bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycolytic Pathway
Authors: Harris Robert A , Harper Edwin T 
Published: April 2015

Abstract

Glycolysis converts glucose into two molecule of the three‐carbon compound pyruvate with the production of two ATPs. Glycolysis provides metabolic intermediates needed for the synthesis of macromolecules, ATP needed to drive energy‐requiring processes and pyruvate needed to complete the oxidation of glucose to carbon dioxide and water. Cells that lack mitochondria (e.g. red blood cells) are completely dependent on glycolysis for ATP. Cells containing mitochondria use glycolysis as a preparatory pathway for the complete oxidation of glucose to carbon dioxide with the production of larger amounts of ATP. Glycolysis produces ATP in emergency situations, for example, when hypoxia prevents ATP production by mitochondria. Oxygen normally suppresses glycolysis because mitochondria maintain ATP at levels that inhibit regulatory enzymes of the pathway (Pasteur effect). Lack of inhibition of glycolysis by oxygen in cancer cells (Warburg effect) is a phenomenon of great interest. Recent studies show that the Warburg effect promotes rapid growth of tumours by providing precursors for macromolecule synthesis.

Key Concepts

Glycolysis refers to a metabolic pathway by which organisms extract energy in the form of ATP during the conversion of glucose into pyruvate and lactate.

Glycolysis produces ATP required for energy‐requiring reactions and processes, for example, ion transport, protein synthesis and reactions catalysed by kinases.

Anaerobic glycolysis (glycolysis in the absence of oxygen) converts the six‐carbon compound glucose into two molecules of the three‐carbon compound lactate with the production of two molecules of ATP.

When oxygen is present, glycolysis produces two molecules of the three‐carbon compound pyruvate which can be used for the synthesis of other molecules or oxidised completely to carbon dioxide and water by the citric acid cycle.

The presence of oxygen suppresses the rate of glycolysis in normal cells because most of the ATP is provided by oxidative phosphorylation (Pasteur effect).

Lack of inhibition of glycolysis by oxygen in cancer cells (Warburg effect) is of great interest as a possible therapeutic target.

The Warburg effect maintains high concentrations of metabolic intermediates needed for rapid growth of tumours.

Phosphorylation of glucose sets up the molecule for splitting into three‐carbon fragments that undergo an oxidation reaction that traps energy by substrate‐level phosphorylation.

Glycolysis is controlled by the properties of three regulatory enzymes: hexokinase, phosphofructokinase 1 and pyruvate kinase.

Glycolysis is subject to feedback inhibition by its end product ATP at the levels of phosphofructokinase‐1 and pyruvate kinase.
Starvation: Metabolic Changes
Authors: Watford Malcolm 
Published: April 2015

Abstract

Animals, including humans, invoke a comprehensive programme of hormonal and metabolic adaptations that enable them to withstand prolonged periods of starvation. The brain is only capable of using glucose or ketone bodies as respiratory fuel. During prolonged starvation, the primary source of glucose is gluconeogenesis from amino acids arising from muscle proteolysis. To spare glucose use (and thus spare muscle protein) most tissues of the body utilise fat‐derived fuels (fatty acid and ketone bodies). As starvation progresses ketone bodies also become the major fuel of the brain, again reducing the need for glucose. High concentrations of ketone bodies result in significant ketonuria with ketones excreted as ammonium salts. The ammonia is derived from the catabolism of glutamine in the kidney with the carbon skeleton being recovered as glucose. This well‐orchestrated pattern of metabolism allows a consistent fuel supply to the brain and other tissues during prolonged starvation.

Key Concepts

Circulating glucose concentrations do not drop below 3.5 mmol L
−1
even in prolonged starvation.

During starvation, the brain must be supplied with fuel in the form of glucose or ketone bodies.

Carbohydrate reserves are depleted after 24 h of starvation.

In prolonged starvation, gluconeogenesis provides the glucose oxidised by the brain.

The major substrates for gluconeogenesis are amino acids derived from skeletal muscle protein breakdown.

Circulating ketone body concentrations rise during prolonged starvation.

During starvation, most tissues utilise fatty acids and/or ketone bodies to spare glucose for the brain.

