bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional Gene Regulation in Eukaryotes
Authors: Latchman David S
Published: April 2013

Regulation of gene transcription is the primary means by which gene expression is controlled to produce different proteins in different cell types or in response to different stimuli. This process is controlled by transcription factors that belong to specific families which are defined on the basis of the different protein domains used to bind to
deoxyribonucleic acid
(DNA). Many transcription factors contain specific activation domains which allow them to activate transcription. In contrast, other transcription factors repress transcription either directly or indirectly by interfering with positively acting factors. Moreover, DNA‐binding transcription factors can also interact with one another and with non‐DNA‐binding coactivators and corepressors so allowing an individual transcription factor to differentialy regulate different genes. In turn, transcription factors are themselves regulated by controlling either their synthesis or by activating them from a pre‐existing inactive state by mechanisms such as ligand binding, phosphorylation or dissociation of an inhibitory protein. These mechanisms allow cellular differentiation events or specific signals to regulate gene expression by altering the synthesis and/or activity of individual transcription factors and thereby altering the expression of their target genes.

Key Concepts:

Regulation of the transcription of DNA into RNA is the key event controlling gene expression.

Transcription is regulated by specific proteins called transcription factors.

Many of these factors act by binding to specific DNA sequences in gene promoters or enhancers.

Transcription factors bind to the DNA via specific DNA‐binding domains which differ between different transcription factor families.

Following DNA binding, some factors activate transcription via specific activation domains.

Other transcription factors can repress transcription either directly or indirectly by interfering with the action of positively acting factors.

In order to regulate gene transcription, transcription factors are themselves regulated by controlling either their synthesis or their activity.

The rate of transcription of a particular gene is therefore determined by the balance between the levels/activity of the activating and inhibitory transcription factors which act on it.
Boyle, Robert
Authors: Hunter Michael
Published: April 2013

Robert Boyle (1627–1691) was a British natural philosopher who pioneered systematic experimentation, using it to vindicate his corpuscularian view of nature. Boyle also argued influentially for the usefulness of science, and reflected deeply on epistemological issues arising from science and on the relations of science and religion.
Clonal Isolation and Plating Efficiency
Authors: Martin Bernice M
Published: April 2013

Viable cultures of cells that were initiated from single cells can be obtained. However, both the isolation of the single cell of interest and the ability to promote proliferation of this cell present challenges. Selection of the single cell can be achieved in a number of ways. Among the methods discussed are a direct approach (cloning cylinders or discs), a theoretical approach (limiting dilution) and isolation using cell sorters. Any of these approaches can be combined with a pre‐seeding technique that will enrich the population of the desired cells in the culture. A number of techniques to address the second challenge, cell proliferation, are also addressed. These include the use of culture ware with a small growth area, increasing the likelihood of cell attachment, the enrichment of the culture medium and the use of feeder layer cells. Because cells differ widely in their characteristics, a combination of techniques can be used.

Key Concepts:

Cloned cells in culture are derived from a single cell.

Each of the cells in a clone should have identical characteristics.

Selection of cells for cloning may be aided by fluorescent molecules and FACS.

The survival and proliferation of the cells that form clones require special conditions.
Differentiation of Somatic Cells, Stem Cells and Stem Cell Variants:In VitroModels
Authors: Danilenko Michael , Coffman Frederick D , Studzinski George P
Published: April 2013

Because conditions of culturein vitrocannot be identical to those in the living system, cell lines culturedin vitroare referred to as ‘model systems’. Not all cell types are capable of differentiationin vitro. Stem cells are of various types, including embryonic stem cells (ESC), mesenchymal stem cells (MSCs), induced pluripotent stem cells (iPSCs), cancer/leukaemia stem cells (CSCs/LSCs),etc.Procedures for studying differentiation in model systems depend on the type of culture that can be employed. Techniques employed include liquid suspension cultures, monolayer cultures and complex culture systems involving semisolid matrices or liquid overlay methods. Cells derived from various tissues can be maintained in culture known as ‘primary culture’. Only a rare human cell in a culture can undergo changes in its molecular machinery known as ‘immortalisation’ which allow it to propagate indefinitely. Recent developments include systems optimised for stem cell differentiation. Suchin vitroculture techniques have applications to the study of differentiation in basic research and clinical applications.

Key Concepts:

Mammalian cells derived from many tissues, the subject of this article, can propagate outside of the body.

Stem cells can differentiate, but provide a reservoir for development of functional cells of various types which is known as ‘lineage expansion’.

Stem cells give rise to progenitor cells (PCs) which can differentiate into mature cells, but have a limited repertoire of lineages of differentiation.

Mature cells can be induced to have the capabilities of stem cells and PCs by introduction of four or less transcription factors (TFs), for example, Oct4, Sox2, Klf4 and c‐Myc, under defined conditions.

