bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaea
Authors: Oren Aharon 
Published: September 2010

AbstractAnalysis of nucleotide sequences of ribosomalribonucleic acid(RNA) led in the 1970s to the recognition of the existence of three domains of life, named Eukarya (Eukaryotes), Bacteria (Eubacteria) and Archaea (Archaebacteria). This classification replaced the earlier accepted Eukaryotes–Prokaryotes dichotomy. The Archaea resemble the Bacteria in cell size and cell structure, but possess many distinguishing features, including lack of peptidoglycan in their cell wall, presence of unique membrane lipids not found in the other domains of life and other unique biochemical and genetic properties. Most cultured Archaea were recovered from extreme environments (high salt concentrations, high temperatures and acidic hot springs). The unique properties of these extremophiles can be exploited in biotechnology. The strictly anaerobic methanogenic prokaryotes also belong to the archaeal domain. Culture‐independent studies show that Archaea are also widespread in nonextreme environments such as seawater and soil, and the properties of a few nonextremophilic Archaea are now being elucidated.Key Concepts:The Archaea form a second lineage of prokaryotes, evolutionarily distant from the Bacteria.Most Archaea are classified within the phyla Crenarchaeota and Euryarchaeota; other archaeal phyla proposed are the Korarchaeota, the Nanoarchaeota, and the Thaumarchaeota.Archaea resemble Bacteria in cell size, morphology and ultrastructure, but differ from the Bacteria in many biochemical, physiological and genetic features.The cell membrane lipids of the Archaea are based on branched (isoprenoid) hydrophobic carbon chains linked to glycerol by ester bonds.Peptidoglycan, the characteristic cell wall constituent of the Bacteria, does not occur in the Archaea.All known methane‐forming prokaryotes belong to the Archaea.Most cultured Archaea are extremophiles that live at high temperatures, low or high pH values or high salt concentrations.Archaea are also widespread in environments not characterised by environmental extremes, but their function in aquatic and soil ecosystems is still poorly understood.Archaea contribute to the autotrophic oxidation of ammonia to nitrite in different ecosystems.Thanks to their unique biochemical features, the Archaea have considerable potential for biotechnological applications.
Glycoproteins
Authors: Merry Tony , Astrautsova Sviatlana 
Published: September 2010

AbstractGlycoproteins are proteins that contain covalently bound oligosaccharides (glycans). Although there are structural features ofN‐ andO‐linked glycans common to all eukaryotes, species‐specific glycosylation reactions create a wide diversity of structures. This is particularly relevant to cell surface glycoproteins although intracellular and even nuclear proteins may be glycosylated. The factors controlling glycosylation are complex and include the protein sequence and structure, specificity of relevant transferase enzymes, availability of donor sugars and other environmental factors. These may all interact so it is not surprising that there is great variety in glycosylation even on the same protein. Glycosylation of proteins is important in such areas as development and interaction with pathogens and provides a means of modifying the function of proteins that is not directly dependent on theirdeoxyribonucleic acid(DNA) template. Interest in the field is growing and advances in analytical technology now make the field accessible to a wider community.Key Concepts:Proteins are frequently modified posttranslationally, the most frequent modification being glycosylation.Glycosylation may play an important role in protein folding through interaction with the chaperones calnexin and calreticulin.It has been calculated that as many as 70% of all proteins may be glycosylated.The glycosylation of a protein may vary extensively depending on the cell in which it is produced which may enable the same protein to function in different ways depending where it is expressed.On the cell surface, glycoprotein glycans are frequently involved in cell–cell interactions.Glycosylation of the same protein may change during development or in maturation, for example in cells of the immune system.Glycosylation differs between species even if they are closely related, for example between great apes and man.Analysis of glycosylation has progressed in recent years and is now almost a routine procedure.Particular features of glycosylation may only have functional significance in a particular time and place but can be widely distributed which can make assignment of function to glycan structure difficult.
Plant Volatiles
Authors: Qualley Anthony , Dudareva Natalia 
Published: September 2010

Abstract

Plants produce an amazing number of chemical compounds that can disperse in the air at ambient temperature. These plant volatiles have served mankind, perhaps since pre‐Neolithic times, as perfumes and flavour compounds. In nature, these compounds attract pollinators and seed dispersers, protect plants through repulsion or intoxication of attacking herbivores, entice predator or parasitoid insects that prey on herbivores, prime defences of neighbouring plants against imminent attack, confer antimicrobial properties critical to defence against pathogens, and mitigate oxidative stresses. Plant volatiles are typically classified into four major categories: terpenoids, fatty acid derivatives, amino acid derivatives and phenylpropanoid/benzenoid compounds, though a number of species‐ or genus‐specific volatile compounds, such as those found in select species of Alliaceae and Brassicaceae, fall outside these categories. This enormous variety is represented by more than 1700 compounds from 90 species.

