‘Genomemark’: Detecting Word Periodicity in Biological Sequences

Abstract

Identifying and predicting the structural characteristics of novel repeats throughout the genome can lend insight into biological function. Specific repeats are believed to have biological significance as a function of their distribution patterns. We have developed ‘GenomeMark,’ a computer program that detects and statistically analyzes candidate repeats. Specifically, ‘GenomeMark’ identifies the periodic distribution of unique words, calculating their χ² and Z-score values. Using ‘GenomeMark,’ we identified novel sequence words present in tandem throughout genomes. We found that these sequences have remarkable spacer sequence distributions and many were genome specific, validating the genome signature theory. Further analysis confirmed that many of these sequences have a specific biological function. The program is available from the authors upon request and is freely available for non-commercial and academic entities.     

Towards the prediction of protein interaction partners using physical docking

Deciphering the whole network of protein interactions for a given proteome (‘interactome’) is the goal of many experimental and computational efforts in Systems Biology. Separately the prediction of the structure of protein complexes by docking methods is a well‐established scientific area. To date, docking programs have not been used to predict interaction partners. We provide a proof of principle for such an approach. Using a set of protein complexes representing known interactors in their unbound form, we show that a standard docking program can distinguish the true interactors from a background of 922 non‐redundant potential interactors. We additionally show that true interactions can be distinguished from non‐likely interacting proteins within the same structural family. Our approach may be put in the context of the proposed ‘funnel‐energy model’; the docking algorithm may not find the native complex, but it distinguishes binding partners because of the higher probability of favourable models compared with a collection of non‐binders. The potential exists to develop this proof of principle into new approaches for predicting interaction partners and reconstructing biological networks.     

Reappraising the early evidence of durophagy and drilling predation in the fossil record: implications for escalation and the Cambrian Explosion

The Cambrian Explosion is arguably the most extreme example of a biological radiation preserved in the fossil record, and studies of Cambrian Lagerstätten have facilitated the exploration of many facets of this key evolutionary event. As predation was a major ecological driver behind the Explosion – particularly the radiation of biomineralising metazoans – the evidence for shell crushing (durophagy), drilling and puncturing predation in the Cambrian (and possibly the Ediacaran) is considered. Examples of durophagous predation on biomineralised taxa other than trilobites are apparently rare, reflecting predator preference, taphonomic and sampling biases, or simply lack of documentation. The oldest known example of durophagy is shell damage on the problematic taxon Mobergella holsti from the early Cambrian (possibly Terreneuvian) of Sweden. Using functional morphology to identify (or perhaps misidentify) durophagous predators is discussed, with emphasis on the toolkit used by Cambrian arthropods, specifically the radiodontan oral cone and the frontal and gnathobasic appendages of various taxa. Records of drill holes and possible puncture holes in Cambrian shells are mostly on brachiopods, but the lack of prey diversity may represent either a true biological signal or a result of various biases. The oldest drilled Cambrian shells occur in a variety of Terreneuvian‐aged taxa, but specimens of the ubiquitous Ediacaran shelly fossil Cloudina also show putative drilling traces. Knowledge on Cambrian shell drillers is sorely lacking and there is little evidence or consensus concerning the taxonomic groups that made the holes, which often leads to the suggestion of an unknown ‘soft bodied driller’. Useful methodologies for deciphering the identities and capabilities of shell drillers are outlined. Evidence for puncture holes in Cambrian shelly taxa is rare. Such holes are more jagged than drill holes and possibly made by a Cambrian ‘puncher’. The Cambrian arthropod Yohoia may have used its frontal appendages in a jack‐knifing manner, similar to Recent stomatopod crustaceans, to strike and puncture shells rapidly. Finally, Cambrian durophagous and shell‐drilling predation is considered in the context of escalation – an evolutionary process that, amongst other scenarios, involves predators (and other ‘enemies’) as the predominant agents of natural selection. The rapid increase in diversity and abundance of biomineralised shells during the early Cambrian is often attributed to escalation: enemies placed selective pressure on prey, forcing phenotypic responses in prey and, by extension, in predator groups over time. Unfortunately, few case studies illustrate long‐term patterns in shelly fossil morphologies that may reflect the influence of predation throughout the Cambrian. More studies on phenotypic change in hard‐shelled lineages are needed to convincingly illustrate escalation and the responses of prey during the Cambrian.     

Images as tools. On visual epistemic practices in the biological sciences

Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is ‘depicting’. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of ‘operational images’ and ‘operational agency’. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center (DKFZ) at Bioquant, Heidelberg, in 2011.     

