bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant Interactions with Herbivores
Authors: Blumenthal Dana , Augustine David 
Published: September 2009

Abstract

Plants are eaten by a tremendous array of herbivores, including almost half of known insect species. Although herbivores consume most plants to some degree, many plants are also relatively well defended, and herbivore populations are often limited by predators. The net result of these processes is that the extent of herbivory, and the strength of its effects on plant populations and ecosystem processes, are highly variable. Herbivores strongly influence plants in aquatic environments, productive environments and environments with nutritious, poorly defended plants or few predators. Effects of herbivores can also be accentuated through positive feedbacks between herbivory and soil resources, in which herbivore‐mediated changes in plant community composition accelerate or decelerate nutrient cycling. Although research on herbivory has focused primarily on natural systems, few of these systems are free of human influence. Humans dramatically change plant–herbivore relationships by removing predators, increasing plant resource availability and moving both plants and herbivores around the globe.

Key concepts

Plants defend themselves effectively, using a combination of chemical defences and physical defences and tolerance.

Plant defence theory aims to explain variation among species and ecosystems in the types and amounts of plant defence.

In addition to plant defences, the extent of herbivory is limited by predation, which can greatly reduce herbivore abundance.

Despite plant defences and predation, herbivores often have strong effects on plants.

Positive feedbacks between plant resources, plant traits and herbivores can increase the influence of herbivores on plants and ecosystems.

Humans dramatically alter plant–herbivore dynamics by moving plants and herbivores, reducing the abundance of predators, increasing nutrient availability and changing the spatial distribution of plant communities.
Palaeoecology
Authors: Seppä Heikki 
Published: September 2009

Abstract

The basis of palaeoecological research is to use the fossil remains preserved in sedimentary deposits to investigate the history and long‐term dynamics of taxa, populations, communities and ecosystems. Palaeoecological methods can also be used for reconstructing past climatic conditions and other environmental factors. Palaeoecological records extend from years to millions of years and can therefore be used for testing the hypotheses of neo‐ecology and biogeography under environmental conditions different and more extreme than in the modern Earth. Palaeoecology provides often the only means to investigate species macro‐ and microevolutionary patterns or rates of speciation and extinction, and slow ecological processes, such as the rise and fall of ecosystems and biomes, species adaptation or migration, and population growth or decline rates. Palaeoecological records also provide unique insights for identifying the ancestry and naturalness of modern ecosystems and are increasingly recognized as sources of baseline information in ecosystem management.

Key concepts:

Ecosystem dynamics over long‐time periods, niche conservatism, hypothesis testing, transfer functions, background for ecosystem management.

Biography information: Heikki Seppä has written the text. He is a Quaternary palaeoecologist and palaeoclimatologist.
History of Antimalarial Agents
Authors: Greenwood David 
Published: September 2009

AbstractMalaria is a debilitating and, in its most severe form, falciparum malaria, a potentially fatal disease. Treatment in the form of powdered bark of the cinchona tree from South America has been available from at least the seventeenth century. Synthetic antimalarial agents were not developed until the twentieth century, stimulated by serious shortages of supply during the two World Wars. The first advances were made in Germany in the interwar period. During and after World War II, further progress was made in Britain and the United States. Inevitably resistance to these agents emerged and became a major problem after the 1960s. Other active chemicals have since been developed, but many have serious side effects and much hope is now pinned on derivatives of a natural product, artemisinin, obtained from sweet wormwood (Artemisia annua) and used for centuries (though not at first for malaria) in traditional Chinese medicine.Key ConceptsMalaria is a potentially fatal disease affecting millions of people, chiefly in tropical countries.A treatment in the form of powdered bark of the cinchona tree from northern South America has been available since the seventeenth century.Cinchona bark contains several antimalarial alkaloids, most importantly quinine.Synthetic antimalarial agents were first developed in Germany in the 1920s and 1930s.The first antifolate compound active against malaria, proguanil, was developed in England during World War II.After World War II, several important synthetic antimalarial compounds, notably chloroquine and pyrimethamine became available for prophylaxis and treatment.From the 1960s resistance emerged as a major issue and quinine once again became the treatment of choice for serious falciparum malaria.Derivatives of artemisinin, a natural product used in traditional Chinese medicine, is being now being successfully used in treatment.
Regulatory Genes in Plant Development:
MADS
Authors: Ma Hong 
Published: September 2009

