bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian Rhythms
Authors: Lear Bridget C , Allada Ravi 
Published: April 2013

Abstract

Daily (circadian) rhythms of behaviour and physiology are prevalent in organisms ranging from cyanobacteria to humans. These rhythms are not simply responses to environmental cues, but are driven by endogenous cellular clocks. Circadian clocks are synchronised to daily environmental cycles to produce 24 h molecular oscillations, which in turn drive rhythmic outputs. The mechanisms that produce circadian rhythms have been elucidated in a number of species, and several features of this system are common to most or all rhythmic organisms. Among animals, the molecular components that make up the circadian clock system are highly conserved, and mutations in human clock genes are associated with specific sleep disorders. Circadian rhythms defects in humans are also associated with other serious conditions such as mental health conditions and metabolic disorders.

Key Concepts:

Circadian rhythms are found in a wide range of organisms.

Circadian clocks utilise transcriptional feedback loops and post‐translational modifications.

Circadian clocks are located in most or all tissues in humans.

Circadian clocks control cell function and physiology through rhythmic gene expression.
Neural Information Processing
Authors: Gabbiani Fabrizio , Midtgaard Jens 
Published: April 2013

Abstract

The central nervous system (CNS) is specialised in processing information originating from a variety of internal and external sources. Its basic information processing units are nerve cells, or neurons. Within the CNS, these elementary building blocks are densely interconnected in hierarchical and parallel pathways. Information originating from sensory neurons in contact with the body periphery is gradually transformed along these pathways to generate specific actions through signals relayed by motor neurons to peripheral organs. The information processing capabilities of animal brains are quite distinct from those of existing man‐made machines, being characterised by their resilience to noise, their capacity to learn and generalise, as well as their ability to participate in complex social behaviours.

Key Concepts:

Understanding neural information processing will require a detailed characterisation of how nerve cells code for sensory stimuli and motor commands, often referred to as the Neural Code.

Neural codes are predominantly based on spikes, which are discrete events in time and space allowing nerve cells to communicate with one another.

Neural codes most likely include spike rate codes and relative spike timing codes.

In many brain areas spikes are sparse across nerve cells and time.

The organisation of such neural codes is only loosely constrained in time and highly flexible.
Hallucinogenic Drugs
Authors: Bonson Katherine R 
Published: April 2013

Abstract

Hallucinogens constitute one of the oldest classes of drugs used by humanity, often in the context of spiritual practices. Classic hallucinogens such as lysergic acid diethylamide (LSD), psilocybin,
N,N
‐dimethyltryptamine (DMT), mescaline and 2,5‐dimethoxy‐4‐methylamphetamine (DOM) produce complex psychological and physical effects, including perceptual changes, cognitive shifts in reality and emotional alterations. These drugs primarily act on serotonin systems through 5‐hydroxytryptamine 2A (5HT
2A
) receptors, with additional activity through dopamine and glutamate systems. Investigation of the neurochemical and behavioural effects of this class of drugs has provided important insights into pharmacology and psychiatric conditions. Given their popularity as recreational drugs, investigation of their actions and effects continues to be an important endeavour. After a long hiatus, clinical studies in humans have resumed with these drugs in laboratories around the world.

Key Concepts:

Hallucinogens have been used for thousands of years by various societies, often in conjunction with spiritual practices.

In present day, hallucinogens remain highly popular as recreational drugs.

The chemical structure of hallucinogens consists of tryptamines (LSD and psilocybin) and phenethylamines (mescaline and DOM).

The potency of hallucinogens is directly correlated to their ability to act as agonists at the serotonin receptor subtype, 5‐HT
2A
.

Drugs that act at sites other than 5‐HT
2A
receptors can also produce hallucinogen‐like effects (e.g. ketamine, MDMA, salvinorin A, nitrous oxide, GHB).

The signature effects of hallucinogens include perceptual changes, alterations in affect and shifts in cognitive ability.

Negative responses associated with hallucinogens include ‘bad trips’ (severe anxiety and a disconnection with reality) as well as rare instances of ‘flashbacks’ and psychotic breaks.

