bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant Interactions with Biotic Factors
Authors: Hartley Susan E
Published: September 2006

Plants interact with a wide variety of other organisms, from microbes to mammals. Interactions such as those with nitrogen‐fixing bacteria are beneficial; those with herbivores, for example, are detrimental. Interactions between plants and other organisms are fundamental to many ecological processes.
Ecological Consequences of Body Size
Authors: Calder William A
Published: September 2006

More of the intraclass evolution of animals has been linked to body size than to any other characteristic. Adult body size exerts a quantitative dominance over how an animal lives and for how long and on its rate of living and extraction of resources from its environment, and consequently on how many of its kind can live simultaneously on a unit of habitat. Size thus determines how the species fits into its ecological community. Continuity is revealed by similar exponents on body mass for functions ranging from metabolism and its physiological support to ecology and conservation. These size‐dependent relationships give us a marvellous basis for understanding ecology and predicting conservation outcomes.
Migration: Orientation and Navigation
Authors: Bairlein Franz
Published: September 2006

Directional or compass orientation does not require a geographically fixed reference whereas goal orientation or true navigation relies on knowledge of the previously experienced goal and the determination of the exact position relative to the goal.
Ecology of Invertebrate Nutrition
Authors: Chapman RF
Published: September 2006

All animals require a number of chemicals for the formation of body structures and for life processes. These nutrient chemicals are similar throughout the animal kingdom because of the basic chemical similarity of all animal life. Most invertebrates acquire the necessary nutrients from their food, but microorganisms sometimes provide nutrients that are lacking in the food and, especially in marine environments, direct uptake of nutrients from the water may be important.
Ecology of Vertebrate Nutrition
Authors: McWilliams Scott R
Published: September 2006

Vertebrate nutritional ecology is the study of the interrelationships between food resources in the environment and the consumptive use of these food resources by vertebrate animals. Consumptive use includes how vertebrate animals procure, digest, absorb and metabolize available foods in the environment to satisfy their requirements for health, growth and reproduction.
Biomechanical Studies of Food and Diet Selection
Authors: Herrel Anthony , Aerts Peter
Published: September 2006

The ways animals acquire food are largely determined by the medium in which they feed. Biomechanical approaches can help explain evolutionary trends and radiations in the feeding system of animals.
Hibernation: Endotherms
Authors: Geiser Fritz
Published: September 2006

The main function of hibernation and daily torpor in mammals and birds is to conserve energy and thus survive during adverse environmental conditions or periods of food shortage no matter if they live in the arctic or the tropics.
Life History Theory
Authors: Yampolsky Lev Y
Published: September 2006

Life history is a general term for the sequence of fitness‐related events and processes occurring during the life of an individual, such as growth, survival and reproduction. Life history theory is a branch of ecology and evolutionary biology that aims to predict and explain the observed patterns in life histories of living organisms.
Latitudinal Diversity Gradients
Authors: Field Richard
Published: September 2006

The diversity of organisms tends to increase from the poles to the equator. This is a remarkably consistent trend over space and time. Many different theories and mechanisms have been advanced to explain the phenomenon; most are likely to be valid at some scale of analysis, and are best considered via a hierarchical framework.
Dispersal: Biogeography
Authors: Wilkinson David M
Published: September 2006

Dispersal is one of the fundamental processes in biogeography crucial to understanding the distribution of organisms and important in understanding the impact of climate change on distributions.
Ecotoxicology
Authors: Calow Peter , Forbes Valery E
Published: September 2006

Ecotoxicology is the description and understanding of impacts of industrial and agricultural chemicals on ecological systems. It is to be distinguished from toxicology because it focuses on the impacts of chemicals on ecological groupings of organisms rather than on individuals.
Urban Ecology: Patterns of Population Growth and Ecological Effects
Authors: Zipperer Wayne C , Pickett Steward TA
Published: September 2006

Although cities have existed for over 6000 yr, scientists are just beginning to understand how the physical, ecological and social components of an urban ecosystem interact and how they are affected by the burgeoning growth of cities and their suburbs. Only through this understanding can we begin to develop sustainable cities that ensure a quality of life for both urban and rural residents and maintain natural habitats for native plants and animals.
Biological Control
Authors: Hokkanen Heikki MT
Published: September 2006

Biological control or biocontrol is a collective term for a set of techniques used to control animal pests, plant diseases and weedy plants. Common to these techniques is the employment of living organisms, biocontrol agents, to control or regulate the numbers of unwanted organisms.
Impact of Genetically Modified Organisms (
GMOs
)
Authors: Paoletti Maurizio G
Published: September 2006

Genetically engineered crops could prove environmentally and economically beneficial; however, current products – especially herbicide‐resistant plants and
Bacillus thuringiensis
‐resistant crops – have potentially serious environmental and economic impacts, similar to the consequences of pesticide use.
Conservation Biology and Biodiversity
Authors: Ricketts Taylor H
Published: September 2006

Conservation biology integrates diverse disciplines within the natural and social sciences, with the goal of preserving the world's biodiversity, or variety of life.
Conservation of Biodiversity
Authors: Paoletti Maurizio G
Published: September 2006

