bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secoviridae: The Amalgamation of the Families
Sequiviridae
and
Comoviridae
Authors: Sanfaçon Hélène 
Published: September 2009

Abstract

Several plant viruses share features with animal and human viruses of the family
Picornaviridae
, including a conserved structure of both the virus particle and the viral genome, expressing viral proteins by proteolytic cleavage of large polyproteins and encoding replication proteins with conserved sequence motifs. Members of the family
Comoviridae
were originally described as the only plant picorna‐like viruses. Other plant picorna‐like viruses were later discovered and classified in the family
Sequiviridae
.
Sequiviridae
and
Comoviridae
are related to each other in phylogenetic studies and share the common property of encoding specialized proteins to enable their movement in the plant. Recently, it was proposed to regroup plant picorna‐like viruses into a single family termed ‘secoviridae’. The proposed family amalgamates the families
Comoviridae
and
Sequiviridae
, and incorporates other plant picorna‐like viruses currently classified in the genera

Sadwavirus

and

Cheravirus

, and the proposed genus ‘

Torradovirus

’.

Key concepts:

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

A recent update in the taxonomy of plant picorna‐like viruses has lead to the creation of the family ‘secoviridae’ which amalgamates the families
Comoviridae
and
Sequiviridae
as well as the existing genera
Cheravirus
,
Sequivirus
and the proposed genus ‘torradovirus’.

Secoviridae share many common characteristics including having both similar virus particle structures and genomic organizations, and requiring a specialized protein to facilitate their movement within the host plant.

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

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

Plant cells infected with secoviridae 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 probably involved in the movement of the virus from cell to cell.

Secoviridae 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.
Lysozyme
Authors: Imoto Taiji 
Published: September 2009

Abstract

Lysozymes are lytic enzymes that hydrolyse glycosidic bonds and are widely distributed in nature. Hen egg‐white lysozyme is the best characterized of all proteins and, as well as serving as a model protein for study, its antibacterial and immune function properties are exploited in medicines and food additives. Basic concepts of enzyme reaction, structure and function of protein, protein chemistry and stability of protein are described. Evolution and diversity in structure and function of lysozyme are also stated.

Key concepts

Fundamental concept on an enzyme reaction is elucidated in an atomic level.

Lysozyme is a model protein for studying on structure and function of protein.

The diversities in structure and function make lysozymes interesting.
m
RNA
Turnover
Authors: Dickson Alexa M , Wilusz Carol J , Wilusz Jeffrey 
Published: September 2009

Abstract

Messenger ribonucleic acid
(mRNA) decay is an important cellular mechanism for regulating gene expression in both bacteria and eukaryotes. The enzymes involved and the factors that modulate their activity have been well‐characterized. Enzymes responsible for mRNA turnover attack either the 5′ or 3′ ends (exoribonucleases) or cleave the RNA in the middle (endoribonucleases). Transcripts generally have specific modifications at their ends, such as the 5′ cap and 3′ poly(A) tail in eukaryotes, to protect them from exonucleolytic decay. RNA‐binding proteins can modulate decay rates by recruiting mRNA degradation enzymes or by altering messenger ribonucleoprotein (mRNP) conformation to favour or impede decay. Here, we describe the enzymes and regulatory factors of the mRNA decay pathways in bacteria and eukaryotes, highlighting similarities between the two. We also discuss how mRNA degradation is regulated by RNA‐binding proteins, and how mRNA turnover pathways are used to identify and degrade aberrant mRNAs.
Cytokines
Authors: Wilson Heather M , Barker Robert N 
Published: September 2009

Abstract

Cytokines are small secreted ‘messenger proteins’ that allow communication between cells. They contribute to a chemical signalling language that controls many processes in multicellular organisms including haematopoiesis, chemoattraction, tissue repair, embryogenesis and virtually all aspects of immunity and inflammation. Cytokine functions are mediated by their binding to specific receptors to initiate intracellular signalling cascades that increase or decrease expression of transcription factors and genes regulating, for example, secretion of effector molecules (including other cytokines), cell proliferation and expression of membrane receptors. They play an important role in many pathologies and indeed measurement of cytokine profiles in patients provides a useful indicator of disease. Due to their multiple functions in disease, therapeutic interference of cytokines, cytokine receptors and their signal transduction pathways offer new treatment options for a range of disorders.

Key concepts

Cytokines are extremely potent, acting at picomolar or femtomolar concentrations.

Cytokines are not produced constitutively but are expressed on stimulation usually acting in an autocrine or paracrine fashion.

Individual cytokines can have many functions and can act synergistically or antagonistically.

Chemokines are a family of cytokines that are principally involved in chemoattraction but also participate in cell activation and angiogenesis.

Cytokine receptors can have similar subunit structures that divide them into families.

