bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction of maximum tsunami run-up due to the interaction with beachfront development – application of single sinusoidal waves
Authors: Goseberg N.
Published: April 2013

Abstract. Experiments are presented that focus on the interaction of single sinusoidal long waves with beachfront development on the shore. A pump-driven methodology is applied to generate the tested waves in the wave flume. The approaching waves firstly propagate over a horizontal bottom, then climbing up a 1 in 40 beach slope. The experiments reported here are confined to the surf similarity parameter of the waves ranging from ξ = 7.69 − 10.49. The maximum run-up of the tested waves under undisturbed conditions agrees well with analytical results of Madsen and Schäffer (2010). Beachfront development is modelled with cubic concrete blocks (macro-roughness (MR) elements). The obstruction ratio, the number of element rows parallel to the shoreline as well as the way of arranging the MR elements influences the overall reduction of maximum run-up compared to the undisturbed run-up conditions. Staggered and aligned as well as rotated and non-rotated arrangements are tested. As a result, nomograms are finally compiled to depict the maximum run-up reduction over the surf similarity parameter.
La promoción y protección de los derechos humanos: organizaciones y mecanismos internacionales: El sistema centroamericano de protección de los derechos humanos
Authors: Guerrero Mayorga Orlando
Published: April 2013

DOI: http://dx.doi.org/10.5377/derecho.v0i8.982 Revista de Derecho No.8 2004 pp.89-100
La fragilidad de los derechos
Authors: Calvo González José Calvo González
Published: April 2013

DOI: http://dx.doi.org/10.5377/derecho.v0i8.987 Revista de Derecho No.8 2004 pp.201-218
Las alteraciones o perturbaciones psíquicas como causas de imputabilidad: especial problemática de la psicopatía
Authors: Vega Gutiérrez Zamyr
Published: April 2013

DOI: http://dx.doi.org/10.5377/derecho.v0i9.992 Revista de Derecho No.9 2004 pp.39-55
El comercio electrónico: antecedentes, definiciones y sujetos
Authors: Robleto Arana Christian Alberto
Published: April 2013

DOI: http://dx.doi.org/10.5377/derecho.v0i9.993 Revista de Derecho No.9 2004 pp.57-74
Trends in asset structure of California hospitals during financial crisis
Authors: Lee Jinhyung
Published: April 2013

The recent financial crises affected US economy as well as healthcare industry. However, how this financial crisis affected the asset investment trend in the hospitals has not paid attention. Thus, this study describes and analyzes the asset investment structure across hospital ownership and size before and after financial crises using California hospitals data from 2005 to 2010. This paper finds that hospitals’ asset structure is significantly different based on ownership and size. Not-for-profit hospitals experience significant drop in financial asset during financial crisis and large not-for-profit hospitals also showed significant changes in fixed and financial assets.
¿Por qué las mujeres en España se jubilan más tarde que los hombres?
Authors: Radl Jonas
Published: April 2013

La relación entre género y jubilación en España es paradójica. La tasade empleo femenino entre los 55 y 64 años es apenas más de la mitadque la de los varones, mientras que la edad media de jubilación esmucho más alta entre las mujeres. Este estudio usa el análisis de lahistoria de acontecimientos para determinar si esa sorprendentediferencia de género se debe a efectos composicionales o de selección.Los datos proceden de un módulo especial de la Encuesta de laPoblación Activa (EPA) de 2006. Un innovador marco metodológicocontrasta los resultados de un modelo de supervivencia «naïf» con losde otro de tipo «duración-selección». Los resultados sugieren que lasmujeres se jubilan más tarde que los hombres sobre todo porqueeconómicamente no se pueden permitir retirarse antes.
El turismo residencial internacional en el nordeste de Brasil: un análisis de partes interesadas Antonio Aledo Tur, Tristan Loloum, Guadalupe Ortiz Noguera, Hugo García Andreu
Authors: Aledo Tur Antonio , Loloum Tristan , Ortiz Noguera Guadalaupe , García Andreu Hugo
Published: April 2013