The aim of conserving biodiversity is to provide strategies and appropriate management to improve and/or maintain diversity of biota and environments in rural and urbanized landscape in a substantial way.
Chemical Ecology
Authors: Grasswitz Tessa R , Jones Graeme R
Published: September 2006

Chemical ecology is the study of the structure, origin and function of naturally occurring chemicals that mediate intraspecific or interspecific interactions. It has developed into a mature science with diverse practical applications. At the heart of the discipline are modern analytical instrumentation, careful observational biology and good bioassay design.
Multivariate Techniques
Authors: Reyment Richard A
Published: September 2006

Multivariate statistical analysis is concerned with the simultaneous examination of two or more variables (in the case of full space) or parts (in the case of simplex space) by means of standard methods of linear algebra and differential geometry. The methods are universally applicable. In the life sciences, multivariate analysis is of wide use in animal and plant taxonomy, quantitative genetics, environmetrics, ecology and aspects of evolutionary biology.
Ecological Modelling
Authors: Pittroff Wolfgang , Pedersen Ellen K
Published: September 2006

Ecological modelling is the use of systems analysis and simulation to mimic complex ecological systems by summarizing available relevant information. The process includes the development of conceptual and quantitative models, and the evaluation and use of the model to answer the specific questions for which the model was built.
Paediatric Congenital Heart Disease
Authors: Anderson Robert H , Redington Andrew N
Published: September 2006

The understanding, diagnosis and treatment of congenital malformations of the heart has been revolutionized over the past few decades, reflecting not only a greater appreciation of the morphological variability to be found within the malformed hearts, but also huge advances in the design and construction of machines available for diagnosis, treatment and life support. Nowadays, despite the anatomical complexity, accurate diagnosis is to be expected in all cases, with the greater majority of patients expected to survive treatment, which is being undertaken progressively earlier in life.
Interspecific Interaction
Authors: Rico‐Gray Victor
Published: September 2006

Organisms are not isolated, and to survive and reproduce most have evolved in ways that require them to use a combination of their own genetic information and that of other species. Hence, interspecific interactions, or interactions between individuals of different species, are one of the most important processes influencing the patterns of adaptation and variation of species.
Microbial Interactions
Authors: Epstein Slava S
Published: September 2006

Microbial interactions are ubiquitous, diverse, critically important in the function of any biological community, and are crucial in global biogeochemistry.
Interspecific Competition
Authors: Joshi Amitabh
Published: September 2006

Interspecific competition is the mutual inhibition of growth rate among populations of different species that have common requirements for shared and limiting resources. Interspecific competition can be a potent force in adaptive evolution and, along with predation and herbivory, is a major factor shaping the structure and species diversity of biological communities.
Mutualism among Free‐living Species
Authors: Armbruster WS , Rosenqvist G
Published: September 2006

Mutualisms are interspecific interactions resulting in benefits to both participants. In symbiotic mutualisms, the species live together for most of their lives. In nonsymbiotic mutualisms, the species interact intermittently.
Soil Resource Conservation
Authors: Lal Rattan
Published: September 2006

Soil is a finite and a nonrenewable resource, unequally distributed geographically, and fragile to misuse and mismanagement. It is a complete form of degradation leading to loss in productivity on‐site, and pollution of water and air off‐site. Soils need to be used, improved and restored.
Sperm–Egg Interactions: Sperm–Egg Binding in Mammals
Authors: Evans Janice P , Hardy Daniel M , Storey Bayard T
Published: September 2006

Fertilization of the mammalian egg occurs through an ordered sequence of reactions in which the sperm adheres to, then penetrates, the zona pellucida. It then binds to and interacts with the egg's plasma membrane, such that the gametes fuse and the egg is activated to form the zygote. These reactions involve specific molecules on sperm and egg that mediate the interactions; malfunction may cause infertility.
Egg Activation
Authors: Kline Douglas
Published: September 2006

The interaction between sperm and egg at fertilization stimulates the egg to begin development, a process known as egg activation. The fertilizing sperm not only contributes its complement of chromatin at fertilization, but also provides the signal that releases the egg from meiotic arrest and permits embryonic development.
RNA
Polymerase
II
Holoenzyme and Transcription Factors
Authors: Hampsey Michael , Reinberg Danny
Published: September 2006

Transcription of protein‐encoding genes requires a host of auxiliary factors that assemble with RNA polymerase II on promoter DNA.
Transcription Activation in Eukaryotic Cells
Authors: Barberis Alcide , Petrascheck Michael
Published: September 2006

Transcription activation is the first step in eukaryotic gene
expression. Gene regulation, which is about turning on and off expression of
specific protein‐coding genes in response to environmental changes, during
development and in differentiated cells, widely occurs at the level of
transcription activation. This is mostly achieved by DNA‐binding proteins that
can control the specificity of the RNA polymerase II enzyme.
Nonlinear Dynamics and Chaos
Authors: Kendall Bruce E
Published: September 2006

Nonlinear dynamics deals with more‐or‐less regular fluctuations in system variables caused by feedback intrinsic to the system (as opposed to external forces). Chaos is the most exotic form of nonlinear dynamics, in which deterministic interactions produce apparently irregular fluctuations, and small changes in the initial state of the system are magnified through time.7
Homo habilis
Authors: Wood Bernard A
Published: September 2006

