bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Futures and the Media
Authors: Jensen Eric 
Published: December 2009

Abstract

Today, public debate over genetic futures takes place within a new societal context. There is a greater emphasis from policymakers on promoting engagement between sciences and publics, and mass media play a key role in this shifting relationship. Media representations of genetic futures are often subject to both positive and negative hype. This tendency towards ‘genohype’ results from the economic imperative of journalistic and entertainment media production. Moreover, symbolic representations from science fiction continue to influence mainstream news coverage of genetics, present and future. The ways in which media representations of genetic futures influence audiences are only partially known; however, it is clear that there is a complex negotiation between existing attitudes, knowledge and values and the messages communicated about genetic futures by both factual and fictional media.

Key Concepts:

Media coverage of genetic futures takes place within a new context for sciences–society relations.

The conventional ‘fact/fiction’ division cannot be consistently upheld in media representations of genetic futures, given the considerable traffic of symbols and ideas across this divide.

The production of media representations of genetic futures relies on information subsidies including press releases, news conferences and other methods of communicating institutionally preferred public relations information directly to the media.

Media can raise the salience of particular issues or aspects of the implications of genetic research, but they cannot consistently or straightforwardly change the opinions that publics hold.
History of Scientific Agriculture: Animals
Authors: Paul Thompson R 
Published: December 2009

Abstract

Domestication of farm animals begins 10 000 years ago. From a wide array of wild animals, only a small number were and, for specifiable reasons, could be domesticated. Trait selection and breeding has been the principal mechanism of animal improvement until the late twentieth century. An understanding of the genetic mechanisms and environmental factors in that process was a twentieth‐century triumph, which enhanced dramatically agricultural animal science. Drawing on physiological, behaviour, genetic, evolutionary and ecological knowledge, sophisticated mathematical models and high speed computing were employed to enhance significantly selection and breeding efforts. Late twentieth‐century agricultural biology began to employ techniques of molecular genetic manipulation (transgenic animals), initially using farm animals as bioreactors. Improvements in cloning, pro‐nuclear injection and use of stem cells can be expected to dominate research and development in twenty‐first‐century animal agriculture.

Key Concepts

The early evolution of animal domestication.

Human and agricultural animal coevolution.

Mechanisms of speciation.

Quantitative genetics aspect of farm animal improvement.

Critical variables in trait farm animal trait selection.

Importance of multiple trait selection.

Animals as pharmaceutical and materials bioreactors.

Challenges and promises of cloning, pro‐nuclear injection and stem cell use in animal agriculture.
Density Dependence and Independence
Authors: Hixon Mark A , Johnson Darren W 
Published: December 2009

Abstract

Density dependence occurs when the population growth rate, or constituent gain rates (e.g. birth and immigration) or loss rates (death and emigration), vary causally with population size or density (
N
). When these parameters do not vary with
N
, they are density‐independent. Direct density dependence, where the population growth rate or gain rates vary as a negative function of
N
, or the loss rates vary as a positive function of
N
, is necessary but not always sufficient for population regulation. The opposite patterns, inverse density dependence or the Allee effect, may push endangered populations towards extinction. Direct density dependence is caused by competition, and at times, predation. It is detected observationally by analysis of abundance time‐series; however, experimental field manipulations provide the most rigorous analytical methods for both detecting and understanding underlying mechanisms. Future directions include expanded and more detailed mechanistic field data integrated with more sophisticated population models.

Key concepts:

Direct density dependence occurs when the population growth rate varies as a causative inverse function of population size or density.

Inverse density dependence – the Allee effect – may occur in a small population, driving it extinct.

Direct density dependence is necessary but not always sufficient for a population to be regulated and may occur simultaneously with density independence.

The ecological mechanisms of density dependence are competition, and in some circumstances, predation (including parasitism and disease).

Density dependence is most commonly tested by examining the relationship between the population growth rate (or individual demographic rates) and population density, either observationally or experimentally.

