bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rubella
Virus
Authors: Frey Teryl K , Matthews Jason D 
Published: April 2013

Abstract

Rubella
virus is a human virus belonging to the family
Togaviridae
and the sole member of the rubivirus genus.
Rubella
virus has a small genome composed of single‐stranded RNA and produces only five proteins. The
rubella
virus replication cycle takes place entirely within the cytoplasm of the infected cell.
Rubella
virus establishes a body‐wide or systemic infection that is manifested by mild symptoms including rash, lymph node swelling and low‐grade fever. However,
rubella
virus is an important human pathogen because it causes a spectrum of serious birth defects known collectively as congenital
rubella
syndrome (CRS) when a mother lacking immunity is infected during the first trimester of pregnancy. CRS can include blindness, deafness, mental retardation, heart malformations and endocrine dysfunctions. Before development of effective live, attenuated vaccines,
rubella
virus was the leading teratogenic agent of an infectious nature. Through use of these vaccines,
rubella
and CRS are controlled in much, but not all, of the world and are targeted for elimination in the Western Hemisphere and Europe.

Key Concepts:

Rubella
virus causes a benign systemic illness characterised by a rash, but is a dangerous teratogen when infection occurs during pregnancy.

Fetal infection by
rubella
virus results in congenital rubella syndrome, a constellation of serious birth defects, particularly deafness, blindness and mental retardation.

Rubella
virus is classified in the
Togaviridae
family and is the only member of the rubivirus genus.

Rubella
virions are pleiomorphic, approximately 70 nm in diameter and consist of a quasispherical capsid containing the genome RNA surrounded by an envelope composed of a lipid bilayer from which protrude glycoprotein spikes.

The
rubella
virus genome is a plus‐polarity RNA, 10 000 nucleotides in length, which encodes only five proteins: P150 and P90, both of which participate in RNA replication in the infected cells, and capsid (C) and envelope glycoproteins 1 and 2 (E1 and E2) which comprise the virion.

In the infected cell,
rubella
virus replication takes place entirely within the cytoplasm.

In the infected cell,
rubella
virus RNA replication, which proceeds through an RNA intermediate, takes place in association with cell membranes.

In the infected cell,
rubella
virion formation takes place in association with the Golgi apparatus and virions are released by exocytosis.

Rubella
virus isolates worldwide cluster into 13 genotypes that fit into two distinct clades with an overall diversity at the nucleotide level of approximately 10%, a very low level for an RNA virus.

Live, attenuated
rubella
virus vaccines, available since approximately 1970, have been used successfully to control or eliminate rubella in developed countries whereas implementation of these vaccines is progressing, but not complete, in undeveloped countries of the world.
Bacterial Origins
Authors: Koch Arthur L 
Published: April 2013

Abstract

One line of descent from the Last Universal Ancestor generated a group of organisms now called Bacteria and another called the Archaea. Both groups are quite diverse and each is quite different; they are collectively called prokaryotes. Before they arose the original first organism had to be able to reproduce and differentiate. This cell must have been able to execute selected chemical reactions to do this. These must have included: (1) a system to energise biosynthesis in order to drive chemical reactions in the biologically useful direction (which could often be in the nonspontaneous direction); (2) a system to duplicate nucleic acids chains by semiconservative replication and (3) an ability for these chains to serve as catalysts for specific biosynthesis. Therefore at least three facilities had to function inside the closed vesicle that then became the First Cell.

Key Concepts:

Few elements were needed for life to start.

More features are common to all life today.

Woese's deductions from ribosome studies of the ontogeny of life led to a breakthrough allowing a more stable taxonomy and phylogeny.

Bacteria are phylogenetically separated from Archaea/Eukarya.

In many cases the phenotypic properties of different organisms correlate with the phylogeny.

Lateral Transfer of Genes was important, but complicates studies of early life.
Codes of Nomenclature
Authors: Krichevsky Micah I 
Published: April 2013

Abstract

Codes of Nomenclature are the agreed conventions for naming biological groups. The various Codes define the rules for constructing the names of biological entities. Different organisations within the The International Council for Science (ICSU) control the individual Codes for zoology, botany, prokaryotes (bacteria and archea) and viruses. With the single exception of viruses, the Codes allow for competing taxonomies. In the other Codes, the competition arises because no judicial systems exist for choosing among the competitors. Only usage dictates the winners. Some organism groups are redundant in coverage between Codes. The Codes differ in defining examples of organism deposit and availability as benchmarks for species. Other codes have been proposed, such as Biocode (treat rationalisation of the ICSU recognised Codes) and PhyloCode (basing the code on phylogenetic criteria).

Key Concepts:

An inherent tension exists between stability of names and changes resulting from further study.

The various rules of nomenclature define the construction of the names of species, albeit somewhat differently in details.