Homo habilis
is an extinct species of hominin, presently included within the genus
Homo
, and best known from sites in East Africa.
Cell Size Control
Authors: Guertin David A , Sabatini David M
Published: September 2006

Growth in biological systems is defined as the accumulation of mass, which leads to an increase in size. In this article, we discuss how cells, organs, and organisms normally control growth, and how deregulated growth can lead to a variety of pathological conditions.
Cognitive Neuroscience
Authors: Platt Michael L
Published: September 2006

Cognition refers to the process of coming to know the world and our place within it. Cognitive neuroscience is the field of inquiry devoted to understanding how the brain enables cognition. Work in this field focuses on defining the neural processes that permit us to perceive and attend to events, determine their meaning and relevance, and respond appropriately. A key discovery in this field was that the higher mental functions, such as attention, memory, emotion, decision‐making and language arise through the activation of dedicated neural circuits localized in discrete areas of the brain. Notably, cognitive neuroscience actively probes subjective states such as emotion, imagery and awareness, which were considered inappropriate for scientific study by behaviourist psychologists of the early and middle twentieth century.
Integrins: Signalling and Disease
Authors: Krissansen Geoffrey Wayne
Published: September 2006

Integrins, the superfamily of cell surface adhesion molecules, do not act as a passive glue, but rather are dynamic molecules that mediate the transfer of information across the membrane in both directions, influencing cell growth, the cell cycle, differentiation, programmed death, survival and motility. They contribute to the pathogenesis of a diverse array of acquired and hereditary diseases, and hence are major targets for therapeutic intervention.
History of Fatty Acids
Authors: Kritchevsky David
Published: September 2006

In the early years of the 20th century the major causes of death were infectious disease, however with introduction of better sanitation, cleaner food preparation and antibacterial drugs the major killers have become degenerative diseases such as heart disease and cancer. Investigating the metabolic role of fat (from synthesis to utilization) may be central to our understanding of the two major causes of death in the developed world, namely, heart disease and cancer.
Discovery of Vitamin A
Authors: Wolf George
Published: September 2006

An account of the ideas and the experiments that led to the discovery of vitamin A.
Atwater, Wilbur Olin
Authors: Carpenter KJ
Published: September 2006

1844–1907 American chemist who pioneered human nutrition research in the USA.
De Beer, Gavin Rylands
Authors: Cain Joe
Published: September 2006

1899–1972 British zoologist, embryologist and historian who studied the relation between embryology and evolution and proved a gifted synthesizer of information on the development of the vertebrate skull and embryological development.
Vesalius, Andreas
Authors: Power Helen J
Published: September 2006

1514–1564 Belgian doctor and anatomist who challenged accepted knowledge on the structure of the human body, raised the status of anatomy among doctors and introduced naturalism into the portrayal of anatomical illustration.
Oxidative Stress‐induced Cellular Senescence
Authors: Toussaint Olivier , Remacle José , Dumont Patrick , Dierick Jean‐François , Pascal Thierry , Frippiat Christophe , Magalhaes Joao Pedro , Chainiaux Florence
Published: September 2006

Replicative senescence is a process in which normal proliferative cells lose replicative potential and acquire biomarkers of cellular senescence as a result of serial passages in culture instead of chronological time. Oxidative stress‐induced premature senescence is the long‐term appearance of the biomarkers of replicative senescence after exposure of human diploid cells to sublethal stress. Cytokine‐induced premature senescence is the long‐term appearance of biomarkers of replicative senescence after repeated exposure of human diploid fibroblasts to proinflammatory cytokines.
Homology and Homoplasy: A Philosophical Perspective
Authors: Amundson Ron
Published: September 2006

Homology refers to the underlying sameness of distinct body parts or other organic features. The concept became crucial to the understanding of relationships among organisms during the early nineteenth century, and it remains important today. Definitions of homology have changed with the progress of biology, and even today different versions are associated with different research agendas. The differences illustrate philosophical issues about the workings of definition and explanation in science.
Human Genome Project: Reassessment and Philosophical Analysis
Authors: Ruse Michael
Published: September 2006

Since the discovery of the structure of the DNA molecule, scientists have attempted to map the human genome. Completion of the project will force us to face the new task of deciding what to do with the information we have acquired.
Philosophy of Biological Classification
Authors: Ereshefsky Marc
Published: September 2006

Essentialism was the prominent philosophy of classification until Darwin's time. Essentialism has been replaced with two philosophies based on evolutionary theory: evolutionary taxonomy and cladism.
Philosophy of Molecular Biology
Authors: Rosenberg Alexander
Published: September 2006

The revolution in molecular biology has made the debate between reductionism and antireductionism in the philosophy of biology a pressing concern among biologists. The adoption of either of these two positions has important implications for the research programme of biology.
Reduction: A Philosophical Analysis
Authors: Sarkar Sahotra
Published: September 2006

The molecularization of biology has led to a renewed interest in the possibility of reducing biological phenomena to physical interactions.
Bioethics of Genetic Testing
Authors: Clayton Ellen Wright
Published: September 2006

Appropriate consideration of the ethical issues surrounding genetic testing is essential to ensure that the knowledge gained from diagnostic techniques is used appropriately.
Global Carbon Cycle
Authors: Sabine Christopher L
Published: September 2006

