bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quinone Cofactors
Authors: Lang Albert , Klinman Judith P 
Published: April 2013

AbstractQuinone cofactors are used by several classes of enzymes, which catalyse the oxidation of biogenic amines and alcohols, to help catalyse these reactions. Before 1990 only one cofactor, the peptide‐derived pyrroloquinoline quinone had been identified. During 1990–2001, however, four new quinone prosthetic groups derived from naturally occurring amino acids were discovered. The first protein‐derived, nondissociable cofactor identified was 2,4,5‐trihydroxyphenylalanine quinone, designated topaquinone (TPQ) in copperamine oxidases. The discovery of TPQ led to the identification of a series of new quinone cofactors, including lysine tyrosylquinone (LTQ) in lysyl oxidase, cysteine tryptophylquinone (CTQ) inquinohaemoprotein amine dehydrogenaseand tryptophan tryptophylquinone (TTQ) in bacterialmethylamine dehydrogenase. These cofactors contribute electrophillic capabilities (and stabilise free radical intermediates) that naturally occurring, unmodified amino acid side chains are unable to provide.Key Concepts:Quinone cofactors are a class of cofactors used by many enzymes to catalyse the oxidation of amines and alcohols.Five quinone cofactors have been characterised: PQQ, TPQ, LTQ, TTQ and CTQ.PQQ is a peptide‐derived cofactor that involves the expression of six genes located within an operon.TPQ is derived from a precursor tyrosine and requires only Cu2+and O2for biogenesis.LTQ is formed by the cross‐linking of a tyrosine residue and a lysine residue, also requiring only Cu2+and O2.TTQ is formed by the cross‐linking of two tryprophan resides, with MauG completing biogenesis.CTQ, the most recently discovered quinone cofactor, is formed by the cross‐linking of a cysteine reside and a tryptophan residue.
Enzymes: The Active Site
Authors: Ghanem Eman , Raushel Frank M 
Published: April 2013

Abstract

Enzymes are highly efficient and specific catalysts. They catalyse biochemical reactions with substantial rate enhancement compared to the uncatalysed reactions. The rate enhancement and specificity of enzymes are derived from a network of general acid/base catalysts, nucleophiles and noncovalent interactions in the active site, the part of the enzyme where cataylsis takes place. In catalysis, binding of the substrate and the transition state in the active site is of critical importance. Enzymes catalyse reactions by preferentially binding the transition state and, therefore, lowering the activation energy of the reaction. Enzymes bind their substrates via a network of weak, noncovalent intermolecular interactions such as hydrogen bonding, hydrophobic and electrostatic interactions. Enzymes utilise several mechanisms to accelerate a reaction such as acid/base catalysis, covalent catalysis and metal ion catalysis. Owing to their integral role in all biochemical pathways, enzymes are an attractive target for drug design and development.

Key Concepts:

Enzymes are biocatalysts that are involved in all forms of biochemical transformations.

Nearly all enzymes are proteins.

Enzymes catalyse reactions with a remarkable rate enhancement due primarily to lowering the energy of the transition state.

The active site is a cavity in the enzyme structure where catalysis occurs.

Amino acid residues in the active site provide the required framework for catalysis.
Vertebrate Embryo: Patterning the Neural Crest Lineage
Authors: Nitzan Erez , Kalcheim Chaya 
Published: April 2013

Abstract

Neural crest (NC) cells form as epithelial progenitors during the process of neurulation, then undergo an epithelio‐mesenchymal transition and become motile. As mesenchymal cells, they migrate through stereotypical pathways, reach their homing sites and differentiate into a large variety of derivatives that are specific and variable along the embryonic axis. These include neurons and glia of the sensory and autonomic nervous system, pigment cells, chromaffin cells of the adrenal gland and mesectoderm in the head region. Given that a few initial progenitors expand and diversify so substantially, the NC provides an excellent model to investigate fundamental questions in Developmental Biology, that is, defining the state of commitment of the different precursors throughout ontogeny, unravelling the nature of cellular interactions among adjacent crest cells and between crest progenitors and their environment, and elucidating the molecular basis of lineage segregation, cell migration and terminal differentiation.

