bluuebunny/crossref_metadata_2025 huggingface dataset:
Foot‐and‐Mouth Disease
Authors: Belsham Graham J , Charleston Bryan , Jackson Terry , Paton David J
Published: March 2009

Foot‐and‐mouth disease (FMD) is an economically important, highly contagious disease of cloven‐hoofed animals characterized by the appearance of vesicles (blisters) on the feet and in and around the mouth. The causative agent,
foot‐and‐mouth disease virus
(FMDV), was the first mammalian virus to be discovered. It has a
ribonucleic acid
(RNA) genome enclosed within a protein coat. The virus replicates very rapidly within the cytoplasm of cells. The RNA genome has to function both as a messenger RNA (mRNA) and as a template for RNA replication. The RNA encodes a single polyprotein which is processed, by
virus‐encoded proteases
, to about 12 mature products which are required for virus replication and assembly. Some of these viral proteins modify host cell activities to block antivirus defence systems. Thus, this small virus displays a remarkably complex array of biological activities.

Key concepts

Foot‐and‐mouth disease has worldwide economic importance.

Foot‐and‐mouth disease virus (FMDV) is able to replicate rapidly in a range of different animals and then spread within the environment.

FMDV uses specific cell‐surface molecules as receptors to gain entry into cells.

The viral RNA displays diverse activities, as a messenger RNA, as a template for RNA replication and as the genome.

The virus‐encoded polyprotein is processed by proteases present within itself to make about 12 different mature products (plus important precursors).

Viral proteins are required both for viral RNA replication and virus assembly, in addition, some also modify specific cellular functions in order to block host antiviral responses.
Poliovirus
Authors: Bradrick Shelton S , Romero José R , Minor Philip D
Published: March 2009

Poliovirus is a well‐characterized member of the Picornavirus family. The picornaviruses are positive strand RNA (
ribonucleic acid
) viruses responsible for many human and animal diseases and the relationships between them have been greatly clarified by molecular data. The atomic structures of polio and several other picornaviruses were solved in the 1980s, and the sequence of many strains determined. The growth cycle involves attachment to a specific receptor found only in Old World monkeys and the higher primates and the viral proteins are synthesized using an internal ribosome entry site in the genome as a single large precursor later cleaved to give the functional viral proteins. The pathogenesis of poliovirus has been intensively studied although many aspects remain poorly understood. Vaccines developed in the 1950s and 1960s are likely to lead to the eradication of the disease in the near future.

Key concepts

Classification of viruses on the basis of sequence comparisons.

History of disease.

Positive strand RNA viruses: classification and recombination between related nonsegmented viruses.

Molecular structure of the picornaviruses.

Receptor site usage and host restriction.

Translation and replication strategies: the internal ribosome entry site.

Pathogenesis of the enteroviruses: localization of replication in different compartments.

Vaccine types, usage and effect in eradication and control programs.
Viruses: Genomes and Genomics
Authors: Williams Çiğdem H , Stanway Glyn
Published: March 2009

The virus genome is the nucleic acid component of a virus which encodes the genetic information. The type of nucleic acid inside the virus particle (
ribonucleic acid
(RNA)/
deoxyribonucleic acid
(DNA), single/double strands) and whether or not the virus uses reverse transcription during replication are fundamental classifications criteria dividing viruses into seven classes. Even within these classes there is great range of genome sizes and organizations, making viruses highly diverse entities. The usually small size of virus genomes makes them particularly amenable to sequencing, and as high‐throughput methods become more commonplace, virus genomics is becoming increasingly prominent. It promises to provide a wealth of new information on the function of virus proteins and nucleic acid structures, virus evolution and how viruses cause disease, which will underpin the development and monitoring of new therapeutic approaches.
Pathogenic Viruses: Clinical Detection
Authors: Zuckerman Mark
Published: March 2009

The clinical and laboratory diagnosis of the viral aetiology of an individual's illness involves understanding their clinical symptoms and signs, how the host's immune system responds to a viral infection, as well as which diagnostic tests are the most sensitive and specific to detect that virus or the host's immune response. Once the choice of test is made, the correct specimen must be collected and the results of these tests interpreted in the context of the clinical picture.
Polytene Chromosomes
Authors: Zhimulev Igor F , Koryakov Dmitry E
Published: March 2009

Polytene chromosomes are specific interphase chromosomes consisting of thousands ofdeoxyribonucleic acid(DNA) strands. For this reason they are very large and display a characteristic band–interband morphology. Polyteny arises in tissues, organs and at developmental stages when there is need for the rapid development of an organ at an unaltered high level of function. Organs containing cells with polytene chromosomes are, as a rule, involved in intense secretory functions accomplished during a short time against a background of rapid growth. Chromosome rearrangements andin situhybridization on polytene chromosomes allow genes to be mapped to a resolution of a few tens of kilobases. Polytene chromosomes allow a specific narrow region to be dissected out with a micromanipulator and a library of DNA clones to be derived from the region.

Key concepts:

Polytene chromosomes are specific type of interphase chromosomes consisting of thousands of DNA strands.

