bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory Processing
Authors: Portfors Christine V 
Published: February 2016

AbstractSound is encoded as action potential trains by the cochlea and transmitted along the eighth nerve into the cochlear nucleus. Central auditory processing exemplifies several general principles of sensory neuronal conduction and control. Information is processed in parallel, with subdivisions of the auditory pathway adapted for specialised feature extraction, and it is hierarchical. The temporal properties of sound mean that the preservation of timing information during auditory processing is of fundamental importance. Timing cues are especially important for encoding the horizontal position of a sound source. Interaural timing differences are encoded by brainstem nuclei with specialised neuronal features. Characteristics of the auditory system have also evolved to encode features present in social vocalisations. The complex interaction between excitation and inhibition in the auditory midbrain enables selective encoding of particular vocalisations by different populations of neurons. Thus, auditory processing has evolved such that behaviourally relevant sounds are efficiently encoded.Key ConceptsThe fundamental organising principle of the auditory system is tonotopy, which is a systematic representation of frequency that starts at the level of the basilar membrane.The ascending auditory pathway is comprised of many nuclei that enable both parallel and serial information processing.The inferior colliculus (the main auditory midbrain nucleus) is the main point of convergence of ascending and descending information.Interaural timing differences are encoded in the medial superior olive (in mammals) and depend on coincidence detection, delay lines and specialised neuronal characteristics.Interaural level differences are encoded in the lateral superior olive (in mammals) and depend on interactions of excitation and inhibition.The barn owl is an exceptional animal that can precisely localise sound in the horizontal and vertical plane by using interaural timing and interaural level differences.A fundamental function of the auditory system is to detect, discriminate and categorise complex sounds such as social vocalisations.Neurons in the inferior colliculus are selective to vocalisations such that a unique neural representation occurs for different vocalisations.The complex interplay between excitation and inhibition in the inferior colliculus results in heterogeneous responses to vocalisations.The mouse auditory system has evolved to utilise cochlear distortions created by overlapping ultrasonic frequencies to encode social vocalisations that have spectral content much higher than the tuning properties of the neurons.
Algal Calcification and Silicification
Authors: Koester Julie , Brownlee Colin , Taylor Alison R 
Published: February 2016

Abstract

The algae represent major producers of calcium carbonate and silica among the world's biota. Calcification involves the precipitation of CaCO
3
from Ca
2+
and CO
3
2
−
ions. Algal calcification by coccolithophores may account for up to half of global oceanic CaCO
3
production. Silicification, the transformation of silicic acid into skeletal material, occurs in a few algal groups. The abundant diatoms represent the major silicifiers, playing a key role in marine silica cycling. Fossilised diatomaceous deposits have long been exploited for building and filling materials. Biomineralisation of calcium and silicon require homeostatic ion controls that are well characterised for Ca
2+
and H
+
in coccolithophores. Calcification occurs in an alkalinised vesicle, while silicification requires an acidic pH. Research on silicification remains focused upon cell wall development. Initiation and development of structures that are mineralised intracellularly requires initiation and regulation by organic components within the vesicles. Low‐temperature, low‐pressure biogenic formation of silica and calcite has potential for biotechnological application in novel industrial processes.

Key Concepts

Organisms across the tree of life are capable of biomineralisation.

Understanding the process of biomineralisation is required to interpret the information contained in biomineral geochemical proxies.

Mechanisms of calcification and silicification include uptake of inorganic ions via protein transporters, intracellular sequestration of those ions and the association of crystal initiation with an organic matrix.

The maintenance of metabolic homeostasis, especially relative to proton flux, is linked to calcification, but less is known about the effect of silicification on homoeostasis.

The adaptive functions of mineralised cellular structures remain hypothetical and are open topics of research.

The biological mechanisms of crystal formation have widespread applications in nanotechnology.
Histocompatibility Antigen Complex of Man
Authors: Mehra Narinder K , Kaur Gurvinder 
Published: February 2016

Abstract

The histocompatibility antigens are cell surface glycoproteins expressed on nucleated cells whose major function is to bind peptides within the cell or from outside and present them at the cell surface for inspection by T cells of the immune system. These antigens are a part of the major histocompatibility complex (MHC), which exists in most vertebrate species and whose products were originally defined as the most crucial elements controlling graft rejection. Human MHC research has revealed human leucocyte antigen (HLA) to be the most polymorphic genetic system in the mammalian genome, and this unique diversity parallels the need for diverse peptide sites within the MHC to combat a fast‐evolving range of pathogens. Clinical screening of HLA polymorphism is now an important prophylactic biomarker system for various diseases and a useful tool for development of peptide‐based vaccination approaches.