Key Concepts:

Plant volatiles are critical in the attraction of pollinators and seed dispersers.

Plants use volatiles to protect themselves from pests and pathogens.

Plants under herbivore attack can alert neighbouring plant species, priming their chemical defences.

Plant volatiles are classified according to their metabolic origins as terpenoids, phenylpropanoids/benzenoids, fatty acid derivatives and amino acid derivatives.

Biosynthesis of plant volatiles is spatially, developmentally and temporally regulated.

Modern techniques for the collection and trapping of plant volatiles (SPME, dynamic headspace sampling) provide sensitive and representative samples for analysis.

Plant volatiles serve humankind as perfumes and aroma compounds, natural flavour constituents, food additives/preservatives, and chemotherapeutics and anaesthetics.
Immune Responses: Primary and Secondary
Authors: Ademokun Alexander A , Dunn‐Walters Deborah 
Published: September 2010

Abstract

Immune responses to antigens may be categorised as primary or secondary responses. The primary immune response of the body to antigen occurs on the first occasion it is encountered. Depending on the nature of the antigen and the site of entry this response can take up to 14 days to resolve and leads to the generation of memory cells with a high specificity for the inducing antigen. The humoral response, mediated by B cells with the help of T cells, produces high‐affinity and antigen‐specific antibodies. This is in contrast with the CD8 T‐cell response which leads to the generation of large numbers of antigen‐specific cells that are capable of directly killing infected cells. Antigen‐specific CD4 T cells, which provide help to B cells in the form of cytokines and other stimulatory factors, can also be expanded upon antigenic stimulation.
The secondary response of both B‐ and T cells is observed following subsequent encounter with the same antigen and is more rapid leading to the activation of previously generated memory cells. This has some quantitative and qualitative differences from the primary response.

Key Concepts:

The innate immune system is the first line of defence against infectious agents. When this is breached, the adaptive immune system provides a more efficient response to clearing pathogens.

The adaptive immune system has the capacity to ‘remember’ previous antigens, a process termed immunological memory.

Antigen‐specific T cells are selected during a primary immune response and expand to produce clones of T cells with high specificity for the activating antigen.

In a B cell primary response to a thymus‐dependent antigen, the immune system selects B cells with a high affinity and specificity for the antigen and these become memory cells.

The selection of B cells with a high affinity for a given antigen occurs in the germinal centres of secondary lymphoid follicles and requires the enzyme activation‐induced cytidine deaminase (AID) and interactions with other immune cells.

The ability to change the isotype of antibody produced (class switching) by a B cell also occurs in germinal centres and requires AID.

In a secondary response to the same antigen, memory cells are rapidly activated. This process is quicker and more effective than the primary response.
Picornaviruses
Authors: Rowlands David J 
Published: September 2010

Abstract

The name picornavirus is derived from
pico
for small and
ribonucleic acid
(RNA), denoting the chemical nature of the genome. Virions are nonenveloped icosahedral particles approximately 30 nM in diameter. The capsid is constructed from 60 copies of each of four structural proteins which account for 70% of the particle mass and enclose the single‐strand genome of 7500–8500 nucleotides. The positive strand genome acts directly as a messenger RNA to template a single polyprotein product. This is subsequently processed by virally encoded proteases into mature active proteins. Several intermediate products have distinct functions to the final fully processed proteins. Replication of the genome is initiated by an uridylated peptide and proceeds via a negative strand intermediate template. Picornaviruses are among the smallest pathogens of vertebrates and are responsible for many important diseases in humans and animals.

Key Concepts:

There are effective vaccines against polio, hepatitis A and foot‐and‐mouth disease viruses. In addition, movement control and slaughter is used to control foot‐and‐mouth disease. There are no licensed drugs for picornavirus infections.

Genome sequence comparisons have replaced biological and biophysical comparisons as the bases for classification within the family.

Picornavirus particles comprise 60 copies each of 4 structural proteins, which form a quasi T1 icosohedral capsid encasing the single strand RNA genome.

The picornavirus RNA genome functions as a messenger RNA to template the synthesis of a single polyprotein, which is posttranslationally processed by viral proteases.

Picornaviruses bind to cell specific surface receptors and this interaction is an important factor in determining host and tissue specificity of each virus.

Picornaviruses cannot gain entry to cells by membrane fusion, as is the case for enveloped viruses, and require special mechanisms to breach cellular membranes and safely deliver the genome into the host cell.

Genome replication occurs in association with virus modified cellular membranes. Viral RNA templates complementary negative strand molecules which in turn template multiple positive strand copies. The synthesis of all RNA molecules is initiated by an uridylated peptide primer.

The mechanisms of transmission of infection play key roles in the epidemiology of picornavirus infections.