The cell environment – other cells, extracellular material – can favour lineage expansion into mature, functional cells and is called a ‘niche’.
Use of Animal Cells and Display Methods for the Production of Human Monoclonal Antibodies
Authors: Tomimatsu Kosuke , Teruya Kiichiro , Shirahata Sanetaka
Published: April 2013

Human monoclonal antibodies have great potential for use in the treatment of various human diseases. An

in vitro

immunisation protocol using human peripheral blood mononuclear cells (PBMCs) was developed to generate human antigen‐specific antibodies. After antigen sensitisation of PBMCs

in vitro

, B cells producing antigen‐specific antibody can be propagated within a week. Heavy and light chain variable region genes were easily amplified from these

in vitro

immunised PBMCs. After generating a combinatorial phage library, antigen‐specific clones were selected by panning rounds. Next, the variable region genes of heavy and light chains of these selected clones were combined with human IgG constant region genes to produce human IgG‐type antibody in mammalian cells. This

in vitro

immunisation method will be applied widely for the production of human monoclonal antibodies for therapeutics by combination with several display methods.

Key Concepts:

In vitro
immunisation method can be used to induce B cells producing antigen‐specific human monoclonal antibodies from human peripheral lymphocytes.

Phage display method can be used to efficiently generate antigen‐specific human monoclonal antibodies.

The combined use of
in vitro
immunisation and phage display methods is beneficial to efficiently establish recombinant animal cells producing antigen‐specific human monoclonal antibodies from a relatively small library.
Pore‐forming Toxins
Authors: Dalla Serra Mauro , Tejuca Martínez Mayra
Published: April 2013

Pore‐forming toxins (PFT) are proteins able to produce well‐structured holes in target cell membrane. They have a very broad taxonomic distribution being produced from bacteria to mammals. Depending on the secondary structure of the membrane‐spanning region, these proteins are categorised into two classes: α‐PFT and β‐PFT. The pore structure of representative members of each class will be described. These proteins can be also classified according to their pore structure:barrel‐staveandtoroidalprotein–lipid pore. In thebarrel‐stavepore the protein molecules provide a continuous interface between the core of the bilayer and the channel lumen, whereas in thetoroidalprotein–lipid pore both polypeptide chains and polar phospholipid headgroups are involved in the building of pore walls. The stoichiometry and the pore diameter depend on the protein, thus the channels can allow leakage of ions, adenosine triphosphate (ATP), proteins and even bacteria. Attacked cells trigger different responses, some promoting recovery of membrane integrity, others transition to a low‐energy‐consumption state, in addition to inflammatory responses and changes in gene transcription.

Key Concepts:

Pore‐forming toxins are proteins produced from bacteria to mammals.

Pore‐forming toxins are classified as α‐PFT and β‐PFT, according to the structure adopted by the transmembrane region.

Pores are nanometre funnel‐like holes that permit the passage of water, ions and small molecules through cell membranes.

PFT form two types of pores, the barrel‐stave and the toroidal protein–lipid pore.

Cells react to pore formation, repair the damage and survive.
Capillary Electrophoresis
Authors: Righetti Pier Giorgio , Guttman András
Published: April 2013

Capillary electrophoresis is an electric field‐mediated microseparation technique that utilises narrow‐bore fused‐silica capillaries (10–100 μm) and high applied electric fields (100–1000 V/cm) enabling short analysis times with high separation efficiency and excellent resolution, whereas the narrow bore capillary readily dissipates the generated Joule heat. The main separation modes of capillary electrophoresis are capillary zone electrophoresis (CZE), micellar electrokinetic chromatography (MEKC), capillary isoelectric focusing (cIEF), capillary gel electrophoresis (CGE) and capillary electrochromatography (CEC). As a truly orthogonal method to high‐performance liquid chromatography (HPLC), capillary electrophoresis is recently gaining high importance in the pharmaceutical, biotechnology and biomedical industries, especially for the analysis of protein therapeutics.

Key Concepts:

Capillary electrophoresis (CE) is a truly orthogonal separation method to chromatography‐based techniques.

CE is a fully automated approach to electrophoresis.

The narrow bore capillaries used in CE enable application of high separation voltages without significant heat generation.

Electroendoosmotic flow (EOF) generates a bulk fluid flow within the narrow bore capillary and therefore one of the driving forces of CE analysis.

The main separation modes of CE are: Capillary zone electrophoresis (CZE) separation is based on free solution mobility; micellar electrokinetic chromatography (MEKC) utilises partitioning of hydrophobic analytes within charged micelles; capillary gel electrophoresis (CGE) applies sieving polymers for size separation of macromolecules; and capillary isoelectric focusing (cIEF) separates amphoteric analytes based on their charge states; and capillary electrochromatography (CEC) based on the interplay between electric field and chromatography‐mediated separations.

CE is one of the emerging separation techniques in the biotechnology, biopharmaceutical and biomedical industries.

