bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA
Structure: Pseudoknots
Authors: Gultyaev Alexander P , Olsthoorn René CL , Pleij Cornelis WA , Westhof Eric
Published: April 2013

An RNA pseudoknot results from Watson–Crick base pairing of a single‐stranded segment, located between two regions, paired to each other, with a sequence that is not located between these paired regions. This leads to a structure with at least two helical stems and two loops crossing the grooves of the helices. Pseudoknots are further stabilised by coaxial stacking between stems and the formation of triple
ribonucleic acid
(RNA) interactions between stems and loops. RNA pseudoknots adopt different folding topologies and are an essential part of various functional RNA molecules, including ribosomal RNAs, ribozymes and riboswitches. In this review, the thermodynamics and main structural features of pseudoknots, important for their function, are discussed: amongst others, viral tRNA‐like structures, ribosomal frameshifter pseudoknots and pseudoknots formed by S‐adenosylmethionine and pre‐queuosine riboswitches upon binding of their respective ligands.

Key Concepts:

The simplest RNA pseudoknot is formed by base‐pairing of nucleotides within a hairpin loop to a complementary sequence outside the hairpin (H‐pseudoknot).

Classical H‐pseudoknots consist of two coaxially stacked helical stems and two loops that cross one deep groove of one helix and the shallow groove of the other helical stem.

Pseudoknots are usually stabilised by coaxial stacking between stems and triple base pairs formed between the bases of the stems and loops.

Many complex pseudoknots may be interpreted as classical pseudoknots containing additional structural elements inserted in the pseudoknot loops.

Pseudoknots are folded in various types of RNA molecules and have diverse functions.

Limited information is available on thermodynamic stability of pseudoknots.

Computer‐assisted prediction of pseudoknots is partially hampered by a lack of knowledge about the thermodynamics of pseudoknot folding.
Experimental Systems in Aquatic Ecology
Authors: Sommer Ulrich
Published: April 2013

The main experimental approaches in aquatic community and ecosystem ecology will be presented along a gradient of scale: unenclosed field experiments, mesocosms with a natural mix of species, microcosms with an artificial mixture of species from cultures, and single species experiments in batch and continuous culture. Experimental manipulations usually consist of the addition or removal of (supposed) key organisms, addition of chemicals or alterations of the physical environment. Selecting the appropriate scale of experimentation is not only a question of technical and financial feasibility but also it has to consider the inevitable trade‐offs between realism and control. Conclusions will be more widely accepted, if they are supported by experiments at a variety of scales.

Key Concepts:

The choice of the appropriate experimental scale has to face an inevitable trade‐off between realism and control.

Unenclosed field manipulations have the highest degree of realism but the least degree of control.

Mesocosms operate with natural species assemblages, permit replication and control of experimental manipulations but are limited in temporal scale (weeks).

Microcosm experiments operate with artificial communities assembled from cultures, offer a high degree of control, but lack the pre‐history a mutual adaptation of the participating species.

Experiments with single or few species rely on the ‘model organism’ concept.

Small‐scale experiments are biased against the detection of slow and space requiring processes.
Primary Succession
Authors: Walker Lawrence R , del Moral Roger
Published: April 2013

Primary succession is the assembly of ecosystems on barren landscapes following severe disturbances that leave little or no biological legacy (lava flows, landslides and mine wastes). The assembly process involves colonisation of newly exposed substrates and subsequent interactions among the colonising plants, animals and soil microbes. Successional trajectories of sequential community replacement then develop, but some may diverge from nearby trajectories, making succession a challenging process to predict. Understanding how plant, animal and microbial communities develop under such extreme conditions is essential for restoration of damaged lands, as restoration is fundamentally the manipulation of successional trajectories by humans. Successional studies also provide insights into loss of biodiversity, climate change and the influences of invasive species on community dynamics.

Key Concepts:

Primary succession is the process of assembly of ecosystems on barren landscapes following severe disturbances that leave little biological legacy.

Primary succession is difficult to predict because it is the net result of many interacting processes including dispersal, colonisation, species interactions and biotic responses to on‐going disturbances.

Restoration is the attempt to manipulate succession and what is known about primary succession can be applied to the amelioration of severely disturbed habitats.

Primary succession provides insights into biodiversity loss, climate change and the influences of invasive species.
Secondary Succession
Authors: Shugart Herman H
Published: April 2013

Secondary succession refers to the sequential changes in vegetation that occur after a disturbance such as wildfires, hurricanes or human alterations. The rate of change in secondary succession is faster than in primary successions. The studies at different scales on the phenomena studied to understand succession has produced contrasting theories on the succession process. Arguments as to whether succession features competition among plants or some sort of positive process where the presence of one species reinforces the subsequent occurrence of another species at the site have produced considerable argument among ecologists. Ecological models that reproduce successional patterns provide insight into this issue as well as in the nature of successional outcomes. Restoration ecology represents a significant application of succession theory.