With the exception of viruses, benchmark examples (Types, Type Specimens, Type Cultures, Type Descriptions, etc.) are required to allow for species comparison and identification.

The published description of a new taxon rarely, if ever, indicates the boundaries of the taxon.

Taxonomies function as useful indexing systems to locate members in biological space and are not absolute.

Both among and within taxa at all levels new information causes changes in views of the centres and borders of taxa.
Catabolic Plasmids
Authors: Schmidt Radomir , Ahmetagic Adnan , Philip Daniel S , Pemberton John M 
Published: April 2013

Abstract

Catabolic plasmids are large (80→1100 kb) linear or circular, accessory deoxyribonucleic acid elements present in the cytoplasm of bacteria from virtually every ecological niche on Earth. Many have a broad host range and can be transferred by cell‐to‐cell contact to a wide range of bacteria. The large catabolic gene clusters carried by these plasmids play a central role in the Earth's carbon cycle, enabling their hosts to degrade and recycle complex naturally occurring molecules such as lignin, the second most abundant plant biopolymer on Earth after cellulose. More recently catabolic gene clusters have evolved the ability to degrade and recycle most man made molecules, including the most toxic and the most recalcitrant environmental pollutants, providing a biological solution to environmental pollution. Catabolic genes have been used to construct novel strains of bacteria which produce biopharmaceuticals such as antibiotics and anticancer agents, biofuels such as ethanol, industrial dyes such as indigo and biodegradable plastics. The very first patent for a genetically modified organism was for the use of catabolic plasmids to degrade oil.

Key Concepts:

Catabolic plasmids are giant bacterial plasmids that encode vast arrays of catabolic gene clusters. They play a central and indispensible role in the Earth's carbon cycle.

Catabolic plasmids are essential for the degradation and recycling of abundant, naturally occurring yet chemically complex plant materials such as lignin.

In addition, there are catabolic plasmids, which enable bacteria to degrade and recycle the most complex, most toxic and the most polluting man‐made molecules including most carcinogens, teratogens and mutagens.

Degradation and recycling of such complex molecules at room temperature and pressure, so called ‘green or eco‐friendly’ chemistry, requires many different enzymes encoded in large arrays of gene clusters. To accommodate these genes on catabolic plasmids they must be very large. Some are in excess of 1000 kb.

Many catabolic plasmids are transferable from one bacterial cell to another by cell‐to‐cell contact. They have an extraordinarily broad host range being able to rapidly confer their catabolic activities on large populations of soil bacteria.

Novel catabolic functions can be produced by rearranging existing pathway genes, combining genes from different pathways to form a new pathway and by fusing segments from a number of pre‐existing catabolic genes into a new catabolic gene.

The genes encoded by catabolic plasmids have been harnessed by humans to produce antibiotics and anticancer drugs, to synthesise biofuels such as ethanol from lignin and to degrade and recycle man‐made environmental pollutants.

The very first patent to be granted for a genetically modified organism was for catabolic plasmids that encoded the degradation of environmental oil spills.
Vaccines: Presentation
Authors: Hochrein Hubertus , O'Keeffe Meredith 
Published: April 2013

Abstract

Vaccines have been the success story of immunology and medicine, saving millions of lives by employing nature's own powerful armoury against pathogens. This armoury known as the immune system has been shaped and optimised for millions of years by coevolution between higher organisms and pathogens including viruses, bacteria, fungi and parasites. The adaptive immune system, which includes antibody‐producing B‐cells and T‐cells, is so powerful that it is able to fight against all foreign intruders, and in most cases controls pathogens of all kinds. Moreover, it develops an immunological memory which allows quick and effective recall responses against previously encountered pathogens. However, there is a caveat with the effectiveness of adaptive immune responses; when compared with the rapid multiplication of viruses and bacteria (hours), adaptive immune responses need a considerable length of time to be effective (days to weeks). The principle of vaccination is to expose the immune system with components of the pathogens it may encounter, allowing the immune system to mount effective measures and immunological memory and thus be prepared to fight the real pathogen if it comes along.

Key Concepts:

The adaptive immune system is able to fight against all types of pathogens.

Vaccinations allow the adaptive immune system to mount effective memory responses without the full pathologies caused by the pathogen.

For optimal immune responses vaccines should contain both foreign material and a danger signal.

Dendritic cells are an important cellular component of danger recognition, and they direct the type of adaptive immune response mounted.