Microfluidics devices integrate the concept of CE with fluidics sample manipulation such as on chip sample preparation.
Macromolecular Structure Determination: Comparison of X‐ray Crystallography and
NMR
Spectroscopy
Authors: Krishnan VV , Rupp B
Published: April 2013

X‐ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are the most powerful and predominant techniques used to experimentally determine the three‐dimensional structures of biological macromolecules at near atomic resolution. X‐ray diffraction (XRD) studies require a crystalisable protein, whereas NMR is suitable for macromolecules in solution. XRD has no size limitations and provides the most precise atomic detail, whereas information about the dynamics of the molecule may be limited. NMR excels in cases where no protein crystals can be obtained and it provides solution state dynamics, but in turn delivers lower resolution structures and is in general limited to molecular weights below approximately 50 kDa. The two techniques can deliver complementary information. Approximately 90% of the experimentally determined macromolecular structures deposited in Protein Data Bank are crystal structures, with NMR dominating the <10 kDa molecular weight range.

Key Concepts:

XRD and NMR are complimentary structure determination methods.

XRD has no size limitations and provides the most precise atomic detail, whereas information about the dynamics of the molecule may be limited.

NMR excels in cases where no protein crystals can be obtained and it provides solution state dynamics, but in turn delivers less detail and in general practice is limited to molecular weights below approximately 50 kDa.
Bergström, Sune
Authors: Ljungström Olof , Normark Daniel
Published: April 2013

Sune Bergström (1916–2004) was a Swedish biochemist and Nobel Prize laureate (1982) for his work on the compounds known as prostaglandins widely distributed in living organisms. Other work dealt with the biosynthesis and metabolism of bile acids. Bergström was dean during1963–1966 and president 1969–1977 of the Karolinska Institutet in Stockholm and chairman of both the board of the Nobel Foundation 1975–1987 and WHO Advisory Committee on Medical Research 1977–1982.
Calorimetry
Authors: Emerson Joseph P , Le Vu H , Lewis Edwin A
Published: April 2013

In biology, particularly in studies relating the structure of biopolymers to their functions, two of the most important questions are: (1) how tightly does a small molecule bind to a specific interaction site? and (2) if the small molecule is a substrate and is converted to a product, how fast does the reaction take place? Because almost any chemical reaction or physical change is accompanied by a change in heat or enthalpy, an isothermal titration calorimeter is an ideal instrument to measure either how much of a reaction has taken place or the rate at which a reaction is occurring. In contrast to optical methods, calorimetric measurements can be done with reactants that are spectroscopically silent (a chromophore or fluorophore tag is not required), can be done on opaque, turbid or heterogeneous solutions (e.g. cell suspensions) and can be done over a range of biologically relevant conditions (temperature, salt, pH,etc).

Key Concepts:

Almost all chemical reactions are accompanied by a change in heat or enthalpy.

Calorimetry can determine the complete set of thermodynamic parameters that characterise binding reactions, for example K, ΔG°, ΔH°, ΔS° and ΔCp.

Binding reactions are typically pH, salt and temperature dependant.
Protein Structure Prediction
Authors: Roy Ambrish , Zhang Yang
Published: April 2013

The goal of protein structure prediction is to estimate the spatial position of every atom of protein molecules from the amino acid sequence by computational methods. Depending on the availability of homologous templates in the PDB library, structure prediction approaches are categorised into template‐based modelling (TBM) and free modelling (FM). While TBM is by far the only reliable method for high‐resolution structure prediction, challenges in the field include constructing the correct folds without using template structures and refining the template models closer to the native state when templates are available. Nevertheless, the usefulness of various levels of protein structure predictions have been convincingly demonstrated in biological and medical applications.

Key Concepts:

Evolution is a general principle to guide protein structure and function predictions.

Proteins of similar sequence have similar 3D structure.

Function of protein is decided by the 3D structure.

TBM using homologous templates has the highest accuracy.

Template structure can be refined by combining multiple templates.

Current physics‐based
ab initio
folding can only fold small proteins.

Threading is an efficient tool for detecting distantly homologous templates.

Membrane protein structure prediction is challenging due to the lack of templates.

Disordered regions exist in protein which does not possess stable structure but has important function implications.
History of Cancer Research
Authors: Morange Michel
Published: April 2013

History of cancer research has always been closely linked with the history of biology. The rise of the cell theory in the middle of the nineteenth century led to a unified conception of cancer, and to a dramatic change in the description of this disease, as well as in its diagnosis and prognosis. Cancer research has been revitalised during the last three decades through the development and transformations of molecular biology. Cancer results from the accumulation of mutations in oncogenes (genes stimulating cell proliferation) and tumour‐suppressor genes (genes limiting cell growth). At least six mutations are necessary for the formation of a tumour. Drugs specifically targeted against these molecular actors of cancer are progressively finding their place in chemotherapy. Simultaneously, new systemic and evolutionary visions of cancer are slowly emerging.

Key Concepts:

Cancer has always been at the forefront of biological research.

Molecular biology has profoundly transformed the vision of cancer.

A succession of somatic mutations is required for the formation of a tumour.