Key Concepts:

Secondary successions are the changes in vegetation that occur after agricultural abandonment or the disturbance of an existing ecosystem. They can be contrasted with primary successions that occur on new substrates.

The concept of succession has a long history in ecology and is a central concept in understanding the dynamics of ecosystems.

There have been and continue to be considerable debate about the nature of succession. The time and space scales considered in ecological succession studies have a pronounced effect on the processes and resultant patterns identified in the studies.

The concept of secondary succession and how it functions is essential a systems theory application in ecology.

Models of ecological succession have developed to investigate the roles of individual species and even of individual plants on determining the patterns of successional change.

Complex nonlinear responses in ecosystems components and the environment can produce complex successions with multiple stable states and multiple paths.

Secondary succession has significant application in the restoration of altered ecosystems.
Soils and Decomposition
Authors: McClaugherty Charles , Berg Björn
Published: April 2013

Soils are dynamic, complex systems of inorganic, organic and biotic components that have the capacity to support plant life. Soils are classified on the basis of their chemical and physical properties. These properties include texture, structure, colour and the nature and properties of soil horizons. Soils are an important component of natural capital, providing for food and fibre production and physical support of cultural infrastructure, but soils are degrading. Soils are the major site for plant nutrient regeneration through the process of decomposition. Decomposition processes also generate long‐term soil organic matter and play an important role in the global carbon cycle. Decomposition of organic matter in soils is accomplished largely by microorganisms, often in association with animals. The rate and course of decomposition is influenced by climate, organic matter composition and nutrient availability from the environment.

Key Concepts:

Soils are dynamic systems composed of organic, inorganic and living components.

Soils are classified according to measurable and observable properties, but there are many different classification schemes around the world.

Key physical characteristics of soils are texture, bulk density and porosity all of which influence nutrient and water dynamics in the soil.

Key chemical properties of soils include acidity (pH), cation exchange capacity (CEC), base saturation, organic matter content and nutrient availability.

Soils are a slowly renewable natural resource that is being degraded worldwide due to erosion, desertification, salinisation and overuse.

Decomposition of organic matter is regulated by climate and the nature and chemical composition of the organic matter.

Soil organisms, particularly microorganisms (fungi and bacteria) and animals, play a major role in the decomposition process.

Decomposition is important in regulating soil nutrient availability to plants.

Soils are an important reservoir for carbon in the global carbon cycle and sequester significant amounts of atmospheric carbon dioxide.
Ecology of Storage and Allocation of Resources: Animals
Authors: Pond Caroline M
Published: April 2013

Most organisms store lipids and/or carbohydrates for energy production during fasting. Lipids store much more energy per unit mass. Long‐chain fatty acids are absorbed and stored almost unaltered, so serve as indicators of natural diets and food chains. Vertebrates and higher arthropods have tissues specialised for lipid storage and management. Adipocytes are 40–85% triacylglycerols and occur in various intra‐abdominal and superficial sites in all tetrapods and some fish. Some mammalian adipose depots have site‐specific properties specialised to local, paracrine interactions with adjacent cells and tissues. In mammals, adipocyte volume is determined by anatomical location, body size and natural diet as well as fatness. The anatomical patterns of relative sizes of adipocytes are similar in all terrestrial mammals but species differ in the relative abundance of adipocytes in each depot. The chemical compositions of storage molecules are adapted to the ecological processes they serve, including migration, hibernation, lactation or unpredictable food supply. Storage of energy and other materials is essential to many aspects of animals' ecology. Adipose tissue can reach 50% body mass before migration or breeding fasts with superficial depots expanding most, especially in large vertebrates.

Key Concepts:

Storage is essential unless nutrients are continuously available.

Storage materials must minimise weight, volume and toxicity; some vitamins and minerals are too toxic to be stored in more than small quantities.

In animals, glycogen and acylglycerols can be safely stored in large quantities and metabolised to produce energy and/or tissues.

Much more energy can be stored as lipid than as glycogen, though the latter is more quickly mobilised.

The chemical composition of storage lipids is adapted to body temperature and the ecological processes that they support. Triacylglycerols of cold‐adapted poikilotherms and hibernating mammals have more unsaturated fatty acids than those of homeotherms.