Most cytokine receptors are heterodimers but some can be homodimers or heterotrimers.

Cytokines exert their effects by activating specific intracellular signalling pathways.

By sharing receptor subunits and signal transducing molecules, many cytokines are known to play redundant and pleiotropic roles.

T‐helper cell subsets are distinguished based on their cytokine secretion whereas the cytokine environment determines which subset will develop.

Excessive cytokine production or activity can lead to several pathologies and cytokine modifiers are showing to be therapeutically effective in modifying cytokine‐mediated diseases.
Cleavage and Gastrulation in Sea Urchin
Authors: McClay David R 
Published: September 2009

Abstract

Cleavage in the sea urchin initially is highly stereotypic and during this time cells are specified transcriptionally to obtain unique molecular identities. A complex series of intercellular signals assist in this diversification of the cells and coordinate their location in the blastula stage embryo. Once the cells are programmed by these early nuclear events the process of gastrulation follows. Gastrulation is characterized by a dramatic morphogenetic rearrangement of cells to form the basic body plan of the organism. In the sea urchin embryo gastrulation occurs in two phases: ingression of the skeletogenic cells and then invagination of the archenteron or the primitive gut.

Key Concepts:

Cleavage is the stage encompassing the earliest cell divisions after fertilization during which cells divide without an increase in embryo mass.

During cleavage, in each cell a combination of transcription factors and signalling between cells establishes gene regulatory networks.

Gene regulatory network states become different in subpopulations of cleaving cells through asymmetric signaling and/or asymmetric inheritance of cytoplasmic determinants, and this process is causal for cell diversification.

Gastrulation in the sea urchin embryo involves two separable morphogenetic processes: ingression of primary mesenchyme cells and invagination of the archenteron, or the primitive gut.

As a consequence of gastrulation, cells of the embryo are rearranged to establish the early body plan of the larval stage.

Most sea urchin embryos develop indirectly. That is, embryogenesis leads to a feeding larval stage, and the larva later metamorphoses into a juvenile, which grows into an adult.
Regeneration of the Urodele Limb
Authors: Stocum David L 
Published: September 2009

AbstractUrodele limbs regenerate via a blastema of progenitor cells derived from differentiated limb cells by a process of dedifferentiation. The blastema grows by mitosis of the progenitor cells under the influence of factors supplied by the wound epidermis and nerves, and is patterned into the new limb structures by molecular interactions between blastema cells.
The Role of Insulators in Genome Organization and Gene Expression
Authors: Baxley Ryan M , Geyer Pamela K 
Published: September 2009

Abstract

Transcription of eukaryotic genomes is regulated by enhancer and silencer input at a gene promoter. These regulatory elements act over large distances and demonstrate limited target specificity, suggesting that constraints exist to increase specificity. Insulators are
deoxyribonucleic acid
(DNA) elements that limit enhancer and silencer action, establishing independent transcriptional domains. Eukaryotic genomes contain a variety of widely distributed insulators. The best characterized are the

Drosophila

Su(Hw)‐dependent insulators and the vertebrate CCCTC‐binding factor (CTCF)‐dependent insulators. Emerging evidence suggests that insulators are not impassable barriers, but are active players in many nuclear functions. Insulator action depends on the organization and properties of local enhancers, promoters and insulators. Two models describing insulator action include (1) formation of independent structural domains that have a global impact on transcription and (2) direct participation in transcriptional regulation that confers specificity to regulatory interactions. Further studies of insulators will provide a richer understanding of transcriptional regulation in eukaryotes.
Natural Antibodies
Authors: Zouali Moncef 
Published: September 2009

Abstract

Natural antibodies are essentially antibodies of the immunoglobulin M (IgM) isotype present in the circulation of normal humans and other mammalian species that have not been previously exposed to deliberate immunization. They are often directed against highly conserved epitopes and often bind to ligands of varying chemical composition with low affinity. This antibody subset contrasts with immune antibodies, which are produced in response to the introduction of antigen to the immune system. Natural antibodies are frequently directed to intracellular structures, rather than to cell‐surface antigens. They have been found to play a role in protection against infectious agents and to exert homeostatic functions. Other investigations suggest that natural antibodies might play a pathogenic role.

Key concepts

A natural antibody is an antibody present in the circulation of an animal or a subject that had not been previously exposed to the corresponding antigen.

Certain B‐lymphocyte subsets, such as B‐1a cells, are committed to natural antibody production.

The antibody repertoire expressed in B‐cell malignancies exhibits several features in common with those of the natural antibody repertoire of healthy subjects.

It is possible that natural antibody production is driven by microorganisms indigenous to the organism, such as bacteria living in the intestine.

Natural antibodies play a role in shaping the B‐cell repertoire and may represent the precursors of antibodies to pathogens.

