bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microviridae: Microviruses and Gokushoviruses
Authors: Cherwa James E , Fane Bentley A 
Published: April 2013

AbstractMembers of theMicroviridaecomprise two subfamilies. The microviruses (Greek for small), which infect free‐living bacteria, are among the fastest known replicating viruses. Gokushoviruses (Japanese for very small) occupy a unique niche, infecting obligate intracellular bacteria, such asChlamydiaandBdellovibrio, or mollicutes, bacteria without a cell wall. All members of the family contain small (4000–6000 bases), circular, single‐strandeddeoxyribonucleic acid(ssDNA) genomes of positive polarity, which are packaged inside small (∼25 nm diameter) T=1 icosahedral capsids. The other icosahedral, ssDNA virus families:Parvoviridae,Circoviridae,NanoviridaeandGeminiviridae; share most of these properties, suggesting a large super family spanning several domains of life. The most well known member of theMicroviridae, ϕX174, has been extensively used to study the fundamental mechanisms of DNA replication and capsid assembly. The latter is uniquely dependent on two scaffolding proteins, and has become a model system for experimental evolution.Key Concepts:Whilst overlapping reading frames increase the amount of genetic information encoded in small genomes, they do not appear to significantly impact the ability of the virus to genetically adapt to selective pressures.Due to the genome's positive polarity, DNA replication must commence before viral genes can be transcribed.Microvirus DNA replication occurs in three distinct stages: (1) ssDNA is first converted to a double‐stranded molecule, (2) amplification of the double‐stranded molecule, (3) single‐stranded genomic DNA synthesis and packaging.Genomic DNA synthesis and packaging are concurrent processes; thus, a genome is not synthesised unless there exists a capsid in which to package it.Gene expression is controlled by the finely tuned interplay ofcis‐acting genetic elements: promoters, ribosome binding sites, mRNA stability sequences and transcription terminators.Microviruses are distinguished by their two scaffolding protein system, whereas Gokushoviruses utilise a single scaffolding protein.Capsid assembly is mediated by scaffolding proteins, which induce conformational switches in the viral coat protein to control the timing and fidelity of morphogenesis.Cell lysis is achieved by inhibiting host cell wall biosynthesis, a mechanism reminiscent of some antibiotics.
Drosophila
Neural Development
Authors: Sprecher Simon 
Published: April 2013

Abstract

The human brain is by far the most complex organ system in terms of cell type variety and interaction between cells. Studies from comparatively simple animal models allow us to genetically dissect the development and function of the nervous system. Advanced molecular genetic tools make the fruit fly

Drosophila melanogaster

a unique and powerful model system to study how during development a complex nervous system develops, how neurons and glia cells are generated and correctly assembled. Many key processes such as proliferation of neural stem cells, neurogenesis, orchestration of spatial and temporal identity, axon guidance and establishment of connectivity have been investigated in fruit flies. Comparative analysis shows that developmental processes as well as genetic pathways acting to build a complex brain are shared between mammals and insects.

Key Concepts:

Along the anteriorposterior and dorsoventral axes transcription factors pattern the nervous system.

Neural stem cells divide asymmetrically to self‐renew and generate committed neural precursors.

Different types of neural stem cells exist to establish different domains of the central nervous system.

Even though the brains of insects and mammals appear quite distinct the overall mode of development are similar.
Genetic Code: Introduction
Authors: Watanabe Kimitsuna , Yokobori Shin‐ichi 
Published: April 2013