Understanding density dependence and regulation within the context of a metapopulation – a population of local populations linked by occasional dispersal – faces major empirical challenges.

Recommended future research on density dependence includes detailed, mechanistic field observations and experiments, as well as modelling of complex dynamics in complex systems, such as metapopulations.
Cornification of the Skin:
A
Non‐apoptotic Cell Death Mechanism
Authors: Candi E , Knight RA , Melino G 
Published: December 2009

Abstract

The most important function of the epidermis is to form a barrier against the environment by means of several layers of terminally differentiated, dead keratinocytes, the cornified envelope (CE). CEs consist of keratins enclosed within an insoluble amalgam of proteins and lipids. Transglutaminase enzymes catalyse the formation of characteristic crosslinks between structural proteins to form the protein part of the CE. Another form of cell death, that is, apoptosis, which has a completely different molecular mechanism and physiological significance, also occurs in the skin. Defects of apoptosis are related to the development of cancer, whereas CE abnormalities are associated with barrier abnormalities and ichthyosis.

Key concepts:

Keratinocyte apoptosis (occurring in basal layer) is an active and rapid, energy‐dependent, gene‐directed biochemical pathway of defensive cell death that does not require de novo protein synthesis and preserves plasma membrane.

Cornification, the keratinocyte differentiation programme (occurring in upper layer), is a slow, coordinated process in space and time, which allows the formation of a layer of dead cells (corneocytes) to create a physical barrier for the skin.

The stratum corneum is composed of tightly attached corneocytes with mostly keratin intermediate filaments (KIFs) embedded into a filaggrin matrix.

The structural proteins of the CE, including involucrin, loricrin, trichohyalin and the class of
small proline‐rich proteins
(SPRs), constitute about 7–10% of the mass of the epidermis. These structural proteins together with lipids (ceramides) form the complete barrier.

Transglutaminase are Ca
2+
‐dependent enzymes that catalyse the formation of
N
ε
‐(γ‐glutamyl)lysine bonds between CE structural proteins to confer the characteristic resistance and insolubility to the skin.

The junctions responsible for intercellular adhesion and for cohesion of the stratum corneum of the epidermis are of two types: (1) the adherence junctions (connecting the actin cytoskeleton of neighbouring cells) and (2) desmosomes (connecting the keratin filament cytoskeleton of adjacent cells).

Proteases are involved in at least three processes in skin differentiation. First, certain cornified envelope precursors require proteolytic processing before cornified envelope formation occurs. Second, the loss of nuclei and mitochondria requires proteolytic processing. Third, desquamation requires proteolysis of the corneodesmosomes.
Positive Selection and Alternative Splicing in Humans
Authors: Gelfand Mikhail S , Ramensky Vasily E 
Published: December 2009

Abstract

Alternative splicing is an important mechanism of generating protein diversity and accelerated genome evolution. The mode of the selection acting in constitutive, major alternative and minor alternative regions of human genes is different. Whereas constitutive and major alternative regions tend to evolve under negative (stabilizing) selection, alternatively spliced exons from minor isoforms experience lower selective pressure at the amino acid level accompanied by weak selection against synonymous sequence variation. The McDonald–Kreitman test uses the nucleotide variation for a gene or a set of genes between and within species to detect the positive Darwinian selection in the presence of negative selection. The results of the test suggest that alternatively spliced exons are also subject to positive selection, with up to 27% of amino acids fixed by positive selection.

Key concepts

Alternative splicing is an important mechanism of generating protein diversity and accelerated genome evolution.

Alternatively spliced regions are often evolutionarily young.

There is a difference in the selection mode in constitutive, major alternative, and minor alternative regions of human genes.

Constitutive and major alternative regions evolve under negative (stabilizing) selection.