The role of asymmetries in animal contests

This paper contains a game theoretical analysis of animal contest situations which are asymmetric in more than one aspect: two opponents may for example be imagined which differ in ‘ownership status’ as well as in ‘relative fighting ability’. The following question is analysed: which aspect may or must be used for conventional settlement in a population ‘playing’ an evolutionarily stable strategy (ESS)? The contestants are assumed to be fully informed about the asymmetric features. In particular, the assessment of relative fighting ability is supposed to be unambiguous and without cost. This assumption of perfect information allows for a decomposition of the ‘evolutionary game’ into sub-games. Therefore an easy procedure for calculating the ESS's can be presented, and simple models are analysed. It is concluded that payoff-irrelevant aspects may be used for conventional settlement of a conflict even if payoff-relevant asymmetric aspects also exist. One of the aspects may, however, be of such strong relevance that, no matter which ESS is played, animals must base their decisions on that ‘dominant’ aspect. It may also occur that two different asymmetric features are each of strong payoff relevance for either of the opponents, such that they have no escalation-suppressing effect. The particular scenario of a conflict between an ‘owner of a resource’ and an ‘intruder’ is used to derive the more general conclusions.     

Comparison of Alimentary Systems in Shelled and Non-shelled Sacoglossa (Mollusca,Opisthobranchia)

The Sacoglossa (= Ascoglossa) comprise a ‘complete’ evolutionary series from species with a large shell into which the animal can withdraw completely, through species with a reduced shell covering only the visceral mass, to shell-less (‘nudibranchiate’) forms some of which have lateral wing-like extensions, parapodia, others bearing leaf-like or cylindrical dorsal appendages, cerata. The Sacoglossa are all specialized suctorial feeders, and almost all are stenophagous herbivores. Hence many anatomical adaptations to a particular food occur in the alimentary system. However, a number of characters seem to reflect phylogenetic relationships as well. Among these are presence/absence, shape, and position of pharyngeal pouches, basic shape of radular teeth, branching pattern of digestive gland, and position of anus. The classificatory significance of these characters is discussed.     

Deficiencies in numerical models of anisotropic nonlinearly elastic materials

Incompressible nonlinearly hyperelastic materials are rarely simulated in finite element numerical experiments as being perfectly incompressible because of the numerical difficulties associated with globally satisfying this constraint. Most commercial finite element packages therefore assume that the material is slightly compressible. It is then further assumed that the corresponding strain-energy function can be decomposed additively into volumetric and deviatoric parts. We show that this decomposition is not physically realistic, especially for anisotropic materials, which are of particular interest for simulating the mechanical response of biological soft tissue. The most striking illustration of the shortcoming is that with this decomposition, an anisotropic cube under hydrostatic tension deforms into another cube instead of a hexahedron with non-parallel faces. Furthermore, commercial numerical codes require the specification of a ‘compressibility parameter’ (or ‘penalty factor’), which arises naturally from the flawed additive decomposition of the strain-energy function. This parameter is often linked to a ‘bulk modulus’, although this notion makes no sense for anisotropic solids; we show that it is essentially an arbitrary parameter and that infinitesimal changes to it result in significant changes in the predicted stress response. This is illustrated with numerical simulations for biaxial tension experiments of arteries, where the magnitude of the stress response is found to change by several orders of magnitude when infinitesimal changes in ‘Poisson’s ratio’ close to the perfect incompressibility limit of 1/2 are made.     

Historical Burden In Systematics And The Interrelationships Of 'Parareptiles'