Human research with hallucinogens has recently been revitalised, augmenting the scientific advances made previously with animal studies.
Learning and Memory
Authors: Reilly Melissa A , Kim Jeansok J 
Published: April 2013

Abstract

An organism's chances for survival are greatly impacted by its ability to learn from previous experience and form memories to modify future behaviour. The search for the
engram
, the physical trace of a memory in the brain, has resulted in a wealth of data beginning to uncover how memories are stored at the molecular‐cellular level. Despite terminology that suggests a unitary nature, modern definitions of memory support the idea of multiple memory systems, unique in both structure and function. Experiments utilising a multitude of techniques support a structural distinction between different types of memory in humans and animals. The method of memory formation appears to be conserved across memory systems, each following a pattern of encoding, storage and retrieval. Though individual memory capabilities do vary slightly across the population, extreme cases have been observed in either direction, such as hyperthymesia (superior autobiographical memory) and amnesia associated with neurological damage (e.g. Alzheimer's disease).

Key Concepts:

Modern neuroscience accepts multiple brain–memory systems.

Memory can be defined in terms of temporal longevity, quality of information, or brain circuits required in its formation and storage.

The medial temporal lobe is a critical system in the formation and storage of declarative memories about facts and events.

Amnesiacs with bilaterally damaged medial temporal lobe system have intact procedural memories.

Understanding the mechanisms of learning and memory is vital to developing treatments for cognitive declines that occur with aging and neurological diseases such as Alzheimer's dementia.
Magnocellular Neurons
Authors: Lemos José R 
Published: April 2013

Abstract

Magnocellular neurons (MCN) are neuroendocrine cells located in the hypothalamus; they are among the largest cells in the brain, and synthesise the hormones
arginine vasopressin (AVP)
and
oxytocin (OT)
. These neuropeptides are secreted from MCN terminals in the neurohypophysis (NH). It is this hypothalamic‐neurohypophysial system (HNS) which allowed the original formulation of the calcium hypothesis for stimulus–secretion coupling.
Vasopressin
is a vasoconstrictor and an antidiuretic and, thus, is involved in fluid homoeostasis.
OT
has recognised functions in parturition and lactation, and has an emerging role as a natriuretic agent. Both hormones may also be central neurotransmitters and have been implicated in stress, social behaviours, learning and memory processes, as well as the development and maintenance of tolerance to ethanol and other drugs of abuse. Furthermore,
OT
has possible therapeutic applications for social disorders.

Key Concepts:

MCNs in the hypothalamus synthesise the peptide hormones, vasopressin and oxytocin.

These neuropeptides are secreted from MCN nerve terminals in the NH.

It is this HNS system which allowed the original formulation of the calcium hypothesis for stimulus–secretion coupling.

AVP is a vasoconstrictor and an antidiuretic and, thus, is involved in fluid homoeostasis.

Oxytocin has recognised functions in parturition and lactation, and has an emerging role as a natriuretic agent.

Both hormones may also be central neurotransmitters and have been implicated in stress, learning and memory processes, social behaviours, as well as the development and maintenance of tolerance to ethanol and other drugs of abuse.

Oxytocin has possible therapeutic applications for social disorders.
Glutamatergic Synapses: Molecular Organisation
Authors: Siddoway Benjamin , Hou Hailong , Xia Houhui 
Published: April 2013

Abstract

One of the best understood and highly organised synapses is excitatory glutamatergic synapses. These synapses consist of post‐synaptic ionotropic glutamate receptors and pre‐synaptic glutamate localised inside pre‐synaptic vesicles. Glutamate binds to α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid subtype glutamate receptors, giving rise to synaptic transmission. However,
N
‐methyl‐
d
‐aspartate subtype glutamate receptors function to induce the change in synaptic transmission, also known as the synaptic plasticity that underlies learning and memory. The subtypes and subunits of glutamate receptors exhibit distinct biophysical properties and play distinct physiological roles critical for synaptic function. The molecular organisation of the synapse includes intracellular scaffolding proteins, intercellular cell adhesion molecules to anchor synaptic architecture and a variety of signalling proteins (kinases, phosphatases, etc.). They function to support and/or mediate the cellular processes critical for synaptic transmission and plasticity, whereas their malfunction leads to diseases where synaptic plasticity is lost, such as Alzheimer disease and mental retardation.