Drugs specifically targeted against the products of oncogenes are progressively entering into clinics.

The growth and expansion of a tumour is seen now as an evolutionary process.

In systems biology, cancer is seen as a new functional state of the cell.

Epigenetic modifications might play a role in the formation of tumours.

The role of cancer stem cells in the development of tumours is still discussed.
Nuclear Magnetic Resonance (
NMR
) of Proteins: Solid State
Authors: Middleton David A
Published: April 2013

Solid‐state nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for examining the structures of protein assemblies and complexes that are unsuitable for analysis by diffraction methods. Structural details are obtained for challenging systems including membrane proteins in lipid bilayers and water‐insoluble fibrillar proteins. High‐resolution spectra of proteins in solid or gel phases lacking long‐range order are obtained with magic‐angle spinning and, for membrane‐embedded proteins, further anisotropic information is gained from spectra of stationary, macroscopically aligned samples. The information obtained defines the secondary structure and global fold of the protein, and also the orientation and topology of membrane proteins within lipid bilayers. These methods have elucidated, amongst other things, the structures of ion channels and their interactions with antiviral drugs and toxins and the molecular architectures of amyloid fibrils associated with Alzheimer's disease and type II diabetes. In addition, the molecular conformations of numerous ligands have been determined in the sites of action within their biological receptor proteins.

Key Concepts:

For solid‐state NMR measurements on biological materials, samples are either macroscopically aligned or are rotated at the magic‐angle.

Solid‐state NMR measurements on aligned membrane proteins provide anisotropic restraints on the orientations of contiguous peptide planes or domains relative to the lipid bilayer.

Magic‐angle spinning provides high‐resolution spectra containing information on isotropic chemical shifts and interatomic distances and torsional angles.

Both approaches require isotopic labelling (
13
C and
15
N supplemented as necessary with deuteration) of the protein.
Resonance Raman Spectroscopy
Authors: Mukerji Ishita
Published: April 2013

Resonance Raman spectroscopy is a vibrational spectroscopic technique that utilises electronic absorption bands to dramatically enhance the magnitude of the signal. It has been used effectively to study protein structure and function. Resonance Raman spectroscopy performed in the UV spectral range can probe the structure of proteins by monitoring the local environment of aromatic side chains. Deep‐UV resonance Raman spectroscopy with excitation wavelengths less than 200 nm can be used to determine secondary structure of proteins by monitoring the frequencies and intensities of amide backbone modes. The ability to monitor both proteins backbone and side chains in kinetic investigations makes this a very powerful technique for investigations of protein folding and amyloid formation.

Key Concepts:

Resonance Raman spectroscopy measures molecular vibrations, which provides information on local environment and H‐bonding. The resonance effect leads to selective enhancement and a simplified spectrum.

Resonance Raman spectroscopy can be used to study samples in a variety of different physical forms such as solutions, gels and fibres.

Time‐resolved techniques involving resonance Raman spectroscopy span a wide time range from picoseconds to seconds. Selective investigation of chromophores, protein backbones and sidechains provides a wealth of dynamic information.

Secondary structure of proteins can be determined using UV resonance Raman spectroscopy, which monitors the amide vibrational modes of the peptide backbone. In particular the amide III
3
mode frequency has a sinusoidal dependence on the Ramachandran Ψ angle.

UVRR spectroscopy is increasingly being used to study protein folding and the association of proteins and peptides into amyloid fibres.
Energy, Radiation and Temperature Regulation in Plants
Authors: Jones Hamlyn G , Rotenberg Eyal
Published: April 2013

The temperature of any plant organ depends on the balance between incoming energy and energy loss. The energy exchanges involved include radiative transfer, sensible heat transfer by convection processes, latent heat transfer as a result of evaporation and transfer to and from storage (by conduction). The radiative transfer is frequently classified into either short‐wave (or solar) radiation and long‐wave (or thermal) radiation; these contribute differently to the overall energy balance. Various biophysical mechanisms are available to plants, through manipulation of the energy balance terms, for temperature regulation. For example, enhanced evaporation can help cool leaves in hot environments, whereas maximising absorption of sunlight can raise the temperature in cold environments. This article outlines the relative importance of these different processes in both leaf and canopy temperature regulation, highlighting differences between treatment of the energy balance at leaf and canopy scales. Examples of applications, such as the measurement of canopy temperature to determine plant water stress or to aid in the selection of drought tolerant varieties of plants, are also discussed.

Key Concepts:

A critical requirement of plants is that they maintain their leaf temperature as close as possible to the optimal temperature for growth; plants have a range of mechanisms that help them to optimise their temperature.

Leaf and canopy temperature are dependent on the leaf energy balance, which itself is dominated by radiant exchanges.

Radiation in natural environments relevant to leaf energy balance is conventionally separated into the ultraviolet (0.2–0.38 μm), the visible (0.38–0.7 μm) and the infra‐red (0.7–100 μm).