Key Concepts

HLA is the most polymorphic component of the human genome. It is a part of the major histocompatibility complex that exists in many animal species.

The major function of HLA molecules is antigen presentation.

High degree of molecular diversity of classical HLA class I and II molecules is a reflection of their direct role as antigen‐presenting molecules against a wide range of pathogens.

The MHC region is characterised by strong linkage disequilibrium between its loci such that conserved ancestral haplotypes can be identified.

There are population‐based differences in allelic distribution of MHC molecules primarily due to historical human migration patterns and varying microbial pressures in different geographical regions.

An individual heterozygous at a particular HLA locus has an added advantage than homozygous as the two different HLA molecules can bind and present a large number of peptides.

The function of the ubiquitous HLA class I gene products (HLA‐A, HLA‐B and HLA‐C) is to present endogenous peptides to responding CD8+ T cells, whereas the class II coded molecules (HLA‐DR, HLA‐DQ and HLA‐DP) have restricted tissue distribution and process exogenous peptides for presentation to CD4+ helper T cells.

The antigen‐binding cleft of HLA class I molecules can bind peptides that are usually nonamers, whereas the HLA class II antigen‐binding cleft can bind longer peptides of 11–18 mers.

Polymorphisms in the MHC have been associated with disease susceptibility, varying rates of disease progression and drug‐induced hypersensitivities.

MHC matching is crucial in donor selection for haematopoietic stem cell and organ transplantation.
Aquaporins: Channels for the Molecule of Life
Authors: Hacke Uwe G , Laur Joan 
Published: February 2016

Abstract

Liquid water has unique properties that make it a universal solvent. Water is an essential component of almost all physiological and biochemical reactions; therefore, its presence is required everywhere within an organism. The circulatory systems of animals and the vascular system of plants move fluids over long distances. In the tallest trees, water moves across a height gradient of 100 m or more, thereby connecting roots and distant leaves. On a cellular and tissue level, water movement is facilitated by intrinsic membrane proteins called aquaporins. These water channels are found in all life forms. Aquaporins have been mostly studied in mammals and plants, where water channels play important physiological roles. This article gives an overview of the discovery, structure and regulation of aquaporins. Their roles in different life forms are discussed.

Key Concepts

Water can diffuse through the lipid bilayer, but without aquaporins flow across membranes is slow.

Aquaporins are integral membrane transport proteins, and they facilitate water movement in cells, tissues and entire organisms.

A single water channel allows the passive passage of more than one billion water molecules per second.

The aquaporin protein family is ancient, and aquaporins can be found in a wide range of organisms.

Aquaporins appear to play important physiological roles in mammals, plants and other organisms.
Evolution of Secondary Plant Metabolism
Authors: Wink Michael 
Published: February 2016

AbstractThe biosynthesis of secondary metabolites (SMs), which are important for the fitness of the plants as defence against herbivores and microbes and also as signal compounds to attract pollinators and fruit dispersers, occurs universally in higher plants and shows very high structural diversity. The evolution of SMs in higher plants rests on variation in the enzymatic manipulation of a relatively small number of primary precursors. Evidence is presented that at least some of the genes encoding key enzymes of biosynthesis probably have reached plants by ancient horizontal gene transfer (HGT), for example, from protobacteria or cyanobacteria which later became mitochondria and plastids. Another source of SMs can be ectomycorrhizal and endophytic fungi; they can directly provide plants with defence compounds or might have transferred their pathway genes into the genome of their host plants times ago.Key ConceptsPlants have evolved secondary metabolites as bioactive substances as a measure to protect themselves against herbivores.Secondary metabolites are part of the innate immune system of plants, used to defend themselves against bacteria, fungi and viruses.Secondary metabolism is dynamic and can react in case of a herbivoral or microbial attack by activating prodrugs, by either increasing the concentration of existing SM or by inducing the synthesis of new SMs (phytoalexins).Secondary metabolites occur in a broad diversity and functionality.Secondary metabolites derive from primary metabolites using a limited number of key pathways. Functional diversity is gained by adding diverse combinations of reactive functional groups.Terpenoids and phenolics are present in almost all plants, whereas alkaloids and other nitrogen‐containing SMs are more common in angiosperms.Some groups of SMs occur in a few restricted plant genera only, which are often not related.The patchy distribution can be due to convergent evolution of the corresponding pathways.Alternatively, the genes for SM biosynthesis have been introduced into the plant genome by horizontal gene transfer from protobacteria (which became mitochondria) and cyanobacteria (which became chloroplast).Some SMs are produced by endophytic fungi, which infect a limited number of often unrelated species. As a consequence, this can also lead to a patchy distribution of SMs.
Epidermis: Outer Cell Layer of the Plant
Authors: Glover Beverley J , Airoldi Chiara A , Moyroud Edwige 
Published: February 2016

