bluuebunny/crossref_metadata_2025 huggingface dataset:
Mercury
Authors: DeVito Stephen C. , Brooks William E.
Published: April 2010

Mercury, used for centuries in many industrial and consumer applications and products because of the unique physical and chemical properties of the metal, is defined as being a hazardous material. The toxic effects of the metal to workers and to the general population as a result of occupational exposure, consumer exposure, and environmental pollution continue to gain worldwide attention. Much effort has been devoted to limiting the production and use of mercury, and finding alternative technologies that are designed to supplant the need for mercury. Overall demand for mercury has decreased throughout the industrialized world and it is likely to continue to decline. The chemistry, properties, natural occurrence, production, processing, economic aspects, environmental releases, uses, and toxicity of mercury are reviewed. Regulatory restrictions imposed by the U.S. Environmental Protection Agency on the production, use, and disposal of the metal are also provided.
Phosphorus
Authors: Brummer J. R. , Keely J. A. , Munday T. F. ,   Updated by Staff
Published: April 2010

The manufacture of elemental phosphorus by the electric furnace route, a mature and worldwide process, is reviewed. The principal product is white phosphorus although some red phosphorus is made from the white for specialty uses. Reduction in phosphorus production capacity has resulted from the detergent phosphate bans in the Western Hemisphere, the construction of wet‐acid purification plants, and increased electric power costs.

Most phosphorus is converted into phosphoric acid or phosphates and is used for cleaning compounds, food and beverages, water and metal treatment, and electronics. The remainder is converted into other derivatives and is used for flame retardants, agricultural chemicals, lubricants, and plasticizers. By‐products of phosphorus manufacture are slag, ferrophos, precipitator dust, and carbon monoxide off‐gas.
Water Treatment, Aeration
Authors: Rajendren Richard B.
Published: April 2010

Aeration for water treatment, the transfer of oxygen, O
2
, from air to water, is well‐studied. The basic purpose of aeration, used primarily for the treatment of wastewater, is to improve water quality for subsequent usage. Aeration can bring about the physical removal of taste‐ and odor‐producing substances such as hydrogen sulfide, H
2
S, and other volatiles as well as the chemical removal of metals (iron, manganese), gases (hydrogen sulfide), and other compounds (organics and inorganics) through oxidation and settling. Additionally, aeration is used extensively for the biological oxidation of both domestic and industrial organic wastes. The function of aeration in a wastewater treatment system is to maintain an aerobic condition. Methods developed to estimate the oxygen demand are biochemical oxygen demand (BOD), chemical oxygen demand (COD), total oxygen demand (TOD), total organic carbon (TOC), and theoretical oxygen demand (ThOD). The oxygen transfer rate for aerators is normally reported at standard conditions. Thus, in order to make meaningful comparisons, the oxygen required for treatment under working or field conditions should be adjusted to standard conditions. Detailed information is given in two basic groups of aerators: Ecto‐type and Endo‐type.
Wheat and Other Cereal Grains
Authors: Wrigley C. W.
Published: April 2010

Wheat, rice and corn (maize) each have world production of 600–700 × 106tons per year. They thus make very significant contributions to the diet of all humanity, as well as contributing to the feeding of animals and to industrial processing. In addition, there are several other cereal species that are grown to a significant extent, particularly barley, rye, oats, sorghum, triticale, and the various species of millet. Starch is the major component of the cereal grains, so it makes the greatest contribution to dietary energy input. The starch component is separated industrially from some cereal grains for further processing into sweetening agents, adhesives, thickening agents, fuel ethanol, and beverages. The gluten protein of wheat makes this cereal uniquely suitable for the production of leavened bread and for many other wheat‐based food products, such as noodles, cookies, cakes, and pasta. Given this range of uses, there are more rigid grain‐quality specifications for wheat than for other cereal species. These include grain color and hardness, protein content, milling quality and dough properties. Starch properties are important quality attributes for both rice and corn, as this component makes a contribution to the cooking and processing quality of both these grains. The cereal grains provide a good balance of nutrition, providing a diet that is low in fats, and offering several nutritional advantages, especially when whole‐grain foods are consumed.
X‐Ray Technology
Authors: Tsuji Kouichi
Published: April 2010

Analytical X‐ray instruments are used to characterize materials in several ways. There are analytical instruments that can produce images of the internal structure of objects that are opaque to visible light. There are instruments used to determine chemical composition of an object, the crystalline phases of solids, and the complete atomic and molecular structure of a single crystal. The determination of particle size, structural information for fibers and polymers and the study of stress, texture, and thin films are applications that are growing in importance and can be examined with X‐ray instruments. This article gives information on the characterization, generation, and properties of X‐Rays, and principles of X‐ray diffraction. Small molecule and macromolecule single‐crystal structure determinations are discussed. These techniques are compared with powder diffraction. X‐ray reflectometers, position sensitive detectors, and area detectors are some of the special instruments designed to measure properties of the new and exotic materials being manufactured. Details on X‐ray fluorescence spectrometry and X‐ray radiography are also given.
Yeasts
Authors: Vaughan Paul , Macreadie Ian G.
Published: April 2010