Natural antibodies could serve as innate recognition receptors, recognizing various bacterial cell wall components or parasites.

Studies of rodents rendered deficient in natural antibodies suggest that this antibody subset is endowed with a homeostatic potential and housekeeping functions, such as recognition and removal of senescent cells and other self‐antigens.

Circumstantial evidence suggests that natural antibodies can be associated with protection against Alzheimer disease, atherosclerosis or cancer development.

B lymphocytes secreting natural antibodies could represent a reservoir capable of mutating their immunoglobulin variable region genes to give rise to high‐affinity pathogenic autoantibodies.
Photosynthesis
Authors: Ort Donald R , Kramer David 
Published: September 2009

Abstract

Photosynthesis is the process that enables higher plants, algae and a broad class of bacteria to transform light energy and store it in the form of energy‐rich organic molecules. In plants and algae, as well as some species of bacteria, photosynthesis removes carbon dioxide from the atmosphere, produces the molecular oxygen we breath and stores energy in biomass. In addition some bacteria use light energy to create energy‐rich molecules, but do not split water to produce oxygen. Photosynthesis is finely regulated to avoid damage caused by excess solar energy. At the same time, though, this regulation also decreases the efficiency of photosynthesis. Current research is aimed at understanding these responses to improve photosynthetic efficiency, thus increasing the production of food and fuel.

Key Concepts:

Photosynthesis is the transformation of light energy to chemical energy by higher plants, algae and certain bacteria.

In higher plants, the initial capture of light energy and conversion to the stable, high‐energy products of NADPH and ATP occurs within and around the thylakoid membranes of the chloroplast. The NADPH and ATP produced are used by enzymes in the stroma to ‘fix’ carbon dioxide and produce carbohydrates.

Although photosynthesis is driven by light, the photosynthetic apparatus must protect itself from excess solar energy which causes a decrease in photosynthetic efficiency.
Nuclear‐Cytoplasmic Transport
Authors: Lange Allison , Corbett Anita H 
Published: September 2009

Abstract

In eukaryotic cells, the genomic
deoxyribonucleic acid
(DNA) in the nucleus is separated from the translational machinery in the cytoplasm by the nuclear envelope. Transport of macromolecules such as proteins and
ribonucleic acid
(RNA) across this membrane is essential for cellular function and requires active nuclear–cytoplasmic transport systems. These systems consist of soluble transport receptors, which recognize and bind cargo in one compartment, mediate transport through nuclear pore complexes embedded in the nuclear envelope and deliver cargo in the target compartment. Disruption of this highly regulated process results in abnormal cell function and is linked to human disease etiology. Understanding the contribution of nuclear protein and RNA transport to cellular organization is one of the major challenges in cell biology.

Key Concepts

Transport into and out of the nucleus occurs through nuclear pore complexes (NPCs), which are large proteinaceous channels that perforate the nuclear membrane.

Proteins destined for import into the nucleus contain a nuclear localization signal (NLS) and proteins destined for export from the nucleus contain a nuclear export signal (NES), each of which targets them for transport.

Soluble transport receptors called importins and exportins or karyopherins recognize and bind macromolecular cargos and facilitate transport through the nuclear pore.

The asymmetric distribution of RanGDP in the cytoplasm and RanGTP in the nucleus controls the directionality of nuclear transport.

Nuclear protein import can be regulated through inter‐ or intramolecular occlusion of the NLS or NES; posttranslation modification of the targeting signal; compartmental sequestration of the cargo protein or altering properties of the nuclear transport machinery including receptors and nuclear pores.

Many classes of RNA are transported via Ran‐regulated, karyopherin‐dependent pathways.

Messenger
ribonucleic acid
(mRNA) export is highly coupled to mRNA processing and is mediated by distinct receptors.

Mutations in nuclear targeting signals and nuclear transport receptors have been linked to several human diseases.
Amino Acid Degradation
Authors: Sawers R Gary 
Published: September 2009

Abstract

Amino acids are valuable metabolic fuels, providing a supply of both nitrogen and carbon for intermediary metabolism and energy for growth. Controlled degradation of amino acids is important in the maintenance of the carbon–nitrogen balance. It is becoming increasingly apparent that imbalance of amino acid degradation can have important consequences for both development and disease. Generally, the first step in degradation of amino acids results in the amino group either being incorporated into other nitrogenous compounds or being excreted as ammonia or urea, whereas the carbon skeleton is catabolized to one of a few common metabolic intermediates. Thus, an understanding of amino acid degradation provides knowledge of the interrelationships between metabolic pathways and helps explain some of the clinical features when deficiencies in amino acid metabolism occur.

Key concepts

Amino acids are important growth substrates for microorganisms.

Tight control of amino acid degradation and cycling maintains the C–N balance.

Glutamate is a key central amino acid in maintenance of the C–N balance.