Recent scientific studies have greatly improved our understanding of carbon cycling at the Earth's surface. The natural exchanges of carbon between the atmosphere, ocean and land are being significantly altered today by human activity.
Walter and Eliza Hall Institute of Medical Research
Authors: Fenner Frank , Cory Suzanne
Published: September 2006

Located in Melbourne, The Walter and Eliza Hall Institute was the first and remains the leading centre for medical research in Australia. It has achieved a major international reputation, initially in virology and more recently in immunology, haematology, cancer and malaria research.
Cold Shock Response in Microorganisms
Authors: Schumann Wolfgang
Published: September 2006

Several species of bacteria are capable of mounting what is known as the cold shock response. This is induced upon a sudden decrease in external temperature and results in the transiently enhanced synthesis of a set of proteins, termed cold shock proteins, that allow the bacteria to adapt to such changes in temperature.
Osborn, Henry Fairfield
Authors: Regal Brian
Published: September 2006

1857

–

1935

American

evolutionary biologist

and powerful, long‐time

head of the American Museum of Natural History, New York.
Boerhaave, Herman
Authors: Galle K
Published: September 2006

1668 – 1738 Dutch physician, chemist and botanist whose teachings helped shape medical school curricula throughout Europe .
Borelli, Giovanni Alfonso
Authors: Galle K
Published: September 2006

1608

–

1679

Italian

physicist and anatomist

who

authored one of the earliest treatments of animal motion based on mechanical principles

.
Leiper, Robert Thomson
Authors: Wilkinson Lise
Published: September 2006

1881

–

1969

British

helminthologist

noted for his seminal

work on life cycles of helminthic parasites and identification of their vectors

.
Shortt, Henry Edward
Authors: Power Helen J
Published: September 2006

1887

–

1987

British

protozoologist and entomologist

who

elucidated the role of sandflies in the transmission of visceral leishmaniasis or kala azar

and who with P. C. C. Garnham

discovered the exoerythrocytic schizonts or tissue stage of mammalian malaria parasites

.
History of Schistosomiasis
Authors: Power Helen Joy
Published: September 2006

The history of schistosomiasis (infection with species of blood flukes or flatworms of the genus
Schistosoma
) is concerned with initial clinical descriptions of the urinary form of the disease; recognition of the aetiology of schistosome worms; discovery of snails as intermediate hosts and completing the life cycle; realization that different worms cause different forms of disease; measures to control and treat the disease.
Glisson, Francis
Authors: Olry Régis
Published: September 2006

1597

–

1677

British

physician

who made the

first accurate clinical description of rickets as well as important contributions to the anatomy and physiology of the digestive system

.
Klebs, Edwin
Authors: Gradmann Christoph
Published: September 2006

1834

–

1913

German

doctor

and

one of the leading medical bacteriologists of the late nineteenth century

.
Margulis, Lynn
Authors: Power Helen J
Published: September 2006

1938

American

biologist

who

developed the serial endosymbiotic theory to account for the evolution of nucleated cells and evolutionary novelty more generally

.
Needham, Joseph
Authors: Witkowski JA
Published: September 2006

1900

–

1995

British

scientist

who

turned from embryology to the history of science

in China.
Noguchi, Hideyo
Authors: Power HJ
Published: September 2006

1876

–

1928

Japanese

microbiologist

who as an original staff member at the Rockefeller Institute in New York worked on a range of

infectious diseases including syphilis and yellow fever

.
Withering, William
Authors: Bynum WF
Published: September 2006

1741–1799 Physician who first popularized the use of digitalis (
Digitalis purpurea
) for the treatment of ‘dropsy’ (oedema) and contributed to the development of Linnaean botany in Britain.
Dioscorides of Anazarbus
Authors: Scarborough John
Published: September 2006

c
AD
40–
c
AD
90 resident in the Eastern Roman Empire, Dioscorides was a Greek‐speaking physician who wrote the long‐influential
Materia Medica
(in Greek) in five books.
Avicenna (Ibn Sina)
Authors: Russell GA
Published: September 2006

980–1037 Physician/philosopher whose works, originally written in Arabic, had a formative influence between the twelfth and seventeenth centuries on medicine, medical education, early modern science and philosophy.
Paracelsus
Authors: Gantenbein UL
Published: September 2006

1493/94–1541 Swiss physician and philosopher of Swabian origin who propelled the development of medicine, chemistry and pharmacology in the Renaissance.
Lind, James
Authors: Bynum WF
Published: September 2006

1716–1794 Scottish naval physician who strongly advocated the curative role of citrus fruits in cases of scurvy, which he established through an innovative clinical trial.
Buchheim, Rudolf
Authors: Oreland Lars
Published: September 2006

1820–1879 German pharmacologist noted for his systematic studies of drugs and their mechanisms of action. During his time as a professor in Dorpat (Tartu in Estonia) he is said to have established, at first in his home, the first laboratory of experimental pharmacology.
The History of Anaesthesia
Authors: Caton Donald
Published: September 2006

Modern surgical anaesthesia began in 1846 with the first successful public administration of ether. The maturation of this branch of medicine developed during the next century and a half as principles of physiology and pharmacology increasingly became part of clinical practice and as practitioners formed societies to promote research and develop standards for education and practice.
History of Salvarsan (Arsphenamine)
Authors: Parascandola John
Published: September 2006