Abstract

MADS‐box genes are found in all major groups of eukaryotes and encode known or putative transcription factors. MADS‐box genes have been phylogenetically defined as type I and type II genes. In plants, type II MADS‐domain proteins typically have the MADS, Intervening, K‐domain,
C
‐terminal (MIKC) domain organization, with conserved MADS and K domains. Many of the plant type II MADS‐box genes have important regulatory functions in development, including the specification of flower organ identities, the control of flowering time, the regulation of meristem identity and the promotion of reproductive organ development. Recent studies have provided further insights into the regulation of MADS‐box genes and uncovered additional functions in controlling the development of various structures, such as embryo, endosperm, gametophyte and roots. In addition, protein physical interaction and genetic studies support the hypothesis that MADS‐box proteins form multimeric protein complexes that regulate specific target genes.
Bacterial Membrane Transport: Superfamilies of Transport Proteins
Authors: Padan Etana 
Published: September 2009

Abstract

The bacterial transport systems enable bacteria to accumulate needed nutrients, extrude unwanted by products and maintain cytoplasmic content of protons and salts conducive to growth and development. Two most widely spread superfamilies of transporters are the ion‐coupled systems that take part in chemiosmotic circuits, and the ABC solute
ATPases
(
adenosine triphosphatases
), whose operation is linked to ATP hydrolysis. The crystal structure of several bacterial transporters has recently been determined, a major breakthrough in the research of transporters. It opened the field to a combined study of structure, function and computation. Several of the structurally deciphered bacterial transporters have eukaryotic orthologues including neurotransmitter transporters that play major roles in health and disease and are major drug targets. Hence, the bacterial transport systems are important both for elucidating the mechanism of transport as well as drug design.

Key concepts:

Crystal structures are essential for understanding the mechanism of transport.

Topology model of transporters obtained from the primary amino acid sequence, the positive‐inside rule and experimental data have been validated by the crystal structure.

Primary transporters utilize external source of energy to drive active transport.

The secondary transporters utilize the energy stored in a pre‐existing gradient to drive transport.

The MFS, major facilitator superfamily, encompasses the largest number of evolutionary related most diverse group of secondary transporters and the extensively studied LacY and GlpT with their crystal structures are educative examples.

Na
+
/H
+
antiporters are essential for sodium and pH homeostasis in all cells and the most studied
Escherichia coli
NhaA with its crystal structure is an educative example.

The sodium‐coupled secondary transporter LeuT is a bacterial homologue of human neurotransmitters transporters and therefore its crystal structure is an essential step in drug design.

The alternating access model is the mechanism of activity of secondary transporters.

The molecules of many secondary transporters exhibit internal symmetry that implies a unique evolution.

The internal symmetry of secondary transporters with the inverted repeats and the interrupted helices in the middle of the membrane is the structural basis of the activity mechanism.
Data Protection Legislation
Authors: Holm Søren 
Published: September 2009

Abstract

Data protection legislation regulates the acquisition, storage, transfer and processing of personal data of all kinds. Human genetic information, whether in digital form or in tissue samples, is by definition personal data and its use will therefore in many cases be governed by data protection legislation. The article introduces the key distinction between data security and wider data protection, and further explores the key legal requirements for data protection. In general, the requirements for legal use of genetic data are informed consent to acquisition and fair processing of any data that are held or generated. The approach to data protection differs between the European Union and the USA and these differences are explained.

Key concepts:

The purpose of data protection legislation is to ensure (1) data security and (2) that data acquisition and processing only occurs in accordance with the law.

Data acquisition usually requires informed consent from the data subject.

There are different rules for the processing of identifiable and nonidentifiable personal data.

There are specific protections in relation to sensitive data, including health data.

Anonymity and nonidentifiability are two different concepts.

Identifiability is only absent if deductive identification is very difficult.

The approach to data protection differs significantly between the European Union and the USA.
Informed Consent: Ethical and Legal Issues
Authors: Holm Søren 
Published: September 2009

Abstract

Informed consent from research participants is a necessary legal and ethical requirement for human genetics research. Valid informed consent relies on giving full information and on the capacity of research participants to consent.
The article describes the historical development of the concept of informed consent in biomedical research and explores its current embedding in international legal documents. It discusses the specific problems of informed consent in fast‐moving research areas and the possible solution in the so‐called ‘broad’ consent. The specific issues raised in relation to consent from minors and other incompetent persons are discussed, as is the research use of old tissue sample and other materials obtained without consent.

Key concepts

Informed consent is a central concept in modern research ethics and law.

Valid consent can only be obtained if the prospective research participant is fully informed and is competent to consent.

In fast‐moving research fields where future research use is difficult to predict, ‘broad’ consent may be used in certain circumstances.

For persons who are incompetent to consent, researchers must often rely on proxy consent (e.g. parents consenting for small children).