Polytene chromosomes have been found in many tissues of the representatives of two orders of insects: Diptera and Collembola, in the macronuclear anlagen of Infusoria, in certain organs and tissues of mammals and also in the cells of the synergids, antipods and endosperm of angiospermous plants.

Polyteny arises in tissues, organs and at developmental stages when there is need for the rapid development of an organ at an unaltered high level of function. Organs containing cells with polytene chromosomes are, as a rule, involved in intense secretory functions accomplished during a short time against a background of rapid growth.

Along the linear axis polytene chromosome have variation in the concentration of the chromatin. Regions of high concentrations are known as chromomeres (bands), and regions with low concentrations are known as interchromomeres (interbands).

The pattern of bands and interbands in each polytene chromosome is specific for the species, and in general is characteristic of that particular chromosome in different tissues or at different developmental stages.

Polytene chromosomes are now considered to be very important objects for the analysis of numerous features of interphase chromosome organization and the genome as a whole.
Lymphocytes: Intraepithelial
Authors: Cheroutre Hilde , Lambolez Florence
Published: March 2009

Intraepithelial lymphocytes (IEL) are small, round mononuclear immune cells, which reside in the paracellular space between nonimmune epithelial cells. They are found in the skin and within the epithelial layer that lines the intestine, the biliary tract, the oral cavity, the upper respiratory tract and lungs and the reproductive tract. The largest population of IEL resides within the epithelium of the small intestine where they form the first line of immune defence against invading pathogens while preserving the integrity of the mucosal barrier.

Key concepts

The lymphocytes located in the epithelium are at the frontline between the self and nonself.

The T‐cell populations from the small intestine are the most important in number and the most diverse in the body.

The T‐cell populations from the epithelium often contain unconventional subpopulation such as CD8aa TCRab+ IEL in the intestine.

Introduction of the new concept of agonist selection for self‐specific CD8aa TCRab+ IEL.

Important function of IEL during immune response against pathogens.
Rubisco
Authors: Portis Archie R , Parry Martin AJ
Published: March 2009

Rubisco, formally known asribulose‐1,5‐bisphosphate (RuBP) carboxylase/oxygenase, is the chloroplast enzyme that assimilates atmospheric carbon dioxide during photosynthesis by combining it with RuBP to form two molecules of phosphoglycerate. However, Rubisco allows oxygen to react with RuBP in addition to carbon dioxide, producing phosphoglycolate, and thereby also initiates the process known as photorespiration. Genetic modification to overcome the limitations of Rubisco would have great agronomic importance.
Heavy Metal Adaptation
Authors: Herrera‐Estrella Luis Rafael , Guevara‐García Angel Arturo
Published: March 2009

Fifty‐three chemical elements fall into the category of heavy metal (HM) defined as the group of elements with densities higher than 5 g cm
−3
. In an ecological sense, any metal or metalloid that causes environmental pollution or that cannot be biologically degraded and is therefore bioaccumulated, should be considered as an HM. HMs are natural components of the Earth's crust, but as a consequence of human activities, in many ecosystems the soil concentration of several HMs has reached toxic levels. The adaptative responses of living organisms to HM contamined environments are efficient processes that include genetical, physiological, anatomical and ecological traits highly conserved in nature. These traits give certain species the ability to survive in toxic concentrations of HM elements. Actually, using multidisciplinary strategies including genomic, genetic, molecular, biochemical, physiological, ecological and agronomic approaches, substantial progress is being made to elucidate the mechanism involved in HM adaptation.
Oxidative Stress
Authors: Fridovich Irwin
Published: March 2009

Respiring organisms derive multiple benefits from molecular oxygen. However, some fraction of the oxygen used is unavoidably converted to dangerous substances such as the superoxide radical (O2−), hydrogen peroxide (H2O2) and the hydroxyl radical (HO). These intermediates of oxygen reduction threaten the integrity of diverse biological molecules and hence the life of cells and organisms. The seeming comfort of aerobes in the presence of oxygen is due to their content of multilayered defences against these reactive metabolites of oxygen. There are superoxide dismutases that eliminate O2−by efficiently converting it to oxygen and H2O2. There are catalases that eliminate H2O2by dismuting it into water plus oxygen and there are also peroxidases that eliminate H2O2and organic peroxides by reducing them to H2O2and to alcohols, respectively. Removing O2−and H2O2prevents the formation of HO. However, no defence is perfect so backing up these frontline defences, that in large measure prevent oxidative damage, are others that repair the damage caused by the reactive derivatives of oxygen and, when that is not possible, eliminate the damaged molecules and replace them with newly synthesized ones.

Key concepts:

The spin restriction facing oxygen reduction that favours the univalent pathway of oxygen reduction.

Superoxide, hydrogen peroxide and hydroxyl radicalare intermediates on the univalent pathway.

These intermediates are reactive and can cause damage.

Defences are essential and have been evolved.

Superoxide dismutases protect against superoxide by converting it to hydrogen peroxide plus oxygen.

There are superoxide dismutases that contain copper plus zinc, manganese, iron or nickel at their active sites.

Catalases protect against hydrogen peroxide by converting it to oxygen plus water.