Yeasts are probably the oldest cultivated organisms: Their use dates to 3000b.c.or earlier. They are eukaryotic organisms, eukaryotes having by definition a defined nucleus surrounded by a nuclear membrane and organized cytoplasmic organelles (mitochondria, peroxisomes, vacuoles, etc). The recognition of yeasts as a group of microorganisms and of their role in fermentation generally preceded their taxonomic classification. They are fungi that exist as single cells during at least some part of their life cycle. They have no photosynthetic ability and are not motile. All the major groups of fungi,Basidiomycetes,Ascomycetes,Phycomycetes, and theFungi imperfecti, include species that have adopted a yeast phase. Yeasts usually reproduce vegetatively by budding or fission, but parasexual and sexual reproduction occur as well in most yeasts. There are extensive and authoritative texts on yeast taxonomy and identification. Among the yeast listed, the genusSaccharomycesis of greatest practical and economic importance for the baking, beer, and wine industries, as well as for the production of biomass. Due to its importance in the study of basic cell biology, reviews ofSaccharomycesgenetics and molecular biology appear regularly. This article emphasizes the biology and industrial use of yeasts, particularlySaccharomyces cerevisiae.
Zirconium and Zirconium Compounds
Authors: H. Nielsen Ralph , H. Schlewitz James , Nielsen Henry ,   Updated by Staff
Published: April 2010

Zirconium is found in at least 37 mineral forms. Occurrence and mining of zirconium are discussed. Zirconium is a highly active metal and is resistant to corrosion by water, steam, mineral acids, alkalies, salts, etc. Zirconium is highly refractory and the ore is cracked with only strong reagents and high temperatures. Various processes to accomplish this, such as electric furnace, caustic fusion, chlorination, flurosilicate fusion, are discussed. Zirconium and hafnium always occur together in natural minerals; separations of these two metals are given. Economic data, analytical methods and safety issues are included. There are many zirconium compounds in the form of hydrides, carbides, nitrides, oxides, halides, organometallics, chalcogenides, oxides, etc, and information is given on many of these compounds.
Bioseparations, Separation Methods in Proteomics
Authors: Garfin David E. , Ahuja Satinder
Published: April 2010

Bioseparationsentail separations of proteins and other materials from biological matrices. In the last few decades, proteins have gained significant importance. For example, monoclonal antibodies and recombinant antibodies are now among the largest classes of proteins that have received FDA approval for therapeutics and diagnostics. The protein engineering market in 2006 was worth almost 67 billion dollars and is predicted to rise to 118 billion dollars by 2011. Development of protein and peptide therapeutics is revolutionizing the biotech and pharmaceutical markets, spurring the creation of next‐generation products with reduced immunogenicity, improved safety and greater effectiveness. Oncology is the dominant therapy for both monoclonal antibodies and other types of engineered proteins.

Proteomicsis concerned with the global investigation of gene and cell functions at the protein level. The goals of proteomics are determination of protein expression levels, post‐translational modifications, protein localization, and protein–protein interactions. One of the important goals of proteomics that deserves special mention here is the discovery and identification of protein biomarkers of disease states.

Of all the biomolecules, proteins present the greatest challenges in bioseparations. The main focus of this article is on the important bioseparations techniques that are most useful for separations and characterization of proteins.
Inductively Coupled Plasma Spectrometry
Authors: Dean John R.
Published: April 2010

The fundamental principles of inductively coupled plasmas as applied to atomic emission spectrometry (AES) and mass spectrometry (MS) are described. Particular attention is given to the formation of an ICP, including spectrometer alignment for AES and MS, and the characteristic temperature of the source. A key component of an ICP is the ability to introduce a range of samples in to the source; different sample introduction approaches are described including the combination of nebulizer/spray chambers, laser ablation and hydride/cold vapor techniques. This is followed by a description of the different types of spectrometers that are used for ICP‐AES and ICP‐MS, as well as a discussion on the types of spectral and nonspectral interferences that arise and their remedies. A direct comparison of the two techniques is then made using the following important variables: detection limits, analytical working range, sample throughput, purchase cost and operating cost. Finally, a brief description of the applications of ICP spectrometry is given. An extensive bibliography is provided, as well as, useful web sites for the major journals that publish articles on the fundamentals and application of the techniques, as well as, a list of current manufactures of the instrumentation.
Ionic Liquids
Authors: Stark Annegret , Seddon Kenneth R.
Published: April 2010

This article deals with the literature on ionic liquids, with the focus on nomenclature, preparation, and handling of the second‐generation ionic liquids. In the older (and some current) literature, ionic liquids are sometimes called liquid organic salts, fused salts, molten salts, ionic melts, NAILs (nonaqueous ionic liquids), room‐temperature ionic liquids, OILs (organic ionic liquids) and ionic fluids. Their most prominent feature, namely the potential of tuning their physical properties to suit a particular application, is discussed in detail. In addition, areas in which ionic liquids are already applied, and in which their properties promise favorable application in transition‐metal catalyzed reactions, are reviewed.

