bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant Tracheary Elements
Authors: Fukuda Hiroo 
Published: September 2010

Abstract

The plant tracheary element is the constituent of vessels and tracheids. Tracheary elements are characterised by patterned secondary wall thickenings and programmed cell death (PCD) at maturity. Their differentiation is induced by plant hormones such as
auxin
, cytokinin and brassinosteroids, and suppressed by a small peptide, tracheary element differentiation inhibitory factor (
TDIF
), secreted from phloem cells. The final determination of tracheary element differentiation is initiated by master transcription factors,
VAD6
and
VND7
(vascular‐related NAC‐domain 7). The secondary wall pattern is formed by guiding the movement of
cellulose synthase
complex in the plasma membrane by the cortical microtubules. The PCD during tracheary element differentiation is initiated by the rupture of the central vacuole in which cell death‐related hydrolytic enzymes have been accumulated. Thus the process of tracheary element differentiation is well understood, so that tracheary element differentiation is an excellent model of cell differentiation in plants.

Key Concepts:

The xylem, which is tissue specific to the vascular plants, is composed of tracheary elements (TEs), parenchyma cells and fibres.

Procambial cells produce the primary xylem containing protoxylem and metaxylem TEs
in planta
.

Typical characteristics of TEs are patterned secondary wall thickenings and programmed cell death (PCD).

TE differentiation is regulated by plant hormones such as auxin, cytokinin and brassinosteroids.

A small peptide secreted from phloem cells prevents procambial cells from differentiating into TEs.

VND6 and VND7 are master transcription factors that initiate TE differentiation.

Microtubules determine the secondary wall pattern by guiding the movement of cellulose synthase complex in the plasma membrane.

During the formation of secondary walls, levels of cellulose and hemicellulose increase and the deposition of pectin ceases, and a little later lignin deposition starts.

The central vacuole plays a crucial role in TE PCD.

A
Zinnia
xylogenic culture is an excellent model system of TE differentiation.
Glycosylation and Disease
Authors: Rhodes Jonathan , Campbell Barry J , Yu Lu‐Gang 
Published: September 2010

AbstractGlycosylation is the process of attachment of sugar molecules, usually in chains (oligosaccharides), to proteins and lipids to form the glycoproteins and glycolipids found in eukaryotic and some prokaryotic organisms. The presence of oligosaccharides on a protein can have substantial effects on its size, stability, charge and antigenicity. The varying structure, branching and substitution of the carbohydrates in an oligosaccharide results in much greater diversity than would be achieved for a peptide with an equivalent number of residues. Acquired alterations in glycosylation occur in cancer and inflammation and may have particularly important functional consequences when they affect mucosae. They also have the potential to affect pathogen–host and other cell–cell interactions. Congenital glycosylation disorders most commonly affectN‐glycosylation and affect development in diverse ways. There is increasing evidence of the importance of interactions between carbohydrate structures and carbohydrate‐binding proteins (lectins) which may be extrinsic (dietary or microbial) or intrinsic (mammalian galectins or siglecs).Key Concepts:Glycosylation occurs asN‐ andO‐linked (mucin type) oligosaccharides (glycans) on glycoproteins and as glycolipids.Variation in sequence, linkage and substitution of carbohdrates in a glycan means that a relatively short glycan can have many more variations (glycoforms) than a peptide with an equivalent number of amino acids.Variations in glycan structure can result from a range of different mechanisms that include altered glycosyltransferase and glycosidase activity, Golgi acidification and structure, donor and acceptor availability.Cell–cell and cell–microbe interactions are often driven by interactions between lectins on one cell and the relevant carbohydrate (glycan) receptor on the other cell.Mucins are heavily glycosylated, particularly withO‐linked glycans and this gives them their protective properties.Mammalian lectins include a family of galactose‐binding lectins called galectins that interact with some of the glycans that show increased expression in epithelial cancers with increased cancer cell to endothelial adherence and increased metastasis as a consequence.Foodstuffs, particularly legumes, contain lectins some of which resist digestion and may have biologically significant interactions with the intestinal epithelium.A wide range of rare congenital dosorders of glycosylation have been recognised – these have many and varied developmental consequences.Some of the developmental glycosylation disorders can be screened for by isoelectric focusing of serum glycoproteins.
Atopy and Asthma
Authors: Yates Anne B , de Shazo Richard D 
Published: September 2010

Abstract

Atopy is the genetic propensity to develop an
immunoglobulin E
antibody response to common allergens. The most common clinical manifestations of atopy are allergic rhinitis, asthma and atopic dermatitis. Asthma is a complex disorder of the airways, involving airway hyperresponsiveness, airflow obstruction that is at least partially reversible, and inflammation of the airways. Although atopy has been identified as the strongest predisposing factor for the development of asthma, not all asthma is allergic in nature. The overall prevalence of asthma has been increasing worldwide for the past few decades, and continues to increase globally. Guidelines for the evaluation and treatment of asthma were developed in the early 1990s, and are revised periodically as research into effectiveness of available medications emerges, and development of new therapies arise.