There catalases with haem iron at the active site and others with manganese.

Peroxidases protect against hydrogen peroxide and against organic peroxides by reducing them to water and to alcohols, respectively.

Removing both superoxide and hydrogen peroxide prevents the formation of hydroxyl radical.

Oxidative stress contributes to multiple pathologies and to normal aging.
Physical Maps of Chromosomes
Authors: Ussery David W
Published: March 2009

Physical maps of chromosomes are a way of visualizing the entire chromosome in a single figure. Physical maps can come in a variety of formats, including actual photographs of chromosomes, genetic maps where the relative locations of genes are mapped, restriction maps showing the location of restriction enzyme cutting sites along the
deoxyribonucleic acid
(DNA), and finally maps based on the known DNA sequence along the entire chromosome.
Autoimmune Disease: Treatment
Authors: Kalden Joachim R , Burkhardt Harald
Published: March 2009

In recent years, substantial progress has been made in understanding the mechanisms of inflammation and autoimmunity, providing new targets for the development of new treatment principles. Tumour necrosis factor α (TNFα) antagonists have been proven as a major progress in the treatment of different rheumatic and chronic inflammatory bowel diseases. The interleukin 1 (IL‐1) receptor antagonist has considerably improved our medication for the systemic juvenile arthritis and periodic fever syndromes, an anti‐IL‐6 receptor monoclonal antibody might be of value as well as abatacept, a cytotoxity lymphocyte‐associated antigen 4Ig (CTLA‐4Ig) fusion protein for the treatment of patients with rheumatic diseases who do not respond to TNF antagonists. The same is true for rituximab, a chimeric anti‐CD20 antibody.

Key concepts

Mode of action and indications for the treatment with traditional and new (cyclooxygenase II, COX‐II, inhibitors), Nonsteroidal anti‐inflammatory drugs (NSAIDs).

Mode of action and indications of steroids for the treatment of autoimmune and chronic inflammatory diseases.

Disease modifying and immunosuppressive drugs, there are different modes of action.

The limitation of surgical approaches in the treatment of autoimmune and chronic inflammatory diseases such as thymectomy, splenectomy and synovectomy.

The limitation of radiotherapy and total lymphoid irradiation for the treatment of autoimmune diseases.

The limitation of plasmapheresis and leucapheresis as treatment principles for autoimmune diseases.

Cellular and juvenile targets for immune intervention in autoimmune and chronic inflammatory diseases.

Biologics for the treatment of autoimmune and chronic inflammatory diseases, modes of actions.

Monoclonal antibodies and fusion proteins for targeting T cells, B cells, cytokines and adhesion molecules.

Mechanisms that could help to reestablish self‐tolerance as well as the ultimate therapeutic goal in autoimmune diseases.
Genetic Variation: Human
Authors: Hollox Edward J
Published: March 2009

Many different types of genetic variation can be observed in the
deoxyribonucleic acid
(DNA) of modern humans. Nevertheless, humans have relatively little genetic variation compared with many other species, suggesting a recent common origin for

Homo sapiens

. Some of this variation may have functional consequences, for example in disease states and complex characters such as stature or intelligence, but much variation in DNA appears to be neutral.
Antiprotozoan Drugs
Authors: Fivelman Quinton L , Yardley Vanessa , Sutherland Colin J
Published: March 2009

Parasitic diseases caused by unicellular protozoa account for a huge burden of morbidity, mortality and economic deprivation across the globe. Current drugs for the treatment of such infections, particularly malaria, trypanosomiasis and leishmaniasis, are inadequate and new therapies are being sought. A review of currently available therapies for protozoal infections of medical importance is presented. Potential new treatments in the drug development pathway are also discussed. There are no registered vaccines available for any protozoal diseases, and only in the case of malaria are there candidate vaccines that have passed beyond Phase I clinical trials.

Key concepts

Understand the worldwide problem of parasitic protozoa and how they cause disease.

Understand the range of treatments available and which is best for a specific disease.

Understand the range of antimalarials available and their basic history.

Understand the limited treatment options available against other coccidian parasites such as
Toxoplasma
and
Cryptosporidium
.

Understand the therapies available for trypanosomiasis and leishmaniasis.

Understand the new therapies against parasitic protozoa currently under development.

Understand the various options available in the design and development of vaccines against malaria and other parasitic protozoa.
Floral Meristems
Authors: Schneitz Kay , Balasubramanian Sureshkumar
Published: March 2009

Meristems refer to a group of undifferentiated dividing cells that are responsible for the formation of plant organs. Floral meristems are a group of dividing cells that give rise to flowers. The formation of a floral meristem and its subsequent fate are under both environmental and molecular control. Several exogenous environmental factors and a complex network of genes control this process.
Trichomes
Authors: Hülskamp Martin , Schellmann Swen
Published: March 2009

A ‘trichome’ (or hair) is an outgrowth derived from the shoot or root epidermis of a plant. Form and distribution of trichomes differ between plant species or genera, but molecular work reveals common regulatory pathway for development of different trichome types within the same plant species and possibly also across plant species.
Systemic Lupus Erythematosus
Authors: Schur Peter H
Published: March 2009