In recent years, many ionic liquids have emerged as environmentally benign alternatives to volatile organic compounds (VOCs, such as trichloromethane, ethanenitrile and dimethylmethanamide), which cause emissions and effectively damage the ecological balance. The merit of ionic liquids, in this respect, is their negligibly small vapor pressure; therefore they are easily retained in a process. This concept has been realized, especially in preparative chemistry, as shown in many examples in this article: when used as solvents in catalytic processes, separation of the solvent (and the catalyst) from the product is facilitated, and recycling is easily possible.
Particle Technology
Authors: Alissa Park Ah‐Hyung , Zhu Chao , Fan Liang‐Shih
Published: April 2010

Particulate systems are involved in numerous industrial processes and are present in various natural phenomena. Particle technology is a term that refers to the field of the science and technology associated with the characterization, formation, processing, and utilization of particles. It is concerned with the systems in which one or more of the components are in the form of particles. Recently, the scope of particle technology has been extended to cover systems containing nanoparticles, aerosols, liquid droplets, emulsions, and bubbles.

Particle technology is an interdisciplinary field. Due to the complexity of particulate systems, particle technology is often treated as art than science. Hence, efforts in synthesizing, measuring, modeling, and developing particle and particulate systems are being pursued actively in both academia and industry. This article describes the fundamental principles governing the key aspects of particle science and technology.
Yeasts, Molecular and Therapeutic Applications
Authors: Macreadie Ian
Published: April 2010

Recombinant DNA technology made possible exciting new uses for yeasts as it did for various other organisms. For yeast, however, the opportunities are greater than for any other organism due to many attributes of yeast. Some of these attributes stem from its exceptionally long, safe and impressive track record. Other opportunities stem from its versatility, stability, variety, and the immense knowledge it has contributed to human health. Some of the recent ways in which yeast are being applied include the production of human therapeutics, the production of new and rare chemical entities, the screening for new drugs, and the elucidation of disease processes, including malaria, cancer and neurodegenerative diseases. In addition, if genetically‐modified foods gain greater acceptance we could see a plethora of new forms of the traditional yeast products. An overview of the new molecular and therapeutic applications of yeast are presented in this chapter.
Zeolites and Other Micro‐ and Mesoporous Molecular Sieves
Authors: Čejka Jiří , Kubička David
Published: April 2010

Zeolites have become indispensable materials for chemical industry being applied as detergents, adsorbents and particularly catalysts. Over the past decades this broad research and application field has experienced rapid development. New zeolite structures were synthesized, fundamental knowledge of micro‐ and mesoporous materials synthesis and characterization was substantially deepened and, consequently, more economical and environmentally acceptable industrial technologies were developped. This chapter summarizes the fundamental as well as practical aspects of zeolite synthesis, the most important properties of zeolites and their implications for practical use together with the main industrial applications. In particular, the attention is focused on zeolite use as adsorbents and catalysts. Zeolite research field was broadened to related materials, including zeotypes, mesoporous molecular sieves, hierarchic systems and metal‐organic‐frameworks. Synthesis, properties, and application potential of these novel and exciting groups of porous molecular sieves are briefly highlighted as well.
Cognition
Authors: Hudkins Robert L. , Marino Michael J. , Williams Michael
Published: April 2010

Therapeutic approaches to ameliorating cognitive dysfunction can be viewed as ends of a continuum, from the prophylactic enhancement of cognitive function to the restoration of function and/or arrest of the decline of cognition that occurs in the aging or traumatized brain. Research in the field of cognition is a high priority as the elderly population increases, with a great need to discover and develop drugs to treat age‐related cognitive disorders, including dementias, as well as cognitive impairments associated with neuropsychiatric disorders, such as schizophrenia. Aspects of cognitive dysfunction also occur in association with several CNS disorders, including Parkinson's disease, AIDS‐associated dementia, stroke, stress, sleep deprivation, depression, and anxiety, as well as with recreational and prescription drug usage and surgical procedures. Cognition is a complex set of processes, including attention, perception, emotion, learning and memory, action, and problem solving. Drugs currently approved for use in the treatment of neurodegenerative disorders such as AD include the cholinesterase inhibitors donepezil, rivastigmine, and galantamine, and memantine, a partial agonist at glutamate receptors. Since none of these drugs works especially well in treating the symptoms of AD, a variety of new chemical entities are currently being explored to identify new cognitive enhancers. This chapter covers the biological aspects of cognition and memory and the medicinal chemistry approaches to targeting cognitive deficits in disease.
Rubber, Guayule
Authors: Cornish Katrina , Schloman William W.
Published: April 2010