Abstract

The epidermis is the protective outer layer of clonally related cells covering all plant organs. It is composed of a number of specialised cell types which differentiate from the basal epidermal cell in adaptively significant frequencies and patterns. The epidermis is unique in developing solely through anticlinal divisions, generating a sheet of cells overlying the rest of the plant. This sheet is connected physically and biochemically to the cell layers below, with information exchange occurring in both directions. The specialised cell types within the epidermis develop either through communication among themselves, or, in some cases, through communication also with the underlying cell layers. Brief descriptions of the molecular genetic control of trichomes, stomata, root hairs and petal conical‐papillate epidermal cells are provided here, along with a summary of the role of the cuticle in epidermal cell morphology and of the interplay between cuticle regulation and cell morphology.

Key Concepts

The plant epidermis is a single layer of clonally related cells.

Plant epidermis fulfils a basic protective function, but specialised cells within the epidermis have specific roles.

The seedling epidermis arises by isolation of the outer layer during embryogenesis. The aerial epidermis and the root epidermis originate later, in the shoot apical meristem and in the root apical meristem, respectively.

Stomatal guard cells allow gas exchange, and their patterning is controlled by cell‐lineage‐based developmental mechanisms.

Trichomes protect the plant from herbivores, and their patterning is controlled by cell–cell interactions.

Root hairs increase surface area for water and nutrient uptake, and are patterned according to positional signals.

The cuticle overlying the epidermis can contribute to epidermal cell shape and function.

There is interplay between the regulation of epidermal cell shape and the regulation of cuticle production.
Hybrid Incompatibility inDrosophila: An Updated Genetic and Evolutionary Analysis
Authors: Fontdevila Antonio 
Published: February 2016

AbstractNegative interactions between independently evolved genes in two species are responsible of incompatibility of their hybrid, manifested by sterility and inviability. The heterogametic sex (XY males inDrosophila) is the most affected and the X chromosome has the largest effect on hybrid incompatibility (HI). These rules of speciation depend on the genetic architecture of HI. Albeit some speciation genes have a major effect, this architecture shows a complex polygenic structure of multiple interactions. HI genes are frequently associated to genetic factors that evolved selfishly by favouring their preferential transmission. Genetic analyses show signatures of positive selection in speciation genes that may favour the role of adaptive evolution. Whether these signatures are compatible with evolution of selfish factors – an idea that is gaining support – still remains a contentious issue. Finally, there is also a current upsurge of evidences in favour of the importance of genetic regulation in the evolution of hybrid incompatibilities.Key ConceptsSpecies must maintain their identity by isolation mechanisms that prevent gene flow among them.In sexual species, hybrid incompatibility, evidenced by sterility and/or inviability, is an isolation mechanism of great importance.The negative interaction in the hybrid between at least two genes that each evolved independently in two species (the BDM model) has been proved by multiple studies.Several genes of major effect (speciation genes) are highly implicated, albeit interacting with other genetic factors, in hybrid incompatibilities.A complex architecture of many genes with multiple interactions among them underlies the hybrid incompatibility.The heterogametic sex is generally more affected by the hybrid incompatibility through interactions between X‐linked recessive genes and partially dominant autosomal genes (the dominant theory).When substituted in a foreign genome, the X chromosome has a larger effect than any autosomal substitution, due to the greater density of speciation genes in the X chromosome.Many speciation genes show signatures of positive selection in their DNA, which suggests, but not always, adaptive evolution.Some speciation genes are associated to genetic factors evolved by genetic conflict, for example, meiotic drive, suggesting that a kind of evolutionary arms race between drivers and suppressors underlies the evolution of hybrid incompatibility.Recently, regulatory divergence rather than divergence in coding sequences is gaining support as a main actor in hybrid incompatibilities.
Regeneration of Organs and Appendages in Zebrafish: A Window into Underlying Control Mechanisms
Authors: Antos Christopher L , Knopf Franziska , Brand Michael 
Published: February 2016