Systemic lupus erythematosus is a chronic inflammatory disease of unknown cause which can affect the skin, joints, kidneys, lungs, nervous system, serous membranes and other organs in the body, in various combinations, especially in young women, and which is characterized by immune abnormalities, in particular antibodies to nuclear constituents. Treatment is based both on preventive measures, alleviation of symptoms, but in particular anti‐inflammatory agents including nonsteroidal anti‐inflammatory drugs, corticosteroids and immunosuppressive medications.
The Aetiologic Spectrum of Cerebellar Ataxia: Inherited Causes of Ataxia
Authors: Todd Peter K , Taylor J Paul
Published: March 2009

Cerebellar ataxia is a frequent finding among patients seen in neurological practice and may result in a wide variety of aetiologies, both acquired and genetic. Inherited ataxia is a large and important subgroup of the ataxic disorders, and includes metabolic ataxias, autosomal recessive degenerative ataxias, autosomal dominant spinocerebellar ataxias (SCAs), X‐linked and maternally inherited ataxias. Hereditary ataxia is reviewed in this article and acquired ataxias are covered in the accompanying article.

Hereditary conditions
account for the majority of ataxic syndromes in children and one‐third to one‐half of patients with adult‐onset ataxic syndromes. Classification by mode of inheritance is a useful way of organizing the hereditary ataxias for both clinical and research purposes, and this approach will be used in this article.

Key Concepts

Understand that there are a wide variety of different inherited causes of ataxia.

Some patients without a family history of ataxia still have the disorder on the basis of a genetic mutation.

Nucleotide expansion disorders are a common cause of dominantly inherited cerebellar ataxia. The majority of these diseases result from a toxic gain‐of‐function mechanism and they demonstrate genetic anticipation, wherein intergenerational expansion leads to disease with earlier onset and often more severe symptom.

Friedreich ataxia is the most common inherited cause of ataxia. It results from decreased expression of the Frataxin protein due to a nucleotide repeat expansion in a noncoding region.

A variety of mitochondrial disorders are associated with ataxia as one of the number of neurologic and systemic symptoms. These diseases result from mutations in either nuclear DNA in genes involved in mitochondrial function or in mitochondrial DNA itself.

Wilson disease is a disorder of copper metabolism that can present with dystonia, ataxia or neuropsychiatric symptoms and is also associated with liver failure. Early treatment can be curative.

Defects in DNA repair underlie many childhood onset forms of inherited ataxia.
Vertebrate Herbivory and Its Ecosystem Consequences
Authors: Oksanen Lauri , Olofsson Johan
Published: March 2009

Herbivory is a process where animals obtain energy and nutrients from vegetative plant parts (leaves, stems, etc.). Herbivory is called grazing, browsing or folivory, depending on the size of the herbivore and the type of plant tissue consumed. The consumption is actually performed by microbes in the digestive system. The role of the animal is to prepare the material and to provide a good environment for the microbes. This requires specializations, making herbivores a distinct animal group. This article focuses on consequences of herbivory by vertebrates. Vertebrate herbivory can change forests to heathlands or grasslands and influence the composition and species richness of the herbaceous vegetation.
Thomas Young
Authors: Weatherall DJ
Published: March 2009

Thomas Young was a remarkable polymath who, as well as working as a physician and contributing widely to the history and practice of medicine, demonstrated that light is a wave, worked out the mechanisms of colour vision and became a leading expert on deciphering hieroglyphic script.
Predator Avoidance
Authors: Abrahams Mark V , Pink Melissa , Klassen Cheryl
Published: March 2009

For prey species to be successful, they must balance the conflicting demands of obtaining the resources necessary for survival while avoiding being killed by predators. This has a hierarchy of approaches that begins with avoiding dangerous (=predators) times and locations, using dangerous locations but adopting behaviours and tactics that assist prey in detecting predators first. If a predator detects them they may also plan for this by staying in groups, thereby diluting the chance of being the individual that is killed or using coordinated group defence. Individuals may also employ toxins or specialized morphologies that deter a predator from attacking or assist in escape. Assuming individual behaviour is not affected by the presence of parasites, prey may also escape predators after capture using specialized morphologies, and even ejecting limbs. Ultimately captured prey may even try to attract other predators with the hope of escaping during the ensuing melee.

Key concepts

Behavioural tradeoffs.

The role of predators in affecting habitat quality.

Costs and benefits of group living.

The role of antipredator morphology.

Batesian and Mullerian mimicry.

The impact of parasites and how they can modify behaviour.

Animal scaling, physics and its impact upon behaviour.

The ecological importance of predators.

Conservation ecology.
Solanum lycopersicum
(Tomato)
Authors: Pavan Stefano , van Heusden Adriaan W , Bai Yuling
Published: March 2009

After its introduction in Europe the tomato (

Solanum lycopersicum

) has gone a long way. Dedicated breeding has resulted in numerous cultivars grown all over the world, differing in all kind of aspects such as yield, shape, resistance, taste and quality. Modern cultivars are sold as hybrids with a very good performance. Since some decades the genetic variation of tomato and wild tomato relatives is conserved and successfully exploited to introgress genes resulting in tomatoes better able to cope with biotic and abiotic stress. Tomato has become a model species for genetic and genomic studies and the sequence of the gene‐rich regions will be determined in the near future.