Guayule (Parthenium argentatum) is a rubber‐producing woody shrub native to the Chihuahuan Desert of northern Mexico and Texas. Guayule produces linear, high molecular weight natural rubber that can have physical properties and applications equivalent to those of Hevea (Hevea brasiliensis) rubber. Guayule rubber can be extracted as a solid bulk polymer or as a latex. Guayule also is one of very few rubber‐producing plants to have ever been used commercially for rubber production. Although guayule rubber was commercially produced in the early part of the last century, more recent efforts to reinstate production have not led to commercial success because the production costs of bulk rubber were too high to permit direct competition with Hevea rubber. Guayule commercialization has been revitalized in recent years by use of the plant to produce low protein hypoallergenic latex, a higher value rubber raw material.
The Dopamine Receptors
Authors: Civelli Olivier , Borrelli Emiliana
Published: April 2010

Dopamine receptors have a prominent place in our understanding of brain function. Drugs blocking dopamine receptors are used as antipsychotic drugs, drugs activating dopamine receptors as relieving Parkinson disease symptoms. Dopamine receptors have been pharmacologically divided into two classes the receptor that activate and the ones that inhibitory second messenger responses. Molecular cloning approaches have shown that this classification indeed hides not two but five receptors. Of particular importance were the discoveries of two additional inhibitory receptors, because they gave hope for the development of better antipsychotic drugs. But understanding novel receptors discovered on the basis of their sequences presents the challenge to search for their function. Although pharmacological tools are being developed targeting the new dopamine receptors, the engineering of mice lines devoid of these receptors and the studies on the gene expression of these receptors have led our major advances in our renewed understanding of the dopamine system.

Key Concepts:

Application of homology screening approaches has revolutionised the search for novel G protein‐coupled receptors.

Molecular biological approaches can lead to the discovery of pharmacologically unexpected receptors.

The new dopamine receptors raised high hopes for the development of new drugs for psychiatric disorders.

In spite of the fact that the new dopamine receptors have been discovered approximately 20 years ago, their role in the organism remains mostly not understood.

The D
4
dopamine receptors carried out the most hopes for the development of new antipsychotic drugs, it is still viewed as involved in the etiology of attention‐deficit disorders.

There is a need for the development of antagonists specific to the new dopamine receptors.
Bacterial Pili and Fimbriae
Authors: Huang I‐Hsiu , Dwivedi Prabhat , Ton‐That Hung
Published: April 2010

Bacterial proteinaceous filaments termed pili or fimbriae are nonflagellar, hair‐like structures protruding from the cell surface that are critical for bacterial virulence and fitness. Present in both Gram‐negative and Gram‐positive bacteria, pili are involved in many processes such as conjugation, adherence, twitching motility, biofilm formation and immunomodulation. Considerably diverse and complex, Gram‐negative pili are formed by noncovalent polymerisation of various pilin subunits; many of these pili require chaperones and usher proteins for their assembly. In contrast, fewer pilus systems have been described for the Gram‐positive counterparts; notably well studied are the heterotrimeric or ‐dimeric pili that are covalently assembled by a transpeptidase enzyme called
sortase
. Here we review the current knowledge of assembly pathways, structure and function of these pili in Gram‐negative and Gram‐positive pathogens.

Key Concepts:

Noncovalent pilus polymerisation is a general mechanism of pilus assembly in Gram‐negative bacteria, including the chaperon‐usher assembly pathway and type IV pilus pathway, which generates noncovalent pilus polymers.

Sortase‐mediated pilus assembly is a general mechanism of pilus assembly in Gram‐positive bacteria that involves a transpeptidase enzyme named sortase, which cleaves pilin precursors at sorting signals between threonine and glycine and involve the side‐chain amino groups of pilin motif sequences to generate covalent links between pilin subunits.

The sorting signal is consisted of an LPXTG motif followed by a hydrophobic domain and a positively charged tail.

The pilin motif is an 11 amino acid sequence of WxxxVxVYPKN located near the
N
‐terminus of major pilin subunits, in which the electron donating lysine residue forms an isopeptide bond with the threonine residue generated from the cleavage of the LPXTG motif of adjacent pilin subunits.

Tissue tropism is referred to as the ability of a pathogen to adhere specifically to some particular epithelial cells.

Phase variation involves switching of surface antigens such as pili that allows a pathogen to evade the host immune system.

Immunomodulation is a process of changing the host's immune system by certain molecules known as immunomodulators including pili that can activate or suppress immune cells.

Dental plaque is one of the most complex bacterial biofilms that is formed by sequential colonisation of initial colonisers such as
Actinomyces
spp. and oral streptococci and late colonisers; this process involves
Actinomyces
fimbriae.

Twitching motility mediated by pili allows translocation between mucosal surfaces, colonisation of host tissues and establishment of biofilms by a pathogen.
Antigens
Authors: Saha Bhaskar
Published: April 2010

The term ‘antigen’ refers to any molecule that is capable of being recognised by the immune system. Such molecules range from simple chemical compounds to complex macromolecules and are specifically recognised by one or more constituents of the innate and adaptive immune systems. In the innate immune system, the pattern recognition receptors recognise the pathogen‐associated specific molecular patterns. In the adaptive immune system, immunoglobulin and T cell‐receptor recognise either specific conformation on the antigen or the amino acid sequence in the peptide, respectively. Although antigens can be recognised by these receptors, all antigens do not necessarily elicit antigen‐specific immune responses; antigens that elicit an immune response are termed immunogens. The capacity to be recognised by these receptors expressed by the cells of the immune system is called antigenicity, whereas the ability to induce an immune response is immunogenicity. Thus all immunogens are antigens but all antigens are not immunogens.