The drug Salvarsan (arsphenamine) was developed and introduced as a chemotherapeutic agent against syphilis in the first decade of the twentieth century by Paul Ehrlich. Although a significant breakthrough in the treatment of syphilis at the time, it was eventually replaced by penicillin.
History of Insulin
Authors: Sneader Walter
Published: September 2006

Failure of the pancreas to produce sufficient insulin results in high blood sugar levels and the development of diabetes. The isolation of insulin in 1922 provided a means of treating diabetes by administering daily injections of the hormone.
History of Antimalarial Agents
Authors: Greenwood David
Published: September 2006

A treatment for malaria has been available from at least the seventeenth century. Synthetic antimalarial agents were not developed until the twentieth century, largely due to the exigencies of the two World Wars.
History of Cortisone and Related Compounds
Authors: Sneader Walter
Published: September 2006

Steroidal hormones were isolated from the adrenal cortex in the 1930s and were synthesized a decade later. Used as drugs, they exhibited serious side effects. These have been largely overcome by the development of chemical analogues.
History of Anticancer Drugs
Authors: Jones Graham B
Published: September 2006

The origins of modern‐day cancer chemotherapies can be traced back to their roots in the nineteenth century.
Invertebrate Nervous Systems
Authors: Matheson Thomas
Published: September 2006

The nervous systems of invertebrates are smaller and contain fewer neurons than those of vertebrates, yet they generate the great diversity and complexity of behaviour that has contributed to the incredible success of these animals.
Coordination, Integration and Behaviour in Invertebrates
Authors: Combes Denis , Simmers John
Published: September 2006

The production of behaviourally appropriate movements requires coordinating neural interactions within an animal's nervous system, the integration of sensory input from the periphery, and instruction from central neuromodulatory commands. Much of our understanding of the neural correlates of adaptive behaviour has derived from studying the simpler nervous systems of invertebrates.
Invertebrate Skeletons
Authors: Willmer Pat
Published: September 2006

A skeleton is any mechanical system that interacts with muscle activity to allow movement and locomotion; the skeleton provides an external force or framework to restore muscles to their relaxed state. Invertebrate skeletons may be hydrostatic or stiff, either type serving to support the body and keep it in shape; stiff skeletons usually also have protective functions.
Osmoregulation in Invertebrates
Authors: Willmer Pat
Published: September 2006

Osmoregulation ensures that a correct balance of salts and water is maintained inside an animal, both in the circulating fluids (blood), and within the cells. It plays a major role in the achievement of homeostasis, especially in freshwater and terrestrial invertebrates.
Invertebrate Metabolism
Authors: Haunerland Norbert H
Published: September 2006

Invertebrates are capable of living in extreme environments and in highly variable conditions. Specific adaptations in their metabolism have evolved to meet these changes.
Theiler, Arnold
Authors: Spargo PE
Published: September 2006

1867–1936 Swiss‐born South African veterinary scientist who played a seminal role in finding cures for many important animal diseases.
Mullis, Kary B
Authors: Witkowski JA
Published: September 2006

1944– American scientist who invented the polymerase chain reaction, an essential tool in molecular genetics.
Postcopulatory Reproductive Strategies
Authors: Snook Rhonda R
Published: September 2006

Male and female reproductive strategies that occur both before and after insemination affect an individual's reproductive success. Sperm competition, cryptic female choice and sexual antagonism are processes that influence fitness following copulation. Males and females may be in conflict over the processes.
Sexual Conflict
Authors: Lessells Kate
Published: September 2006

Sexual reproduction leads to evolutionary conflict between males and females over the amount of parental investment each makes and many other aspects of reproduction.
Embryophyta (Land Plants)
Authors: Kenrick Paul
Published: September 2006

Almost all plants that live on land are classified as Embryophyta, with the exception of some terrestrial algae. Embryophyta includes a remarkable diversity of forms and some of the largest living organisms on Earth.
Musci (Mosses)
Authors: Newton Angela E
Published: September 2006

Mosses are members of the green plant lineage, showing alternation of generations, with an unbranched persistent sporophyte generation dependent on the dominant leafy gametophyte generation. They are the third most speciose group of land plants, and are important members of most terrestrial ecosystems.
Bryophytes (Liverworts)
Authors: Brown Elizabeth A
Published: September 2006

The liverworts are a group of green land plants that diverged before the dominant land plants such as angiosperms and gymnosperms. Together with mosses and hornworts, liverworts differ from all other land plants in having a free living gametophyte (a plant with only one set of chromosomes) as the dominant generation.
Pteridophytes (Ferns)
Authors: Yatskievych George
Published: September 2006

Pteridophytes (vascular cryptogams or ferns and fern allies) comprise about 12 000 species of primitive vascular plants; they do not produce flowers or seeds and reproduce instead via spores. They occur in most terrestrial habitats and also in some aquatic communities. Some species are very beneficial to humans, but the group also contains important species of weeds.
Poaceae (Gramineae)
Authors: Peterson Paul M
Published: September 2006

The grass family (Poaceae or Gramineae) is the fourth largest flowering plant family and contains about 11 000 species in 800 genera worldwide. Twenty‐three genera contain 100 or more species or about half of all grass species, and almost half of the 800 genera are monotypic or diatypic, i.e. with only one or two species.
Brassicaceae (Mustard Family)
Authors: Al‐Shehbaz Ihsan A
Published: September 2006