Key concepts:

Mexico is presumed to be the most probable region of tomato domestication, and Peru the centre of diversity of tomato wild relatives.

The cultivated tomato has been renamed from

Lycopersicum esculentum

to
Solanum lycopersicum
.

Tomatoes can be used either for fresh consumption or for processing.

Heirloom cultivars are older tomato varieties; in greenhouses nowadays mainly hybrid cultivars are grown.

Tomato cultivars grow either indeterminate or determinate.

The cultivated tomato has 12 wild relatives. These wild tomatoes have a large genetic diversity, which has contributed greatly to the breeding of modern tomato cultivars.

Several institutions are nowadays dedicated to the conservation of the genetic variation present within

S. lycopersicum

and in tomato wild relatives.

Tomato is a model species for classical genetic and genomic studies. It has a chromosome number of 2n=2x=24 and a modest genome size (950 Mb/haploid genome).

Tomato genomic data are freely available at the SOL Genomics Network database (SGN;
http://sgn.cornell.edu
).
Patent Issues in Biotechnology
Authors: Bently Lionel , Sherman Brad , Hubicki Stephen
Published: March 2009

In both European and US law, biotechnological products may be patented if they fulfil the normal requirements of patent law that they are novel, nonobvious and useful for industry. In practice this means that biological molecules, including genes, that have been isolated from nature and are susceptible of industrial application are capable of protection, as are processes of isolating and purifying biological molecules.
Tooth Morphogenesis and Patterning: Molecular Genetics
Authors: Saffron Tucker Abigail
Published: March 2009

Teeth develop by a series of epithelial–mesenchymal interactions that govern not only where the tooth will form within the developing jaw, but also what type of tooth will develop. Before any sign of tooth development is observed, the patterning information regarding what type of tooth will form has already been determined. Thus an incisor forms in the distal jaw, whereas the molars form more proximally at the back of the jaw. Then, as the tooth develops, a signalling centre, known as the enamel knot, is set up at the centre of the tooth germ, which controls the shape (morphogenesis) of the tooth and the number of cusps which form. The genes involved in these patterning processes are starting to be elucidated and experiments involving knockout mice and misexpression studies have given insights into the molecular genetics of tooth morphogenesis.

Key concepts:

How a tooth develops in the embryo?

How tooth identity is determined – i.e. to develop as a molar or incisor?

How tooth shape is controlled – i.e. number of cusps?
Eye: Proteomics
Authors: Steely H Thomas , Clark Abbot F
Published: March 2009

Vision is our most precious sense, and numerous ocular diseases, including age‐related macular degeneration, glaucoma and diabetic retinopthay, are responsible for visual impairment and blindness in hundreds of millions of individuals worldwide. In the past several years, a number of advances have been made to better understand ocular biology and diseases. Research in ocular proteomics of ocular tissues and cells such as the trabecular meshwork, retina, optic nerve head, retinal pigment epithelium, cornea, lens, sclera, tears, aqueous humour and vitreous humour, has allowed the identification of eye proteins and protein modifications that are involved in ocular development, ageing and disease. This provides an important foundation for better understanding ocular biology and disease pathogenesis.

Key Concepts:

The eye is a unique sensory organ.

A wide variety of proteomics techniques are being used to identify proteins and protein modifications that are involved in ocular development, ageing and a wide variety of ocular diseases.

Eye proteomics can be very challenging due to the very limited quantity of ocular tissues and fluids available for analysis.

Posttranslational protein modifications are commonly associated with a variety of ocular diseases, including glaucoma, macular degeneration and cataracts.

Serum proteomics is being used to examine systemic effects of specific ocular diseases.
Abscisic Acid (
ABA
)
Authors: Cutler Adrian J
Published: March 2009

Abscisic acid (ABA) is a phytohormone found in all higher plants that mediates responses to abiotic stress conditions and controls stomatal aperture. It is also involved in seed development and is associated with seed dormancy. ABA is biosynthesized in higher plants from carotenoid precursors. ABA acts via a complex signalling process leading to both short‐term changes in ion channel activity and long‐term effects on gene expression.
Restoring Rivers and Streams
Authors: Ardón Marcelo , Bernhardt Emily S
Published: March 2009

Increasingly, management agencies are attempting to reverse degradation to rivers through ecosystem restoration, whereby efforts are made to remediate, improve or return degraded rivers back to their historic form and function. River restoration has become a booming industry throughout the developed world, with a wide variety of methods currently employed. Common activities include: reshaping channels back to historic or reference dimensions, planting riparian vegetation, and constructing high‐quality habitat for fish. The goals driving these restoration projects are also diverse, ranging from improving water quality to achieving improved aesthetic and recreational benefits. Restoration efforts may improve local conditions by reducing bank erosion, reducing stream temperatures and increasing dissolved oxygen concentrations, but to date there has been little empirical evidence for catchment‐scale improvements in water quality, aquatic biodiversity, or recovery of sensitive aquatic taxa.