A proxy must make a decision to consent based solely on considerations of the best interest of the incompetent person.
Interests of the Future Child
Authors: McLean Sheila AM 
Published: September 2009

AbstractModern technology makes it possible for intending parents to make certain choices about the characteristics of their future children, when they seek to establish a pregnancy usingin vitrofertilization (IVF) combined with pre‐implantation genetic diagnosis (PGD). Moreover, choices about whether or not to continue with a pregnancy are also available in those countries where prenatal screening and pregnancy termination are available. Although by and large these decisions are seen as reflecting the rights of people to make free, uncoerced choices (the concept of reproductive liberty) others condemn them either as eugenic or as amounting to killing children. However, increasing emphasis on the commitment to future generations may increasingly impact on the reproductive decisions made by prospective parents. Arguably, the concept of reproductive liberty may be modified by the notion of intergenerational justice.Key conceptsAn understanding of the concept of reproductive liberty.An understanding of the concept of intergenerational justice.An understanding of the arguments for and against the use of Pre‐implantation Genetic Diagnosis.
Haemophilias: Gene Therapy
Authors: Callaghan Michael , Kaufman Randal J 
Published: September 2009

Abstract

Haemophilia A and B are the two most common severe congenital bleeding disorders and each is corrected with infusion of a single plasma protein. Preliminary data from animal models and from clinical trials in humans suggest that gene therapy may be effective in the haemophilias. Advances in vector technology combined with improved trangenes and knowledge of factors VIII and IX secretion in target tissues over the past several years have improved the prospects of gene therapy for the haemophilias.

Key Concepts

Understand the roles of factors VIII and IX in the intrinsic coagulation cascade.

Understand that both haemophilia A and B are caused by single gene mutations inherited in an X‐linked recessive pattern.

Understand the clinical features of haemophilia A and B.

Understand that haemophilia A and B are excellent models for gene therapy because of the wide range of protein levels that can be both therapeutic and not toxic.

Understand issues that determine target tissue suitability for gene therapy.

Understand the importance of efficient transgene transfection and secretion and the role of bioengineered transgenes.

Understand the potential for accumulation of unfolded or misfolded protein accumulation with overexpression of a transgene in a target tissue and the possibility of toxicity through induction of the unfolded protein response.

Understand the advantages and disadvantages of available vector technologies including: nonviral delivery systems, retroviral vectors, adenoviral vectors and adeno‐associated viral vectors.

Become familiar with results from gene therapy clinical trials in the haemophilias.

Become aware of the ethical and regulatory considerations in haemophilia gene therapy.
Wetland Communities
Authors: Sharitz Rebecca R , Batzer Darold P 
Published: September 2009

Abstract

Wetland communities are assemblages of individuals of different species (plants, animals, microorganisms) living and interacting together in habitats that have water at or near the surface of the ground, or where the land is flooded by shallow water, for much of the year. These organisms are adapted to life in saturated soil conditions, which can include intermittent flooding, anoxia and potentially harsh water and soil chemistries. Wetland communities may be broadly grouped into coastal, including salt marshes, tidal freshwater marshes and forested mangrove swamps; and inland, including freshwater marshes, freshwater swamps, riparian wetlands (along streams and rivers) and peatlands (including bogs and fens). Hydrological conditions such as the source, depth, flow rate and timing of water presence are the fundamental determinants of the composition and structure of wetland communities.

Key Concepts

Definition and classification of wetland communities.

How wetland and upland communities differ in species richness and composition.

Successional development of wetland communities.

Abiotic and biotic factors affecting wetland community composition.

How competition and facilitation affect wetland plant community composition.

Effects of herbivory and predation on wetland communities.

Threats to wetland communities and wetland losses.
RNA
Silencing and its Suppressors in the Plant‐virus Interplay
Authors: Valli Adrián , López‐Moya Juan José , García Juan Antonio 
Published: September 2009

Abstract

Viruses are obligate intracellular parasites that need to evade the host defences targeted against them. In plants, activation of
ribonucleic acid
(RNA) silencing is among the most powerful responses against viruses. To overcome this defence, both
deoxyribonucleic acid
(DNA) and RNA plant viruses make use of viral products able to interfere with silencing mechanisms, and known collectively as RNA silencing suppressors (RSSs). RSSs present an extraordinary diversity in modes of action, and therefore, their study is providing valuable information about the different silencing pathways in plants. This article reviews our knowledge on RSSs, including the experimental systems used to identify them, and the mechanisms by which they act. Finally, the additional effects that they cause in the network of silencing pathways, and hence the need of a tight control of their activity, are also considered.

Key concepts:

Argonaute: Family of proteins that contain certain conserved domains, such as PIWI domain (found in Piwi, or P‐element‐induced wimpy testis in
Drosophila
, and related proteins) and PAZ domain (found in Piwi, Argonaute and Zwille proteins). Proteins of this family are the main components of RNA silencing effector complexes.