Key Concepts:

Antigens are those molecules that are specifically recognised by the receptors of the innate and adaptive immune systems.

Immunogens are those molecules that are able to elicit immune responses with negative or positive effects such that immune responses are suppressed or activated, respectively.

Haptens are small molecules that are able to bind antibodies but are unable to evoke an immune response.

All immunogens are antigens but all antigens are not immunogens.

Toll‐like receptors in the innate immune system recognise many patterns on antigens whereas recognition with finer specificity is executed by immunoglobulin and T‐cell receptors, the constituents of the adaptive immune system.

The ability to rearrange the genes of the receptors (B‐ and T‐cell receptor) in the adaptive immune system creates a huge repertoire of antigen‐specificity and memory whereas such a feature is not available with the receptors of the innate immune system.

B‐cell receptors recognise virtually any antigens in a conformation‐dependent manner and do not need any processing of the antigen for its recognition whereas the T‐cell receptor recognition of an antigen depends primarily on the sequence of amino acids in the peptide.

T‐cell receptors recognise primarily peptide antigens in association with major histocompatibility complex molecules that necessitates processing of the antigens before the recognition.
Closteroviridae
Authors: Martelli Giovanni P , Candresse Thierry
Published: April 2010

Closteroviridae
is a family of plant viruses with filamentous, helically constructed particles showing distinct cross‐banding and varying in length from 650 nm (species with fragmented genome) to over 2000 nm (species with monopartite genome). The genome is a single‐stranded, positive‐sense RNA (
ribonucleic acid
), with size varying from 13 000 to nearly 19 000 nucleotides, thus being among the largest known for plant viruses. The family comprises three genera,

Closterovirus

,

Ampelovirus

and

Crinivirus

, which differ in genome type (monopartite, bipartite or tripartite) and size, and in epidemiological behaviour. Closteroviruses are transmitted by aphids; ampeloviruses by pseudococcid mealybugs and soft scale insects and criniviruses by whiteflies. These viruses are mostly phloem‐restricted, are all transmitted with a semipersistent modality regardless of the type of vector and are pathogenic to a wide range of herbaceous and woody crops, to which they may cause extensive damage. Control is based on preventive measures such as sanitary selection, sanitation and induction of resistance, primarily through conventional breeding.

Key concepts:

Closteroviridae
is a growing family of plant viruses with three genera.

All members of the family have filamentous virions with open particle structures and distinct cross‐banding.

Closteroviral genomes are among the largest for plant viruses and are highly diversified also within each genus.

The family represents a monophyletic lineage that has evolved in a modular way.

A characterizing trait of the genera is the type of vectors that mediate transmission from host to host.

Virus particles are primarily restricted to the phloem from where they are acquired by the vectors.

Virus dissemination over long distances is mediated by infected propagative material, rather than vectors.

Most members of the family have a restricted natural host range.

Many cause serious, if not devastating, epidemics to herbaceous and woody crops.

Disease control relies on preventive measures aimed at reducing vector populations and sources of inoculum.

Sanitary selection and sanitation are efficient means for producing certified stocks.
Virus Diseases of Grapevine
Authors: Martelli Giovanni P
Published: April 2010

There are more than 20 recognized virus and virus‐like diseases of grapevines (VitisandMuscadiniaspp.). Many have a clear‐cut detrimental effect on the vines, that is stunting, reduced vigour, malformation of the leaves and twigs, foliar discolourations ranging from reddening to chlorotic or bright yellow mottling, ringspots and line patterns. The productive life of the vineyards can be shortened and the quantity and quality of the crop badly affected. Prevailing disease agents are viruses transmitted by nematodes (nepoviruses and sadwaviruses), pseudococcid mealybugs and soft‐scale insects (closteroviruses and vitiviruses). Infected propagation materials (scions and rootstocks) are the major way for long‐distance dissemination of diseases, several of which have now a worldwide distribution and have entered areas where the grapevine industry is expanding. Control is based on preventive measures such as sanitary selection, sanitation and induction of resistance through conventional breeding or genetic engineering.

Key concepts:

Virus and virus‐like diseases are a major threat to the world's grapevine industry.

The world of grapevine‐infecting viruses is the most variegated among woody crops.

Prevailing viruses are soil‐borne and mealybug‐transmitted.

Spreading of diseases and their agents is mediated by infected propagative material and vectors.

Nursery productions have played, and still do, a major role in disease dissemination.

Disease control relies on preventive measures aimed at reducing vector populations and sources of inoculum.