Radiation coming from the sun is often termed short‐wave radiation, about half of which is in the visible region, a small amount in the ultraviolet, and the remainder in the near infra‐red (0.7–3 μm).

Long‐wave, or thermal radiation is conventionally taken as the radiation between 3 (or sometimes 4) μm and 100 μm. The radiation emitted by natural surfaces as a function of their temperature is primarily in this wave‐band.

The thermal radiation emitted by any body increases according to the fourth power of the temperature (Stefan–Boltzmann's law).

Leaf and canopy temperatures depend on the exchanges of energy between plants and the atmosphere both through radiation exchange and by means of sensible heat and latent heat fluxes.

Leaf temperature therefore depends on the radiation climate (time of day, cloud cover and type, etc.), atmospheric conditions (wind speed, temperature, etc.), the soil conditions (soil type, water content, etc.) and the canopy properties (such as plant morphology, density, height, etc.) that together affect the size and ratios of the radiant, sensible and latent heat fluxes.

Measurement of leaf temperature using infra‐red thermometry or thermography can be used to detect plant water‐deficit stress and to screen plants for their drought tolerance.
Dispersal: Biogeography
Authors: Wilkinson David M
Published: April 2013

Dispersal is one of the fundamental processes in biogeography, crucial to understanding the distribution of organisms. The most basic distinction between different types of dispersal is between organisms that disperse using their own energy and those that use energy from the environment. Dispersal can lead to two main patterns of range expansion. Either a population can slowly expand from the margins of its geographical range or a small number of individuals can disperse to a new location some distance from the current edge of the species range, or a combination of both of these processes can occur. Humans have assisted the dispersal of many organisms to new parts of the world – sometimes leading to problems when they become pests in their new range. Understanding dispersal is also important in attempting to predict how organisms will respond to climate change.

Key Concepts:

There are three fundamental processes in biogeography: evolution, extinction and dispersal.

The most basic distinction between types of dispersal is between organisms that disperse using their own energy (active dispersal) and those that use energy from the environment (passive dispersal).

Much of biodiversity is microscopic; organisms of this size can often be easily dispersed by air or water currents.

Many larger animals are capable of dispersal under their own power, especially ones that can fly such as birds and bats.

Individual organisms can sometimes appear at a location well outside their normal range, such individuals are referred to as vagrants.

There are two main patterns of range expansion ‘diffusion’ and ‘jump dispersal’.

Vicariance biogeography is an alternative to dispersal biogeography, which downplays the importance of dispersal, replacing it with the idea that a taxon's range can be divided by the formation of physical barriers.

A key applied question is whether organisms will be able to disperse at a speed that will allow them to track future climate change.

Human influence has had a big role in reducing the effects of dispersal barriers by moving organisms around the world.

When a species is dispersed to another part of the world by human actions, its main parasites and predators can be left behind; occasionally this can cause a dramatic increase in its population at the new site and the introduced organism can become a pest species.
Ecological Biochemistry
Authors: Que Hee Shane
Published: April 2013

Ecological biochemistry is the study of the role of biochemistry and chemistry in the ecological relationships of different organisms in their abiotic environment. In the middle of the nineteenth century, it was found that insect herbivores could be repelled by chemicals emitted by, or eaten in, a target plant. Development of toxicology, biochemistry, ecology as disciplines and of analytical chemistry techniques allowed the molecular basis to be determined in 1968 when cardiac glycosides (cardenolides) of milkweed were shown to cause young blue jays to vomit up partially eaten Monarch butterflies and to avoid butterflies. Numerous chemical signalling systems were soon found for many host–predator and/or host–benefactor interactions of many species. The advent of genomic techniques in the twenty‐first century has allowed the genetic basis of these interactions to be examined in recent research, a trend that will also apply for future research.

Key Concepts:

Ecological biochemistry focuses on the identification and quantification of molecules that interact with a different organism and the mechanism of the interaction.

Ecological biochemistry also features the fate and transport aspects of molecules that interact with a different organism.

Ecological biochemistry also features how the interacting molecule is produced and that mechanism.
Mutualism Among Free‐living Species
Authors: Armbruster WS , Rosenqvist G
Published: April 2013

Mutualisms are interspecific interactions resulting in benefits to both participants. In symbiotic mutualisms, the species live together for most of their lives. In nonsymbiotic mutualisms, members of the interacting species live apart most of the time and interact intermittently. Common mutualisms among free‐living species include various plant–animal mutualisms, such as pollination and seed dispersal, and a number of animal–animal mutualisms such as cleaning and parasite‐removal services (e.g. oxpeckers and cleaning wrasses). The evolutionary stability of these mutualisms is a topic of current research interest, in which mutualism may easily slip into unbalanced relationships wherein one partner exploits the other.

Key Concepts:

Mutualisms among free‐living species are ecologically important, providing critical services for the maintenance of populations and functioning of ecosystems.