AbstractThe genetic code establishes the relationship between all 64 possible arrangements of triplets (codons) of the four nucleotide bases contained in either DNA (A, T, G and C) or RNA (A, U, G and C) and the 20 amino acids that are used to construct proteinsvia‘translation’ system as well as signals of translation initiation and termination. The historical events from 1950s to 1960s that contributed to the deciphering of the genetic code led to the development of the field of molecular biology. In 1960s, the genetic code was established to be ‘universal’ for all living organisms. However, from late 1970s, variations of genetic code have been found in various genetic systems. Variations of genetic code promote studies on the origin and evolution of the genetic code.Key Concepts:Genetic code is the correlation between nucleotide triplet and the corresponding amino acid.Genetic code consists of 64 triplet codons and sometimes ‘degenerate’.Central dogma states that genetic information flows unidirectionally from DNA to proteinviaRNA as an intermediary.A cell‐free protein system contains ribosome, S100 fraction, tRNA, amino acids, ATP, an energy recycling system and a template.Termination codon consists of UAG (amber codon), UAA (ochre codon) and UGA (opal codon), which code for no amino acid but instead cause protein synthesis to terminate.Initiation codon is AUG, which initiates protein synthesis with formyl‐methionine in bacteria and phage.Universal genetic code shows the way of assignment of 64 triplet codons to each of 20 amino acids and 3 termination codons, which is common to almost all extant organisms – bacteria, yeasts, viruses, plants and animals.
Semaphorins
Authors: van Erp Susan , Jeroen Pasterkamp R 
Published: April 2013

Abstract

The semaphorins are an evolutionary conserved family of intercellular signalling proteins known to deliver guidance cues to growing axons and migrating cells during development. Semaphorins bind with high affinity to several distinct receptor families on the cell surface, including the neuropilins and plexins. The interaction of semaphorins and their receptor complexes triggers elaborate intracellular signalling pathways that in many cases regulate the cytoskeleton to control growth cone or cellular morphology. However, semaphorins also regulate cellular processes not directly related to changes in cytoskeletal dynamics such as apoptosis or cytokine release. Defects in semaphorin function have been associated with a variety of human diseases including amyotrophic lateral sclerosis, spinal cord injury and cancer, and studies have been initiated to use semaphorin proteins as therapeutic targets in human disorders.

Key Concepts:

Semaphorins are bi‐functional guidance cues mediating attractive and repulsive chemotactic responses.

Semaphorin receptor complexes are composed of ligand binding, signal‐transducing and modulatory subunits.

Context‐dependent changes in receptor or signalling components determine the downstream effect of semaphorins.

Semaphorins can act as ligands and receptors, a process called bi‐directional signalling.

Secreted and membrane‐associated semaphorins regulate various aspects of neural circuit development.

Signalling cues that function downstream of semaphorin receptors includes protein kinases and small GTPases.

Semaphorins have been implicated in various human diseases and may serve as therapeutic targets.
Ephrins
Authors: Kilari Sreenivasulu , Wilkinson George 
Published: April 2013

AbstractEphrins are cell surface proteins which bind to the Eph family of receptor tyrosine kinases. Cell surface‐attached ephrin‐A ligands principally activate EphA receptors, and transmembrane ephrin‐B ligands primarily activate EphB receptors. Ephs and ephrins influence many developmental processes, including compartmentalisation, cellular migration, axon guidance and angiogenesis. These developmental functions arise as Ephrin–Eph interactions shape cellular behaviours, including adhesion, migration and synaptic plasticity. Eph receptors communicate with the cytoskeleton through differential activation of small GTPases downstream of their tyrosine kinase activity. In addition to stimulating Eph receptors, ephrins signal within the cell which expresses them, a phenomenon termed ‘reverse signalling’. Ephrin‐B reverse signalling relies in part on phosphorylation of the cytoplasmic tail and recruitment of cytoplasmic proteins. Both ephrins and Ephs can modify internalisation and trafficking of other cell surface effector molecules.Key Concepts:Ephrins are implicated in numerous developmental events centred around cell‐contact‐dependent signalling.Ephrin ligands and Eph receptors participate in axon guidance, and graded expression of this system is implicated in the topographic mapping of the retinotectal projection.Ephrins also critically control synaptic function.In the vasculature, EphB4 and ephrin‐B2 are required for angiogenesic remodelling of the primitive vascular plexus.Ephrins both stimulate Eph receptor tyrosine kinases and transduce ‘reverse’ signals in the cells which express them.The specific outcome of Eph–ephrin engagement depends on cellular context and on the involvement of other signalling components.
Idiotypes
Authors: Gavalchin Jerrie 
Published: April 2013