Key Concepts:

NC progenitors are multipotent at the population level and become differentially restricted during ontogeny.

Lineage segregation in the trunk is likely to begin before NC emigration from the neural tube.

Epithelio‐mesenchymal transition of NC progenitors is orchestrated by a network of secreted factors (BMP/noggin and Wnt1) acting in concert with adhesion molecules, RhoGTPases, extracellular matrix components and cell intrinsic determinants.

NC cells migrate stereotypically to their homing sites and migration seems to be largely channelled by interactions between inhibitory environmental signals and NC cells expressing their cognate receptors.

Contact inhibition mediated by noncanonical Wnt signalling contributes to the directionality of NC migration.

Specification and subsequent differentiation of NC progenitors into the various phenotypes are regulated by reiterative signals (i.e. BMPs, Wnts) that induce lineage‐specific codes of transcription factors.

In spite of undergoing early fate restrictions
in vivo
, some NC cells, even following differentiation, retain significant plasticity as evidenced by
in vitro
analysis.
Potexviruses and Carlaviruses – Short Filamentous Viruses
Authors: Martelli Giovanni P , Rubino Luisa 
Published: April 2013

Abstract

Potexviruses and carlaviruses are plant‐infecting viruses belonging to the family
Aphaflexiviridae
and
Betaflexiviridae
, respectively. Both have slightly flexuous filamentous particles measuring 470–580×13 nm (potexviruses), and 610–700×12–15 nm (carlaviruses). Virions contain 94–95% protein and 5–6% positive sense, single‐stranded
ribonucleic acid
c
. 5800–7000 nucleotides (nt) (potexviruses) and 7900–9000 nt (carlaviruses) in size. Both virus types have a genome with a similar structural organisation, comprising five (potexviruses) or six (carlaviruses) open reading frames, three of which, known as the ‘triple gene block’, encode polypeptides that facilitate virus movement within the host. Natural hosts of both virus types are herbaceous (weeds, ornamentals, vegetables) rather than woody plants. Many potexviruses are agents of severe diseases, whereas a high percentage of carlaviruses induces symptomless infections. Transmission of potexviruses in nature is, by and large, by mechanical contact, whereas carlaviruses are transmitted primarily by aphids with a nonpersistent modality.

Key Concepts:

Potexviruses and carlaviruses infect primarily herbaceous hosts after mechanical or vector‐driven transmission, respectively.

Particles of both genera are filamentous and slightly flexuous and accumulate in aggregates in the cytoplasm of parenchyma cells.

Demarcation of species within the genera takes into account molecular and biological criteria.

Both genera are characterised by the presence of the so‐called triple gene block that provides the support for virus movement in infected hosts.

Potexviruses and carlaviruses constitute models for virus replication, movement and encapsidation studies.

Control is based on preventive measures, such as sanitary selection, production of virus‐free seed lots and resistance through conventional breeding and genetic engineering.
Virus Diseases of Tropical Crops
Authors: Geering Andrew D W , Randles John W 
Published: April 2013

Abstract

Virus diseases are serious constraints to the productivity and profitability of a wide range of tropical crops. Identification of the causal viruses and understanding their epidemiology is the key to estimating the incidence and economic impact of the diseases they cause, and to devising virus management strategies. Epidemics result from interactions between virus, host plant, vector and environmental factors, and every epidemic can be considered to be a unique pathosystem in which each of the components contributes to the epidemic, and in which none are limiting. Pathogen diagnosis is the key to managing diseases, and we list 18 crops, their main virus/viroid diseases and pathosystem descriptors for each. Six types of pathosystem are described on the basis of the mode of spread, and the different management strategies applicable to each are discussed. The Ninth Report of the International Committee on Taxonomy of Viruses (2012) is an essential reference for virologists working with tropical crops.

Key Concepts:

Identification of viruses or viroids is the key to managing the diseases they cause.

Koch's rules are applied to establish causal associations between viruses/viroids and disease.

Viruses/viroids are identified by their biological, morphological and genetic properties using classical and molecular methods.

The universal database for viruses/viroids published by the International Committee on Taxonomy of Viruses is the resource for classification.

Rapid diagnostic methods rely on nucleotide sequence comparisons with publicly available data bases.