Some migratory birds maximises energy density and efficient mobilisation of the storage lipids during prolonged flight by adaptive desaturation.

Specialised lipid storage tissues include the arthropod fat body and vertebrate adipose tissue that sequesters large quantities of triacylglycerols.

Vertebrate adipocytes are nearly spherical cells, 0.01–4 nL in volume, specialised to take up, hold and release storage lipids and to the regulation of appetite and metabolism.

In mammals, the mean volume of adipocytes is determined by anatomical location, body size and natural diet as well as by fatness.

Some mammalian adipocytes have site‐specific properties specialised to paracrine interactions.
Biomechanical Studies of Food and Diet Selection
Authors: Herrel Anthony , Van Wassenbergh Sam , Aerts Peter
Published: April 2013

The ways animals acquire food are largely determined by the medium in which they feed. As water is dense and viscous, resistive forces are important and affect the way prey can be captured resulting in the independent evolution of suction feeding in many vertebrate groups. Alternatively, on land, gravitational forces play an important role and will affect prey capture and transport by imposing limits on the use of adhesive forces and thus tongue‐based capture and transport. Biomechanical approaches involving the analysis of movements and forces can, combined with theoretical models, help explain the selective pressures operating on the feeding system. As such, these approaches may help explain the divergence of the feeding system in animals occupying different ecological niches and may help us understand the proximate factors driving adaptive radiations.

Key Concepts:

The density of the medium animals live in determines their prey capture strategy.

Prey capture using suction has evolved independently in many vertebrate groups.

Tongues work only on land.

Trade‐offs are inherent to mechanical systems.

Biomechanical models are limited by the quality of the input data used.

Tooth morphology and wear are powerful indicators of feeding ecology.

Functional approaches can help explain ecomorphological patterns.

The feeding system and prey mechanical defences co‐evolve.
Behavioural Ecology
Authors: Hager Reinmar , Gini Beatrice
Published: April 2013

Behavioural ecology investigates how animal behaviour is adapted to the physical and social environment of individuals. Over the past 40 years behavioural ecology has been established as a field of research in which both empirical and theoretical studies analyse how evolution has shaped animal behaviour through the process of natural selection. The underlying premise is that individuals adopt strategies (behaviours) that maximise their fitness, that is, the contribution of their genes to future populations. Behavioural ecology seeks to understand why a specific behaviour confers a fitness advantage to an individual given a set of ecological and social conditions. The adoption of methods from genetics, physiology, bioinformatics and developmental biology has greatly expanded the tool kit with which questions in behavioural ecology are addressed.

Key Concepts:

Behavioural ecology is the study of how animal behaviour is adapted to the physical and social environment through natural selection.

Key concepts in behavioural ecology are the comparative approach, game theory, the optimality approach.

Animals are assumed to tradeoff between costs and benefits of different behaviours, for example between maximising food intake or reproduction at a given time.

Competitive interactions often evolve into evolutionary stable strategies, situations where frequency‐dependent dynamics are in equilibrium.

Conflicts exist between species, between members of a species and between genetic elements within individuals; these often result in arms races where exploitation and defences evolve progressively in response to each other.

New molecular, genetic and bioinformatic tools are opening up new questions in behavioural ecology, for example in phenotypic plasticity and epigenetics.
Biogeographical Regions
Authors: Huggett Richard
Published: April 2013

Species are not uniformly distributed over the globe. The largest regions of animal and plant assemblages are biogeographical regions, each bearing a distinctive fauna and flora. Some families and even some orders of animals are endemic to particular biogeographical regions; other families are shared by two or more regions; a few families are cosmopolitan and found in all regions. The delineation of traditional biogeographical regions was rather subjective. Recently, increased availability of global species range maps, the development of new multivariate techniques and improved computational power have led to quantitative regionalisations that are broadly similar to traditional regions but do show differences. The transition zones between are sometimes gradual, as in the junction between the Oriental and Australian faunal regions. The state of biogeographical regions is under threat from such human activities as habitat destruction and fragmentation and the introduction of alien species, and it will decline without conservation measures.

Key Concepts:

Regions (in biogeography) are spatial units of varying scales carrying comparatively distinct sets of animals and plants.

Faunal and floral elements are groups of species sharing a similar pattern of geographical distribution.

Biogeographical provincialism is the tendency of different geographical regions to house unique species, genera or families.

Endemism is the state of being unique to a specific geographical region, such as a continental landmass, a biogeographical region or a habitat.

Transition zones (in biogeography) are regions where one biogeographical region grades into another, and contrasts with sharp borders.