The interrelationships within the clade comprised of turtles, pareiasaurs, and procolophonid-like taxa are investigated via a cladistic analysis incorporating 56 characters. A single most parsimonious tree was found (80 steps, c. i. = 0·8) in which the successive outgroups to turtles are: pareiasaurs, Sclerosaurus, lanthanosuchids, procolophonoids (=Owenetta, Barasaurus and procolophonids), and nyctiphruretians (= nycteroleterids). Thus, as suggested recently by other workers (Reisz, in Fischman, 1993) turtles are the highly modified survivors of a radiation of poorly-known reptiles commonly called ‘parareptiles’. Pareiasaurs are united with turtles on the basis of twenty unambiguous derived features which are absent in other basal amniotes (=‘primitive reptiles’) and reptiliomorph amphibians: for example, the medially located choana, enlarged foramina palatinum posterius, blunt cultriform process, fully ossified medial wall of the prootic, opisthotic-squamosal suture, lateral flange of exoccipital, loss of ventral cranial fissure, thickened braincase floor, ‘pleurosphenoid’ ossification, reduced presacral count, acromion process, trochanter major, reduced fifth pedal digit, and presence of transverse processes on most caudals. Recent phylogenetic proposals linking turtles with captorhinids, with dicynodonts, and with procolophonoids are evaluated. None of the proposed traits supporting the first two hypotheses is compelling. The procolophonoid hypotheses is supported by only one synapomorphy (the slender stapes). All other synapomorphies proposed in favour of the above groupings either occur in many other primitive amniotes, or are not primitive for turtles, or are not primitive for the proposed chelonian sister-group. Nyctiphruretus and Lanthanosuchids and nycteroleterids, often considered to be seymouriamorph amphibians, are demonstrated unequivocally to be amniotes. The ‘rhipaeosaurs’, currently considered to be pareiasaur relatives, are shown to be a heterogenous assemblage of seymouriamorphs, therapsids and nycteroleterids. The phylogeny proposed here indicates that many of the traits of the earliest known turtle, Proganochelys, previously interpreted as unique specialisations, also occur in pareiasaurs and other near outgroups of turtles, and must instead represent the primitive chelonian condition: for example, the wide parietals and the short quadrate flange of the pterygoid. The sequence of acquisition of chelonian traits is discussed: many features once thought to be diagnostic of turtles actually characterize larger groupings of procolophonomorphs, and must have evolved long before the chelonian shell appeared. These traits include most of the chelonian-pareiasaur synapomorphies listed above, and many others which characterize more inclusive groupings found in this analysis. In putting Proganochelys much closer to the main line of chelonian evolution, in elucidating the sequence of acquisition of chelonian traits, and in reducing greatly the number of differences between turtles and their nearest relatives, this study helps bridge one of the major gaps in the fossil record. The failure of previous cladistic analyses to identify correctly the nearest relatives of turtles is attributed to biased character selection, caused by an over-reliance on cranial characters deemed ‘important’ by earlier workers, and by a tendency to shoehorn ‘parareptile’ taxa into phylogenies derived from analyses restricted to ‘mainstream’ groups such as synapsids, diapsids, turtles, and ‘captorhinomorphs’. Many of the synapomorphies that resolve turtle origins are postcranial, and the three nearest outgroups to turtles are all highly bizarre groups which were dismissed as ‘too specialized’ by early workers and continued to be inadequately assessed even by workers using a cladistic framework.     

The ‘n’ effect in molecular recognition

The cooperativity which exists in crystal melting and many biological molecular recognition phenomena arises from extended arrays of weak interactions. We present a correlation between the melting temperature of a crystal and the intermolecular energy (which is evident only when compounds possessing several or many internal rotors are excluded). The correlation is used as the basis for a model of crystal melting which is capable of estimating the melting temperature of crystals. This model provides the basis for an understanding of the sharpness of the crystal melting transition for organic and inorganic substances. The cooperativity illustrated by the extended arrays of weak interactions, or the ‘n’ effect, is extended to analogous order/disorder transitions in biological systems, such as the ‘melting’ of DNA and RNA duplexes, providing insights into the physical properties of these structures.     

A neutral terminology to define 'invasive' species

The use of simple terms to articulate ecological concepts can confuse ideological debates and undermine management efforts. This problem is particularly acute in studies of nonindigenous species, which alternatively have been called ‘exotic’, ‘introduced’, ‘invasive’ and ‘naturalised’, among others. Attempts to redefine commonly used terminology have proven difficult because authors are often partial to particular definitions. In an attempt to form a consensus on invasion terminology, we synthesize an invasional framework based on current models that break the invasion process into a series of consecutive, obligatory stages. Unlike previous efforts, we propose a neutral terminology based on this framework. This ‘stage‐based’ terminology can be used to supplement terms with ambiguous meanings (e.g. invasive, introduced, naturalized, weedy, etc.), and thereby improve clarity of future studies. This approach is based on the concept of ‘propagule pressure’ and has the additional benefit of identifying factors affecting the success of species at each stage. Under this framework, invasions can be more objectively understood as biogeographical, rather than taxonomic, phenomena; and author preferences in the use of existing terminology can be addressed. An example of this recommended protocol might be: ‘We examined distribution data to contrast the characteristics of invasive species (stages IVa and V) and noninvasive species (stages III and IVb)’.     

Advanced-level Biology—A Possible Approach

Teachers' conscious priorities in selecting topics for teaching rarely include the ‘biology/social science interfaces’; neither are many usually aware of the existence and implications of ‘hidden ideologies’ in the curriculum. This paper gives several examples of such interfaces, and stresses the point that only by redirecting the education of teachers can their awareness and priorities be suitably altered.     