Mutualisms among free‐living species may be evolutionarily more labile than symbiotic mutualisms, in which the former may more commonly ‘degenerate’ into exploitative relationships.

A key factor in the ecology and evolution of mutualisms among free‐living species is signalling between spatially distant organisms, usually with behaviour, volatile chemicals and/or colour. The degree of honesty (or dishonesty) of such signalling is another topic of current research interest.
Individual‐based Models in Population Ecology
Authors: Lomnicki Adam
Published: April 2013

The individual‐based approach is a concept of population ecology that rests on the premise that population properties should be derived from properties of individuals. It was developed due to conceptual advances in evolutionary biology in the second half of the twentieth century and as a consequence of access to computers. The advances in biology have allowed the rejection of the notion of adaptations of units of natural selection other than individuals whereas the computers made possible the simulations of very complex phenomena in many fields of science, engineering and economy. Investigations of individual variation have shown its origin and its impact on population dynamics. Computer simulations of particular ecological systems, especially those of economic and conservation importance, have proven to be very useful and able to discover relations that cannot be found out by analytical inquiries. It seems that in the future the individual‐based approach will be fully integrated into theoretical and applied ecology.

Key Concepts:

Individual plants and animals differ not only in their sex and age but also in other phenotypic features.

Individual differences affect resource partitioning by individuals within the population, explain the mechanisms of scramble or contest competition and consequently the conditions for population stability and persistence.

Absolutely equal resource partitioning by population members makes population stability and persistence impossible.

By itself, individual variation in resource partitioning is not sufficient for population persistence and its ability to survive sudden drop in the availability of resources; some degree of resource monopolisation is required.

The best examples of situation in which we can observe monopolisation of resources are populations of plants competing for light and birds or other animals defending individual territories.

The important ecological phenomenon – despotic distribution which forces some individuals to move into worse habitat where their fitness is lower is possible only with some degree of monopolisation of available resources.

Another ecological phenomenon – the existence of the source and sink system, which is important in population dynamics, can be maintained due to resource monopolisation by some population members.

Individual variability and individual properties, as well as spatial population structure are difficult to describe by general models with analytical solutions but computer simulations make their description much easier and the exploration of their consequences much more effective.

Computer simulation of ecological phenomena uses methods and concepts developed in other fields of science and technology, like agent‐based models or complex adaptive systems.

Agent‐based models are used not only for the study of population dynamics but also to explain collective animal behaviour and other population or community‐level phenomena.
Dinosaur Behaviour
Authors: Horner John R
Published: April 2013

Dinosaur behaviour concerned with reproductive activities and life history strategies can be hypothesised from the fossil record through studies of geology and comparative biology. Dinosaurs constructed rimmed earthen nests in which they deposited from 12 to 30 eggs. The eggs were incubated either by rotting vegetation or direct body heat produced by the parent as they brooded the eggs like birds. Dinosaurs nested in colonies like birds, and returned to the same nesting areas on a regular basis. Some hatchling dinosaurs were nest‐bound or altricial, and were brought food by their parents. These kinds of baby dinosaurs grew very fast in the confines of their nests. Gigantic accumulations of dinosaur skeletal remains indicate that many dinosaurs, particularly the ceratopsians and hadrosaurs lived in large aggregations or herds and may have migrated to find food. The skulls of many dinosaurs possess elaborate bony structures including horns, spikes, domes and shields that have been interpreted as defensive features. Recent studies showing that these features change shape during growth suggest that they are actually for species recognition, particularly so that the adults could recognise juveniles and the juveniles could recognise adults. Nesting grounds, large accumulations of skeletons and cranial display features all indicate that dinosaurs were very social animals.

Key Concepts:

Dinosaurs laid eggs in nests and lived in colonies.

Plant‐eating dinosaurs may have incubated their eggs using rotting vegetation.

Meat‐eating dinosaurs incubated their eggs by sitting on them, much like birds.

Some dinosaurs cared for their young by bringing them food.

Dinosaurs, particularly hadrosaurs and ceratopsians, travelled in gigantic herds.

The horns and spikes and shields found on the skulls of dinosaurs were most likely used for species recognition rather than defence.
Salk Institute
Authors: Olby Robert
Published: April 2013

Nearing its first half‐century of research, the Salk Institute has risen to prominence among major research Institutes in the life sciences. The location, the very favourable working conditions and the Institute's growing reputation have attracted outstanding scientists, both young and old. Jonas Salk and the architect, Louis Kahn, worked together to achieve a unique design, and the result has made the Institute a mecca for the student of twentieth century architecture. Although some restraint was put on Salk's broad vision for the Institute's research agenda by his eminent advisers, Salk had Kahn revise his vision of the kind of facilities the scientists would need. The final result embodied a more limited plan than Kahn had originally envisaged. Both functionally and visually the design and character of the buildings have proved remarkably successful.
Wilson, Edward O.
Authors: Ruse Michael
Published: April 2013