Danger signals are recognised at the molecular level by pattern recognition receptors, for example, TLR, NLR, RLH and C‐type lectins.
Antibody‐dependent Cellular Cytotoxicity (ADCC)
Authors: Teillaud Jean‐Luc 
Published: April 2013

AbstractAntibody‐dependent cell‐mediated cytotoxicity (ADCC) is the killing of an antibody‐coated target cell by a cytotoxic effector cell through a nonphagocytic process, characterised by the release of the content of cytotoxic granules or by the expression of cell death‐inducing molecules. ADCC is triggered through interaction of target‐bound antibodies (belonging to IgG or IgA or IgE classes) with certain Fc receptors (FcRs), glycoproteins present on the effector cell surface that bind the Fc region of immunoglobulins (Ig). Effector cells that mediate ADCC include natural killer (NK) cells, monocytes, macrophages, neutrophils, eosinophils and dendritic cells. ADCC is a rapid effector mechanism whose efficacy is dependent on a number of parameters (density and stability of the antigen on the surface of the target cell; antibody affinity and FcR‐binding affinity). ADCC involving human IgG1, the most used IgG subclass for therapeutic antibodies, is highly dependent on the glycosylation profile of its Fc portion and on the polymorphism of Fcγ receptors.Key Concepts:Antibodies bound to target cells (virus‐infected or tumour cells) and Fc receptors expressed by cytotoxic cells are the major actors of ADCC.IgG and IgA can trigger ADCC by binding specifically to FcγR and FcαR, respectively.ADCC mechanisms that lead to target cell death vary depending on effector cells that are recruited by antibodies.FcγRIIa and FcγRIIIa polymorphism impact ADCC efficacy by IgG1 antibodies.Engineering FcIgG either by introducing point mutations or by modifying the glycosylation profile allows to optimise IgG1 antibodies for enhanced ADCC.Bispecific antibodies that bind activating molecules expressed by cytotoxic cells and tumour cells can mimic classical ADCC.
Complement System and Its Role in Immune Responses
Authors: Oikonomopoulou Katerina , Reis Edimara S , Lambris John D 
Published: April 2013

Abstract

The complement system is a network of more than 50 plasma proteins and receptors, which have the role of mediating innate and adaptive host defence mechanisms, whereas they also participate in various (patho)physiological processes. The primary functions mediated by complement proteins include phagocytosis of foreign elements (bacteria, viruses, particles

etc

.), cell lysis, inflammation, solubilisation of immune complexes, apoptotic cell clearance and enhancement of humoral immune responses. Dysregulation of complement activity has, therefore, been connected to various diseases, including autoimmune conditions, thrombotic pathologies and infections.

Key Concepts:

Complement is a multiprotein network of plasma proteins and cell surface receptors.

Complement is an evolutionary conserved system.

Complement participates in innate and adaptive immunity.

Complement dysregulation and deficiencies are connected to disease.
Transfer
RNA
Structure
Authors: Westhof Eric , Auffinger Pascal 
Published: April 2013

Abstract

Transfer ribonucleic acid (tRNA)
molecules that participate in the elongation step of protein synthesis on the ribosome have a conserved secondary structure, known as the cloverleaf, and fold into a common three‐dimensional architecture. The conservation of the global L‐shaped 3D fold is assessed by the more than 100 available crystal structures showing tRNAs in native states or in complexes where tRNAs are bound to various interacting systems such as cognate synthetases, editing, modification and processing enzymes or full ribosomes. These tRNA crystal structures display a whole range of structural adaptability features encoded in their sequence and underlying their various functions. Thus, as the number of available structural data expands, the concept of a unique tRNA structure fades out for that of an ensemble of interconnected and environmentally dependant tRNA structures.

Key Concepts:

tRNAs display a huge sequence variability.

tRNA molecules fold with a conserved secondary structure.

The conservation of the secondary structure originatesbase covariations in Watson–Crick pairs of helices.

The tertiary folds of tRNAs present a striking adaptability.

The structural adaptabilities of tRNAs stem from the molecular neutrality present among the various noncovalent interactions.

Only a minimal number of conserved tertiary interactions are preserved.

The maintenance of some non‐Watson–Crick pairs is key for the three‐dimensional structure.

As a consequence of structural adaptability, tRNAs have acquired a greatdiversity in biological systems.

The structure and function of tRNAs is modulated by the type and concentration of the ions surrounding them.
Drosophilaas an Experimental Organism for Functional Genomics
Authors: Dow Julian AT 
Published: April 2013