Key Concepts:

River restoration: The process of assisting the recovery of an ecosystem that has been degraded, damaged or destroyed.

Rehabilitation: The act of restoration to an improved or former condition.

Compensatory mitigation: Creation, restoration, enhancement or preservation of a river, stream and/or wetland designed to offset permitted losses of ecosystem function.

Natural channel design: Restoration of the dimension, pattern and profile of a disturbed river system by emulating the natural, stable river.

Meander: Curvature of stream channels, measured as high levels of sinuosity (S shape).

Floodplain: Flat area adjacent to rivers that is subject to erosion and deposition due to flooding outside of the channel.

Riparian forest: Vegetation alongside a river channel that provides important services to rivers such as shades, organic material inputs, sediments and nutrient retentions.
Vagus Nerve Stimulation for Epilepsy
Authors: Baaj Ali A , Benbadis Selim R , Vale Fernando L
Published: March 2009

Epilepsy refractory to medical management continues to pose a problem to clinicians. Vagus nerve stimulation (VNS) is a safe and effective treatment for patients with refractory epilepsy who are not surgical candidates. Although the mechanism is still poorly understood, several clinical trials have demonstrated its efficacy and safety. VNS has become the most widely used nonpharmacological therapy for the treatment of drug‐resistant epilepsy.
Invasion of Introduced Species
Authors: Simberloff Daniel
Published: March 2009

Species introduced deliberately or inadvertently by humans to areas outside their native ranges affect native species in many ways. Some impacts, such as predation and herbivory, are obvious, but others are subtle and may result from complex, sometimes indirect interactions of more than two species. No habitat or area is immune to impacts of introduced species, but some sorts of sites, such as anthropogenically disturbed areas and oceanic islands, are particularly prone to invasions. Arrival of a new invader may lead to evolution by both the invader and native species with which it interacts.
Water Transport by Epithelia
Authors: Reuss Luis
Published: March 2009

Water transport in epithelia can occur down an established concentration gradient, in which case it is indisputably osmotic. In other epithelia, water transport occurs in the absence of or even against differences in the osmolalities of the adjacent solutions. In the latter case, water flow is in the same direction as the net solute flux and in near‐isosmotic proportions. The pathways and mechanisms of water transport in this class of epithelia remain controversial, but the prevailing views are that water flow is largely transcellular, via both water pores (
aquaporins
,
AQP
) and the phospholipid bilayer, with little contribution of other membrane proteins. In addition, solute–solvent flux coupling is not a molecular, but a thermodynamic phenomenon, i.e. water transport is driven by small differences in osmolality between epithelial fluid compartments created by solute transport. Paracellular water flow is likely to be small relative to transcellular water flow.
Viruses of Fish
Authors: Russell Peter H , Dixon Peter F
Published: March 2009

Viruses can infect many species of fish and have become most apparent on fish farms. The more virulent viruses can result in haemorrhages, ascites and death. They have been spread between countries by stock fish, ornamental fish, eyed eggs and/or wild fish and so cheap vaccines are still needed to reduce the risk to fish farmers and dealers. However, if infection of fish occurs between vaccination and export then vaccinated excretors can transfer disease between countries.

Key concepts:

The more serious fish viruses usually result in haemorrhages, ascites and death.

New fish viruses continue to be recognized.

Fish viruses do not infect man.

Fish viruses can spread globally and into new species of fish.

Vaccines exist for only a few viruses.

The first of all commercial DNA‐vaccine was made for infectious haematopoietic necrosis virus of farmed Atlantic salmon in Canada.

Vaccines are needed for fry and for the emerging viruses of warm‐water fish.

Vaccines reduce but do not obviate excretion of virus.
Herpes Simplex: Viruses and Infections
Authors: van Hal SJ , Dwyer DE
Published: March 2009

Human herpes viruses 1 and 2 (HSV‐1 and HSV‐2) are among the most common human viral pathogens. Various epidemiological factors determine the infecting HSV type with significant changes in the epidemiology of genital herpes and HSV‐1 infections especially in developed countries. Following transmission of HSV to a susceptible person, symptomatic or asymptomatic infection may result with localized disease, the most common manifestation. HSV then establishes latency in the dorsal root ganglia which enables subsequent reactivation. The risk and rate of reactivation are dependent on numerous host factors and the infecting viral subtype. The number of diagnostic tests has increased with molecular methods improving our understanding of asymptomatic viral shedding. Antiviral therapy ameliorates the clinical manifestations and improves survival in neurological disease. Prophylactic antiviral strategies have been formulated for recurrent disease, but vaccine trials do not yet show clinically relevant benefit.