Edward O Wilson is the most distinguished living evolutionist. He has made seminal contributions to ant taxonomy, to island biogeography, to the importance of pheromones (chemical methods of communication) and to social behaviour (sociobiology). He has also been active in conservation projects, much concerned to promote biodiversity, and he has in later years turned his attention to philosophical and social issues, arguing that evolution provides a firm foundation for the study of ethics and epistemology.
m
RNA
Untranslated Regions (
UTRs
)
Authors: Mignone Flavio , Pesole Graziano
Published: April 2013

Eukaryotic messenger
ribonucleic acids
(mRNAs) possess a tripartite structure that comprises a 5′ untranslated region, a coding region made up of the amino acid coding triplet codons and a 3′ untranslated region. During nuclear maturation of primary transcripts, both ends of mRNA are post‐transcriptionally modified through the addition of a 7‐methyl‐guanosine cap structure at the 5′ end and a polyadenosine tail at the 3′ end. Untranslated regions are involved in the post‐transcriptional regulation of gene expression by modulating mRNA stability, nucleo‐cytoplasm transport, subcellular localisation and translation efficiency thus allowing a fine control of the protein product. This regulatory activity is mediated by
cis
‐acting oligonucleotide elements that interact with binding proteins and noncoding RNAs through a combination of primary and secondary structures.

Key Concepts:

UTRs are involved in the post‐transcriptional regulation of gene expression.

UTRs regulate mRNA stability, nucleo‐cytoplasm transport, subcellular localisation and translation efficiency.

Alternative splicing can result in mRNAs encoding the same protein under the control of different UTRs.
Polyploidy and Paralogous Chromosome Regions
Authors: Lundin Lars‐Gustav , Larhammar Dan , Hallböök Finn
Published: April 2013

Polyploidisations, that is, genome doublings, have taken place on numerous occasions during the evolution of animals and plants. The resulting duplicated chromosome regions can be recognised by their similar repertoires of gene families. Duplicated genes or regions within a genome are referred to as paralogous, and each set of related chromosome regions comprise a paralogon. In the ancestor of vertebrates, before the origin of the gnathostomes (jawed vertebrates), two tetraploidisations took place, abbreviated 2R for two rounds of tetraploidisation. A third tetraploidisation, 3R, happened before the radiation of the true bony fishes, the teleosts. Paralogues resulting from tetraploidisations are called ohnologues in honour of Susumu Ohno, who proposed the vertebrate tetraploidisations. Paralogous genes can undergo either subfunctionalisation (become more specialised) or neofunctionalisation (evolve novel functions). The vertebrate tetraploidisations seem to have paved the way for many gnathostome innovations such as jaws, limbs, an advanced nervous system and a complex adaptive immune system.

Key Concepts:

Polyploidisations have happened on numerous occasions in plant evolution and several times in vertebrate evolution.

A paralogon is a set of related chromosome regions resulting from duplications, usually tetraploidizations.

Paralogous genes can undergo either subfunctionalisation (become more specialised), neofunctionalisation (evolve novel functions) or loss.

The tetraploidisations in vertebrate evolution are thought to have facilitated evolution of new functions and structures.

After tetraploidisations, rearrangements scramble the chromosome regions, thereby obscuring the relationships.

The tetraploidisations do not only generate copies of single genes. Since all genes are duplicated, whole networks of genes or pathways are duplicated, such as the phototransduction pathway.

The total number of genes are doubled after a tetraploidisation event. However, the number of genes is later reduced due to different mutations such as deletions.
XYY
Syndrome
Authors: Goobie Sharan , Prasad Chitra
Published: April 2013

XYY syndrome is a genetic condition in which males have 47 chromosomes instead of the usual 46 chromosomes. The karyotype is written as 47,XYY as these males have an extra Y chromosome. XYY occurs in approximately one in 1000 live male births and falls into the category of sex chromosome aneuploidy. Males with XYY often have tall stature but otherwise are not significantly different in physical appearance compared to other men. They are generally healthy; however, some XYY men can have learning disabilities or behaviour problems. It is possible that the information we know about XYY syndrome in the medical literature may be biased, as healthy, developmentally normal males do not often have a reason to have a karyotype performed. We may overestimate some of the problems associated with XYY such as learning disabilities and behaviour problems, as these are common reasons for children to have a karyotype.

Key Concepts:

Males with XYY syndrome have 47 chromosomes, which includes an extra Y chromosome.

Males with XYY syndrome appear physically normal, however often have tall stature.

Males with XYY syndrome generally have normal intelligence, however some may have learning disabilities or behaviour issues.

Males with XYY syndrome do not have criminal tendencies as suggested in the older literature.
Sequence Finishing
Authors: Beasley Helen , Grafham Darren , Willey David
Published: April 2013

Sequence finishing can be described as the manual enhancement of assembled shotgun sequence data to improve regions of low quality or close gaps in the sequence. Shotgun sequencing data can be whole genome derived or from clone‐based entities such as bacterial artificial chromosomes (BACs) or other plasmid based vectors such as fosmids. Sequence finishing can be achieved using a combination of laboratory and computational techniques to produce a highly accurate and complete deoxyribonucleic acid (DNA) sequence.