The Great American Interchange was the intermingling of South American and North American faunas starting 6 million years ago when a string of islands and then a permanent land connection bridged the ocean gap between North American and South American landmasses.

Habitat loss and fragmentation is one of the chief drivers of biodiversity loss and change in biogeographical regions.

Alien species (also called exotic, introduced and nonnative species) are species accidentally or purposefully carried to areas outside their natural range by humans.
Environmental Impact Assessment
Authors: Noble Bram F
Published: April 2013

Environmental impact assessment (EIA) is a systematic process designed to identify and predict the potential impacts of human activity on the biophysical and human environment. It also functions as an environmental management tool to identify measures to avoid, mitigate or compensate for those effects. EIA is intended to be an iterative process to follow‐up to projects postimplementation to determine actual environmental outcomes, interpret and communicate information about those outcomes and investigate opportunities for improved project environmental performance. Originating from the United States’ National Environmental Policy Act of 1970, EIA is now amongst the most successful and widely practiced environmental management tools in the world.

Key Concepts:

EIA is an aid to decision making through which concerns about the potential environmental consequences of proposed projects are assessed before those projects become a reality.

Screening in EIA ensures that assessments are done when needed and not done when not needed.

Scope is essential to good EIA and the goal is to focus on a select set of environmental components that are deemed important from scientific, public or regulatory perspectives and are likely to be adversely affected by the project.

The underlying intent of EIA is to allow project proponents, managers and decision makers to enhance the benefits of proposed development projects and to mitigate potentially adverse impacts to the point of acceptability.

EIA must be applied early in the development planning processes if it is to be influential in project design and decision making.

Information gained in EIA follow‐up studies, after the project is implemented, provides feedback to improve predictions and mitigation and management programmes, and an opportunity to learn for subsequent project proposals.
Conservation Biology and Biodiversity
Authors: Pennington Derric N , Ricketts Taylor
Published: April 2013

Human population growth and the corresponding increase in human consumption rate are leading factors contributing to biodiversity degradation and loss worldwide. Conservation biology integrates diverse disciplines within the natural and social sciences, with the goal of preserving the world's biodiversity, or variety of life. This chapter defines biodiversity and different metrics of diversity, and summarises how biodiversity is distributed, emphasising important patterns both across space and taxonomic groups. Next it describes the major threats to global biodiversity. It examines how people assign values to biodiversity, with a focus on ecosystem services. Finally, it highlights future challenges of conservation biology to protect biodiversity as well as human well‐being. Making conservation more relevant to policy makers, and people in general, requires integrated research to understand the provision of ecosystem services, their relationship to biodiversity and the tradeoffs of resource use decisions.

Key Concepts:

Conservation biology is an interdisciplinary endeavour that aims to balance the natural resource uses of a growing human population while sustaining a functioning and diverse biosphere for future generations.

Biodiversity is a hierarchical concept that includes the diversity of alleles, genes, individuals, populations, species, communities and ecosystems.

Each level of biodiversity serves an important function, and human activities can affect biodiversity at any level of organisation.

Biodiversity is unevenly distributed, both across spatial and temporal gradients and across taxa.

Human population growth and the corresponding increase in human consumption rate are impacting land cover, biogeochemical cycling, water quality and availability, and other major features of the world that is contributing to biodiversity degradation and loss.

Biodiversity has both intrinsic value and utilitarian value; the latter is derived from the ecosystem services, or the essential goods and services that ecosystems provide to humanity, including food, medicine, building materials, clean water and flood control.

Quantifying ecosystem services can make conservation more relevant to policy makers and people in general, and research is needed to understand the provision of ecosystem services, their relationship to biodiversity, and the tradeoffs of resource use decisions.
Satellite Remote Sensing of the Environment
Authors: Bamber Jonathan L , Schumann Guy
Published: April 2013

Satellite remote sensing of the environment is a relatively young science, beginning in earnest in the 1970s. Since then, rapid developments in sensor technology, computer power and data storage capabilities have resulted in remarkable advances in what can be observed, at what resolution and with what accuracy. Here, we summarise the fundamental physical concepts and the types of sensor that have been used for observing the biosphere, hydrosphere, oceans and ice at the surface of the Earth.

Key Concepts:

Satellites can provide global, synoptic coverage of key parameters such as albedo, surface temperature, soil moisture, rainfall, primary productivity in the surface oceans, and vegetation cover.

There is a continuous time series of visible and infrared observations covering the last four decades. Much of these data are freely available.

Improvements in technology mean image resolution of less than a metre is achievable, greatly improving classification accuracy.