Sanitary selection and sanitation are most efficient means for producing certified stocks.
Bacterial Replication Fork: Synthesis of Lagging Strand
Authors: Tanaka Taku , Masai Hisao
Published: April 2010

How can an antiparallel DNA (deoxyribonucleic acid) strand be duplicated by aDNA polymerasethat synthesises DNA in only one direction? This paradox of DNA synthesis on the lagging strand was dissolved by discovery of Okazaki fragments. The major components of the bacterial replication fork includereplicative helicase,primaseandDNA polymerase. The loading ofreplicative helicase,DnaB, is the most critical step for assembly of a primosome, a protein complex responsible for duplex unwinding and primer RNA (ribonucleic acid) synthesis at the replication fork.DNA polymerasemay be an asymmetric dimer, each of which may concurrently synthesise leading or lagging strand. Several different modes of primosome assembly have been identified in bacteria. AtoriC(origin of chromosome),DnaA‐dependent primosome is assembled for initiation of a round of DNA replication, whereasPriA‐dependent primosome is assembled at stalled replication forks to facilitate replication restart.

Key Concepts:

Initiation of DNA replication: DNA replication is initiated by the initiator protein, which specifically recognises and binds to the origin sequence and recruits other primosome components including a DNA helicase.

Leading and lagging strands: Leading strand is the one in which the direction of DNA chain elongation and overall fork movement is the same and lagging strand is the one in which they are opposite.

Replicative helicase: An enzyme which catalyses continuous unwinding of the parental duplex DNA at the replication fork.

Replication fork: The site of DNA replication where two replicating single‐stranded DNA separates.

Primer RNA: A short stretch of RNA, the 3′‐terminus of which is utilised by DNA polymerases for DNA elongation.

Primosome: A name given to the protein complex capable of duplex DNA unwinding and primer RNA synthesis at the replication fork.

Stalled replication fork: A replication fork the movement of which is blocked by internal and external ‘replication stress’ including DNA damages and depletion of nucleotide precursors.

Replication restart: The process of reassembly of primosome at a stalled replication fork to resume DNA chain elongation.
Poxviruses
Authors: Pickup David J
Published: April 2010

Poxviruses are brick‐shaped, enveloped viruses, each containing a linear, double‐stranded DNA (
deoxyribonucleic acid
) genome of 130–380 kilobases (kb). Several family members, including

variola

,

monkeypox

,

cowpox

,

vaccinia

,

orf

and

molluscum contagiosum viruses

, cause disease in humans. Smallpox, which was caused by

variola virus

, was once responsible for the deaths of millions each year. In 1796, Jenner showed that inoculation of material from a cowpox lesion could protect against smallpox: Vaccination had been introduced into medicine. Moreover, through the use of

cowpox

and

vaccinia virus

vaccines, the dread disease of smallpox was eradicated from the natural environment. Although

variola virus

, the principal poxvirus pathogen, is no longer a public health hazard, the poxviruses have continued to be the focus of intense study because they provide unique systems for investigation of mechanisms important in molecular biology, viral pathogenicity and immunity. Attenuated poxviruses now provide some of the most promising contemporary platforms for broad‐spectrum, live‐virus vaccines.

Key concepts

Variola virus
, which causes smallpox, is one of the most virulent human pathogens.

Variola virus
is the only virus eradicated from the natural environment.

Jenner showed that infection with cowpox could protect against infection with smallpox.

Cowpox virus
was the original vaccine, hence the name vaccine, from the Latin word
vacca
for cow.

The worldwide eradication of the disease of smallpox was achieved by immunization with vaccines containing live
vaccinia viruses
(viruses similar to, but more attenuated than,
cowpox virus
).

Except for
variola virus
and
molluscum contagiosum virus
(MCV), most of the poxvirus diseases of humans are zoonoses (diseases transmitted to humans from animals).

Among viruses, the poxviruses are unusually independent of host cell functions, employing mainly viral enzymes for viral gene transcription and viral DNA replication in the cytoplasm of infected cells.

Poxviruses do not establish latent infections.

Poxviruses possess many accessory genes that are not required for virus replication
in vitro
, but which are advantageous for virus replication
in vivo
.

Most of the accessory proteins encoded by poxviruses of vertebrates interfere with either innate or adaptive immune responses.
Viral Capsids and Envelopes: Structure and Function
Authors: Lucas William
Published: April 2010

Virus particles contain the viral genome packaged in a protein coat called the capsid. For some viruses, the capsid is surrounded by lipid bilayer that contains viral proteins, usually including the proteins that enable the virus to bind to the host cells. This lipid and protein structure is called the virus envelope, and is derived from the host cell membranes. The capsid and envelope play many roles in viral infection, including virus attachment to cells, entry into cells, release of the capsid contents into the cells, and packaging of newly formed viral particles. The capsid and envelope are also responsible for transfer of the viral genetic material from one cell to another. These structures also determine the stability characteristics of the virus particle, such as resistance to chemical or physical inactivation.

Key concepts:

Viral genetic material is packaged inside protein structures called capsids.

Viruses are divided into two groups: enveloped viruses are surrounded by an outer lipid membrane; nonenveloped viruses lack this membrane.