Up to 27% of positions in minor alternative regions may be experiencing positive selection.
Mutation Rate of Non‐
Cp
G
DNA
Authors: Furano Anthony V , Walser Jean‐Claude 
Published: December 2009

Abstract

Base substitutions (mutations) change the informational content of
deoxyribonucleic acid
(DNA). Therefore, understanding the determinants of the base mutation rate is a fundamental problem in biology. Biochemically, mutations are a function of the fidelity of DNA replication, damage and repair. Each can be affected by nucleotide composition and context. However, various downstream factors determine the ultimate survival of these mutations in a population, including natural selection and chance (genetic drift). The result in mammals is two dramatically different mutation rates. The C of most CpG dinucleotides mutates approximately 10‐ to 50‐fold faster than Cs in other contexts or any other nucleotide (i.e. in non‐CpG sites). But, the non‐CpG mutation rate also varies between different genomic regions. Here we address the difference between CpG and non‐CpG mutation rates and the factors that are correlated with the variance in non‐CpG rates. A predominant one is CpG content.

Key concepts:

Evolutionary processes determine the extent to which the base substitutions (mutations), which result from biochemical errors inherent in the processes that replicate and maintain the integrity of the genome, contribute to the mutation rate experienced by a population.

These biochemical mutations are a function of the fidelity of DNA replication, the efficiency with which replication errors and DNA damage are repaired and whether DNA repair processes themselves produce errors in undamaged DNA.
Evolution of Nuclear Receptor Pseudogenes
Authors: Fairbanks Daniel J 
Published: December 2009

Abstract

Nuclear receptors (NRs) are transcription factors with
deoxyribonucleic acid
(DNA)‐binding and ligand‐receptor domains. When activated by ligands, they bind to the regulatory regions of target genes to regulate transcription. NR genes comprise relatively large gene families derived from a single metazoan parent gene through evolutionary duplication and divergence, which often produces duplication (unprocessed) pseudogenes. However, no NR duplication pseudogenes have been found in genomes examined to date. A small number of NR retropseudogenes (processed pseudogenes), and a single unitary pseudogene have been identified in the annotated human, chimpanzee, mouse and rat genomes. The unitary pseudogene (

ψ
FXR
β

) is exclusive to catarrhines and arose via mutational inactivation of the

FXR
β

gene, which is an active gene in murids. The human‐specific

ψ
ERR
α+

pseudogene arose through duplication of a DNA segment containing the

ψ
ERR
α

–retropseudogene and is an example of a duplication retropseudogene. The murid

ψ
Rev‐erb
β

and

ψ
LRH1

pseudogenes are examples semiprocessed retropseudogenes.

Key concepts

There are relatively few nuclear receptor pseudogenes in vertebrate genomes.

Identified nuclear receptor genes consist of retropseudogenes and a single unitary pseudogene.
P53 and Cell Death
Authors: Wolyniec Kamil , Haupt Sue , Haupt Ygal 
Published: December 2009

AbstractThe p53 transcription factor emerges not only as the most important tumour suppressor, but also as an intriguing scientific puzzle characterized by immense functional complexity. P53‐mediated apoptosis is a well‐established tumour suppression mechanism forming a critical barrier to tumourigenesis. Intense research into the mechanism of p53‐induced apoptosis revealed an involvement of p53 in the extrinsic and intrinsic cell death pathways, reactive oxygen species signalling and antisurvival responses. Notably, p53 exerts its effects by various direct and indirect mechanisms engaging transcriptional activation or repression of target genes as well as transcriptional independent modes of action. Importantly, more than 20 years of intense research has paved the way for a rational design of selective anticancer therapies aimed at restoration of p53 functionality in cancer cells.Key concepts:Apoptosis (programmed cell death) is a fundamental cellular process during development, maintenance of tissue homeostasis, and in cellular response to stress.P53 function is compromised in most cancer cases either by direct mutations (50%) or by indirect mechanismsP53 is a transcriptional factor that binds to specific target DNA sequences to either transcriptionally activate or repress genes.P53 activates multiple apoptotic signalling pathways (extrinsic and intrinsic) thereby promoting an efficient apoptotic response.The majority of pro‐apoptotic activities of p53 are mediated through the induction of specific apoptotic target genes, e.g.Bax,PumaandNoxa.P53 also contributes in the mitochondrial outer membrane permeabilization due to its relocalization to mitochondra and interaction with Bcl‐2‐family members.Harnessing p53 for cancer therapy is a promising strategy to combat cancer by reactivating pro‐apoptotic function in neoplastic cells.
Difference Gel Electrophoresis (
DIGE
)
Authors: Granlund Irene , Hall Michael , Schröder Wolfgang P 
Published: December 2009