AbstractIdiotypes are unique determinants of an immunoglobulin or T‐cell receptor that can function as antigens. Responses to idiotypes, which include anti‐idiotypic (Id) antibody (Ab)‐producing B cells and idiotype‐specific T cells, form a network that regulates their production, referred to as the idiotypic network. In an immune response, antibody 1 (Ab1) is produced in response to an antigen, and anti‐Id Ab produced to Ab1 (Ab2) may bind in the antigen‐combining site (Ab2β) or the framework region (Ab2γ) of Ab1. As Ab2β can fit in the paratope of an antigen receptor of B or T cells, it mimics the three‐dimensional structure and is the internal image of antigen, and has the potential to activate Ab1 precursors reactive with the antigen. These findings have led to the use of Ab2β as an immunogen to elicit specific immune responses to foreign pathogens, as probes to study cell surface receptors and as immune therapy for tumours.Key Concepts:Idiotypes are unique determinants located in the variable region of antigen receptors on B cells (immunoglobulin, Ig) and T cells (T‐cell receptor, TCR).Antibody 1 (Ab1) is produced in response to an antigen and Ab2 produced to Ab1 may react with the antigen‐combining site (Ab2β, internal image of antigen) or the framework region (AB2γ) of the antibody molecule.The interaction of clones of B and T cells that express distinct idiotypic specificities to regulate the immune response is referred to as the idiotypic network.The idiotypic network can be exploited to elicit specific immune responses to foreign pathogens, to study cell surface receptors and as immune therapy for tumours.
Immunological Memory
Authors: Zanetti Maurizio 
Published: April 2013

Abstract

Immunological memory is a distinct characteristic of the immune system and it relates to its ability to remember antigens on pathogens, tumour cells, tissue of the immunological self, and cells and tissues derived from other individuals of the species and mount an immunological response of greater magnitude and with faster kinetics upon re‐encounter of the same antigens. This property provides an advantage in the course of protective responses against pathogens and tumour cells, but represents a threat in the case of allogeneic cell or tissue transplant. During the past decade considerable progress has been made in the elucidation of the multiple cellular and molecular mechanisms regulating the induction and maintenance of immunological memory. Although our understanding remains imperfect, the current cumulative information allows one to recognise operational patterns and identify those principles that will aid in the design of better vaccines and better understanding the role of immune system in protection against disease.

Key Concepts:

Immunological memory represents an important aspect of the immune response in mammals.

Immunological memory exists for both B lymphocytes (antibody producing cells) and for T cells.

Memory responses by the immune system occur according to only partially understood operational principles.

Memory responses form the basis for the effectiveness of vaccines against pathogens and cancer cells.

Memory responses protect the individual and the species against the threat of pathogens and cancer cells.
Neonatal Immunity
Authors: Tregoning John S 
Published: April 2013

Abstract

Both our innate and adaptive immune responses are reduced in function at birth. This leads to an increased risk of infection coinciding with a period of maximum exposure to new pathogens, caused by the move from the sterile environment of the womb to the infectious environment of the world. However, not every new antigen seen is dangerous to the newborn, and a balance is required to ensure an appropriate immune response and avoid inflammatory responses to benign antigens. To supplement the period of immune immaturity, the mother transfers passive protection, principally antibody, to the child. Vaccines can be used in early life, but the reduced function of the neonatal immune response reduces the efficacy of vaccines, which are otherwise effective in adults, necessitating research on infant‐specific formulations.

Key Concepts:

The neonate immune system is reduced in capacity and can be described as hyporesponsive.

The immune system develops in a programmed series of cell maturation events.

Moving from the controlled, sterile environment of the womb to the outside world has a critical impact on the newborn's immune system.

Reduced pattern recognition by neonatal antigen‐presenting cells leads to the observed hyporesponsive phenotype.