Where present, the envelope contains the viral proteins, which mediate binding to host cells. Where no envelope is present, this function is carried out by the outer capsid proteins. In general, nonenveloped viruses are more stable and can survive much longer in the environment.

Capsids and envelopes determine the method of viral entry into and exit from host cells.
Nerve‐dependent Tissue and Organ Regeneration
Authors: Mescher Anthony L
Published: April 2010

The anatomical and functional restoration of parts removed from an organism is known as regeneration. In the regenerating amphibian limb and in tissue regeneration in certain sensory organs, this process occurs under the influence of nerves. In other systems, such as liver regeneration and most instances of tissue repair, nerves are not required. One determinant of whether nerves are required for regenerative growth may be the degree of vascularization in the injured, responding tissue or organ. The early, nerve‐dependent blastema of the regenerating limb is almost completely avascular except in its overlying skin. The molecular basis of the nerves’ growth‐promoting effect is not known. Of the candidate molecules proposed, the nutritive factor
transferrin
, which is also released from capillaries, fits most closely to what is known of the neural effect in limb regeneration. Other candidates proposed as mediators of this activity include Fibroblast growth factors (FGFs),
neuregulins
and anterior gradient protein (nAG).

Key Concepts:

Amphibian limb regeneration and other examples of epimorphic (blastema‐based) regeneration usually depend on trophic factors provided by peripheral nerves.

All nerve types can supply the growth requirement, which appears to be a nutritive factor that sustains cell cycling rather than a mitogenic signal to trigger cell cycling in dedifferentiating limb cells.

Other nerve‐dependent regenerating systems, such as regeneration of taste buds and corneal repair, lack a direct, extensive vasculature.

Regenerating systems not requiring nerves, such as liver regeneration and seasonal regrowth of antlers, are not epimorphic and the regenerative process does not involve a blastema.

Candidate factors for the neural effect include neuregulins, the newt anterior‐gradient protein (nAG), and the plasma‐derived trophic factor transferrin.

Transferin is transported and released axonally and is required for cell cycle progression in a manner consistent with the effects of denervation on limb blastema cell proliferation.
Lens Induction
Authors: Kondoh Hisato
Published: April 2010

Lens tissue develops from the embryonic head ectoderm through its interaction with the retinal primordium, the optic vesicle. This developmental mechanism has served as a paradigm of embryonic tissues induction. The application of modern techniques for gene manipulation and monitoring gene activities in developing embryonic tissues have revealed the two optic vesicle‐dependent mechanisms that underlie the lens induction process: local activation of the cooperative transcription factorsSOX2(SRY‐related‐HMG‐box 2) andPAX6(paired box 6) in the head ectoderm; and elimination of the influence of the cephalic neural crest, which is otherwise inhibitory to lens development. Lens induction reciprocally influences the development of the optic vesicle and organizes the lens‐centered optic cup. The action ofSOX2andPAX6is also common to other lens‐generating processes, including during lens regeneration from the dorsal iris in the newt eye, and lens transdifferentiation from the pituitary primordium as occurs in certain mutant embryos.

Key concepts:

Tissue induction is the process of deriving new cell types from a tissue through interaction with another tissue.

Transcription factors are proteins that regulate gene transcription by binding to the gene regulatory regions of DNA.

Signalling molecules, which are often proteins, are secreted from a group of cells, bound by receptors on another group of cells, and cause changes in the cells that bind the molecules.
Immunity: Humoral and Cellular
Authors: Harrison Leonard C , Unglik Gary , Honeyman Margo C
Published: April 2010

The immune system evolved to recognise infectious pathogens. Discrimination between self and nonself is a critical property of the immune system that enables it to eradicate pathogens without harming the host. Immune responses to pathogens are affected initially by the innate immune system, which reacts rapidly to generic pathogen‐associated molecules and primes the adaptive immune system, which is slower to react but has exquisite specificity and memory. Here, we outline the spatial framework of the immune system and define its mobile and fixed elements. A range of cell types (including antigen‐presenting cells and lymphocytes) and soluble components (including complement, antibody, cytokine and chemokine proteins) circulate and communicate between the bone marrow and lymphoid tissue structures to maintain immune surveillance.

Key Concepts:

The immune system is designed to recognise, react to and eradicate ‘nonself’, in particular infectious pathogens.

The immune system comprises fixed and mobile elements.

The elements of the immune system sequentially mediate innate immunity, providing acute, generic defences and adaptive immunity, providing highly specific, long‐lasting defences.

The specificity and diversity of adaptive immunity is based on genetic polymorphism of the receptors for antigens on T and B cells and of the major histocompatibility complex (MHC) molecules that bind antigenic peptides recognised by the T‐cell receptor.

