bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Magnetic Resonance (
NMR
) of Proteins: Solid State
Authors: Middleton David A 
Published: April 2013

Abstract

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

Abstract

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

Abstract

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

AbstractDispersal 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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

Abstract

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.