The first step in amino acid degradation is removal of the α‐amino group.

Key steps in amino acid degradation include deamination, catalysed by pyridoxal phosphate‐dependent transaminases, oxidoreductases or carbon–oxygen lyases, decarboxylase reactions and carbon skeleton rearrangements catalysed by isomerases.

Carbon skeletons arising from amino acid breakdown are channelled into central metabolism.

Production and excretion of urea and uric acid by animals and birds and reptiles, respectively, avoids the accumulation of toxic levels of ammonia in blood and tissues.

Metabolic products derived from
l
‐serine are essential for cell proliferation and a functional nervous system.

Absence of key enzymes or imbalance in amino acid degradation leads to severe disease states, such as phenylketonuria and methylmalonic aciduria.
Bioinformatics
Authors: Tramontano A 
Published: September 2009

Abstract

Bioinformatics is a discipline at the intersection of biology, computer science, information technology and mathematics. It aims at integrating and analysing a wealth of biological data with the aim of identifying and assigning a function to each of the parts list of a living organism and understanding the incredibly complex processes that define life at a systems level. It is applied, for example, in the construction of genetic and physical maps of genomes, gene discovery, the inference of the molecular function and three‐dimensional structure of their products, the interpretation of the effect of gene variations on the phenotype, the reconstruction of interaction and signal transduction pathways and the simulation of biological systems. Bioinformatics is an essential part of modern biology and a key player in the quest for a complete systems‐level understanding of a living cell and of an organism.

Key concepts

Biological data are being produced at an unprecedented speed and need to be organized and integrated.

Bioinformatics, or computational biology, is the discipline that uses computational tools for analysing biological data and adds ‘biological’ value to them.

The complete DNA sequences of many genomes, including
Homo sapiens
, have been elucidated and need to be annotated, that is, associated to their biological function.

Proteins, the products of genes, perform most of the functions of life.

The function of a protein can be deduced by its evolutionary history or by analysing the three‐dimensional shape that it assumes.

The evolutionary history of a protein (a gene) can be deduced by comparing its sequence with those of all other known proteins (or genes).

The number of possible three‐dimensional structures of a protein is almost infinite and the correct one cannot be selected, as of today, on the basis of first principles.

Empirical methods, based on evolution or on the body of experimental knowledge on protein structures, can be used to infer the unknown structure of a protein.

The future challenge of bioinformatics is to use and combine available data on sequences, three‐dimensional structures, interactions, abundance and temporal patterns of expression to obtain a systems level understanding of life.
Lipoproteins: Genetic Disorders
Authors: Soutar Anne K 
Published: September 2009

AbstractThe primary function of plasma lipoproteins is to transport newly synthesised or dietary lipids in the circulation; these water‐insoluble substances include triacylglycerol, cholesterol and fat‐soluble vitamins. Mutations in genes for the many enzymes, receptors and structural proteins that regulate lipoprotein metabolism and transport are often detrimental to health, and may increase the amount of normal lipoproteins, result in accumulation of abnormal lipoproteins or cause lipoprotein deficiencies. Some defects increase the risk of coronary heart disease, whereas other deficiency disorders cause neurological and/or gastrointestinal symptoms. Genetic disorders of lipoprotein metabolism highlight the importance of lipid transport and metabolism in normal human physiology.Key ConceptsNormal regulation of plasma lipoprotein metabolism is critical for transport of lipids and fat‐soluble vitamins in the circulation.Once secreted from cells in the liver or intestine, lipoproteins undergo many complex metabolic changes in the blood circulation brought about by enzymes and their cofactors, exchange factors and cell‐surface receptors.Variation in the genes for these proteins can alter their function and cause changes in the composition, concentration and/or function of plasma lipoproteins that are frequently deleterious to health.Several defects in lipoprotein metabolism result in increased risk of premature coronary heart disease because of cholesterol deposition in the blood vessels, whereas others lead to neurological symptoms due to deficiency of fat‐soluble vitamins.The inheritance pattern varies: most known lipoprotein disorders are monogenic, with either autosomal dominant inheritance, where heterozygous carriers are affected or autosomal recessive inheritance, where heterozygous carriers are apparently unaffected. Some dominantly inherited disorders have a gene dosage effect, where homozygous individuals are more severely affected than heterozygous ones.Some gene variants only have a marked physiological effect in a particular genetic or environmental background, so not all carriers are affected.Families exist who have a clinical phenotype characteristic of a known monogenic disorder, but who have no detectable defect in the known causal genes; this suggests that novel genes still remain to be identified that influence lipoprotein metabolism.One of the commonest inherited disorders, familial combined hyperlipidaemia, is not monogenic and requires several gene variants to be present for symptoms to be manifest. These variants are also unlikely to be the same for all families.