The mother provides some immune protection to the child, especially via antibodies in breast milk.
Infertility: Immunological Aspects
Authors: Francavilla Felice , Barbonetti Arcangelo 
Published: April 2013

Abstract

Naturally occurring antisperm‐antibodies (ASA) exert an impairment to fertility, which is related to the extent of sperm autoimmunisation. It determines the degree of the interfering effect on sperm penetration through the cervical mucus independently from the antigenic specificity of ASA. Whether or to what extent an ASA‐interfering effect occurs, in each individual patient, downwards from the impairment of cervical mucus penetration is still hard to establish. The main reasons are the inability of current diagnostic tests to determine the antigenic specificity of ASA and to quantify the antibody density on the sperm surface, the main determinants of the ASA‐impairment at level of sperm/oocyte interaction. The current empirical treatment strategy (intrauterine insemination as first line‐treatment) would give way to a more rational one, with the development of tests detecting ASA directed against defined fertilisation‐related antigens.

Key Concepts:

Immunological infertility refers to couple infertility due to antisperm‐antibodies (ASA) occurring in the male or female partner.

Antisperm‐antibodies (ASA) exert an impairment to fertility, which is related to the extent of sperm‐immunisation.

The impairment of sperm penetration through the cervical mucus represents the primary mechanism of ASA interference with fertility.

An ASA interference at the level of gamete interaction can occur or not, depending on the relevance of the specific antigens, targeted by natural ASA in each individual patient, to the fertilisation process.
Baculoviruses
Authors: Guarino Linda 
Published: April 2013

Abstract

Baculoviruses are large, complex
deoxyribonucleic acid
(DNA) viruses that infect arthropods. The viruses are highly pathogenic and a few members have been successfully exploited as biological control agents for agricultural and forestry pests. With the exception of a virus pathogenic to silk moths (

Bombyx mori

nucleopolyhedrovirus (NPV)), most baculovirus research is geared towards increasing virulence. The type species of baculoviruses,

Autographa californica

NPV, is widely used as a eukaryotic expression system for the production of vaccines and other proteins of medical and biological importance. Baculoviruses are also good model systems for the study of apoptosis, DNA replication, transcription, pathogenesis, membrane fusion and virus infectivity.

Key Concepts:

Baculoviruses are rod‐shaped, enveloped viruses of 30–60 nm in diameter and 250–300 nm in length.

Baculoviruses infect insects of the orders Lepidoptera, Diptera and Hymenoptera.

Baculoviruses have been genetically engineered to be highly efficient eukaryotic expression systems.

Baculoviruses are unusual in making two different infectious forms: occluded virus for spreading infection from insect to insect and budded virus for spreading of viral infection within an infected insect.

Baculoviruses have circular‐double stranded genomes, ranging from 80 to 180 kb.

Baculoviruses use actin filaments for intracellular transport.

Baculovirus DNA is infectious.

Baculoviruses use host RNA polymerase for synthesis of early genes and encode a viral RNA polymerase for transcription of late genes.

Baculovirus infection spreads through the tracheal system.

Baculoviruses have been successfully used to control insect pests.
Cytomegaloviruses
Authors: Chatterjee Archana , Livingston Robyn , Harrison Christopher J 
Published: April 2013

AbstractThe cytomegaloviruses are a common, ancient group of viruses that are widely distributed in the animal kingdom. They have a complex biology with a highly restricted host range. These viruses spread easily in the human population, causing mostly asymptomatic infection. This large reservoir of latent infection however, is a significant threat to high‐risk patients including immunocompromised hosts and the fetus in nonimmune pregnant mothers. Although a limited number of antiviral agents for treatment and prophylaxis in selected patient groups, as well as other adjunctive therapies have become available over the past few decades, newer, less toxic medications and a safe and effective vaccine remain in the research realm. Other areas still to be investigated include identification of the site of viral latency, characterisation of the targets of acute infection, determination of the exact role of virus and host immune response in disease and latency.Key Concepts:The cytomegaloviruses (CMVs) belong to the family of deoxyribonucleic acid (DNA) viruses known asHerpesviridae.CMVs have complex biology and are widely distributed in nature, yet each animal species has its own CMV.The prevalence of human CMV infection varies with age, geographic location, cultural and socioeconomic status, race or ethnicity and child‐rearing practices.In most cases, human CMV infection in normal hosts is asymptomatic, but it can cause a mononucleosis syndrome similar to that fromEpstein–Barr Virus(EBv) infection.The greatest risk from CMV is in immunocompromised patients and infants born to nonimmune mothers who develop primary infection during their pregnancy.CMV has been one of the most important opportunistic infections in patients with AIDS.Antiviral agents used to treat severe CMV disease include ganciclovir, valganciclovir, foscarnet, cidofovir and fomivirsen.Passive immunoprophylaxis with CMV hyperimmunoglobulin (CMVIG) in post‐transplant patients, premature newborns at risk for postnatal infection and pregnant women is controversial.Blood/organ donor screening, ‘leucocyte‐reduction’ in donated blood, handwashing and other hygienic measures can reduce the spread of CMV.Newer therapeutic agents and a vaccine are under development.
Developmental Biology: Mathematical Modelling of Development
Authors: Maini Philip K , Baker Ruth E 
Published: April 2013