The Brassicaceae (Cruciferae) or mustard family is a well‐defined group that includes many vegetable crops (cabbage, broccoli, Brussels sprouts, cauliflower, horseradish, turnip, radish, watercress, etc.) and the model organism,Arabidopsis thaliana. It is easily recognized by the flowers with four petals in the form of a cross and by the pungent taste of its crushed leaves.
Conifers
Authors: Whetten Ross W
Published: September 2006

Seed‐bearing plants are divided into two major groups: the flowering plants, or angiosperms, and a more ancient lineage, the gymnosperms. The largest and most widespread group within the gymnosperms is the conifers, which are present worldwide and play important ecological and economic roles in some regions.
Illiciales
Authors: Sampson F Bruce
Published: September 2006

The order Illiciales is a member of the basal subclass of angiosperms, the Magnoliidae, and is made up of two small families. The family Illiciaceae contains one genus,
Illicium
, which has about 42 species, and the family Schisanraceae, which contains two genera –
Kadsura
(24 species) and
Schisandra
(about 25 species), including the Chinese star anise.
Nymphaeales
Authors: Les Donald H
Published: September 2006

The Nymphaeales comprise an angiosperm order commonly known as ‘water lilies’. All members of the order are aquatic plants that typically possess floating leaves.
Amborellales
Authors: Sampson F Bruce
Published: September 2006

The order Amborellales consists of a single plant,Amborella trichopoda, which is considered to be the basal‐most surviving flowering plant.
Alismatales (Water Plantains)
Authors: Haynes Robert R , Les Donald H
Published: September 2006

The Alismatales comprise an angiosperm order commonly known as ‘water plantain’. All members are aquatic or wetland plants with vegetation totally submersed and flowers floating or emergent, or with floating leaves and floating or emergent flowers, or with emergent vegetation and flowers. Most species have a totally submerged juvenile phase, and some species, for example
Baldellia ranunculoides
,
Luronium natans
,
Ottelia ovalifolia
,
Ottelia alismoides
, and
Blyxa alternifolia
, develop submerged cleistogamous flowers.
Arecales (Palms)
Authors: Dransfield John
Published: September 2006

Arecales is the order of monocotyledonous angiosperms that includes the palms. Palms are economically very important, have distinctive morphology and a fossil record that extends from the middle of the late Cretaceous to the present day.
Geraniales (Geranium)
Authors: Bakker Freek T
Published: September 2006

The angiosperm order Geraniales, as currently informally recognized, contains about 800 species, some of which are of economical and horticultural importance. Geraniales mainly comprises three families: Geraniaceae (geraniums, pelargoniums), Melianthaceae, a family of 18 species, Ledocarpaceae totalling 12 species in three genera, and Vivianiaceae, a small family containing a single genus with six species.
Oxalidales
Authors: Bradford Jason
Published: September 2006

Oxalidales are an order of flowering plants comprising six families that contain approximately 2000 species in 58 genera. Most Oxalidales are trees, shrubs or woody vines inhabiting the wet tropics, particularly on mountains, and warm temperate zones, especially in the southern hemisphere.
Root Nodules (Rhizobium, Legumes)
Authors: Brewin Nicholas J
Published: September 2006

Legume root nodules provide a built‐in supply of nitrogen fertilizer. Nodules arise from a symbiotic association with soil bacteria termed rhizobia that have the capacity to convert atmospheric nitrogen into a form that is available for plant growth.
Cucurbitaceae (Vine Crops)
Authors: Wehner Todd C , Maynard Donald N
Published: September 2006

The Cucurbitaceae or vine crop family is a distinct family without any close relatives and includes many important vegetables such as cucumber, melon, watermelon, squash, pumpkin and gourds.
Cornales (Dogwood)
Authors: Xiang Jenny Qiu‐Yun
Published: September 2006

Cornales is a relatively small, but diverse, plant order of flowering plants belonging to the asterids clade. It contains trees, shrubs, lianas, and rhizomatous and rarely aquatic herbs that occur from cold temperate regions to the tropics, rarely in subarctic zones. Common representatives include flowering dogwood, bunchberry, cornelian cherry, black gum, hydrangea, mock orange, and blazing star.
Asterales (Sunflower)
Authors: Smissen Rob D
Published: September 2006

The flowering plant order Asterales, is dominated by the sunflower or daisy family (Asteraceae).
Boreal and Temperate Forests
Authors: Vankat John L
Published: September 2006

The Earth's latitudinal gradient of forests encompasses boreal to temperate deciduous to temperate evergreen forests (as well as tropical forests). In addition, there are several variants of the temperate evergreen forest and there are montane forests at high elevations. Boreal and temperate forests differ in environment, structure, composition and disturbance.
Fluctuating Asymmetry
Authors: Tomkins Joseph L , Kotiaho Janne S
Published: September 2006

Fluctuating asymmetry refers to small random deviations from perfect symmetry in bilaterally paired structures; it is thought to reflect an organism's ability to cope with genetic and environmental stress during development and its utility as an indicator of such stresses is based on the assumption that perfect symmetry is an
a priori
expectation for the ideal state of bilateral structures. Fluctuating asymmetry has been used as an indicator of individual quality in studies of natural and sexual selection and as a bioindicator tool for environmental monitoring and conservation biology.
Enzymes: Phosphopantetheine‐dependent
Authors: Crump Matthew P , Shoolingin‐Jordan Peter M
Published: September 2006