Variable coverage and sequence gaps can occur across whole genome shotgun or a particular BAC or fosmid owing to the random nature of shotgun sequencing and the composition of a given piece of DNA can be prohibitive to both the cloning and sequencing process. A targeted approach is required to provide a more cost effective means of improving any regions of low quality and to close gaps that remain after initial shotgun sequencing.

Key Concepts:

Gaps exist in shotgun sequence for various reasons including structural elements, which can interrupt the sequencing reaction and variation in coverage owing to chance.

Directed finishing to close gaps in shotgun DNA sequence is labour intensive compared with high throughput shotgun sequence generation.

Good quality complete DNA sequences facilitate genome annotation and comparative sequencing studies.
Adoption Studies
Authors: Yates William R
Published: April 2013

Adoption studies are one form of clinical genetic study designed to evaluate genetic and environmental influences on phenotype. In adoption studies the index cases and controls are adoptees. The adoption study design provides a unique opportunity to examine gene and gene by environment interactions for a variety of behavioural, psychiatric and medical disorders. Adoption genetic studies provide some challenges related to the issues related to adoption (atypical biological parent profiles, differences in adoptive parents compared to nonadoptive parents and the stress of learning about being an adoptee). Recently, molecular genetic strategies have been applied to samples of adoptees. Advancing privacy issues have made it more difficult to design and carry out adoption research.

Key Concepts:

Adoption studies provide a unique research model where biological genetic effects can be estimated.

Adoption studies can be helpful in uncovering gene–environment interactions in complex behavioural and psychiatric disorders.

Adoption genetic studies utilise a variety of statistical techniques including calculation of odds ratios, logistic regression, log‐linear statistical monitoring and path analysis.

Recent advances in adoption study research have occurred by combining molecular genetic techniques to the genetic and environmental data of adoptees.

Increased privacy concerns and privacy laws related to biological parent anonymity have made adoption studies more difficult to design and implement.
Metabolism: Hereditary Errors
Authors: Groop Leif , Rosengren Anders
Published: April 2013

Inherited metabolic diseases can be both monogenic and polygenic. The monogenic forms are usually rare and are characterised by early onset. Examples include maturity‐onset diabetes of the young (MODY), phenylketonuria and
glycogen
storage diseases. The polygenic metabolic diseases result from a complex interaction of genetic variants and environmental factors. Type 1 and type 2 diabetes are typical examples. Important progress has been made in unravelling the genetic background of the common forms of diabetes. For type 2 diabetes, close to 50 loci have been consistently associated with increased disease risk. The findings have provided novel pathophysiological insights and suggest that type 2 diabetes occurs when the pancreatic islets fail to compensate for the increased insulin demands in states of insulin resistance. The exact disease mechanisms associated with the genetic variants are however in most cases not completely known. Novel approaches, including
deoxyribonucleic acid (DNA)
sequencing, are likely to give a more comprehensive picture of the genetic background.

Key Concepts:

Genetic factors play an important role in most metabolic disorders.

Monogenic metabolic diseases such as MODY have high penetrance and early onset.

The common metabolic disorders have typically a polygenic inheritance.

Type 1 and type 2 diabetes have a complex pathogenesis and result from a combination of environmental and genetic factors.

Genome‐wide association studies have identified a large number of disease susceptibility variants for type 2 diabetes.

Identification of genetic risk variants is invaluable for improving the pathophysiological understanding.
Digenic Inheritance
Authors: Vockley Jerry
Published: April 2013

Monogenic inheritance refers to genetic control of a phenotype or trait by a single gene. For a monogenic trait, mutations in one (dominant) or both (recessive) copies of the gene are sufficient for the trait to be expressed. Many traits are not determined so simply, and either involve the interaction of many genes with (multifactorial inheritance) or without (polygenic inheritance) environmental effects. Less commonly, the interaction of only two genes is required for expression of a phenotype, a mechanism referred to as digenic inheritance. In this situation, mutations in at least one copy of each gene are required for the expression of a phenotype. A growing number of human diseases with a digenic inheritance pattern are being described, a phenomenon that is likely to increase with moredeoxyribonucleic acid(DNA) sequence data being generated through clinical‐based exome and genome sequencing efforts.

Key Concepts:

Traditional mendelian patterns of inheritance are controlled by mutations at a single genetic locus.

Many human disorders are caused by more complex patterns of inheritance.

Digenic inheritance refers to mutation on two genes interacting to cause a genetic phenotype or disease.

Triallelic inheritance is a special case of digenic inheritance that requires homozygous mutations at one locus and heterozygous mutations at a second locus to express a phenotype.

Digenic inheritance is probably best though of as being on a continuum that includes modifier effects of monogenic inheritance and polygenic or multifactorial inheritance.