AbstractUnderstanding how structures (e.g. hair, teeth, feathers, limbs and pigmentation patterns) arise from the initially unstructured fertilised egg is one of the key challenges in developmental biology. Mathematical models enable us to investigate how certain biochemical and/or biophysical processes interact to produce pattern and form. They provide a unifying theme for spatio‐temporal patterning across a vast range of biological applications by suggesting a set of underlying principles for pattern formation. Such models suggest that patterns and structures must have certain properties and these predictions motivate experiments. The results of such experiments help refine models and lead to more precise predictions. In this way, modelling, combined with experiment, can be a powerful investigative tool in helping unravel the complexity of morphogenesis (the formation of structure) in biology.Key Concepts:Patterning arises due to short‐range activation, long‐range inhibition.Mathematical models suggest constraints on development.Instabilities emerge from stabilising processes.Pattern properties can be mechanism‐independent.It is the integration of biochemical and biophysical processes that lead to structure formation.
Regeneration of Muscle
Authors: Grounds Miranda D 
Published: April 2013

Abstract

Muscle regeneration is the process by which damaged skeletal, smooth or cardiac muscle undergoes biological repair and formation of new muscle in response to death (necrosis) of muscle cells. The success of the regenerative process depends upon the extent of the initial damage and many intrinsic and environmental factors. Key cellular events required for regeneration include inflammation, revascularisation and innervation, in addition to myogenesis where new muscle is formed. In mammals, new muscle formation is generally excellent for skeletal muscle but poor for cardiac muscle; however a greater capacity for regeneration of cardiac muscle is seen in fish and some anurans. These aspects of regeneration are discussed with respect to myogenic stem cells, molecular regulation, ageing and implications for human therapies, with a strong focus on skeletal muscle. Other situations of muscle damage and restoration that do not involve necrosis (e.g. sarcomere disruption and atrophy) are here not considered as regeneration.

Key Concepts:

Necrosis is required for muscle regeneration.

Inflammation is essential to remove necrotic tissue and initiate myogenesis.

New blood vessel formation is required after major injury of muscles.

Skeletal muscle has an excellent capacity for regeneration. The major source of myogenic precursor (stem) cells is still considered to be the satellite cell, although other cells lying outside the myofibre may contribute to myogenesis.

The source of the myogenic precursor cells (myoblasts) varies between conventional tissue regeneration and epimorphic regeneration (where mature cells dedifferentiate).

The microenvironment, including the extracellular matrix, affects all aspects of regeneration, for example, the muscle precursors and their capacity for new muscle formation (and fibrosis impairs myogenesis).

Reinnervation is essential for functional recovery of skeletal muscle.

Excellent myogenesis can occur in geriatric muscle, although systemic factors essential for regeneration, for example, inflammation and innervation, may be suboptimal.

Mammalian heart muscle has a very poor capacity for regeneration and severe damage (e.g. heart attack) results in fibrosis and impaired function.

In contrast, the hearts of vertebrates such as salamanders and zebrafish can regenerate; the new heart muscle is derived from the dedifferentiation and proliferation of mature cardiomyocytes. It is hoped that an understanding of mechanisms involved in these situations will present opportunities to induce regeneration of damaged human cardiac muscle.