Nonspecific costimulation via surface‐interacting molecules or soluble cytokines and chemokines shapes the differentiation of T and B cells in the adaptive immune response.
Plant Defences against Herbivore Attack
Authors: Schardl Christopher L , Chen Feng
Published: April 2010

Plants deploy a number of defences against attack by insects and other herbivores. Direct defence is conferred by plant products and structures that deter or kill the herbivores. Chemical toxins and deterrents vary widely among plant species, and some typical toxins include alkaloids, terpenoids, steroids, phenylpropanoids and precursor compounds that, on damage of the plant tissue, can be degraded to cyanide or other toxic molecules. Physical defences include thorns, barbs and unpalatable tissues. Other defences are indirect, such as defensive symbioses with microbes, harbouring protective ants or recruitment of parasitoids and predators that attack the herbivores. Recent experiments, and deployment of transgenic plants with Bt toxins, demonstrate the potential for novel plant defences in agriculture.

Key Concepts:

Plants employ various direct and indirect mechanisms to defend against herbivores.

Direct defences include chemical defences and physical defences such as tissue toughness, thorns and barbs.

Chemical defences against herbivores are numerous and diverse.

Direct chemical defences can be toxic or deterrent to herbivores, or reduce nutritive value of the plant tissues.

Some chemical defences act indirectly, for example, by attracting wasps that are parasitic to the herbivores.

According to optimal defence theory, young tissues of high value to plant fitness tend to be chemically defended, whereas older tissues have relatively strong physical defences.

Chemical defences, especially induced chemical defences, are tightly regulated mainly through the jasmonate signalling pathway.
Eicosanoid Biosynthesis
Authors: Fernandez Ana Z , Fatima Garces Maria , Alvarado‐Castillo Claudia P , Estrada Omar
Published: April 2010

Eicosanoids are the major products derived from the cellular metabolism of arachidonic acid by the enzymescyclooxygenase,lipoxygenaseandepoxygenases. The eicosanoids comprise several compounds, which include prostaglandins, thromboxanes, prostacyclins, leukotrienes, lipoxins and epoxyeicosatrienoic acids. They represent the major group of metabolically active lipids, exerting their functions through different mechanisms, that is by receptor binding and intracellular signalling pathway modulation. Their effects are diverse, acting on every cell of the body, with a short half‐life. A tight regulation on the processes of formation and inactivation or clearance is fundamental to prevent the exacerbation of their effects. Although initially they were strictly linked to inflammatory processes, recent evidences point out their homeostatic counterpart. Thus, there are eicosanoids involved in vasoconstriction/vasodilatation balance, thrombotic/antithrombotic balance and inflammation/anti‐inflammation balance. This article will focus on the enzymes involved in the formation of these lipids.

Key concepts:

Eicosanoids are important lipid mediators involved in cellular homeostasis.

Most eicosanoid effects are mediated through specific receptors.

Inhibition or activation of the key enzymes involved in the biosynthesis of eicosanoids has encouraged the development of new therapeutics approaches.
Quaternary Life on Land
Authors: Elias Scott A
Published: April 2010

The Quaternary is the most recent geologic period. The glaciations that characterise this period began about 2.6 million years ago. There have been roughly 50 glacial–interglacial cycles during the Pleistocene Epoch which comprised all of the Quaternary except the current interglacial interval, the Holocene. Pleistocene biota mostly responded to the series of rapid dramatic climatic changes by migrating to regions of acceptable climate. The constant reshuffling of biological communities led to the formation of many combinations of species for which there is no modern analogue. The end of the last glaciation saw the extinction of large numbers of large mammals (the Pleistocene megafauna) in Eurasia, Australia and the New World. The Late Pleistocene saw the rise and geographic dispersal of humans, including Neanderthals in Europe and southwest Asia, and modern humans who spread out of Africa into Europe, Asia, Australia and eventually the New World.

Key concepts:

Rapid climate change characterised most of the Quaternary.

The Quaternary and Late Tertiary saw the evolution of modern ecosystems.

Nonanalogue biological communities formed during the Pleistocene, as the ranges of individual species responded independently to climate change.

The Late Pleistocene–Holocene transition saw a major extinction event among megafaunal mammals.

The Pleistocene was also the most important interval of human evolution and dispersal.
Petals
Authors: Drea Sinéad
Published: April 2010

Petals are often the most obvious organ within a flower because they provide visually arresting targets for varied pollinators and show corresponding adaptions in form, colour and scent. When present, they are located in the outer layers of a flower (the perianth) surrounding the male and female reproductive organs, the stamens and carpels. Their development is a consequence of a regulatory hierarchy of meristem determining genes, organ identity genes and downstream target genes. The gene hierarchy involves transcription factors from varied families and is regulated at transcriptional and posttranscriptional levels, involving microRNAs (
ribonucleic acids
) and targeted protein degradation. The nature of the gene and protein interactions determining and controlling many aspects of petal development have been teased apart in dicotyledonous flowers of

Arabidopsis

,

Antirrhinum

and

Petunia

and in recent years, this knowledge has been used to explore the evolution of these developmental genetic systems across the angiosperms.

Key concepts:

Molecular genetics has identified key regulators of petal development in model species.

Petal initiation and subsequent development is regulated by a range of transcription factor types.

Petal characteristics such as colour, shape and scent are related to pollination mechanisms.

Ethylene is important in petal senescence.