Epidemics are driven by virus, vector, host, environment, time and human activity.

Vector–virus interaction is the main determinant of the rate, range, timing and pattern of disease spread.

Viruses/viroids of tropical plants have unique pathosystems.

A full description of a pathosystem is required to sustainably manage virus epidemics.

Management of epidemics can be achieved by destabilising or down‐regulating one or more components of the relevant pathosystem.
Plant Virus Satellites
Authors: Xu Ping , Roossinck Marilyn J 
Published: April 2013

Abstract

Plant virus satellites are molecular parasites of plant viruses that rely on a helper virus for replication but do not supply any essential function to the helper virus. They can affect the accumulation of the helper virus and alter the host symptoms induced by the helper virus. They include satellite viruses, satellite ribonucleic acids (RNAs) and satellite deoxyribonucleic acids (DNAs). Size, genome structure and replication strategies vary greatly among plant virus satellites. Some plant virus satellites have been used as biocontrol reagents or as vectors to express exogenous genes. They have also been used as reporters for studying the evolutionary mechanisms of the helper virus.

Key Concept:

Plant virus satellites depend on a helper virus for replication, but they may use different host factors.

Plant virus satellites do not provide any essential function for the helper virus.

Plant virus satellites have varied effects on their helper viruses and hosts, including reduction in virus titer and exacerbation or attenuation of symptoms.

Some plant satellite RNAs use ribozymes to resolve multimers generated during replication.

Satellite DNAs are the symptom determinants in an increasing number of crop diseases caused by geminiviruses.
Bacteriophages with
ss
RNA
Authors: Olsthoorn René , van Duin Jan 
Published: April 2013

Abstract

The single‐stranded
ribonucleic acid
(ssRNA) phages are small icosahedral viruses which infect their host via F‐ or polar pili. The best‐characterised are those infecting

Escherichia coli

, a Gram‐negative bacterium found in the gut and faecal sewage. The ssRNA phages are members of the
Leviviridae
family, which includes the two genera
Levivirus
and
Allolevivirus
. The family presently comprises about 100 isolates including the well‐known MS2 and Qβ coliphages.Their genome size ranges from 3400 to 4300 nt and codes for four proteins. The genome of ssRNA phages adopts a unique structure that regulates translation of the four genes, confers RNase resistance in the bacterial cytoplasm, ensures recognition by replicase and facilitates encapsidation by capsid or coat proteins. The interaction between RNA and coat protein by virtue of its high specificity and strength is used in many molecular biological applications.

Key Concepts:

ssRNA phages are members of the
Leviviridae
family which comprises the genera
Levivirus
and
Allolevivirus.

ssRNA phages infect their hosts via pili.

The nonenveloped quasi‐icosahedral shell of the virion has a
T
=3 surface lattice.

RNA inside the virion is structured.

The genome encodes four types of proteins: maturation, coat, lysis and replicase.

Replication requires the use of host proteins.

Translation of the genes is regulated by RNA secondary structure.

Forced evolution experiments reveal constraints on RNA secondary structure.

Phage particles can be used to display foreign epitopes.

RNA phages are used as indicator organisms for the presence of pathogens in drink and surface water.
Neural Crest: Origin, Migration and Differentiation
Authors: Kelsh Robert N , Erickson Carol A 
Published: April 2013

Abstract

The neural crest is a population of cells that emigrates from the dorsal neural tube during early embryogenesis and migrates extensively to give rise to a myriad of cell types. Patterns of migration are controlled largely by extracellular cues in the environment. Neural crest cells are initially multipotent. Cell fate specification – the selection of an individual cell fate from all the possibilities available to a multipotent progenitor – is likely to involve a series of steps, in which cells become progressively restricted to individual fates, a process that is likely to begin while still in the dorsal neural tube, but which then is usually completed during, or even after migration. Extracellular cues in the migratory and postmigratory environment act together with intrinsic transcription factors to ensure that specific fates are chosen. Together, these result in expression of one or more transcription factors that activate or cement a gene regulatory network that establishes and maintains expression of the differentiated phenotype.

Key Concepts:

The neural crest is an important tissue, as reflected in its nickname, ‘the fourth germ layer’.