Glucose utilisation by the brain is decreased during prolonged starvation as the brain utilises ketone bodies as the major fuel.

High concentrations of ketone bodies result in significant excretion of ketones.

Urinary ketones are excreted as ammonium salts derived from the renal metabolism of glutamine with the carbon skeleton being recovered through renal gluconeogenesis.
Secoviridae: A Family of Plant Picorna‐Like Viruses with Monopartite or Bipartite Genomes
Authors: Sanfaçon Hélène 
Published: April 2015

Abstract

Members of the family
Secoviridae
, referred to as secovirids, are plant viruses that share features with animal and human viruses of the family
Picornaviridae
and other insect or marine viruses of the order
Picornavirales
. These common features include a conserved structure of the icosahedral virus particles, the expression of viral proteins by proteolytic cleavage of large polyproteins and viral replication proteins with conserved sequence motifs, including the viral RNA‐dependent RNA polymerase and protease. Secovirids also share the distinguishing feature of encoding specialised proteins that enable their movement in plant and counteract plant defence mechanisms, such as RNA silencing. The family
Secoviridae
includes eight genera. Members of the genera
Comovirus
,
Fabavirus
,
Nepovirus
,
Cheravirus
,
Sadwavirus
and
Torradovirus
have a bipartite positive‐strand RNA genome, whereas members of the genera
Sequivirus
and
Waikavirus
have a monopartite genome.

Key Concepts

Many plant viruses are related to animal and human viruses of the family
Picornaviridae
and to other picorna‐like viruses infecting algae and arthropods.

A recent update in the taxonomy of plant picorna‐like viruses has led to the creation of the family
Secoviridae
which amalgamates the previous families
Comoviridae
and
Sequiviridae
as well as the genera
Cheravirus
,
Sequivirus
and
Torradovirus
.

Secovirids share common characteristics including having both similar virus particle structures and genomic organizations and requiring specialised proteins to facilitate their movement within the host plant or counteract plant defence mechanism.

Secovirids produce their proteins in the form of large polyproteins that are cleaved at specific sites by a viral protease.

Replication of the viral RNA occurs in large protein complexes in association with intracellular membranes from the host.

Plant cells infected with secovirids generally display tubular structures that are composed of the viral movement protein, contain virus‐like particles and traverse the cell wall. These tubular structures are involved in the movement of the virus from cell to cell.

Secovirids can be transmitted through seeds and pollen or with the help of nematode or arthropod vectors and their spread in the field is largely dependent on their mode of transmission.

Some secovirids have been successfully exploited as plant vectors, allowing epitope presentation for vaccine production, expression of proteins in plants and silencing of endogenous plant genes.
Viruses and Plant Disease
Authors: Loebenstein Gad 
Published: April 2015

Abstract

Viruses are submicroscopic obligate intracellular parasites that replicate only inside the living cells of other organisms. They contain nucleic acid (either
RNA
or
DNA
) and may cause a disease. Viruses are considered to be a life form, because they carry genetic material, reproduce and evolve through natural selection. Their size varies between 15 and 2000 nm (10
−9
m). Plant viral genomes encode between 1 and 12 proteins. Direct and indirect economic effects of major virus diseases such as citrus tristeza, cassava mosaic, virus diseases of potato and sweet potato, cacao swollen shoot, whitefly‐transmitted viruses in tomato and plum pox in stone fruits are described.

Key Concepts

This is a brief introduction to plant viruses and virus diseases.
Membrane‐Containing Bacteriophages
Authors: Poranen Minna M , Bamford Dennis H , Oksanen Hanna M 
Published: April 2015