Abstract

One of the largest challenges in proteomics today is to be able to quantify the composition and amount of proteins found in a specific cell or tissue at a defined time point. Difference gel electrophoresis (DIGE) is a gel electrophoresis‐based technique for protein quantification in complex mixtures. In DIGE the high resolution of two‐dimensional gel electrophoresis is combined with the excellent dynamic range obtained by fluorescent tag labelling of protein samples. The output of DIGE experiments provides information about how many proteins display changed expression levels on a specific treatment. In addition, proteins of interest can be excised and identified with conventional mass spectrometry techniques and further analysed by other biochemical methods.

Key concepts:

DIGE is a gel‐based technique for relative protein quantification in complex protein samples.

Experimental design, sample preparation and data analysis are all critical steps of a DIGE experiment.

Labelling of protein samples is performed by either a minimal or saturation labelling procedure.

Use of an internal standard minimizes gel to gel variation and provides increased power to the experiment.

For protein identification poststaining of gels is necessary when a minimal labelling procedure has been used.

DIGE can also be used for other applications such as native gel electrophoresis of protein complexes.

The DIGE technique is constantly being improved and continues to be an important method in functional proteomics.
Metapopulation Ecology
Authors: van Nouhuys Saskya 
Published: December 2009

Abstract

A metapopulation is a spatially structured population that persists over time as a set of local populations in balance between local extinction and colonization. Starting in 1969, and accelerating since the early 1990s, mathematical models of metapopulations have shown the importance of landscape connectivity and dispersal for persistence of a species or of interacting species. Some metapopulation models have been fit to empirical data. Although pure metapopulations may be rare, there are many empirical studies in which metapopulation processes, primarily local colonization and extinction, have been useful in explaining dynamics of natural and experimental systems. Metapopulation ecology is used in conservation biology and in population genetics where it influences genetic structure, the rate and trajectory of evolution and even what traits are under selection. Finally, communities of species that are distributed in a landscape potentially form metacommunity, which is a concept that shares important characteristics with metapopulations.

Key concepts:

A metapopulation is made up of semiindependent local populations.

In a metapopulation there is interplay between local and regional population dynamics.

While few species may live as metapopulations in the strict sense, many species depend on metapopulation processes. That is, a species regional persistence depends on asynchronous local dynamics and dispersal.

Predator–prey and competitive interactions may persist on a landscape scale due to metapopulation processes.
Plant Communication
Authors: Heil Martin 
Published: December 2009

Abstract

Plants can use volatile organic compounds released from herbivore‐infested neighbours to anticipate future enemy pressure and adjust their defensive phenotype accordingly. The most likely explanation for the evolution of this phenomenon is that plants use volatile signals for within‐plant signalling, that is, to mount a systemic response to local damage in as yet undamaged parts. The benefits of this within‐plant signalling are obvious and the same remains true for the receivers of cues that allow them to anticipate upcoming enemy attack. By contrast, no study has demonstrated that the emitting plant benefits from warning its neighbours. The question remains open whether this signalling phenomenon represents communication or, rather, eavesdropping.

Key concepts:

Plants are sessile organisms and require phenotypic plasticity to cope with a rapidly changing and in part unpredictable environment.

Plants express induced systemic resistance to herbivores and pathogens.

Plants can anticipate future enemy attack by perceiving cues that are released from damaged neighbours.

Volatile organic compounds play multiple roles in the resistance of plants to pathogens and herbivores.

Communication is defined differently, making it difficult to clearly apply the term ‘plant communication’ to signalling between plants.