Radar remote sensing is proving particularly useful for observing the hydrological cycle due to its all‐weather day/night capability.
Human Disease: Effects of Economic Development
Authors: Butler Colin D , Powles John , McMichael Anthony J
Published: April 2013

Since palaeolithic times economic development has had mixed effects on the burden of human disease and injury. Pre‐modern agrarian populations with universal early marriage probably experienced the least favourable levels of health and survival, in many cases worse than their hunter‐gatherer ancestors. Over recent centuries, favourable effects of economic development on health have been ascendant. Child and adult survival have improved markedly in recent decades in most developing countries. However, many important health problems arising from economic development remain unsolved, including tobacco addiction, physical inactivity and obesity, to environmental contamination and disruption (including, now, systemic environmental changes such as climate change). The improvement in global food security has also stalled. Unless corrected, these interacting issues may undermine global public health.

Key Concepts:

Economic development has mixed but generally positive health effects, especially in recent centuries.

Economic development involves several transitions – agricultural, technological, industrial, demographic, nutritional, epidemiological and sustainability.

Knowledge is central to the epidemiological and demographic transitions.

These transitions are causally intertwined in complex ways.

Development can lead to transitional ‘overshoot’, for example from high to low fertility, from under to over caloric intake and from under to overconsumption of environmental resources.

Global population health is threatened by declining environmental health determinants, which risks a consequential decline in social health determinants.

Dominant measures of economic development omit negative externalities (adverse effects which impinge on public goods, other people, or future generations), thus providing excessively optimistic progress indicators.

There is an urgent need for a ‘sustainability transition’, entailing a shift to renewable energy, ecological conservation and enhanced equity.

This could be assisted by new metrics of economic growth and human well‐being.

There is a possibility that paths of economic development will continue to diverge, leading to an ‘enclave’ world with sections of the human population being ‘left behind’ whilst progress continues elsewhere.
Deforestation, Forest Management and Governance
Authors: Lisa Klenk Nicole , Mabee Warren , Gong Yazhen , Bull Gary Q
Published: April 2013

The world's forests are a major source of material and fuel, a vast reservoir of biodiversity and they also provide valuable ecological services such as hydrological cycling and carbon sequestration. They play an important role in carbon accounting schemes under the Kyoto Protocol and the UN Programme on Reducing Emissions from Deforestation and Forest Degradation (REDD). As such, the impacts of global deforestation are of critical social, ecological and political significance. The primary causes of deforestation are well understood and will likely be exacerbated as new demands for forest products develop. Innovative governance arrangements, such as third party certification schemes and co‐management, have increasingly sought a role in alleviating deforestation alongside governmental forest policy‐making. Continued decreases in deforestation rates will depend on changes in how forests are valued and managed through multi‐level governance arrangements.

Key Concepts:

Energy production account for more than 50% of all wood uses.

There is concern that woodfuel use is one of the drivers of deforestation, but it is often difficult with available statistics to understand just how important this driver is.

Deforestation is mainly caused by economic forces, governance failures and politico‐ethical failures.

Given the rapid global loss of biodiversity, mainly due to deforestation in tropical areas, primary and selectively logged forests are of critical importance in tropical forest conservation.

Forest carbon sequestration is explicitly allowed in the Kyoto Protocol as a tool to meet emission reduction targets.

Without stricter governance oversight, carbon emissions mitigation initiatives such as the UN Programme on REDD can enable the usurpation of land and resource rights from indigenous communities in developing countries.

Decreasing the rate of deforestation requires the participation not just of governments but of local communities, indigenous peoples and citizens for decision‐making and monitoring in forest policy and management.
Dinosaur Feeding
Authors: Norman David B
Published: April 2013

Many dinosaurs can be relatively easily partitioned, on the basis of their tooth morphology and skeletal form, into those that were classically sharp‐toothed, agile and fast‐moving carnivorous theropods such as
Coelophysis
,
Velociraptor
and
Tyrannosaurus
. Alternatively others had comparatively blunt teeth, were rather heavy‐legged and barrel‐bodied herbivorous sauropodomorphs, for example,
Diplodocus
, cerapods, for example,
Triceratops
and armoured thyreophorans, for example,
Sauropelta
. However, some dinosaurs, as we shall see (e.g. heterodontosaurs, therizinosaurs, alvarezsaurs and spinosaurs) exhibit anatomies that cannot be so readily categorised; these challenge our understanding of likely feeding behaviours. For these latter creatures a more comparative–deductive approach must be adopted. Detailed investigation of such ‘atypical’ types, as well as the more classic morphologies, suggests that some dinosaurs exploited morpho‐functional solutions to the problems posed by feeding that are not seen among present‐day animals.