Neural crest cells give rise to many different cell‐types.

Neural crest cells are induced at the boundary of the developing neural plate and prospective epidermis.

Neural crest induction depends on BMP signalling in the prospective epidermis and Wnt signalling from the underlying mesoderm.

These signals induce neural crest in two phases, specification of the neural plate border, and specification/maintenance of definitive neural crest.

Neural crest migration patterns are complex, and usually specific to the derivative fate adopted.

Neural crest migration is controlled by the environmental distribution of repellent and attractive/permissive signals, with cell‐type specific receptor expression in the neural crest cells determining their response.

While some or all neural crest cells are initially multipotent, specification of individual derivative fates likely results from progressive fate restriction.

Neural crest fate specification involves a combination of intracellular and extracellular factors.

Fate specification results from transcriptional activation of key genes encoding (a combination of) specific transcription factors.

These transcription factors activate and maintain the fate‐specific gene regulatory networks that characterise each cell‐type.
Neurogenesis in
Drosophila
Authors: Jarman Andrew 
Published: April 2013

Abstract

Neurogenesis is the process by which neurons are born during the development of an animal. The nervous system entails great cellular diversity and is the most complex of any organ system. A developing animal needs to harness sophisticated cellular and genetic mechanisms to ensure the orderly generation of large numbers of neurons in the right places and times, and in the right numbers. A long history of molecular genetic studies in the fruit fly,

Drosophila melanogaster

, has provided many insights into how this is achieved. Neurogenesis involves the initial patterning of the ectoderm, the formation of neural precursor cells from the ectoderm and the formation of neurons from these precursors through fixed lineages involving asymmetric cell division. Many of the concepts uncovered apply to neurogenesis in other animals. Indeed, many of the molecular mechanisms are highly conserved.

Key Concepts:

The fruit fly has relatively few neurons in its nervous system, making it tractable to detailed developmental analysis.

The arrangement of these neurons is, as far as is known, very precisely determined by the mechanisms controlling neurogenesis during development.

Neurons are the progeny of neural precursor cells that derive from the ectoderm.

The precursor cells are specified by the action of proneural transcription factors, which are opposed by Notch signalling in the process of lateral inhibition.

At their formation, the precursors are already specified to contribute specific neuronal progeny via fixed lineages of cell division.

For the PNS, neural precursor identity is endowed by proneural factors, their cofactors.

For the CNS, neuroblasts have unique identities according to their location, due to their inheriting different combinations of ectodermal patterning factors.

Within the fixed division lineages, cellular diversity arises through asymmetric cell division, which is driven largely by asymmetrically localised and inherited cell fate determinants.
Catalytic
RNA
Authors: Burke Cassandra R , Lupták Andrej 
Published: April 2013

Abstract

Ribonucleic acid
(RNA) molecules have diverse roles in biological systems. Although some code for proteins or act to translate codons to amino acids, others fold into specific shapes that endow them with the ability to catalyse specific chemical transformations. These catalytic RNAs, ribozymes, are responsible for protein synthesis,
transfer RNA
(tRNA) processing, self‐splicing of certain introns, self‐scission during rolling circle replication of some single‐stranded RNA viruses and cofactor‐dependent gene regulation in bacteria. Other ribozymes have been evolved

in vitro

to perform a wide variety of transformations. Two of these, tRNA aminoacylase and RNA polymerase ribozymes, are featured here because molecules with such capabilities are thought to have existed on early Earth, before proteins took over as the dominant biological catalysts. Most of the ribozymes have been shown to perform multiturnover catalysis and thus act as true enzymes, either in their natural, biological form or as engineered constructs.

Key Concepts:

RNA molecules can fold into specific conformations and accelerate chemical transformations, thus acting as catalytic biomacromolecules, ribozymes.

Ribozymes can accelerate chemical reactions by many orders of magnitude.

Many ribozymes are capable of multiturnover catalysis, acting as enzymes.

Protein synthesis templated by mRNA is catalysed by ribosomal RNA.

Most ribozymes are phosphoryl transferases.

In vitro
selected ribozymes have been shown to catalyse a wide variety of reactions.