AbstractViruses exhibit vast diversity in their form and function and are by far the most numerous (estimates 1030–1032) organisms on earth. The largest group among viruses is bacteriophages (phages), the viruses that infect bacteria, with over 6000 identified members. Vast majority of the phages are composed of protein and nucleic acid with a head–tail morphology. Polyhedral, filamentous or pleomorphic phages comprise only less than 4% of the described bacteriophages, and a minority of these has lipid constituents in addition to nucleic acid and protein. These membrane‐containing bacteriophages form a diverse group of viruses and the major virus morphotypes are represented by the members of the virus familiesCorticoviridae,Tectiviridae, CystoviridaeandPlasmaviridae. The lipids as a bilayer can either form the outermost layer of the virion or be enclosed within the virus capsid. In both cases, the viral membranes are involved in cell entry processes.Key ConceptsMembrane‐containing bacteriophages are a diverse group of bacterial viruses.Bacteriophages with a membrane are usually sensitive to organic solvents and detergents.Lipids in the viral membrane have a bilayer structure.The virion proteins are all virus specific, but lipids are derived from host cytoplasmic membrane.During virus morphogenesis, the virus‐specific membrane proteins exclude host proteins during formation of the viral membrane.The viral protein‐rich membranes have an essential role during entry mediating the translocation of the genome across the bacterial cell envelopes.
Immunoglobulin Superfamily
Authors: Natarajan Kannan , Mage Michael G , Margulies David H 
Published: April 2015

Abstract

The immunoglobulin (Ig) superfamily (IgSF) consists of a group of proteins that exploit the structural robustness and fundamental stability of the Ig fold for a wide assortment of functions across a broad span of evolutionary time, extending from microorganisms to humans. Several classification schemes, based on three‐dimensional structure or amino acid sequence patterns, have been developed to assist in understanding functional and evolutionary relationships. Although the best‐understood activities of IgSF members are related to immunological recognition, a number of related molecules participate in developmental and homeostatic phenomena. Manipulation of the IgSF by recombinant methodologies including bacteriophage and yeast display offers
in vitro
approaches to increase the available diversity of novel structures for almost limitless functions.

Key Concepts

Immunoglobulin domains can be recognised by their three‐dimensional structure and organisation of secondary structural components.

Common features of
β
‐sheet organisation and stabilisation by a disulphide bond permit sub‐classification of the immunoglobulin superfamily (IgSF) members into V, C1, C2 and I set IgSF folds.

Although exploited extensively for functional roles in immune recognition, such as for antibodies and T‐cell receptors (TCR), the immunoglobulin fold is also found in a wide variety of structures employed in cell–cell interactions.

The immunoglobulin fold offers a stable core upon which variable loops are grafted providing a scaffold for many functions.

Various display technologies have been used to generate high‐affinity antibodies and TCR.
Inflammation: Chronic
Authors: Kumar Rakesh K , Wakefield Denis 
Published: April 2015

Abstract

Chronic inflammation may result from failure to eliminate an irritant that causes acute inflammation, from an autoimmune response to a self‐antigen, or may be caused by an innately chronic irritant of low intensity that persists. It is a biologically distinct pattern of response in tissues that is characterised by simultaneous inflammation and repair. Recruitment and activation of macrophages is typical of chronic inflammation and is often accompanied by recruitment of cell types participating in an immunological response, notably T lymphocytes. Significant destruction of tissue may occur. Repair, which involves induction of granulation tissue, may lead to subsequent scarring. The chronic inflammatory response is regulated by the coordinated action of various cytokines and growth factors. Many common and clinically important diseases result from chronic inflammation, and this process also contributes to other diseases which are not primarily identified as inflammatory.

Key Concepts

Chronic inflammation is a key process underlying many common and important diseases, as well as other disease states which are not obviously inflammatory.

Compared to acute inflammation, chronic inflammation is a biologically distinct pattern of response, characterised by simultaneous inflammation and repair.

Macrophages and their derivatives are key participants in a chronic inflammatory response.

The immune response contributes to the pathogenesis of many chronic inflammatory diseases.

Chronic inflammation is regulated by a complex interaction among cytokines that promote inflammatory cell recruitment/activation and growth factors that promote healing.
Reproductive Immunology
Authors: Chaouat Gérard 
Published: April 2015

