bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertebrate Herbivory and Its Ecosystem Consequences
Authors: Oksanen Lauri , Olofsson Johan 
Published: March 2009

AbstractHerbivory 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.
Predator Avoidance
Authors: Abrahams Mark V , Pink Melissa , Klassen Cheryl 
Published: March 2009

AbstractFor 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 conceptsBehavioural 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

Abstract

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

Abstract
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

AbstractTeeth 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

Abstract

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

Abstract
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

AbstractIncreasingly, 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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

AbstractHuman 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 conceptsClassification of human herpes virusesStructure and replication of HSVPathogenesis of HSVLatencyImmunological responses to HSVEpidemiology of HSVInteraction between HSV and HIV infectionClinical manifestations and complicationDiagnostic modalities for HSV detectionAntiviral therapy and strategies used in the treatment of HSVPreventative strategies and vaccines
In VivoAnalysis of Membrane Fusion
Authors: Palfreyman Mark T , Jorgensen Erik M 
Published: March 2009

AbstractMembranes 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 conceptsFusion 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

AbstractExisting 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 conceptsProtected 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

Abstract

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

AbstractThe 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 conceptsIntroduction 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.