Addressing teachers' concerns about teaching evolution

Evolution was introduced into the senior secondary school Life Sciences curriculum in South Africa for the first time in 2008. Research in other countries shows that evolution is an extremely controversial topic to teach, raising serious concerns for teachers. Curriculum change theory dealing with ‘stages of concern’ suggests that teachers implementing a new curriculum move through a predictable series of types of concerns, and that if their initial concerns are not addressed then teachers are slow to move on to more important task-related matters. This has serious implications for both professional development programmes and the development of support materials for teachers: information about teachers' concerns is needed so that those having to support teachers can do so on an informed basis. This article identifies the concerns of 125 secondary school teachers having to teach evolution for the first time. Data was gathered using an activity-based questionnaire administered in a workshop setting to four different groups of biology teachers attending inservice workshops on the teaching of evolution, at stages progressively closer to the implementation date. The majority of concerns identified were early-stage ‘self-concerns’, dealing with personal worries and a need for information. Implications of the findings for providing support for teachers with concerns about teaching evolution are discussed.     

The National Centre for School Biotechnology

Giving land an ecological value is a problem in many student projects. This paper suggests a method which is suitable for a range of abilities

Any methods used by students for evaluating the ecological or conservation value of an area under study need to be relatively simple, as it is unlikely that they will have a specialist knowledge of ecology. The most frequently used criteria in site evaluation are difficult to apply at secondary education level, and a method has been developed which relies only on recognition of major habitat types and landscape features. The example used is a comparison of two possible sites for location of a sewage treatment works, and a ‘total ecological score’ is obtained for each site. This can then be used to calculate possible ‘units of ecological damage’ in the event of a development on the land. Damage can also be categorized as reversible or irreversible to allow for reinstatement and mitigation work. Students can then incorporate these estimates as part of a wider impact analysis and decision-making process and the methods can be applied to any development.     

Teaching evolution using a card game: negative frequency-dependent selection

Teaching biological evolution can be difficult on a number of levels, be it student confusion arising from prior conceptions and the controversy surrounding evolution, or simply because the material is complex. Games and simulations can help to convey complex topics and also to increase variety in teaching methods. Here I describe a card game that can be used to teach the advanced topic of protected polymorphism in higher education settings. Protected polymorphism is allelic variation resulting from negative frequency-dependent selection; when the fitness of an allele increases when it becomes rare, the allele will be ‘protected’ from extinction. Negative frequency-dependent selection is proposed to maintain genetic variation in nature, which is required for evolution by natural selection. Protected polymorphisms primarily play a role in biological interactions, such as immune systems, plant-pathogen interactions, sexual selection and predator-prey interactions. The card game described here uses plant pollination alleles as an example. The game is played using eleven stocks of traditional playing cards per group of about six students. Specific topics addressed include negative frequency-dependent selection, polyploidy, dominance, selfing and inbreeding depression.     

Is the “Histone Code” an Organic Code?

Post-translational histone modifications and their biological effects have been described as a ‘histone code’. Independently, Barbieri used the term ‘organic code’ to describe biological codes in addition to the genetic code. He also provided the defining criteria for an organic code, but to date the histone code has not been tested against these criteria. This paper therefore investigates whether the histone code is a bona fide organic code. After introducing the use of the term ‘code’ in biology, the criteria a putative organic code such as the histone code must conform to in order to be recognised as an organic code are described. Our current knowledge of histones and their major post-translational modifications, and the specific protein binding domains that recognise and translate these into specific biological effects, is then reviewed in detail. The histone modification system is then placed in the context of an organic code and it is concluded that it fulfils all the requirements of an organic code. The marks produced on histones by processes such as acetylation and methylation act as organic signs that are translated into unique biological effects, their biological meanings. These translations are accomplished by effector proteins that consist of a binding domain that recognises a specific histone mark and a regulatory domain that mediates the biological effect. Crucially, these domains can be experimentally interchanged between different effector proteins, thus altering the rules that specify the relationships between sign and meaning. The effector proteins therefore fulfil the role of adaptor molecules.     

Structure and in vitro cytocompatibility of the gastropod shell of Helix pomatia

Distinguishing features of biological constructions are high stability and adaptation to their environment. Beside biocompatibility, nontoxicity and degradability these characteristics are demanded for new biomaterials in the field of tissue engineering. This study investigated the chemical composition, the organization and the in vitro osteoconductive potential of the terrestrial gastropod shell (Helix pomatia) on CAL72 and human osteoblast-like cells. Chemical composition of the biomaterial was examined by X-ray diffraction (XRD) and scanning electron microscopy (SEM) was performed to analyze the architecture of the snail shell and the morphology of the seeded cells. A double staining procedure (FDA/PI) and a proliferation test (EZ4U) assessed the viability of the cells. Microscopical images showed the multilayered architecture of the aragonite shell with hexagonal crystals on the inner side. The cells spread well on the biomaterial and the highest proliferation rate could be measured with CAL72 cells on the inner shell surface. The osteoconductive effects of this natural biomaterial could encourage further experiments in the field of tissue engineering.