Key Concepts:

Glutamatergic synapses are critical for our brain function.

Synaptic plasticity is critical for proper neuronal circuit formation.

Synaptic plasticity is the cellular model for learning, memory and other experience‐dependent brain functions.

History of neuronal activity plays a significant role in synaptic protein composition, which in turn governs synapse‐to‐nucleus signalling.

Scaffolding proteins, in addition to signalling proteins and receptors, are critical for synaptic plasticity.

Extrasynaptic NMDA receptor signalling plays distinct roles from synaptic NMDA receptor signalling.
Action Potentials: Generation and Propagation
Authors: Egri Csilla , Ruben Peter C 
Published: April 2013

Abstract

All cells maintain a voltage across their plasma membranes. Only excitable cells, however, can generate action potentials, the rapid, transient changes in membrane potential that spread along the surface of these unique cells. Action potential generation and propagation occurs through, and is regulated by, the function of voltage‐gated ion channels – proteins with ion‐selective pores that span the cell membrane. Ion channels undergo changes in their structural conformation in response to changes in the electrical field across the membrane. These structural changes cause the opening of pores – channels – through which ions can flow down their electrochemical gradient. The charge carried by ions creates an electrical current and rapidly alters the membrane potential with time‐ and voltage‐dependent properties. This rapid, transient membrane potential change is called the action potential. Action potentials transmit information within neurons, trigger contractions within muscle cells, and lead to exocytosis in secretory cells.

Key Concepts:

All cells maintain a voltage difference across their plasma membranes.

Action potentials are all‐or‐nothing, transient changes in membrane potentials of electrically excitable cells that carry important cellular information.

Influx of sodium ions through voltage‐gated sodium channels is responsible for the upstroke of the action potential, whereas efflux of potassium ions through voltage‐gated potassium channels is responsible for the falling phase.

Propagation of action potentials depends on gating kinetics of ion channels and intracellular and membrane resistances.
Dopamine
Authors: Bannon Michael J , Bannon Erin E , Bannon Kellen T 
Published: April 2013

Abstract

Dopamine is a neurotransmitter (or chemical messenger) found in diverse organisms ranging from simple invertebrates to humans. It is also a required intermediate in the formation of the neurotransmitters noradrenaline and adrenaline. Although found in a number of vertebrate tissues, dopamine's most important effects are due to robust expression in a relatively small number of central nervous system neurones that have widespread projections. Dopamine signalling affects a correspondingly wide variety of physiological functions, from gastrointestinal motility and pituitary hormone release, to voluntary movements, motivation and reward, and higher cognitive processes. Although dopamine neurotransmission is normally a highly regulated process, drugs have been developed to modify its signalling. Some commonly used drugs affect dopamine neurotransmission indirectly (by changing its synthesis, release, reuptake or inactivation), whereas other drugs more directly mimic or block the actions of dopamine at its biological targets (i.e. multiple cell surface dopamine‐responsive receptors). An astonishingly broad range of central nervous system disorders (including Parkinson disease, schizophrenia, attention deficit hyperactivity disorder, and sleep disorders), and other medical conditions (such as nausea, excessive pituitary hormones, gastrointestinal disorders, and cardiovascular shock) are currently treated using such drugs.

Key Concepts:

Dopamine is a neurotransmitter in the brain and elsewhere, as well as an intermediate in the biosynthesis of the neurotransmitters noradrenaline and adrenaline.

Dopamine synthesis is regulated by a rate‐limiting enzyme, and its extracellular concentrations controlled by an active recapture mechanism and several metabolic enzymes.

The effects of dopamine are mediated by a family of G protein coupled receptors linked to distinct intracellular signalling pathways.

Though relatively few in number, dopamine‐containing neurons originating in the mammalian midbrain send branching fibres that innervate widespread areas of the forebrain.