El presente artículo analiza el sistema de actores implicados en eldesarrollo turístico-residencial en el destino turístico de Pipa, en lacosta del nordeste brasileño. El estudio contempla los efectos sociopolíticosdel boom inmobiliario (2001-2008) orientado a la promoción deurbanizaciones cerradas de segunda residencia. Se utiliza el método deAnálisis de Partes Interesadas (API) para identifi car las distintasfunciones y posiciones de los actores en un socioespacio turísticoexpuesto a intereses inmobiliarios y transnacionales. El métodoempleado revela una confi guración social desigual y confl ictiva. Losresultados muestran que el turismo residencial internacional modela laconfi guración sociopolítica local, fortaleciendo a unos actores(constructoras, inmobiliarias) y colocando a otros en situación dedependencia (poblaciones locales, municipios).
La salida del desempleo de extranjeros y españoles. Efectos del contexto económico
Authors: Muñoz Comet Jacobo
Published: April 2013

En este artículo se estudian las transiciones hacia el empleo de laspersonas que se encuentran desocupadas y que han trabajadoanteriormente. Para ello se utilizan los fi cheros de fl ujos de la Encuestade Población Activa. Los análisis se han realizado para dos periodoseconómicos diferentes: de expansión (2005-2007) y de recesión(2008-2010). Los resultados muestran que durante los años de bonanzalos extranjeros procedentes de Latinoamérica y de Europa del Estetenían una probabilidad mayor de abandonar el desempleo. Esto es asíuna vez controladas variables socio-demográfi cas y relacionadas con elúltimo puesto de trabajo. Esta ventaja, sin embargo, desaparecedurante la época recesiva. Asimismo, el efecto de algunos factores queinfl uyen en la probabilidad de recuperar el empleo, como el capitalhumano, cambia dependiendo de la fase del ciclo económico.
El problema de la libertad en Norbert Elias en diálogo con las neurociencias
Authors: Romero Moñivas Jesús
Published: April 2013

Este artículo se centra en la teoría sociología de la libertad propuestapor Norbert Elias, frente a las clásicas concepciones fi losófi cas. Enprimer lugar, se analizan los rasgos básicos que el sociólogo alemánrechaza de las teorías metafísicas de la libertad. A continuación, sedesarrollan los pilares básicos sobre los que se asienta la teoría socialde la libertad de Norbert Elias. Finalmente, se desarrollan brevementedos ejemplos empíricos clásicos: los casos de Luis XIV y Mozart. Contodo ello se pretende mostrar que la concepción de Elias puede ser unainterlocutora válida en el actual debate científi co sobre la libertad,especialmente en las neurociencias.
Reexaminando la migración a partir del Informe sobre Desarrollo Humano 2009
Authors: Lacomba Vázquez Joan , Benlloch Domènech Cristina
Published: April 2013

Desde los años setenta el vínculo entre migración y desarrollo ha venidoapareciendo como un importante tema de debate político y científi co.Como muestra de un renovado interés, en el año 2009 el Programa deNaciones Unidas para el Desarrollo publicó el Informe sobre DesarrolloHumano titulado «Superando barreras: movilidad y desarrollohumanos». En este artículo, revisamos algunos de sus datos con el fi nde cuestionar ciertos lugares comunes en torno a la relación entre fl ujosmigratorios internacionales y procesos de desarrollo. Nuestra principalconclusión es que el vínculo entre ambos no se produce en un únicosentido, ni obedece a patrones generalizables, más allá de laconstatación de que son los países con un desarrollo humano mediolos más afectados por la migración, pero también los más benefi ciadospor ésta.
Treating the Mother, Protecting the Unborn: The Motherisk Approach
Authors: Koren Gideon
Published: April 2013

Pregnant women and their unborn babies are excluded from most pharmaceutical research. We have to convince regulatory agencies worldwide that, by not demanding research of drug safety and effectiveness in pregnancy from pharmaceutical agencies, we are orphaning pregnant women from progress in therapeutics and causing both themselves and their unborn babies tremendous unacceptable risks.
Cerebellar Plasticity
Authors: Ito Masao
Published: April 2013

The remarkable recuperative capability of the cerebellum to compensate for lesion‐induced functional deficits has long been known. A well‐studied example is the vestibular compensation that follows unilateral labyrinthectomy, involving the cerebellar flocculus. More recently, however, the implications of cerebellar plasticity have expanded to include changes induced experience‐dependently. Various forms of motor adaptation and motor learning in physiological ranges are included in this term. For example, the vestibuloocular reflex exhibits a marked cerebellum‐mediated adaptability to a change imposed on the visual–vestibular relationship. Many other reflexes and voluntary movements exhibit similar plasticity via respective areas of the cerebellum. Moreover, certain morphological changes have been noted to occur under behavioural and social impositions as evidence of a role of cerebellar plasticity at such a high level of control. These various forms of cerebellar plasticity appear to be triggered by performance errors, which provoke synaptic plasticity in neuronal circuits of the cerebellum.