Picornaviruses are responsible for a wide range of clinical diseases resulting from multiple factors such as receptor specificity, tissue‐specific susceptibility, virulence and the mechanisms of transmission.
Monoclonal Antibodies
Authors: Zola Heddy 
Published: September 2010

Abstract

Antibodies bind other molecules strongly and specifically and are therefore useful as reagents in research, diagnosis and therapy. Antibodies taken from the blood of immunised animals are a mixture of different antibodies produced by different cells (they are described as polyclonal). Monoclonal antibodies are antibodies with a unique specificity, generally made by cloning cells containing a particular antibody gene set to produce a population of identical cells, derived from a single cell, which all produce the same antibody. Monoclonal antibodies are therefore much more specific than polyclonal antibodies. Monoclonal antibodies can be made in cell culture and are therefore also more reproducible from batch to batch than polyclonal antibodies. Monoclonal antibodies have become the preferred reagents in many research and diagnostic applications and are increasingly used in therapy of cancer and immunological disorders, generating a multi‐billion dollar industry.

Key Concepts:

Antibodies form part of the mammalian immune response, binding to foreign molecules to neutralise or remove them.

By injecting an animal with a target molecule, we can make an antibody that binds the target molecules strongly and specifically.

One immune cell makes just one antibody, but from the blood, we get a mixture of the antibodies produced by many immune cells.

By isolating a single immune cell making a single antibody of interest and converting it to a dividing, growing clone of cells (cloning the cell), we can make large quantities of identical antibody – monoclonal antibody.

Monoclonal antibodies provide specific reagents for almost any molecular structure above a minimal size.

Monoclonal antibodies can be used to identify, quantify, isolate or remove the target molecule in complex biological mixtures or in tissues.

Monoclonal antibodies can be injected into patients to remove harmful components ranging from toxins to cancer cells.

Advances in molecular biological technologies make it possible to modify monoclonal antibodies to achieve therapeutic objectives with minimal side effects.
Natural Killer (
NK
) Cells
Authors: Vivier Eric , Ugolini Sophie 
Published: September 2010

Abstract

Natural killer (NK) cells are a discrete subset of lymphocytes of the innate immune response. They are rapid mediators of cytotoxicity against a variety of ‘stressed cells’ that include microbe‐infected cells, transformed cells or cells in distress as a result of physical or chemical injuries. NK cells are also potent producers of a large spectrum of cytokines, including
interferon γ
(IFNγ) and
interleukin 10
(IL‐10). Through these functions, they act as both effector and regulatory cells of the immune response.

Key Concepts:

NK cells are lymphocyte of innate immunity that sense a variety of stressed cells and participate to their elimination.

NK cells are regulatory cells that contribute to the innate immune response and to the shaping of the adaptive immune response.

The study of NK cell biology has been instrumental in revealing various mode of immune detection: missing self‐recognition and stress‐induced cell recognition.

The manipulation of NK cell recognition strategies leads to the development of innovative therapeutic settings from allogeneic bone marrow transplantation to the injection of blocking anti‐KIR monoclonal antibodies.
Peptide Bonds, Disulfide Bonds and Properties of Small Peptides
Authors: Gilbert Hiram F 
Published: September 2010

AbstractThe peptide bond links amino acids into head‐to‐tail polymers in proteins as peptides. Chemically, the peptide bond is an amide with restricted rotation about the carbon–nitrogen bond. This restricted rotation combined with free rotation around the alpha carbon of the linked amino acids define the three‐dimensional structure of all proteins. The structure of a peptide or protein can be further stabilised by introducing disulfide crosslinks, a chemical oxidation between two sulfhydryl groups of the amino acid cysteine stabilise specific conformations of peptides and proteins. Small peptides, which often function biologically as hormones or other signalling molecules can also be useful model systems for investigating protein structure and function. The introduction of disulfide bonds and a change in conformation between thecisandtransconformations of the proline peptide bond may be a barrier to the rapid formation of the proper protein structure. In the cell, enzymes are present to catalyse these processes.Key Concepts:The conformational flexibility around the alpha carbon of peptides connected by peptide bonds accommodates an enormous number of structures depending on the protein sequence.Disulfides are chemical crosslinks between or within polypeptides that adds stability to the overall structure.Conformational transitions involving proline residues in a protein can slow protein folding due to a slow conformational transition.The enzymes protein disulfide isomerase and peptidyl proline isomerase function in the cell to catalyse slow chemical and configuration changes that retard protein folding.
Membrane Lipid Biosynthesis
Authors: Vance Jean E 
Published: September 2010

Abstract

Biological membranes consist of a complex array of proteins and lipids that create selective permeability barriers in cells. Another function of membrane lipids is their degradation to generate ‘lipid second messengers’ that can regulate important cellular functions such as cell division and cell death. The major membrane lipids of eukaryotic cells are the glycerophospholipids, the sterols and the sphingolipids. The most abundant glycerophospholipids in eukaryotic cells are phosphatidylcholine and phosphatidylethanolamine, each of which is synthesised by two independent pathways. The glycosphingolipids consist of structures in which ceramide is attached to a variety of oligosaccharide chains to create an enormously diverse class of lipids that are highly enriched on the cell surface. In mammalian cells, cholesterol is the most abundant sterol in membranes, whereas plants and fungi do not contain cholesterol

per se

but instead contain sterols that are related to cholesterol; prokaryotic membranes do not contain sterols.