AbstractThe ability to regenerate organs and appendages is not universal among animals. Humans have a rather limited capacity to regenerate after an injury, while other vertebrates such as the zebrafish are capable of regenerating many anatomical structures. It is unknown why different vertebrates have such differences in regenerative capacity, so studying animal models that do regenerate will allow us to know what is needed to regenerate. Zebrafish research is not only able to tell us what mechanisms are involved in regeneration, but it also shows us that there are different regeneration strategies: some use stem cells while other create progenitors from differentiated tissue cells. This article details how zebrafish uses and regulates either differentiated tissue cells or stem cells to regenerate. We focus on four structures – fin appendage, brain, spinal cord and heart – and describe how current cell and molecular discoveries from these regenerating fish structures contribute to our understanding of general principles of regenerative biology.Key ConceptsThe zebrafish is a remarkablein vivomodel to understand the stem/progenitor cell biology and molecular mechanisms involved in appendage and organ regeneration.Studying how the zebrafish regenerates its fins, its nervous system and its heart will provide information on how endogenous cell populations (whether fully differentiated or stem cells) are activated and concertedly controlled to regenerate compound structures.Different zebrafish tissues use different strategies to regenerate: some convert differentiated tissue cells to progenitor cells while other draw from stem cell pools.Zebrafish appendages and hearts regenerate primarily from the residual differentiated tissues.Zebrafish nervous tissue regenerates from resident stem cell populations.
Translational Readthrough of Premature Termination Codons in a Therapeutic Context
Authors: Bidou Laure , Sandra Blanchet , Olivier Namy 
Published: February 2016

Abstract

Coding sequences are defined between a start and a stop codon. The appearance of a nonsense mutation in a coding sequence creates a premature termination codon (PTC), preventing the correct production of the corresponding protein by interrupting translation and inducing the degradation of the transcript via the nonsense‐mediated mRNA decay (NMD) pathway. Over the past 10 years, there has been considerable interest in the possibility of suppressing in‐frame PTCs for therapeutic purposes. Indeed, some drugs have been shown to promote PTC readthrough by binding to mammalian ribosomes, thereby partially restoring the synthesis of a full‐length protein in cultured mammalian cells and animal models. This translational suppression strategy represents a promising therapeutic approach for genetic diseases and cancers due to a PTC.

Key Concepts

The stop codons in humans are UAA, UAG and UGA, and they are recognised by release factors.

Near‐cognate tRNA‐binding codons display base pairing for only two of the three bases of the codon.

Stop codon readthrough is the process by which the ribosome incorporates a near‐cognate tRNA at the stop codon.
Monogenic Autoinflammatory Diseases
Authors: Verbsky James , Gallagher Joel 
Published: February 2016

Abstract

Defects in the immune system that result in spontaneous inflammation are termed autoinflammatory disorders. In contrast to autoimmune diseases, they are not mediated by autoantibodies or autoreactive lymphocytes. Prominent features include fevers and rash, although other symptoms are observed. Flares are typically episodic and vary in severity, but do not worsen over time as in autoimmune disorders. Recent improvements in genetic technologies have led to the characterisation of multiple autoinflammatory syndromes. Prior to understanding the underlying mechanisms, these were treated with systemic anti‐inflammatory medications such as NSAIDs or glucocorticoids, which have adverse side effects. Advances in understanding the underlying etiologies have led to the discovery of novel options for targeted treatments.

Key Concepts

Autoinflammatory syndromes are characterised by fevers, rash, arthritis, myalgias and various other symptoms, although each syndrome may not present with all of these.

Autoinflammatory syndromes are related to the innate arm rather than the adaptive arm of the immune system.

The autoinflammatory syndromes typically first present in childhood.

The inflammasome and interleukin 1 (IL‐1) are key mediators in many autoinflammatory syndromes.

Genetic testing provides a definitive diagnosis of the underlying etiology of autoinflammatory syndromes.

Understanding the various pathways of autoinflammatory syndromes provides multiple targets of novel treatment modalities.
Local Adaptation in Plants
Authors: Lascoux Martin , Glémin Sylvain , Savolainen Outi 
Published: February 2016

AbstractLocal adaptation reflects the fact that local populations tend to have a higher mean fitness in their native environment than in other environments and in other populations introduced in their home site. Starting in the 1920s a large number of reciprocal transplant and common garden experiments, as well as studies of populations along environmental clines, have demonstrated that local adaptation is widespread in plants. One remaining challenge is to understand how populations become locally adapted and to characterise the genes involved in this process. Theoretically, local selection at single loci will promote local adaptation and gene flow will decrease it. For quantitative traits, the situation is more complex, and strong local adaptation can even be established and maintained in the presence of higher gene flow. The genetic basis of local adaptation will evolve through time, and eventually trade‐offs between alleles at a locus may occur in the different environments (antagonistic pleiotropy).Key ConceptsLocal adaptation is widespread in plants but its genetic basis is still poorly known.Local adaptation is the property of a group of populations in a given set of environments.Local adaptation depends primarily on the balance between selection and migration.The genetic architecture of local adaptation, in particular the presence of trade‐offs, is likely to be variable among species as it will depend, among other things, on the time since the populations diverged or the amount of gene flow between them.