Phosphopantetheine‐dependent enzymes are a group of multifunctional or individual enzymes including fatty acid synthases, polyketide synthases and nonribosomal polypeptide synthases, all of which utilize the 4′‐phosphopantetheine moiety attached to an acyl carrier protein or a peptide carrier protein. The terminal thiol group of 4′‐phosphopantetheine is covalently attached to any of a number of acyl groups in the form of a thiol ester to facilitate acyl transfer and nucleophilic activation.
Nick Translation
Authors: Woodward K
Published: September 2006

Nick translation is a rapid and easy method of labelling duplex DNA with radioactive or chemically modified nucleotides. The technique is based on the ability of DNase I to introduce random nicks in the target DNA and the simultaneous exonuclease and polymerase activity of
Escherichia coli
DNA polymerase I to replace existing nucleotides with labelled nucleotides (Kelly
et al.
, 1970; Rigby
et al.
, 1977).
Reverse Transcription and PCR
Authors: Woodgate L , Mills K
Published: September 2006

The ability to study comparatively the expression of messenger RNA (mRNA) populations from different samples has become accessible by the novel application of reverse transcription (RT), together with the polymerase chain reaction (PCR), to isolate gene sequences which can then be visualized by displaying on a sequencing gel. Differentially expressed transcripts can be analysed by Northern blotting or semiquantitative PCR to confirm differential expression. Utilization of various primer combinations facilitates the isolation of approximately 15 000 mRNA species, which represents gene expression in a mammalian cell at any one time.
Calibration of a Transilluminator for UV Fixation of DNA to Nylon Filters
Authors: Southern Edwin M
Published: September 2006

One method of fixing DNA to filters prior to hybridization analysis is to use ultraviolet light to crosslink the DNA to the filter.
Immunization of Mice for Monoclonal Antibody Production
Authors: Liddell JE
Published: September 2006

Monoclonal antibody production requires the immunization of laboratory mice with an immunogenic protein and test sampling of antiserum. For smaller, less immunogenic proteins and peptides, conjugation of the molecule to a carrier protein is necessary before immunization.
Enzyme‐linked Immunosorbent Assay (ELISA) to Measure Pure Protein
Authors: Liddell JE
Published: September 2006

Enzyme‐linked immunosorbent assay (ELISA) is used to measure the concentration of a soluble protein. The protein is coated to an assay plate and detected using a three‐step detection process. A colour change is observed which is proportional to the concentration of protein bound to the plate.
Immunodiffusion
Authors: Liddell JE
Published: September 2006

Immunodiffusion is one of the earliest and simplest methods of studying antibody–antigen reactions. It involves the migration of antibody and antigen towards each other in a semisolid agar gel. A visual precipitate is formed where the concentrations become equivalent. Qualitative information is also obtainable on cross‐reacting molecules
Dideoxy Sequencing of DNA
Authors: Wilton S
Published: September 2006

The enzymic sequencing approach uses a DNA polymerase to synthesize transcripts that have been terminated at specific bases. A primer anneals to a complementary region on the template strand and acts as a starting point for DNA synthesis, which occurs in the presence of a mixture of deoxyribonucleotides (building blocks) and specific dideoxyribonucleotides (chain‐terminators). Originally four separate reactions were set up, each with a base‐specific chain‐terminator. Separation of these reaction products on a DNA sequencing gel will generate a ladder of bands indicating the position of each terminated base relative to the end of the sequencing primer. A homogeneous sequencing template should generate a single band in one of the four lanes where a band in the ‘A stop’ lane indicates an ‘A’, a band in the ‘C stop’ lane represents a ‘C’ and so on. In this manner it is possible to deduce the DNA sequence of the target template by identifying consecutive bands in one of the four lanes of the ladder. Since DNA synthesis occurs in the 5′ to 3′ direction, the sequence is read 5′ to 3′ from the bottom to the top (origin) of the gel. Although it was originally suited to the sequencing of single‐stranded DNA templates, there have been many advances in the chemistry of enzymatic sequencing, including the application of thermostable DNA polymerases and fluorescent dye‐terminators as used in automated DNA sequencers.
Direct Sequencing of PCR Products
Authors: Wilton S
Published: September 2006

Direct sequencing of PCR products allows immediate and detailed analysis of those particular fragments without the extra steps associated with cloning. Although cloning of PCR products is now routine, there are still extra steps (which may take several days) in obtaining the recombinant sequencing templates. In addition to this extra effort, it is then necessary to sequence at least four independent recombinants to ensure that the average sequence has been obtained, so as to detect differences in the cloned sequences reflecting errors introduced during the PCR. Prior to the introduction of the thermostable polymerases and cycle sequencing, double‐stranded sequencing of either PCR products or plasmid DNA was less efficient and more difficult than sequencing single‐stranded templates. Fluorescent sequencing chemistry and template preparation have advanced to such a state where it is now possible to generate hundreds of bases of sequence information from the same primers used in the original PCR. Further sequence information can be obtained using ‘internal’ primers.
Direct Labelling of Proteins with
125
I
Authors: Gjøen Tor , Berg Trond
Published: September 2006