Key Concepts:

Lipid bilayers provide the fundamental architecture of biological membranes.

Cellular phospholipid levels are tightly regulated.

Major classes of phospholipids are made by more than one pathway.

Acyl chain composition of phospholipids can be modified by deacylation.

The cholesterol‐lowering statin drugs regulate cholesterol biosynthesis at the step catalysed by 3‐hydroxy‐3‐methylglutaryl‐CoA reductase.
Adrenaline and Noradrenaline
Authors: Goldstein David S 
Published: September 2010

AbstractNoradrenaline and adrenaline are catecholamines that play major roles in regulation of the ‘inner world’ of the body by the brain. Noradrenaline (synonymous with norepinephrine), the main neurotransmitter of the sympathetic nervous system, is responsible for tonic and reflexive changes in cardiovascular tone. Adrenaline is a key determinant of responses to metabolic or global challenges to homeostasis, such as glucoprivation, and of manifestations of emotional distress. In contrast with the view that the sympathetic nervous and adrenomedullary hormonal systems function as a unit (the ‘sympathoadrenal system’) to maintain homeostasis in emergencies, across a variety of situations adrenaline responses are more closely linked to responses of the hypothalamic‐pituitary‐adrenocortical system than of the sympathetic nervous system. The sympathetic noradrenergic system is active even when the individual is at rest and maintains tonic levels of cardiovascular performance. Adrenoceptors in the membranes of effector cells determine the physiological and metabolic effects of catecholamines.Key Concepts:Noradrenaline and adrenaline are catecholamines.Noradrenaline is the main neurotransmitter of the sympathetic nerves in the cardiovascular system.Adrenaline is the main hormone secreted by the adrenal medulla.The sympathetic noradrenergic system plays major roles in tonic and reflexive changes in cardiovascular tone.Adrenaline is a major determinant of responses to metabolic or global challenges to homeostasis.Adrenaline responses to stressors are more closely linked to responses of the hypothalamic‐pituitary‐adrenocortical system than of the sympathetic nervous system.The sympathetic noradrenergic system is active even when the individual is at rest and maintains tonic levels of cardiovascular performance.Adrenoceptors in the membranes of effector cells determine the physiological and metabolic effects of catecholamines.Beta‐adrenoceptors mediate stimulatory effects of catecholamines on the rate and force of the heartbeat; stimulation of vascular alpha‐adrenoceptors produces vasoconstriction and increases blood pressure, and stimulation of vascular beta‐adrenoceptors – especially beta‐2 adrenoceptors in skeletal muscle – produces vasodilation.Catecholamines affect cardiovascular functions by actions at adrenoceptors on cardiovascular cells, in the nervous system, and in the kidneys.
Tiering on Land – Trees and Forests (Late Palaeozoic)
Authors: Cleal Christopher Jonathan 
Published: September 2010

Abstract

Trees with woody trunks first appeared in Middle Devonian times (390 MYA). However, a number of other types of Palaeozoic plants also achieved large sizes, most notably the arborescent lycopsids. The tropical wetlands of late Carboniferous and early Permian age (320–280 MYA), often referred to as the coal swamps or coal forests, were dominated by the arborescent lycopsids. Because of the unusual growth and reproductive strategies of these plants, and the water‐logged and low pH substrates, the ecological structure of these forests was quite different from most modern‐day forests. Rather than there being a vertical stratification of the vegetation controlled by light availability, there was a lateral ecological partitioning of the habitats controlled mainly by substrate conditions.

Key Concepts:

The late Palaeozoic coal forests were relatively open habitats, and therefore, light levels were not significant in controlling their ecological partitioning.

Substrate conditions were most important for controlling plant distribution in the coal forests, resulting in a lateral ecological partitioning, rather than a vertical tiering as is typical in most modern‐day forests.

The rapid determinate growth of the arborescent lycopsids that dominated the coal forests meant that huge amounts of peat were generated, which are now preserved as coal.

The coal forests were a major carbon sink during the late Palaeozoic times and had a significant impact on levels of atmospheric carbon dioxide and global climates.