Key Concepts:

Tooth morphology provides direct information about the potential diets of long‐extinct animals.

Skeletal morphology provides information about the mechanics and potential lifestyle of long‐extinct animals.

Morphology and lifestyle interpretations based on dinosaur skeletons contain information that is relevant to deductions concerning their probable diets.

Jaw mechanics and tooth wear patterns provide objective information about bite forces and the movement of food caught between the teeth.

Carnivores typically eat meat and have predatory habits, but such animals are not exclusively predatory because today many are also known to take carrion opportunistically.

Herbivores typically eat plant material, but some classically herbivorous reptiles (such as land iguanas) are also known to eat eggs, young mammals or chicks, as well as carrion; these considerations also apply to animals such as rodents. So such apparently clear cut human definitions are evidently not as clear in real life.

Finite Element Modelling and Beam Theory have been used to augment information about the range of feeding styles in dinosaurs.

Pleurokinesis is a cranial mechanism that allows classically reptilian herbivores (i.e. ornithopod dinosaurs) to develop a power stroke, during jaw closure, by mobilising the lateral walls of the skull. This enables oral processing (repetitive chewing) of plant material.

Co‐evolutionary relationships (between dinosaurs and plants) in the fossil record, notably with respect to the coincident timing of the evolution of angiosperms (flowering plants) and diversification of herbivorous dinosaurs, cannot be proved.
Dinosaurs and The Origin of Birds
Authors: Clark James M
Published: April 2013

The evolutionary relationships of birds have been debated ever since the discovery of a fossil bird,Archaeopteryx, in 1861, that has bird‐like feathers but reptilian teeth and a long bony tail. Recent discoveries of feathered dinosaurs have confirmed analyses of bird relationships beginning in the 1970s that placedArchaeopteryxand birds within one group of dinosaurs, the Theropoda. Recognition of this relationship and discovery of a variety of new species have allowed evolutionary biologists to study for the first time many aspects of the transition from ground‐living theropods to flying birds. Many new details about the evolution of feathers, reproductive features of birds and flight have emerged from these fossils and continue to emerge as new fossils are found. The precise relationships of birds to theropods is still debated, but the scansoriopterygids, dromaeosaurs and troodontids are amongst the closest relatives of birds.

Key Concepts:

The closest living relatives of birds are the crocodilians and together they form the group Archosauria.

The origins of birds lie with fossil archosaurs, which include dinosaurs, the flying reptiles called pterosaurs and the many fossil relatives of crocodilians.

Evolutionary relationships are studied using cladistic analysis of similarities shared amongst different species.

Cladistic analyses strongly support birds being closely related to a subgroup within the theropod dinosaurs called Coelurosauria and especially with the scansoriopterygid, dromaeosaur and troodontid coelurosaurs.

Fossil coelurosaurs with feathers from China provide convincing evidence that birds are coelurosaurs, and that during the course of evolution feathers arose before flight.
Patenting Plants and Plant Products
Authors: Ergenzinger Edward R , Williams Jeff
Published: April 2013

The United States approach to protect newly developed plant varieties has fed a booming agribusiness industry, but the United States differs from many other parts of the world in terms of its views on patenting plants and public attitudes regarding genetically modified foods. This article reviews the relevant forms of intellectual property protection available to plant breeders in the United States, which includes the Plant Protection Act, the Plant Variety Protection Act, and utility patents under the Patent Act. These forms of protection are compared with the standard conventions available in Europe. Two brief discussions follow. First, the role of public attitudes in acceptance of genetically modified crops is reviewed. This is followed by a brief overview of the ethical and legal context related to bioprospecting.

Key Concepts:

The United States plant breeders have three forms of intellectual property protection available for use: PVPA, PPA and utility patents.

The United States and European patent systems have been aligned to allow for more uniform international enforcement of patents.

Bioprospecting has the potential to uncover powerful new discoveries, but ownership rules must be interpreted for both equity and efficiency concerns.

The United States and European consumers generally have differing opinions of the safety of genetically engineered crops.
Molecular Farming in Plants
Authors: Hoja Ursula , Sonnewald Uwe
Published: April 2013

The commonly used term ‘molecular farming’ describes the large‐scale production of valuable proteins in transgenic plants, including antibodies, vaccines, other pharmaceuticals and industrial proteins. Compared to traditionally used systems such as microbial cultures, plants offer many advantages with respect to economy, quality and safety. Especially attractive is the possibility to power protein production using natural sunlight and atmospheric carbon dioxide. Furthermore, transient expression systems offer the possibility to rapidly produce personalised pharmaceuticals otherwise impossible. Several production systems including algae, mosses, tissue‐ and cell cultures have been reported, enabling contained protein production. Combining these cell‐based production systems with newly developed photo‐bioreactors promises powerful solutions for cost‐efficient and safe manufacturing of valuable proteins. However, constraints concerning protein yield and public acceptance must be overcome before the plant's full potential can be exploited.