Key Concepts:

In general terms, plasticity implies the capability of the nervous system to change its structure and function to adapt to new bodily and environmental conditions.

The history of research on the cerebellum contains rich cases of compensatory recovery that occurred after lesioning the cerebellum or other tissues of the brain and body, which represent cerebellar plasticity in the original sense.

The notion of cerebellar plasticity has now been expanded to include physiological changes occurring in cerebellar neurons under certain functional and environmental impositions, broadly embracing various forms of motor adaptation and motor learning.

The various forms of cerebellar plasticity appear to be commonly underlain by unique error‐learning mechanisms of cerebellar neuronal circuits based on plasticity at individual synapses (synaptic plasticity).
Circadian Rhythms
Authors: Lear Bridget C , Allada Ravi
Published: April 2013

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

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

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

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

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

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

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

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

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

Gram‐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

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

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

Hyphae 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.
Yeast Artificial Chromosomes
Authors: Arnak Remigiusz , Bruschi Carlo V , Tosato Valentina
Published: April 2013

Yeast artificial chromosomes (YACs) are shuttle‐vectors that can be amplified in bacteria and employed for the cloning and manipulation of largedeoxyribonucleic acid (DNA)inserts (up to 3 Mb pairs) in the yeastSaccharomyces cerevisiae. Artificial chromosomes can be conveniently built and modified in yeast cells usingin vivohomologous recombination, a novel process known as ‘recombineering’. The capacity of YACs to accommodate large DNA fragments is exploited to clone clusters of genes surrounded by their native DNA context, where regulatory elements are located. This is important for biotechnology, when YACs are used for engineering genetic determinants of new biochemical pathways for production of secondary metabolites and for heterologous protein expression. YACs can be retrofitted with the appropriate selectable markers and transmitted to cells of different organisms allowing the generation of transgenic animals. Finally, YACs are largely employed in the production of full‐scale genomic libraries, for mapping and functional analysis purposes.

Key Concepts:

Yeast artificial chromosomes (YACs) represent the top instruments for the study of eukaryotic genomes and for mobilisation of large genetic elements among bacteria and eukaryotes.

YACs behave like naturally existing chromosomes, provided that they are of the proper size, showing comparable stability.

YACs can be manipulated directly by classical genetic engineering as well as by modern recombineering technology.

Properly retrofitted, YACs can be used in many different organisms, for cloning or genome analysis.

Chromosomal translocation can be studied using disposable YACs that do not harbour genetic information essential for cell function.
Archaeal Membrane Lipids and Applications
Authors: Sprott G Dennis
Published: April 2013

Membrane lipids ofArchaeaare unique and distinct from those found inEukaryaandBacteria. The polar lipids consist of isoprenoid chains, 20–40 carbons in length and usually saturated, which are attachedviastable ether bonds to the glycerol carbons at thesn‐2,3 positions. Polar head groups differ at the genus level of diversity and consist of mixtures of glyco groups (mainly disaccharides), and/or phospho groups primarily phosphoglycerol, phosphoserine, phosphoethanolamine or phosphoinositol. Phosphocholine headgroups are rarely found. Extremely halophilic archaea are characterised by headgroups consisting of phosphoglycerolphosphate‐O‐methyl, and sulfated‐sugars. Some of these archaea synthesise cardiolipin analogues. The inherent stability and unique features of archaeal lipids makes them a useful biomarker for Archaea within environmental samples, including ocean sediments. The polar lipids ofArchaeacan be used to make liposomes (closed vesicles referred to as archaeosomes) with characteristics that are useful for applications in biotechnology. Archaeal‐like polar lipids are being synthesised to optimise the properties of archaeosomes to serve as next‐generation adjuvants and drug delivery systems.

Key Concepts:

Archaeol (2,3‐diphytanyl‐sn‐glycerol), and variations thereof, define the polar lipids of the domain of life,Archaea.

The structures of polar lipids biosynthesised provide a useful taxonomic feature to assign an isolate to the Genus level of classification.