Key Concepts:

Asthma is a common but complex disorder of the airways, involving variable and recurrent symptoms, airway obstruction, inflammation and bronchial hyperresponsiveness.

Symptoms of asthma include coughing, wheezing, shortness of breath and feelings of chest tightness or pain with breathing.

Onset of asthma usually begins early in life, although adult‐onset of asthma may occur.

Genetic predisposition, as well as environmental factors, play a role in the development of asthma.

Treatment of asthma centres around control of chronic inflammation, avoidance of triggering factors and treatment of acute bronchospasm when needed.

Individuals over 65 may have a decreased perception of breathlessness and air hunger. Therefore, the use of clinical symptoms to diagnose and treat seniors may underestimate the severity of airways obstruction.
Mixed
T
‐ and
B
Lymphocyte Deficiency Disorders
Authors: Vihinen M 
Published: September 2010

Abstract

Mixed immunodeficiency diseases are intrinsic defects of the immune system affecting both B and T cells and thus the adaptive immune system. Mixed or combined immune deficiencies may also be associated with or secondary to other diseases. Patients have severe symptoms and the condition can be fatal unless properly treated. Early and reliable diagnosis is in many instances crucial for the efficient treatment of these diseases since delayed diagnosis and management can cause severe and irreversible complications, even the death of the patient. Combined immunodeficiencies, which are a heterogeneous disease group, appear throughout the immune system and affect several crucial genes and proteins. The symptoms and signs vary significantly between the different forms of combined immunodeficiencies.

Key Concepts:

Combined immunodeficiency affects both B and T cells.

Lymphocytes are white blood cells including B and T cells.

Haematopoietic stem cell transplantation, the intravenous infusion of autologous or allogeneic stem cells collected from bone marrow, peripheral blood or umbilical cord blood, reestablishes haematopoietic function in patients.

V(D)J recombination is genetic recombination which randomly selects and assembles segments of genes encoding specific proteins in the immune system.
Galen of Pergamum
Authors: Nutton V 
Published: September 2010

Abstract

G
alen
,
ad
129–216, Greek physician, anatomist and physiologist, was the most influential of ancient doctors. His combination of erudition, logic and practical skills convinced many contemporaries of his supreme merits, and his theories came to dominate learned medicine in medieval Europe and in the Islamic world. He saw himself as continuing the work of Hippocrates of Cos in medicine, and of the physicians of early Alexandria in anatomy, systematising the notion that health and disease depended on an individual balance or imbalance of four fluids, or humours, blood, bile, black bile and phlegm. He was a prolific dissector, almost entirely of animals, and his description of the body, bolstered by an exuberant rhetoric, remained largely unchallenged until the sixteenth century CE.
Tetrahymena
Cell Culture
Authors: Zhang Siwei , Ling Zihui , Wang Shulin , Nozawa Yoshinori , Umeki Shigenobu 
Published: September 2010

Abstract

Tetrahymena

, a free‐living unicellular eukaryote, is a ciliate considered to be the most highly developed protozoan, because it possesses specialised organelles that perform each of the cell functions. This pear‐shaped microorganism (30×50 μm) can be found in almost all freshwater environments, including even natural hot springs in which a thermotolerant strain can live. One distinct feature that sets ciliate apart from other multicellular eukaryotes is the possession of two functionally different nuclei – macronucleus, which is transcriptionally active and responsive for the somatic function of cells, and micronucleus, which is transcriptionally silent and serves as germinal nucleus during mating.

Tetrahymena

grows easily to high density. Its relatively large size, nuclear dimorphism and other unique genetic characteristics make it a good model system to study the molecular, cellular and genetic processes of cells.

Key Concepts:

Ciliates are unicellular organisms that execute many biological activities observed in multicellular organisms.

Tetrahymena
cells can survive under extremely dangerous conditions such as cold, pH alterations and osmotic stress.