Key Concepts:

Plant‐based production of proteins can be done in a wide range of systems including different species, tissues and organelles, for each protein the best combination must be identified.

Light‐driven production of bioactive‐proteins offers an eco‐friendly and sustainable alternative to conventional production systems.

Transient expression of proteins offers the possibility to cost efficiently produce customised pharmaceutical proteins.
Regeneration of Functional Neuronal Connections After Injury in the Central and Peripheral Nervous System
Authors: Schwab Martin E , Buchli Anita D
Published: April 2013

During development both the peripheral nervous system and the central nervous system (CNS: brain and spinal cord) are very plastic and can adapt well to nerve fibre damage. In the mature organism, however, major differences exist in the molecular processes of nerve fibre regeneration in peripheral nerves and the CNS of higher animals and humans. Thus, spontaneous nerve fibre regeneration and functional recovery can occur only in the peripheral nervous system. In the adult CNS, specific molecules that suppress growth and block regeneration have been found. Some of the mechanisms blocking fibre regeneration can be experimentally influenced in animal models. They lead to nerve fibre regeneration and, importantly, to improved recovery after spinal cord injury or stroke. Several approaches are currently in the preclinical stage and some of them are being tested in human PhaseI/II clinical trials.

Key Concepts:

During development regeneration and functional recovery of the injured PNS and CNS take place.

Within the critical period of early postnatal life neuronal circuits are shaped by experience; the critical period is a time window with enhanced brain plasticity.

In the adult CNS spontaneous regeneration is strongly limited in contrast to the PNS where nerve fibres regenerate over long distances leading to functional recovery.

Axonal regeneration and plasticity in the mature CNS are restricted by growth inhibitory molecules found in particular in myelin, as well as inhibitory factors present in the glial scar and the extracellular matrix.

After acute CNS injury, secondary damage involving different cell types, secreted factors as well as ECM molecules at the site of primary damage leads to more tissue loss, eventually resulting in the formation of a glial scar.

After nerve axotomy or crush the distal nerve stump degenerates; this process is called Wallerian degeneration.

In the CNS, plasticity is defined as the functional adaptation of surviving tracts and anatomical areas of the CNS; this includes cellular and molecular modifications at the level of the synapse, and changes on the cellular level leading to the formation of new circuits through sprouting and anatomical reorganisation.
Altruism – A Philosophical Analysis
Authors: Clavien Christine , Chapuisat Michel
Published: April 2013

Altruism is a malleable notion that is understood differently in various disciplines. The common denominator of most definitions of altruism is the idea of unidirectional helping behaviour. However, a closer examination reveals that the term altruism sometimes refers to the
outcomes
of a helping behaviour for the agent and its neighbours – that is, reproductive altruism – and sometimes to what
motivates
the agent to help others – that is, psychological altruism. Since these perspectives on altruism are crucially different, it is important to use a clear terminology to avoid confusion. In particular, we show that the notion of altruism used by biologists profoundly differs from the ones used by philosophers, psychologists and economists in cross‐disciplinary debates about human altruism.

Key Concepts:

Reproductive altruism refers to a behaviour that increases other organisms' fitness and permanently decreases the actor's own fitness.

It is important to distinguish reproductive altruism from cooperation, in which both partners gain direct fitness benefits.

Reproductive altruism decreases the direct fitness of the altruist and thus its persistence in the course of evolution requests an ultimate explanation.

Kin selection, the indirect transmission of genes through relatives, is the key process explaining the evolution and maintenance of reproductive altruism.

Psychological altruism refers to an other‐directed motivation to help and increase others' welfare independently of self‐directed calculations.

Psychological altruism is a proximate mechanism; in contrast to reproductive altruism, it may confer direct fitness benefits.