New polar lipid structures are being reported as the field expands to encompass novel isolates.

These unique polar and neutral isoprenyl lipids can be used as biomarkers of archaea in environmental samples.

Archaeal lipids can serve as a rich source for novel molecules not commonly found in nature, such as β‐l‐gulose.

Archaeal polar lipid mixtures hydrate to form lipid membrane vesicles (archaeosomes) with bilayer, unilayer or a combination of uni and bilayer structure.

Archaeosomes are generally nonfusogenicin vitro, but fusion can be dramatic for certain compositions by exposure to the combination of acidic pH, calcium and glycosidase.

Archaeosomes function as safe vaccine adjuvants in mammals imparting long‐lasting CD8+T‐cell immunity and antibody responses.

Isoprenoid lipids that retain the key archaeal‐lipid features are being synthesised to optimise their properties as vaccine adjuvants and delivery systems.
Magnetotaxis in Prokaryotes
Authors: Lefèvre Christopher T , Frankel Richard B , Bazylinski Dennis A
Published: April 2013

Magnetotaxis refers to the behaviour of some motile, aquatic, bacteria that orient and swim along magnetic field lines. These microorganisms, called magnetotactic bacteria (MTB), contain intracellular structures known as magnetosomes, which are nano‐sized, magnetic, iron‐mineral crystals, each enveloped by a biological (phospholipid bilayer) membrane. Magnetosomes are usually arranged in chains within the cell, providing it with a permanent magnetic dipole moment that facilitates location and retention in the cell's preferred habitat at or below the oxic–anoxic interface in the water column or sediment. Although all MTB are motile by means of flagella and have a cell wall structure characteristic of Gram‐negative bacteria, their diversity is reflected by the large number of different morphotypes found in environmental samples of water or sediment, and by phylogenetic analysis of both cultured and uncultured organisms.

Key Concepts:

Prokaryotes (bacteria), like eukaryotes, internally compartmentalise and contain organelles.

The prokaryotic flagellum rotates clockwise and counter clockwise thereby propelling the cell during swimming.

Magnetotaxis is bacterial motility directed by a magnetic field.

Magnetotactic bacteria contain intracellular, nano‐scale, membrane‐enveloped, magnetic iron‐mineral crystals called magnetosomes.

Magnetosomes impart a permanent magnetic dipole moment to cells of magnetotactic bacteria causing them to behave as miniature, motile, compass needles.

Magnetotaxis works in conjunction with aerotaxis to increase energy transduction in magnetotactic bacteria.

Genes for magnetosome formation are clustered in a region of the genomes of magnetotactic bacteria known as a magnetosome gene or genomic island.

Magnetotactic bacteria are important in the cycling of a number of important elements including carbon, iron, nitrogen and sulfur.
Phototaxis: Microbial
Authors: Allan Claire Y , Fisher Paul R
Published: April 2013

Phototaxis in its broadest sense is light‐regulated movement of motile organisms (microorganisms in the case of microbial phototaxis), usually resulting in their attraction to (positive phototaxis) or avoidance of (negative phototaxis) illuminated regions. Prokaryotes often use a time‐biased random walk strategy under which they choose directions randomly, but move for longer time periods in the chosen direction when that direction happens to be correct. They use type I sensory rhodopsin photoreceptors and two‐component histidine kinase‐mediated phosphotransfer systems to regulate flagellar movement. Eukaryotic microbes by contrast can sense and respond to the direction of light by regulating the direction of movement. Phototransduction pathways in eukaryotic microbes appear to involve protein phosphorylation/dephosphorylation at serine or threonine residues, and the responsible kinases and phosphatases are regulated by second messengers. This review focuses on select representative organisms from each of the three taxonomic domains whose photosensory signal transduction pathways have been studied. Although many components of the signal transduction pathways controlling phototaxis have been identified, there is still much to be elucidated.

Key Concepts:

Phototaxis enables microorganisms to position themselves in an environment that is optimal for survival.

Organisms from all three taxonomic domains display phototaxis with differing photosensory signal transduction pathways.

Photosensory signal transduction pathways in eubacteria and archaea involve the coupling of signals from photoreceptors to the same signalling pathways as are used by these organisms for chemotaxis.