Brain dopamine influences learning and execution of voluntary movements, motivation, reward, attention and working memory.

Disturbances in dopamine neurotransmission have been implicated in a number of CNS disorders, but shown most conclusively in Parkinson disease and drug abuse.

Drugs that modify CNS dopamine neurotransmission are used to treat a variety of disorders including Parkinson disease, schizophrenia, attention deficit hyperactivity disorder, sleep disorders, and nausea.

Dopamine receptors outside of the CNS are targets in the medical treatment of excessive pituitary hormone release, certain gastrointestinal disorders, and cardiovascular shock.

The extensive study of this simple neurotransmitter system has led to fundamental discoveries regarding cellular and molecular mechanisms contributing to normal brain function and human disease.
Bacterial Flagella
Authors: Hughes Kelly T , Erhardt Marc 
Published: April 2013

Abstract

Bacteria propel themselves through liquid or over semisolid media using rotation of a propeller‐like organelle, the flagellum. Flagellar rotation is energised by the membrane ion gradient and flagella enable bacteria to swim towards nutrients and away from harmful substances. The flagellum is a sophisticated, molecular nanomachine. To build a flagellum, more than two dozen proteins need to assemble in an ordered process. The accurate size and subunit composition of each substructure of this nanomachine is achieved by coupling gene expression to the assembly state. Major components of the flagellum assemble outside the cytoplasmic membrane. A specialised protein export system, termed ‘type‐III secretion’ transports flagellar substrates across the inner membrane. A flexible coupling structure, the hook, connects the membrane‐embedded basal body to the rigid, extracellular filament. The length of this flexible joint is tightly controlled in

Salmonella enterica

and hook length is determined by intermittent secretion of a molecular ruler.

Key Concepts:

Bacteria swim through their environment by rotating an extracellular appendage, the flagellum.

Rotation of the flagellum is energised by influx of protons through stator proteins that are attached to the cell body.

The bacterial flagellum consists of three major parts: (1) the basal body as the engine, (2) a flexible joint structure that connects the engine to (3) the long external filament.

Assembly of the flagellum involves dozens of proteins and the coordination of gene expression to the assembly state of the flagellum.

A specialised protein export system, a type‐III secretion apparatus, is responsible for the export of flagellar secretion substrates, for example, most external parts of the flagellum.

Protein export

via

the type‐III secretion system is dependent on the proton‐motive force.

The length of the flexible joint structure that connects the filament to the basal body is highly regulated to a final length of 55 nm in
Salmonella
. A molecular ruler determines the final length and catalyses a switch in secretion specificity from early to late‐substrate secretion mode.
Streptomycete Spores
Authors: Elliot Marie A , Flärdh Klas 
Published: April 2013

AbstractGram‐positive bacteria of the genusStreptomycesare major inhabitants of soil and grow as branching hyphae, strikingly like the filamentous fungi. Whereas their mycelium is multicellular, dispersal and long‐term survival are achieved by unicellular spores. Spore formation is part of a complex developmental cycle involving dedicated reproductive aerial hyphae. The long apical cells of the aerial hyphae are divided into chains of tens of prespore compartments, which in turn mature into thick‐walled spores with condensed nucleoids and low metabolic activity, primed for dispersal and survival. Aerial hyphae and spore surfaces are coated with a proteinaceous fibrous sheath. This highly hydrophobic sheath is required for aerial hyphal emergence, and may aid spore dispersal and interaction with various interfaces. When exposed to appropriate environmental conditions, spores rehydrate and swell. Cell polarisation is required for the emergence of a germ tube, which develops into a mycelium by apical growth and side‐branch formation.Key Concepts:Streptomycesspores are distinctly different from bacterial endospores.Spores develop from dedicated reproductive structures called aerial hyphae.Streptomycesspores are formed by division of long, multigenomic hyphal cells into unigenomic compartments.A thick spore wall is assembled from within the maturing spore and contributes to quiescence and resilience.Spores are dehydrated, accumulate trehalose and have condensed nucleoids.An outer fibrous sheath confers surface hydrophobicity to aerial hyphae and spores.Germination involves rehydration, symmetrical swelling and establishment of polar growth leading to germ tube emergence.
Algal Metabolism
Authors: Beardall John , Raven John A 
Published: April 2013