To avoid misunderstandings, it is important to identify which form of altruism is at stake in interdisciplinary literature about human altruism.
Homology and Homoplasy: A Philosophical Perspective
Authors: Amundson Ron
Published: April 2013

Homology refers to the underlying sameness of distinct body parts or other organic features. The concept became crucial to the understanding of relationships among organisms during the early nineteenth century. Its importance has vacillated during the years between the publication of Darwin's
Origin of Species
and recent times. For much of the twentieth century, homology was regarded as nothing more than evidence of common descent. In recent times, however, it has regained its former importance. It is regarded by advocates of evolutionary developmental biology as a source of evidence for developmental constraint, and evidence for biases in phenotypic variation and the commonalities in organic form. The recent growth in understanding of developmental genetics has made possible a new theory about the mechanical causes of homology, which was impossible under the naïve views regarding genetic causation that were available during most of the twentieth century. This new theory, proposed by Günter Wagner (2007), states that homologies of character are due to the development of a certain kind of genetic regulatory network called a character identity network.

Key Concepts:

For much of the twentieth century, the concept of homology was regarded as secondary in importance to adaptation, with homology regarded as merely the evidence for common ancestry.

Recent advances in molecular biology and developmental genetics have enhanced the importance of homology, and it has regained the importance that it had during the nineteenth century.

One might expect homologous characters to develop from identical embryological precursors, but this is not correct; paradoxically, homologous traits can have distinct embryological origins.

This ‘paradoxical’ fact about homology has led to great frustration among those who have attempted to explain the developmental basis of homology.

Recent developments in developmental genetics may have given us a way to explain the ‘paradoxical’ nature of homology.
Medical Futility
Authors: Loeben Gregory S
Published: April 2013

Medical futility is a concept that has been heavily debated since the late 1980s. It is increasingly invoked in end‐of‐life decision‐making as a way to both describe certain situations and to justify refusing treatment as a response to those situations. As the emphasis on patient autonomy has grown, so have demands for treatment that the medical team thinks are inappropriate because they are insufficiently beneficial. The concept of medical futility addresses these treatment demands. Futility judgments have been categorised as physiologic, quantitative and qualitative depending upon the nature of the claim being made. Despite an ongoing dialogue about the nature of these judgments, there is still widespread disagreement about the appropriate use of the concept as a justification for limiting treatment.

Key Concepts:

Medical futility is a concept used both to describe certain treatment and as a justification for refusing certain treatment.

There is significant disagreement about exactly what medical futility means, in what situations it should be applied, and what justification it ultimately provides for refusing treatment.

Medical futility can usefully be distinguished into physiological, quantitative and qualitative futility.

The debate over medical futility can be seen as arising from several factors: the development of modern technology, the rise of patient autonomy as a dominant value in Western medicine, and growing concern with cost control.

Medical futility can only be determined relative to particular goals and futility judgments require us to consider what we think the appropriate function and goals of medicine should be.

Institutional policies about medical futility generally focus on fair procedures for resolving futility disagreements rather than on a universal definition.
Bioethics of Gene Therapy
Authors: Resnik David B
Published: April 2013

Gene therapy in human beings raises a variety of important ethical, legal and social issues. Somatic gene therapy (SGT) is similar to other forms of medical treatment in that the goal is to treat or prevent diseases in individuals. SGT raises questions concerning safety and efficacy of treatments and protection for human research subjects. Germline gene therapy is different from traditional medicine because it involves manipulation of the human genome to prevent the birth of children with genetic diseases. Germline gene therapy has been much more controversial than SGT, because it creates risks not only to patients but also to future generations, and because it may lead to genetic enhancement. Genetic enhancement raises a number of difficult issues, including the ethics of changing human traits, parental control over children's lives, exacerbation of discrimination and social inequalities and eugenics.

Key Concepts:

Advances in genetics and biotechnology in the 1970s and 1980s made possible the first somatic gene therapy experiments, which took place in the 1990s.

Somatic gene therapy has had some successes but still faces significant technical challenges.

Somatic gene therapy can pose significant risks to patients and some have died in somatic gene therapy experiments.

Germline gene therapy has been more controversial than somatic gene therapy because it involves deliberate, inheritable changes in the genome.

Germline gene therapy poses risks not only to patients but also to future generations.

Germline gene therapy raises difficult ethical questions related to tampering with human nature, enhancing human traits, parental control over children, discrimination, social justice and eugenics.

The distinction between therapy (which aims to prevent or treat disease) and enhancement (which aims to improve human traits), plays a key role in debates about gene therapy.

The therapy/enhancement distinction is not as clear as some have assumed, because the concept of disease is not purely objective and includes social, cultural and ethical dimensions.

Investigators and institutions should take appropriate steps to protect the rights and welfare of gene therapy patients participating in clinical research.

In thinking about the balance of benefit and risks of a gene therapy study, it is important to consider the safety and efficacy of the proposed research and the availability of alternatives.