Phototransduction pathways in eukaryotic microbes appear to involve protein phosphorylation/dephosphorylation at serine or threonine residues, and the responsible kinases and phosphatases are regulated by second messengers.
Rhizosphere
Authors: Lynch James M , de Leij Frans
Published: April 2013

The rhizosphere is that part of the soil ecosystem where plant roots, soil and the soil biota interact with each other. These interactions are often of benefit to plants, improve soil fertility and enhance the degradation of toxic chemicals. Rhizodeposition from plants is the key energy supply for the rhizosphere biota. Mineral nutrients are supplied by the soil matrix, organic residues and biological nitrogen fixation. The interactive biotic community includes microorganisms, protozoa and soil fauna. Some organisms are beneficial whereas others are harmful. Some deleterious organisms can be suppressed in a variety of biological control strategies. The key physical factors governing rhizosphere activity are temperature, water availability, oxygen, pH and soil structure. The rhizosphere has strong influences on agriculture, and the bioremediation of contaminated and degraded land.

Key Concepts:

Rhizodeposition from roots generates the energy substrates for rhizosphere organisms.

Mineral nutrients are provided by the soil matrix, organic residues and biological nitrogen fixation.

Microorganisms interact with protozoa and soil fauna in the rhizosphere.

Deleterious organisms can be suppressed by beneficial organisms in biological control.

Temperature, water availability, oxygen, pH and soil structure govern biotic activity.

The rhizosphere activity can optimise crop production and remediate contaminated and degraded land.
Herpesviruses (Human)
Authors: Whitley Richard J
Published: April 2013

Human herpesviruses are a family of eight
deoxyribonucleic acid
(DNA) viruses. There are three subfamilies, reflecting size and sites of latency. The alphaherpesviruses consist of
Herpes simplex virus type 1
(HSV‐1),
Herpes simplex virus type 2
(HSV‐2) and
Varicella‐zoster virus
(VZV), all of which have a predisposition to infect neuronal tissues and establish latency in sensory ganglia. The betaherpesviruses are
Cytomegalovirus
(CMV),
Human herpesvirus 6
(HHV‐6) and
Human herpesvirus 7
(HHV‐7) which infect endothelial cells and secretory glands. Finally, the gamma herpesviruses are
Epstein
–
Barr virus
(EBV) and
Kaposi sarcoma‐associated herpesvirus
(KSHV or HHV‐8). These viruses commonly infect humans but generally cause only trivial disease. However, in high‐risk patient populations (e.g. the newborn or immunocompromised host) disease can be associated with significant morbidity and mortality. Therapy exists for many but not all of the resultant diseases.

Key Concepts:

Human herpesviruses are a family of eight
deoxyribonucleic acid
(DNA) viruses:
Herpes simplex virus type 1
(HSV‐1),
Herpes simplex virus type 2
(HSV‐2),
Varicella‐zoster virus
(VZV),
Cytomegalovirus
(CMV),
Epstein‐Barr virus
(EBV),
Human herpesvirus 6
(HHV‐6),
Human herpesvirus 7
(HHV‐7) and
Kaposi sarcoma‐associated herpesvirus
(KSHV or HHV‐8).

Membership in the
Herpesviridae
family is based on the structure of the virion, and herpesvirus is categorised into three subfamilies and six groups (classified A–F) based on genomic sequence arrangement.

Replication of herpesviruses occurs in a multistep process, though this process is considered inefficient, with a high ratio of noninfectious to infectious viral particles.

Latency is established in specific host cells, and the latent viral genome may be either extrachromosomal or integrated into host cell DNA.

Reactivation of latent virus can be triggered by such stimuli as stress, menstruation and exposure to ultraviolet light, though reactivation in not clearly understood from a biochemical of genetic standpoint.

The definitive diagnosis of a herpesvirus infection usually requires either isolation of virus or the amplification of viral DNA by molecular techniques, namely polymerase chain reaction (PCR).

A critical factor for the transmission of HSV‐1 and HSV‐2 is the requirement for intimate contact between a person who is shedding virus and a susceptible host.

Varicella‐zoster virus
is one of the most common encountered by humans, and is generally transmitted via airborne routes. Varicella (chicken pox) is the manifestation of primary infection, and Herpes zoster (shingles) is the recurrent form, resulting from latent virus. Vaccines are available for the prevention of both these types of infection.

Infections due to HSV, VZV and CMV are the most amenable to therapy with antiviral drugs.