Tetrahymena
cells possess rapid adaptation machineries to regulate biological processes including cell division, conjugation and cell death against intracellular and extracellular stresses.
Mitochondria: Methods for Preparation
Authors: Mühlenhoff Ulrich 
Published: September 2010

AbstractMitochondria are the main energy providers of the cell. Procedures developed for the isolation of pure and intact mitochondria have contributed considerably to the understanding of the complex biochemical functions of mitochondria, as they permit the application of detailed biochemical and biophysical techniques to the investigation of this organelle. This article describes the principles underlying the procedures for the isolation of mitochondria from a large variety of tissues and the techniques for assessing the quality of mitochondrial preparations. Special emphasis is given to cell fractionation protocols for the isolation of mitochondria from model organisms, includingSaccharomyces cerevisiae,Arabidopsis thaliana, cultured mammalian cells, and for the isolation of hydrogenosomes and mitosomes from amitochondriates. The special requirements for the determination of the mitochondrial proteome by high‐throughput mass spectrometry are discussed.Key Concepts:Cell fractionation is a summary term for the isolation of cell organelles and subcellular fractions from tissues and cultivated cells.Equilibrium centrifugation, a centrifugation technique by which particles are separated by virtue of their different densities in density gradients, is the most common technique for the preparation of highly enriched mitochondrial fractions.Differential centrifugation, a centrifugation technique by which subcellular particles are separated by virtue of their differences in sedimentation rates, is the most common technique of cell fractionation protocols.The mitochondrial proteome represents the whole set of proteins found within mitochondria.Mitosomes and hydrogenosomes are mitochondria‐related organelles from protists.A model organism is an experimental organism that is representative for a whole group of species. Models that are easy to manipulate tend to be the most widely used.A subcellular marker is a selected biomolecule that is confined to a specific organelle or suborganellar compartment and that may be used to determine the presence of this compartment in a subcellular fraction.The subfractionation of mitochondria involves techniques that allow the physical separation of individual mitochondrial compartments.The quality of a mitochondrial preparation is determined by the degree of other contaminating organelles, the level of specific mitochondrial activities and the degree of mitochondrial integrity.
Microinjection into
Xenopus
Oocytes
Authors: Sigel E 
Published: September 2010

Abstract

Microinjection of genetic information in the form of complimentary
ribonucleic acid
(cRNA) into the

Xenopus

oocyte leads to the functional expression of the encoded proteins. In this novel environment, exogenous proteins may be functionally characterised under well‐defined conditions. Complimentary
deoxyribonucleic acid
(cDNA) coding for the protein may be mutated, the altered cDNA transcribed and polyadenylated

in vitro

to the corresponding cRNA and the function of the resulting altered protein is compared with that of the wild‐type protein. The oocyte is a major expression system used in membrane protein structure–function studies. It is especially popular for expression of membrane transport proteins such as carriers and ion channels. In another approach, total messenger RNA (mRNA) may be prepared from a tissue of choice, microinjected into oocytes, the encoded functions characterised and the encoding genetic information isolated.

Key Concepts:

Proteins can be ‘transplanted’ into the
Xenopus
oocyte.

The
Xenopus
oocyte may be used as a test tube for newly introduced protein functions.

Genetic information in the form of cRNA may be prepared
in vitro
from the coding cDNA.

The
Xenopus
oocyte translates foreign microinjected cRNA.

The
Xenopus
oocyte is favourite expression system for structure–function studies.

Expression cloning can identify genes purely based on protein function.
Crystallisation of Nucleic Acids
Authors: Holbrook Elizabeth L , Holbrook Stephen R 
Published: September 2010

AbstractHigh‐resolution three dimensional structure analysis by X‐ray diffraction requires large, well‐ordered, single crystals. The crystallisation of nucleic acids has become the limiting step in their structural analysis by X‐ray crystallography. Nucleic acids may be isolated from native sources or synthesised chemically or enzymatically. Purification to homogeneity may be achieved by thin layer chromatography, polyacrylamide gel electrophoresis, column chromatography or combinations of these methods. Approaches to crystallisation have included batch methods, dialysis, evaporation, interface diffusion and vapour diffusion. The most widely and successfully used technique is hanging‐drop vapour diffusion. Sparse matrix screening has allowed exploration of the vast crystallisation space with the limited amount of nucleic acid available. Developments in synchrotron radiation and cryocrystallography have allowed use of smaller crystals for structure determination. High‐throughput robotic crystallisation uses less material thus allowing more crystallisation experiments from a given amount ofdeoxyribonucleic acid(DNA) orribonucleic acid(RNA).Key Concepts:The most complete structural description of a DNA or an RNA molecule is achieved through high resolution X‐ray crystallography.Nucleic acid crystallisation depends on synthesis of large quantities of homogeneous DNA or RNA.Material for crystallisation can be prepared by purification of native material, chemical synthesis or enzymatic synthesis.Purification to homogeneity implies a single form of oligomeric state and modification in addition to a single species.Purification methods include thin layer chromatography (TLC), polyacrylamide gel electrophoresis (PAGE) and liquid chromatography (LC).The most widely used method for crystallisation is vapour diffusion in either a hanging drop or sitting drop format.High‐throughput robotic crystallisation allows setup of a greater number of experiments while using less nucleic acid material.The size of crystal needed for X‐ray diffraction analysis has been sharply reduced with the use of powerful synchrotron radiation and computer programs.To date, over 2000 DNA and 1000 RNA crystal structures have been reported in public databases such as the Nucleic Acid Database and the Protein Data Bank. Most of these structures are nucleic acid complexed with protein or ligands.
Duve, Christian Rene De
Authors: Fry Iris 
Published: September 2010