Dicer: Ribonuclease belonging to the RNase III family. Dicer‐like enzymes cleave hairpin or double‐strand RNA molecules into short RNA duplexes of 20–24 nucleotides with a 2‐nucleotides overhang at the 3′ ends, which are key components of the RNA silencing pathways.

microRNA (miRNA): Endogenous single‐strand RNA of 20–21 nucleotides, which derives from a hairpin precursor. miRNAs are incorporated into RISC, guiding it, by base complementary, to silence endogenous mRNAs.

RNA‐dependent RNA polymerase (RdRP, RDR): Enzyme able to synthesize RNA using RNA as template. These enzymes are involved in amplification steps of RNA silencing.

RNA‐induced silencing complex (RISC): Multicomponent complex including an Argonaute protein and a short RNA. RISC can silence mRNAs by endonucleolytic cleavage, decay acceleration and translation inhibition.

RNA‐induced transcriptional silencing complex (RITS): Multicomponent complex including an Argonaute protein and a short RNA that silence gene expression by inhibiting or downregulating the transcription activity.

RNA silencing: General term used to describe different events triggered by small RNAs to induce transcriptional or posttranscriptional gene downregulation in a sequence‐homology manner.

RNA silencing suppressor (RSS): Factor (usually a protein) with the capacity to interfere with the onset of RNA silencing or with its maintenance. The expression of viral RSSs is the most common strategy that plant viruses use to escape from RNA silencing.

Short interfering RNA (siRNA): Small RNA of 20–24 nucleotides derived from Dicer‐mediated cleavage of a double‐stranded RNA precursor. One of the strands of the siRNA is incorporated in RISC or RITS to guide their RNA silencing effector activities.
Analysis of the Amphioxus Genome
Authors: Satoh Noriyuki 
Published: September 2009

AbstractAmphioxus or cephalochordates are small fish‐like marine invertebrates. The sequenced genome ofBranchiostoma floridaeis approximately 520 Mb in size and estimated to contain approximately 21 900 protein‐coding loci. Comparison of the amphioxus genome with genomes of other animals made a great impact on the resolution of the long‐standing question of the origin of vertebrates. First, chordates are monophyletic group, in which cephalochordates represent the most basal extant chordate lineage, with urochordates sister to vertebrates. Second, there is highly conserved synteny between the cephalochordate and vertebrate genomes. This allows reconstruction of 17 ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes. Third, the two rounds of genome‐wide duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates. Fourth, whereas most duplicate genes have been lost, a disproportionate number of genes are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.Key conceptsThe phylum Chordata consists of the subphyla Cephalochordata (amphioxus), Urochordata (ascidians) and Vertebrata, and these three groups are characterized by possession of a notochord, a hollow dorsal neural tube, a perforated pharyngeal region and a post‐anal tail.Chordates are monophyletic group in which cephalochordates represent the most basal extant lineage, suggesting a free‐living ancestor of chordates.Seventeen ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes are revealed by highly conserved synteny between the two genomes.The two rounds of genome‐wide gene duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates.A disproportionate number of genes which were produced by the genome‐wide duplication are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.
Recombination Rates in Drosophila
Authors: Stevison Laurie S , Noor Mohamed A F 
Published: September 2009

AbstractRecombination occurs during meiosis to produce new allelic combinations in natural populations, making it important for studying evolution. The model systemDrosophilahas been crucial for understanding the mechanics underlying recombination and assessing the association between recombination rate and several evolutionary parameters.Drosophilawas the first system in which genetic maps were developed using recombination frequencies between genes. Linkage maps have been subsequently developed in many biological systems, including humans. Fungal systems have been helpful in highlighting the mechanics of recombination and identifying particular enzymes that perform various steps in the process; however, similar proteins have been identified inDrosophila. Further,Drosophilahas been used to determine genetic and environmental conditions that cause variation in recombination rate. Finally,Drosophilahas been instrumental in elucidating associations between local recombination rate and nucleotide diversity, divergence and codon bias, as well as helping determine the causes of these associations.Key ConceptsRecombination refers to either independent assortment or crossing over, both of which are responsible for introducing genetic variation during meiosis.Drosophilahas been crucial in the development of genetic mapping techniques, which have been extended to other organismal systems including humans.Fungal systems have been critical to the discovery of the underlying mechanics of crossing over.Several key environmental conditions that cause recombination rate variation have been identified primarily inDrosophila.Recombination rate variation within a genome is in part due to ‘hotspots’ that concentrate double‐strand breaks to particular regions of the genome.The demonstrated relationship between nucleotide diversity and recombination rate inDrosophilahas been repeated in many organismal systems.The relationship between recombination rate and genetic divergence has been less repeatable between different organismal systems, due to either mechanical or evolutionary processes.