Volatile organic compounds serve as signals exchanged among plants and carnivores and likely also serve as plant hormones.
Immunity, Granzymes and Cell Killing
Authors: Waterhouse Nigel J , Susanto Olivia , Sedelies Karin A , Trapani Joseph A 
Published: December 2009

Abstract

Cytotoxic lymphocytes protect us from viral infection and cancer by directly killing tumour cells, or cells harbouring a virus. One crucial mechanism they use to kill their targets is known as the ‘granule exocytosis’ pathway. This involves secretion of a potent mix of toxins, resulting in transfer of granule proteases (granzymes) from the killer cell into the target cell, where they cleave various intracellular substrates to activate diverse signalling pathways to cell death. Access to the target cell cytosol depends on a pore‐forming protein toxin, perforin. Because granule exocytosis is a crucial part of the body's natural defence against such dangerous cells, understanding how granzymes kill their targets may yield novel strategies and identify new molecular targets for anticancer or antiviral therapies.

Key Concepts:

The critical role of cytotoxic T lymphocytes and natural killer cells is to eliminate abnormal cells, thereby defending higher organisms against intracellular infection.

An important additional function of cytotoxic lymphocytes also encompasses their role in surveillance against transformed cells.

Perforin and granzymes synergize to kill target cells. Perforin is critical to this process and its role is to enable granzyme proteases to access key substrates in the target cell.

Granzyme B is the most potent pro‐apoptotic granzyme, as it shares with caspases the capacity to cleave its substrates after key aspartate residues.

Cytotoxic lymphocytes have developed a plethora of different signalling pathways to bring about target cell death. This is critically important as viruses are adept at blocking cell death to maximize their opportunity for viral replication and spread to uninfected cells.

Apart from inflicting cell death, granzymes have additional functions such as directly interfering with viral replication and in cytokine processing, leading to amplification of the inflammatory response to pathogens.

Dysregulation of cytotoxic T cell function can sometimes lead to adverse effect such as autoimmune tissue damage.
Platypus Genome Provides Unique Insights into Early Mammalian Evolution and Monotreme Biology
Authors: Grützner Frank 
Published: December 2009

Abstract

Whole‐genome sequence has been available from species of two mammalian subclasses (marsupials and eutherian mammals) but not monotreme mammals. Monotremes (platypus and echidna) are the most distant living mammalian relatives to humans, which diverged more than 160 million years ago. In addition to the key phylogenetic position they also feature fascinating biology (e.g. egg‐laying, venom, electroreception and multiple sex chromosomes). The recently completed draft genome of the duck‐billed platypus fills this gap in comparative genomics, and provides unique insights into the evolution of mammalian genes, regulatory mechanisms and nonprotein‐coding sequences. The platypus genome project also revealed first insights into the gene sets underlying the unique biology of monotremes.

Key concepts:

Monotremes are the most basal mammalian group of egg‐laying mammals (including platypuses and echidnas) that provide unique insights into the evolution of mammals.

Mammals are a group of animals, which share fur, mammary glands and a placenta. This group includes eutheria (e.g. humans and mice), metatheria (e.g. kangaroos) and prototheria (egg‐laying platypus and echidna).

Genomics describes the analysis of sequences of whole genomes.

In Comparative Genomics information on genomes of various species is compared to provide insights into the evolutionary change of different aspects of genomes (e.g. chromosomes, genes, regulatory regions and repeats).

Rapid progress in large‐scale DNA sequencing technology allows Genome Projects to determine the sequence of entire genomes of a rapidly growing number of organisms.

Genome composition describes basic characteristics of whole genomes including size, estimated gene number, repeat content and base pair composition.

Genome analysis provides a prediction of most of the genes in a genome, which reveals presence or absence of genes and gives insights into function and evolution of typical characteristics of the species.

All genetic information generated by publicly funded genome projects or published by individual researchers are deposited in Genome databases (also called genome browsers like UCSC or ENSEMBL) which allow searches and comparisons of billions of sequences of hundreds of species.