Abstract

Algal metabolism concerns the biochemical and transport processes by which algae take up nutrients and convert them into the materials needed for growth, reproduction and defence of the organisms. Many of the metabolic processes that occur in algae are common to those found in other living organisms. This commonality is described, but emphasis is given to those major metabolic processes in algae that are unique to, or differ in detail from, those of other organisms. This includes mechanisms of light harvesting, carbon acquisition and aspects of nitrogen (N) and sulfur (S) assimilation as well as formation of unique secondary metabolites. In addition the consequences of growth in extreme environments, such as nutrient limitation and exposure to extremes of visible and UV light, for algal metabolism are considered. The exploitation of algal metabolism and its products in biotechnology is also briefly described.

Key Concepts:

Algal metabolism shares many features in common with that of other living organisms but also differs in unique respects.

Algal metabolism gives rise to a range of unique compounds, including secondary metabolites, some of which have toxicity to other organisms.

Algal metabolism is modulated to a large extent by environmental factors such as nutrient availability and extremes of temperature and light.

Algal metabolism can be exploited to produce compounds of biotechnological importance. These include pigments, nutraceuticals and oils for biodiesel.
Phycology
Authors: Borowitzka Michael A 
Published: April 2013

Abstract

Phycology is the study of algae. However, just what algae are is difficult to define, because they belong to many different and unrelated taxonomic groups and include both prokaryotic and eukaryotic representatives. Broadly speaking, the algae comprise all, mainly aquatic, plants and plant‐like chlorophyll
a
‐containing organisms that can use light energy to fix carbon from atmospheric carbon dioxide (CO
2
) and evolve oxygen, but which are not specialised land plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose. Besides being a principal source of oxygen, algae are important primary producers in many, mainly aquatic, habitats and are the source of a number of important commercial products and molecules.

Key Concepts:

The algae are a very diverse group of plants and plant‐like organisms but which are not specialised land plants like mosses, ferns, coniferous trees and flowering plants.

The algae include both prokaryotic and eukaryotic organisms.

Algae are key providers of oxygen on earth and are the basis of aquatic food webs.

Algae have a wide range of commercial applications.

Endosymbiosis has played an important part in the evolution of the algae.
Hyphal Growth
Authors: Harris Steven D 
Published: April 2013

AbstractHyphae are tubular structures that constitute the basic unit of a fungal mycelium. It is the efficient growth of hyphae that plays a crucial role in fungal colonisation of a substrate. Hyphal growth is driven by localised cell surface expansion and cell wall deposition at the hyphal tip. Spatial and temporal regulatory mechanisms enforce this growth pattern by controlling the recruitment of the morphogenetic machinery, which consists of the cytoskeletal and vesicle trafficking elements that mobilise the precursors needed for growth. In addition to the establishment and maintenance of hyphal polarity, the ability to regulate the termination of polarised growth is likely to be important because it facilitates transitions from hyphal growth to development or pathogenesis. Hyphal growth presumably evolved as an adaptation that enabled filamentous fungi to efficiently colonise terrestrial habitats.Key Concepts:Hyphal growth is the defining feature of filamentous fungi.The morphogenetic machinery consists of those elements of the cytoskeleton and vesicle trafficking components that are needed to drive extension of the hyphal tip.The Spitzenkörper is a vesicle supply and transit centre located at the hyphal tip that is required for optimal rates of tip extension.The spatial separation of exocytosis and endocytosis within the hyphal tip complex enables rapid tip extension.The direction of hyphal extension is regulated by a microtubule‐based marking system that conveys positional information to the morphogenetic machinery.Reactive oxygen species and calcium appear to serve as signals that regulate tip growth and the emergence of branches.Duplication cycle describes the events that encompass the doubling of cell mass and nuclear numbers during hyphal growth.The termination of polarised hyphal growth is often a key prerequisite for development and pathogenesis.The hyphal mode of growth appears to have independently evolved on multiple occasions during evolution.