Abstract
Born in 1917, Belgian cytologist and biochemist who in 1974 was awarded the Nobel Prize for Physiology or Medicine for his discoveries of the cellular organelles, the lysosome and the peroxisome. Since the 1980s, De Duve contributed to the theoretical understanding of the origin and evolution of life.
Phosphorimager
Authors: Van Kirk C , Feinberg LA , Robertson DJ , Freeman WM , Vrana KE 
Published: September 2010

Abstract

Phosphorimaging is a form of solid‐state liquid scintillation where radioactive material can be both localised and quantified. Similar to traditional autoradiographic techniques (in that it relies on high‐energy particle decay), phosphorimaging can recognise radiolabelled
deoxyribonucleic acid
(DNA),
ribonucleic acid
(RNA) and protein targets in a variety of sample preparations, such as gels, blots, homogenised tissues, cell populations, arrays and tissue slices. Although more expensive than traditional X‐ray film technology, phosphorimaging is more sensitive, develops images more rapidly and has a greater dynamic range than X‐ray film, which has made it a popular choice for several applications in molecular biology. Current applications include, but are not limited to,

in situ

hybridisation, ligand‐binding pharmacology, as well as Southern, northern and western blotting.

Key Concepts:

Phosphorimaging allows for both localisation and quantification of targets.

Potential targets include radiolabelled DNA, RNA, proteins and posttranslational protein modifications.

Phosphorimaging can be performed on media including gels, homogenised samples, cell populations, arrays and tissue slices.

Phosphorimaging identifies and quantifies its target through the measurement of light emitted from excited electrons returning to their ground state. These electrons are stimulated to higher energy levels by radioactivity emitted from the target and light is released as the electrons return to their ground state.

Although phosphorimaging is more expensive and has lower resolution than traditional X‐ray film detection and quantification methods, phosphorimaging affords greater sensitivity, faster image development, reusable detection plates and enhanced linear dynamic range.
Sexual Conflict
Authors: Bonduriansky Russell 
Published: September 2010

Abstract

Although females and males share a common interest in successful reproduction, the sexes often maximise their reproductive success (fitness) in mutually incompatible ways. Two basic forms of sexual conflict are recognised:
Interlocus sexual conflict
reflects a conflict of interest over the outcome of an interaction between sexes (e.g. to mate or not?), with some genetic loci evolving to enhance male fitness at females’ expense and other loci evolving to promote female fitness by mitigating male‐imposed harm. This conflict drives the evolution of sexually antagonistic male strategies such as coercive behaviours and morphologies, toxic ejaculates and infanticide, and female counter‐adaptations that confer resistance to such strategies.
Intralocus sexual conflict
reflects divergent selection on a shared trait whose expression is influenced by the same loci in both sexes, such that selection on one sex can displace the other sex from its phenotypic optimum. It selects for genomic adaptations that permit the evolution of sexual dimorphism.

Key Concepts:

Sexual conflict arises because strategies that maximise the fitness of one sex can reduce the fitness of the other sex.

Two basic forms of sexual conflict are recognised:
interlocus
(between genetic loci) and
intralocus
(within a genetic locus).

Interlocus sexual conflict is a conflict of interest over the outcome of some interaction (e.g. to mate or not?), mediated by different genetic loci in each sex.

Sexual conflict can lead to sexually antagonistic coevolution and sexual ‘arms races’, whereby adaptations that benefit males at females’ expense select for counter‐adaptations in females that mitigate male‐imposed harm.

Interlocus sexual conflict is manifested in a variety of traits that increase male reproductive success but harm females in the process, including behavioural harassment and coercion, morphological armaments such as genital spines and chemical manipulation via ejaculate components or pheromones.

Intralocus sexual conflict is a conflict of interest over the expression of a shared trait that is subject to sex‐specific patterns of selection but influenced by the same genetic loci in both sexes.

Intralocus sexual conflict selects for modifications to the genetic basis of trait expression that allow each sex to evolve towards its phenotypic optimum, resulting in sexual dimorphism.

Intralocus sexual conflict challenges the ‘good genes’ model of sexual selection because females that mate with high‐quality males may produce low‐quality daughters.

Sexual conflict may increase the costs of sexual reproduction, reduce mean fitness in populations and (in theory) even promote population extinction.

The study of sexual conflict has become one of the most important and dynamic areas in evolutionary biology.