebrates that adapt to metal-based antifouling biocides on ship hulls may be more likely to be introduced to and establish in metal-polluted environments. We tested this idea by studying clonal variation in tolerance to, and ability to recover from, exposure to copper in a widespread invasive marine bryozoan, Watersipora subtorquata. We cloned colonies of this organism to independently test multiple environments in a genotype by environment design, and then created a genetic variance-covariance matrix. Genotypes were exposed to a gradient of copper concentrations and growth measured during exposure and after a recovery period. There was a significant genotype × environment interaction in growth during exposure and recovery. We found clonal variation in tolerance and ability to recover from exposure to copper, with growth during exposure apparently trading off against growth after exposure. A weak genetic correlation between growth during and after exposure further indicated that they are separate traits. Overall, the genetic variation within this population indicates that there is considerable potential for adaptation to copper, but this comes at a cost to growth in unpolluted environments.     

Dissociations between the behavioral effects of LSD and tolerance development during ontogeny in cats: a novel approach to the study of tolerance mechanisms

The characteristic behavioral effects of d-lysergic acid diethylamide (LSD) in cats first appeared at approximately 25 days of age and increased rapidly in magnitude over the next 10 days. However, 25 day old kittens showed no tolerance to the repeated administration of the drug. While the behavioral response to the initial dose of LSD remained relatively constant between 35 and 112 days of age, the tolerance gradually became more pronounced throughout this time period, reaching an adult level of virtually complete tolerance at 112 days. These findings provide new insight into the nature of the relationship between the primary drug action and the development of tolerance, and suggest a new strategy for investigating the neural bases of tolerance, i.e., examining the neurochemical effects of repeated LSD administration in kittens during various stages of tolerance development.     

Plant powder teabags: a novel and practical approach to resolve culturability and diversity of rhizobacteria

We have developed teabags packed with dehydrated plant powders, without any supplements, for preparation of plant infusions necessary to develop media for culturing rhizobacteria. These bacteria are efficiently cultivated on such plant teabag culture media, with better progressive in situ recoverability compared to standard chemically synthetic culture media. Combining various plant‐based culture media and incubation conditions enabled us to resolve unique denaturing gradient gel electrophoresis (DGGE) bands that were not resolved by tested standard culture media. Based on polymerase chain reaction PCR‐DGGE of 16S rDNA fingerprints and sequencing, the plant teabag culture media supported higher diversity and significant increases in the richness of endo‐rhizobacteria, namely Gammaproteobacteria (Enterobacteriaceae) and predominantly Alphaproteobacteria (Rhizobiaceae). This culminated in greater retrieval of the rhizobacteria taxa associated with the plant roots. We conclude that the plant teabag culture medium by itself, without any nutritional supplements, is sufficient and efficient for recovering and mirroring the complex and diverse communities of rhizobacteria. Our message to fellow microbial ecologists is: simply dehydrate your plant canopy, teabag it and soak it to prepare your culture media, with no need for any additional supplementary nutrients.     

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

Background  

The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space.