Key concepts

Classification of human herpes viruses

Structure and replication of HSV

Pathogenesis of HSV

Latency

Immunological responses to HSV

Epidemiology of HSV

Interaction between HSV and HIV infection

Clinical manifestations and complication

Diagnostic modalities for HSV detection

Antiviral therapy and strategies used in the treatment of HSV

Preventative strategies and vaccines
In VivoAnalysis of Membrane Fusion
Authors: Palfreyman Mark T , Jorgensen Erik M
Published: March 2009

Membranes provide a barrier that allows chemical reactions to be isolated from the environment. The plasma membrane, for example, delineates self from nonself, and thus must have played an essential role in the evolution of life. Yet under numerous circumstances it is equally important that membranes be breached. Numerous forces oppose the spontaneous fusion of membranes; thus, specialized proteins have evolved to fuse membranes. The most well‐understood fusion proteins are the viral fusion proteins and the SNARE proteins used in the secretory pathway. In addition, recent discoveries have lead to models for the fusion of organelles such as mitochondria and peroxisomes, as well as for cell–cell fusion. Despite the diverse structures of fusion proteins, it is possible that they function to drive membranes through a series of common lipid intermediates. Here we review the mechanisms of fusion for biological membranes, and highlight the similarities and differences in these processes.

Key concepts

Fusion proteins are thought to lead membranes through the common set of lipid intermediates: lipid stalk, hemifusion diaphragm and pore formation.

There are three known classes of viral fusogens: type I, II and III.

Type I and II are structurally unique yet undergo similar structural rearrangements during membrane fusion.

Viral fusion proteins are initially present only on a single membrane and must insert a fusion peptide into the target membrane to accomplish fusion.

SNAREs are used throughout the secretory pathway.

SNAREs are present on both membranes destined to fuse.

SNAREs and viral fusion proteins play an active role in all steps of the fusion process.

Multimerization of viral fusion proteins and SNARE proteins is needed for fusion to occur.

The fusogens used in cell–cell fusion are not evolutionarily conserved.

The coordinated action of Fzo1 and Mgm1 is needed to fuse the inner and outer membranes of mitochondria.
Strategies of Reserve Selection
Authors: Cabeza Mar , van Teeffelen Astrid
Published: March 2009

Existing protected areas contain only a biased sample of the Earth's biodiversity. This is because conservation has to compete with other land‐uses. Limitations in space and budget highlight the importance of effective and efficient conservation strategies. In this context, questions like what elements of biodiversity should we focus on, and where to protect them, are difficult to answer. The field of spatial conservation planning has evolved to address these questions, with attention to cost‐efficiency, representativeness, adequacy, flexibility, threat and vulnerability. It encourages politicians and conservation planners to set quantitative conservation goals, and offers tools to prioritize among large sets of species, ecosystem types and areas. The implementation of this approach is becoming essential in order to halt the loss of biodiversity in a world of increasing human population and increasing demand for natural resources.

Key concepts

Protected areas have long been established opportunistically resulting in inefficient spending of conservation funds.

Scoring methods rank individual sites according to their conservation value, but cannot guide the design of networks efficiently.

Complementarity‐based approaches instead, evaluate the value of the network as a whole, thus achieving cost‐efficiency in reserve network design.

Aiming at representation of species or ecosystems in reserves is insufficient. Conservation goals and their derived targets should aim at persistence if biodiversity loss is to be halted.

To achieve cost‐efficiency, targets have to be explicit and quantitative.

A large suit of tools exists to aid conservation decision‐making under conditions where data is incomplete or of poor quality – typical for biodiversity data. More or better data is indispensable, but meanwhile decision‐making can proceed.

Although the perfect biodiversity surrogate does not exist, basing the design of reserve networks on information for a number of taxa produces promising results.

Connectivity of reserve networks promotes the persistence of species in fragmented landscapes.

One‐size‐fits‐all solutions do not always exist. Species or habitats may require different conservation actions, leading to inevitable trade‐offs.

Although spatial prioritization has been mostly used to locate protected areas, it can be used to assist the identification and location of most suitable management actions.
Secondary Cell Walls
Authors: Zhong Ruiqin , Ye Zheng‐Hua
Published: March 2009

Secondary cell walls are the major constituent of tracheary elements and fibres in wood, which is the most abundant biomass produced by plants. They provide strong mechanical strength to tracheary elements and fibres, and ultimately to plant organs. The principal components of secondary walls are cellulose, hemicellulose and lignin. Cellulose microfibrils together with hemicelluloses form the main load‐bearing network in secondary walls, in which lignin is impregnated to form another crosslinked network to provide hydrophobicity and more rigidity. The biosynthesis of secondary walls is a highly coordinated developmental process that involves a coordinated expression of secondary wall biosynthetic genes regulated by a cascade of transcription factors. Because secondary walls in the form of wood and fibres are the most abundant, renewable plant products, understanding how they are constructed will provide novel strategies for genetic improvement of wood and fibres to better suit our needs.

Key concepts

Cell walls are the plant ‘exoskeleton’ that dictates the cell shape and collectively the plant form.

The ability for plant cells to make secondary cell walls is considered to be one of the most important evolutionary landmarks for vascular plants.

Secondary cell walls are the main constituent of tracheary elements and fibres of wood, which is the most abundant biomass produced by land plants.

Secondary cell walls in tracheary elements and fibres provide mechanical strength to plant organs.