AbstractReproductive immunology is an interdisciplinary science, which deals with the role of immunocytes and cytokines in reproduction and, as a consequence, immune control of fertility and sexually transmitted diseases. In this article, we briefly discuss Veterinary Reproductive Immunology and then go back to the triggering concepts and focus on the foetus as an allograft paradox, if any (alternate theories to the self/non‐self vision of immunity, for which viviparity is not a problem, are dealt with). We then deal with various aspects of the materno‐foetal relationship at cellular and molecular level, both in the established pregnancy and at implantation. This leads us to discuss implantation failure(s) and recurrent spontaneous abortion as well as immune control of fertility and control of STDs.Key ConceptsThe foetus is usually seen as an allograft in mother's womb, which should be rejected by maternal immune system.The placental (allo) antigenicity is severely reduced.A complex cytokinic network specifically regulates some aspects of maternal immunity while sparing trophic and angiogenic circuits.Uterine natural killer cells are a specialised subset with limited cytotoxicity but trophic, immunoregulatory and angiogenic properties.Deregulations of the cytokinic uterine environment can lead to sterility.Regulatory T cells are important in placental pregnancy, and their deletion enhances pregnancy loss.Immune interception of fertility is feasible.
Regeneration of the Urodele Limb
Authors: Stocum David L , Crawford Karen 
Published: April 2015

AbstractUrodele limbs regenerate via a blastema of mesenchymal cells derived from muscle, connective tissue and nerve sheath cells in the vicinity of the amputation surface by a process of histolysis, dedifferentiation and release of stem cells. Blastema cells replicate their DNA, arrest in G2 and accumulate under an apical epidermal cap (AEC). G2 arrest is broken by factor(s) expressed by the AEC that bind to receptors on the blastema cell surface. Expression of these factors is dependent on factor(s) provided by axons reinnervating the AEC. The blastema cells proliferate and are patterned into new limb structures by suites of signalling factors such as retinoic acid, sonic hedgehog and Wnt, in addition to homeobox transcription factors that endow the cells with positional identities expressed as axial gradients on the cell surface. The degree to which the early blastema is determined is controversial, with some evidence arguing for developmental plasticity and other evidence arguing that the blastema is self‐organising.Key ConceptsUrodeles are unique in their ability to form a regeneration blastema in response to amputation.The cells of the regeneration blastema are derived from resident stem cells and/or by the reprogramming (dedifferentiation) of differentiated cells.Blastema cells derived from the different limb tissues redifferentiate in a lineage‐specific manner, but blastema cells derived from fibroblasts can also transdifferentiate into cartilage and tendon.The apical epidermal cap (AEC) of the wound epidermis is induced by regenerating nerve axons to produce a mitogen(s) that drives the proliferation of blastema cells.Patterning of the blastema involves region‐specific contributions of limb cells, lineage‐specific redifferentiation of blastema cells, interactions between blastema cells of different positions to eliminate discontinuities and sorting out of blastema cells with different cell surface adhesion.Cell interactions are mediated during axial patterning of the blastema by several signalling molecules and homeobox transcription factors.How the axial pattern and limb type of the early blastema is determined, whether by induction, self‐organisation or both, remains controversial.
Vesicle Transport Assay
Authors: Wöllert Torsten , Langford George M 
Published: April 2015

Abstract

Eukaryotic cells contain an extensive cytoplasmic network of actin filaments and microtubules that function as tracks for vesicle transport. The ability to visualise vesicle movement along both sets of filaments advanced rapidly when
in vitro
vesicle transport (motility) assays were developed. These assays utilise super‐resolution, contrast‐enhanced DIC microscopy to detect structures below the resolution of the light microscope including vesicles as small as 100 nm and microtubules 25 nm in diameter. Images are captured in real time and stored digitally for subsequent analysis. The standard motion analysis parameters include vesicle type, velocity, distances and path length.
In vitro
motility assays enabled the identification of important factors that are essential for the regulation of intracellular transport including motor proteins and their membrane receptors, the formation of hetero‐motor complexes and transported cargoes.

Key Concepts

The cytoskeleton contains actin filaments and microtubules, both of which serve as tracks for vesicle transport.

Vesicle transport is the directed movement of membrane vesicles on filaments of the cytoskeleton.

Microtubules function as intracellular tracks for transport of vesicles by two classes of motor proteins, kinesins and dyneins.

Actin filaments serve as tracks for vesicle transport by myosin motors.

Motor proteins are mechanochemical nanomachines that use the energy of ATP for muscle contraction, cell motility, cell division and transport of different cargoes along the cytoskeleton.