AbstractAlthough historically the classical model for the understanding of development, the fruit‐flyDrosophila melanogasteris valuable for study for three reasons: as an organism in its own right, as an inexpensive, genetically powerful model for human function and disease, and as a model for economically important or harmful insects, such as vectors of disease. The sophisticated genetic tools that distinguishDrosophilafrom other model organisms or insects allow great spatial and temporal precisions both in genetic intervention, and in the expression of genetically encoded sensors for second messengers or intracellular environmental variables. Combined with other, novel functional readouts, it is now possible to move towards an understanding ofDrosophilaas a metazoan organism composed of distinct and individually tractable tissues that interact and integrate to produce a functioning whole.Key Concepts:Drosophila melanogasteris a small, easily reared insect with a short lifecycle.The key advantages ofDrosophilaare a balance between genetic power and biomedical relevance, and rapidity and low cost of generation and maintenance of mutant and transgenic stocks.The genetic toolbox available forDrosophilaallows precise intervention in specific, defined cells in an otherwise normal organism, opening unique opportunities for functional biology.Approximately 70% of human genes have clearDrosophilahomologues, allowing the modelling of many human diseases in flies.Drosophilaalso shares approximately 70% of its genes withAnopheles gambiae, the mosquito vector of malaria.Our understanding of fly development is now mature: new phenotypes are required to provide a global functional genomic understanding.An exciting challenge for the future is functional biology; understanding how the different tissues and control systems interact to make a working, successful organism.
Peptidoglycan
Authors: Young Kevin D 
Published: April 2013

Abstract

Peptidoglycan is the rigid, but flexible, macromolecule that surrounds and protects individual bacterial cells. It supplies the foundation for bacterial cell walls, defines an organism's shape and anchors protein complexes and extracellular organelles to the cell surface, all while remaining porous enough to admit essential nutrients and large compounds. Peptidoglycan fragments trigger neighbouring microorganisms to grow or to modify their own walls, serve as maturation signals for vertebrate immune systems and may be used to manipulate the immune system for the benefit of pathogenic organisms. Because it is unique to bacteria, peptidoglycan is one of the most valuable targets to which antibiotics may be directed. Although the components of peptidoglycan are known and we have a basic understanding of its biosynthesis, there remains a great deal to learn about its three‐dimensional organisation, its biological properties and activities, and how it expands and divides during bacterial growth.

Key Concepts:

Peptidoglycan is the basic component of the bacterial cell wall, which is the protective structure that surrounds and protects most bacteria.

Peptidoglycan is composed of numerous glycan (sugar‐based) polymers that are covalently crosslinked to one another by short peptide side‐chains, creating a single bag‐like macromolecule called the sacculus.

Penicillin‐binding proteins are responsible for the final stages of peptidoglycan synthesis, but additional proteins modify peptidoglycan in numerous ways in different bacteria.

Because of its complexity, the exact three‐dimensional structure of peptidoglycan is not known, but it is thought to look like a net with pores 2–5 nm in diameter.

Large protein complexes and organelles are embedded in or are threaded through peptidoglycan, indicating that enzymes must degrade peptidoglycan in a limited way to create holes in which these structures may be assembled.

Bacteria can change the composition and perhaps the structure of their peptidoglycan, depending on growth conditions and in response to their environmental surroundings.

Peptidoglycan is constantly being broken down, recycled and renewed as bacteria grow and divide.

Bacteria use peptidoglycan fragments to signal or manipulate other microorganisms or even human and animal immune systems.

Because peptidoglycan is unique to bacteria, the enzymes that synthesise it are some of the most important targets for antibiotic therapy.
Bacteriophages
Authors: Maniloff Jack 
Published: April 2013

Abstract

Bacteriophages (phages) are viruses that infect most, if not all, bacteria in the domains Bacteria (eubacteria) and Archaea (archaebacteria). Most (96%) phages have tailed phage morphology, with the rest having a polyhedral, filamentous or pleomorphic morphology. Phage genomes are a single‐ or double‐stranded, linear or circular,
deoxyribonucleic acid (DNA)
or
ribonucleic acid (RNA)
molecule. An exception is the cystovirus genome, which consists of three RNA molecules. Most phages produce a lytic infection, which typically involves phage attachment to the cell surface, injection of phage nucleic acid into the cell, intracellular expression of phage genes to produce nascent phage nucleic acid and proteins, assembly of progeny phages, and cell lysis to release progeny phages. In some situations, instead of a lytic infection, some phages remain latent in infected cells – a process called lysogeny. As bacterial predators, phages affect global biogeochemical cycles.

Key Concepts:

Bacteriophages (phages) are viruses that infect most, if not all, bacteria in the domains Bacteria (eubacteria) and Archaea (archaebacteria).

Most (96%) phages have tailed phage morphology, with the rest being polyhedral, filamentous or pleomorphic.

Phages genomes are a single‐ or double‐stranded, linear or circular, DNA or RNA molecule, except cystoviruses, which have a genome of three molecules of linear double‐stranded RNA.

Most phages have a lytic infection cycle, in which an infected cell produces nascent phage nucleic acid and proteins, which are assembled into progeny phages and released by cell lysis.

Some phage infections are lysogenic, in which the intracellular phage remains latent and the cell continues to grow.

Bacteria have a type of adaptive immunity, the CPISPR system, against phages and plasmids.

As bacterial predators, phages affect global biogeochemical cycles.