Secondary cell walls in tracheary elements are deposited in specific patterns, including helical, annular, scalariform, reticulated and pitted patterns.

The principal components of secondary cell walls are cellulose, hemicelluloses and lignin.

Cellulose is synthesized by the cellulose synthase complexes located at the plasma membrane.

Hemicelluloses, including glucomannan and xylan, are synthesized at the Golgi and then secreted via vesicles into the cell walls.

Lignin is synthesized through dehydrogenative polymerization of monolignols,
p
‐coumaryl alcohol, coniferyl alcohol and syringyl alcohol, which is catalysed by oxidases including peroxidases and laccases.

The biosynthesis of secondary cell walls is regulated by a transcriptional network comprising of a cascade of transcription factors.
FusariumandFusarium–Cereal Interactions
Authors: Nicholson Paul
Published: March 2009

The genusFusariumcurrently includes over 80 species. This number is increasing as studies based upondeoxyribonucleic acid(DNA) sequence comparison become more common. The majority ofFusariumspecies are associated with plants and many are important plant pathogens. This review introduces the species of greatest significance with respect to cereal crops. As well as causing significant yield loss, many of the species produce a range of secondary metabolites (mycotoxins) that are harmful to human and animal consumers. Studies are unravelling the genetics of mycotoxin biosynthesis and regulation but work is still required to understand the role of these compounds in the life cycle of the producing fungi.

Key concepts

Introduction to fungal diversity in relation to theFusariumgenus and its relationship to cereal crops.

Species concepts: morphological, biological and phylogenetic.

Genetic basis of mycotoxin biosynthesis.

Role of mycotoxins and other secondary metabolites in plant–pathogen interaction.
Epidemiology of Plant Disease
Authors: Jeger Michael J
Published: March 2009

Epidemiology is the science of disease in populations, in this article plant populations. It is a quantitative discipline with strong conceptual foundations and practical applications. Epidemics of plant diseases have had major impacts on agricultural and horticultural crops and on forest‐tree populations with major socio‐economic and political consequences. An epidemiological tool‐kit includes methodologies for analysing disease progress in time and space, the derivation of key parameters determining the rate of epidemic progress, and the extent of control required for disease management. The complexity of biotic interactions affecting plant epidemics is shown by introducing genetic variation in host and pathogen, the role of disease vectors in transmission, and higher level interactions involved in biological control. The importance of disease in wild plant communities is assessed. With the increased recognition of the landscape connectedness of crop plants, natural communities and invasive species, some additions to the epidemiological tool‐kit are proposed.

Key concepts

Infection cycle: The components of the pathogen life cycle in a host population. For a fungal pathogen this would include the sequence infection, colonization, sporulation and dispersal (to a new host, completing the cycle).

Integrated disease control: The use of different methods of disease control – chemical, cultural, biological and host resistance – within a decision‐based approach to disease management.

Disease triangle: A recognition that a disease (epidemic) is a consequence of the interaction of a virulent pathogen population with a susceptible host population in a conducive (biotic and abiotic) environment. With plant virus diseases the ‘triangle’ is often extended to include explicity the vector.

Basic reproductive number: The number of secondary infected units (plants, plant parts) caused by the introduction of one infectious unit into a susceptible host population, curing that unit's period of infectiousness.

Intraspecific diversity: Genetic variation occurring within a plant host and/or pathogen population; such variation can determine the level of compatibility in a host–pathogen interaction as expressed in gene‐for‐gene recognition systems. It is used in disease control strategies based on multilines and varietal mixtures.

Evolutionary epidemiology: An attempt to integrate population genetic and population dynamic approaches in epidemiology so that the evolutionary dynamics of plant pathogen populations can be studied and managed.

Landscape epidemiology: A recognition that plant disease epidemics occur at the landscape scale, and are influenced by aspects of the wider environment including features such as topography, watersheds, human activity and the conjunction of cropland and semi‐natural vegetation.
Metabolic Effects of Caloric Restriction
Authors: Baur Joseph A
Published: March 2009

Caloric restriction (CR) improves health and increases longevity in organisms from yeast to mammals. Studies in rodent models show that CR suppresses a wide range of diseases that contribute to human morbidity and mortality such as cancer, cardiovascular disease and diabetes. Although the metabolic and physiological changes induced by CR have been investigated for over 70 years, the precise mechanism by which it is able to slow the progression of age‐related degeneration remains a subject of much debate. This article summarizes our current understanding, including recent findings that implicate specific enzymes and signalling pathways in the process. Further study of CR may provide insight into the nature of aging and reveal new opportunities to improve the quality and quantity of human life.

Key concepts

Reducing energy intake in the absence of malnutrition (caloric restriction) improves health and extends longevity.

Caloric restriction causes widespread changes in physiology and metabolism, many of which are distinct from fasting responses.

Manipulation of specific genetic pathways can block or mimic some responses to caloric restriction.

Insulin/IGF‐1 signalling is consistently implicated in the mechanism of caloric restriction.

Neither aging nor its retardation by caloric restriction is understood, however much of the available data is compatible with the Free Radical Hypothesis.