The superfamily of myosin motor proteins found in eukaryotic cells is known to contain over 20 different classes and of these, 12 classes are found in vertebrates, including humans.

The kinesin superfamily is subdivided into 15 classes and the dynein family is grouped into axonemal and cytoplasmic dyneins.

Motor protein defects are associated with diseases including Griscelli syndrome, Usher syndrome, myopathies, deafness, tumour progression and metastasis.

Differential interference microscopy, also known as Nomarski microscopy, uses polarised light to enhance gradients in the optical path length and phase shifts in unstained, transparent biological specimens.

Cell‐free extracts are important tools for cell biologists and have a variety of applications including cell cycle studies, intracellular transport mechanisms, signal transduction events and maintenance of cell architecture.
Protein Import into Peroxisomes: The Principles and Methods of Studying
Authors: Fujiki Yukio , Okumoto Kanji , Honsho Masanori 
Published: April 2015

Abstract

Peroxisomes are essential intracellular organelles that involve many metabolic processes, such as β‐oxidation of very long‐chain fatty acids and synthesis of plasmalogen and bile acids as well as generation and degradation of hydrogen peroxide. These peroxisomal functions are fulfilled by strictly and spatiotemporally regulated compartmentation of the proteins catalysing these reactions. Defects in peroxisomal protein import results in inherited peroxisome biogenesis disorders in humans. Peroxisomal matrix and membrane proteins are synthesised on free ribosomes but transported into peroxisomes by distinct pathways determined by specific targeting signals and their receptors. The mechanism by which this is achieved has been clarified by identification of many
PEX
genes and the products named peroxins, the essential factors for peroxisome biogenesis. This article introduces several basic methods to investigate protein import into peroxisomes.

Key Concepts

Peroxisome plays an essential role in various metabolic pathways.

Deficiency of peroxisomes in human causes severe foetal genetic diseases, peroxisome‐deficient disorders.

Functions and the integrity of peroxisomes are archived by proper import of both matrix and membrane proteins into peroxisomes.

Peroxisomal proteins are encoded by nuclear DNA, synthesised in cytosolic free ribosomes and post‐translationally imported into pre‐existing peroxisomes.

Peroxisomal matrix and membrane proteins are translocated into peroxisomes via different pathways in a manner dependent on their distinct targeting signals.

Many of peroxins encoded by
PEX
genes are responsible factors for peroxisome biogenesis and are involved in the import of peroxisomal proteins.

Various experimental approaches have elucidated the molecular mechanisms underlying peroxisome biogenesis.

Post‐translational import of peroxisomal proteins into isolated peroxisomes can be reproduced
in vitro
.

Semi‐permeabilised cells, in which only the plasma membrane is selectively permeabilised, are used to investigate peroxisomal protein import, as with living cells.
F
ol,
H
ermann
Authors: Dröscher Ariane 
Published: April 2015

Abstract

Hermann Fol (1845–1892) – Swiss marine biologist and microscopist – made important contributions to the clarification of the process of fertilisation and to the study of the anatomy and development of marine organisms. He observed and depicted very neatly how the spermatozoon penetrates and transfers its nucleus into the egg cell. He also pioneered experimental embryology and experimental teratology, artificially inducing multiple fertilisations. Fol's greatest love, however, was marine biology. He undertook numerous expeditions with his boats and devised several oceanographic apparatuses. In late 1881, he co‐founded today's
Observatoire océanologique de Villefranche
.
K
horana,
H
ar
G
obind
Authors: Grote Mathias 
Published: April 2015

Abstract
Har Gobind Khorana (1922, Raipur, British India – 2011, Concord, MA, USA) was an Indian‐American biochemist most well known for his contributions to the elucidation of the genetic code in the 1960s, which earned him a share in the 1968 Nobel Prize in physiology or medicine. Later on, Khorana's laboratory at the Massachusetts Institute of Technology worked on molecular membrane biology. Khorana's scientific life stands exemplarily for the increasing role of chemical strategies in the life sciences (nowadays epitomised in the fields of ‘chemical’ or ‘synthetic biology’), as well as for the internationalisation of science in the second half of the twentieth century.