To quantify binding to receptors and endocytosis of protein ligands, radioactive labelling with
125
I is still the most widely used technique. It combines high sensitivity with simple analysis and is the method of choice for most applications. Radioactive iodine can be directly coupled to tyrosine residues or via adducts that accumulate in the cells at their site of degradation.
Production of Monoclonal Antibodies
Authors: Liddell JE
Published: September 2006

Monoclonal antibodies are the secreted products of a hybridoma cell line that is created from the fusion of an antibody‐producing lymphocyte and a histocompatible myeloma cell. The hybrid cell inherits the ability to survive in tissue culture from the parent myeloma cell and the capacity to produce antibody from the parent lymphocyte. Each hybrid cell can develop into a clone of identical cells producing identical antibodies that bind to one epitope. Production of such monoclonal cell lines from the fusion mixture requires several rounds of dilution and selection on the basis of specific antibody secretion. Once established, the pure cell line can be stored frozen and recovered to produce unlimited quantities of identical antibodies as required. The vast majority of monoclonal antibodies are derived from mouse cells, although it is also possible to produce them from rat cells. There are a few human monoclonal antibodies derived from hybridomas, but these tend to be very difficult to establish and maintain. All the steps required to make mouse monoclonal antibodies are described here.
Affinity Purification of Antibodies
Authors: Liddell JE
Published: September 2006

This method produces the purest sample of antibody, containing only antibodies that react with the desired antigen, free of all other immunoglobulins. It is based on affinity chromatography, in which antigen is bound to a solid phase to which specific antibody is bound and then eluted off.
Denaturing Gel Electrophoresis of
RNA
and
DNA
Using Urea–Polyacrylamide Gels
Authors: Southern Edwin M
Published: September 2006

At high concentrations, urea is able to denature both DNA and RNA and polyacrylamide gels containing urea at 7 mol L
−1
can be used to separate nucleic acids under denaturing conditions.
Denaturing Formamide Polyacrylamide Gels for Separating
RNA
and
DNA
Authors: Southern Edwin M
Published: September 2006

RNA and DNA can be separated under denaturing conditions using formamide polyacrylamide gels. Polyacrylamide gels are generally used for molecules and fragments between 6 bp and 1000 bp.
Pulsed‐field Gel Electrophoresis of DNA
Authors: Southern Edwin M
Published: September 2006

Conventional electrophoresis is not useful for DNA larger than 50 000 base pairs (bp). For large DNA molecules up to 7 million bp (7 Mb) it is necessary to use pulsed‐field electrophoresis. This protocol describes how the procedure is carried out.
Site‐directed Mutagenesis Using PCR
Authors: Jones P
Published: September 2006

PCR‐based site‐directed mutagenesis is used to study gene expression, protein structure–function relationships, and vector modification. This technique uses a three‐stage PCR with optimized parameters for each stage and the use of a ddNTP‐blocked fragment to produce a final mutant product.
Nuclear Run‐on Assays
Authors: Bates N , Hurst H
Published: September 2006

The nuclear run‐on assay is used to measure the transcriptional activity of selected endogenous genes. Nuclei are isolated from appropriate cells using techniques that keep engaged RNA polymerase complexes bound to genomic DNA. Subsequent incubation with the four ribonucleotide triphosphates, one of which is radiolabelled, allows polymerase complexes to progress several hundred base pairs along the genome, producing short, radioactive RNA molecules. After purification, the RNA species of interest are detected by hybridization to appropriate DNA sequences immobilized on a membrane. The amount of specifically hybridized RNA is proportional to the number of engaged polymerase complexes and therefore reflects the transcriptional activity of the gene in the intact cell.
Isolation of DNA from Agarose Gels using Agarase
Authors: Southern Edwin M
Published: September 2006

One of the major advantages of low gelling temperature agarose is that it is easy to recover DNA and RNA from the gel by melting it and extracting it with phenol. This basic procedure may be improved by including an agarase digestion step.
Electroblotting of Gels
Authors: Southern Edwin M
Published: September 2006

Quite often the gel electrophoretic migration pattern of individual components in a sample is determined not by analysing the gel but rather by analysing an image of the gel created by blotting the gel on to membrane. One of the simplest procedures is capillary blotting but this takes several hours and cannot be used with polyacrylamide gels. The transfer of nucleic acids can be speeded up by electroblotting.
Manual Dot Blotting
Authors: Beauchamp J
Published: September 2006

DNA blots can be prepared without specialized apparatus, though the results are less good than those obtained by manifold blotting. However, the technique may be useful for ‘in‐house’ purposes such as roughly comparing the levels of nonradioactive labelling of probes. Only very small volumes of sample can be used.
Single‐step Method of Total RNA Isolation by Guanidine–Phenol Extraction
Authors: Chomczynski Piotr
Published: September 2006

The single‐step method isolates total RNA from a variety of sources including tissues and cells from human, animal, plant, yeast, bacterial and viral origins. The method is based on liquid‐phase separation resulting in sequestration of pure RNA into the aqueous phase. RNA is precipitated from the aqueous phase, dissolved, reprecipitated and washed with alcohol. The entire procedure can be completed in less than 4 h.