The existence of ribozymes supports the RNA World hypothesis.
Spleen
Authors: Steiniger Birte 
Published: April 2013

AbstractThe spleen is a secondary lymphoid organ present in all vertebrates, which monitors the blood. It consists of sessile stroma cells (fibroblasts), migratory cells of the immune system and blood‐filled spaces and vessels. Splenic functions and microanatomy differ according to the species investigated. Certain functions such as immunological monitoring of bloodborne antigens, destruction of intravasal microorganisms and aged or abnormal blood cells, are more or less invariant. In rodents and humans the spleen is composed of two large compartments, the white pulp and the red pulp. The white pulp harbours dense accumulations of more or less migratory lymphocytes and antigen‐presenting cells, which crawl on a meshwork of specialised fibroblasts. The red pulp is composed of connective tissue cords containing arterioles and capillaries and of sinuses, which represent a spleen‐specific initial part of the venous circulation. The connective tissue of the red pulp cords is filled with blood and represents the only place where an open circulation occurs in the body. In addition, the cords harbour a dense population of specialised macrophages and some plasma cells. The article describes the microanatomical compartments of rat and human spleens, the course of B lymphocyte immune reactions in rodent spleens and the consequences of splenectomy in humans.Key Concepts:The spleen monitors the antigen composition of the blood.The monitoring is predominantly carried out by lymphocytes recirculating through the spleen in the white pulp and by sessile macrophages in the red pulp cords.Specialised fibroblasts recruit lymphocytes and macrophages to their compartments with the help of several mechanisms, such as secretion of chemokines or expression of certain adhesion molecules.The splenic red pulp cords are the only location in the body with an open circulation. This means that blood flows in spaces not lined by any barrier‐forming cells such as endothelia.The open circulation thus permits a direct contact between the blood and resident macrophages.In rodents and humans the spleen contains a special type of B lymphocytes, the marginal zone cells. These cells recognise polysaccharide antigens and are easily activated to become antibody‐secreting plasma cells.In humans, splenectomy leads to the loss of marginal zone‐type B cells in the blood and to a reduced resistance against bacteria with polysaccharide capsules. This is especially relevant in children.The susceptibility to overwhelming post‐splenectomy infections in humans may be due to loss of the marginal zone and its special stromal cells in combination with loss of the large phagocyte compartment in the splenic red pulp.
Major Histocompatibility Complex: Interaction with Peptides
Authors: Liu Jun , Gao George F 
Published: April 2013

Abstract

T‐cell‐specific immunity functions in a major histocompatibility complex (MHC)‐dependent manner. MHC molecules present antigenic peptides on the surface of cells to be recognised by specific T‐cells. MHC class I and class II molecules possess highly similar structural features used to load peptides. Specifically, both contain peptide‐binding grooves formed by two α‐helices and eight β‐strands. In the peptide‐binding groove, specific amino acids compose pockets that accommodate the corresponding side chains of the anchor residues of the presented peptides. Peptide‐binding preferences exist among different alleles of both of MHC I and MHC II molecules, which are mainly dependent on amino acid polymorphisms in the peptide‐binding grooves of MHC chains. Aside from the common binding of peptides to MHC molecules, the currently determined structures of post‐translationally modified peptides to MHC molecules demonstrate that the modified groups have important roles in the peptide–MHC interaction. The illumination of the binding features of peptides to MHC molecules has aided our understanding of T‐cell‐specific immunity and the development of T‐cell epitope‐related vaccines.

Key Concepts:

MHC I and class II molecules fold into a highly similar conformations featuring a peptide‐binding groove to present T‐cell epitopes.

Peptide‐binding grooves of MHC I molecules are composed of two α‐helices and eight β‐strands formed by one heavy chain, while MHC II uses two domains from different chains to construct the peptide‐binding groove.

Peptides bind to MHC molecules through primary and secondary anchor residues protruding into the pockets in the peptide‐binding grooves.

Peptide preferences are dependent on the amino acids polymorphisms comprising the anchor pockets, which are related to the various alleles of MHC.

The conformations of peptides presented by MHC I molecules are length‐dependant.

The modified groups of post‐translationally modified peptides have important roles in the peptide–MHC interaction.

MHC is called HLA, human leucocyte antigen, in human; H‐2 in mice.