bluuebunny/crossref_metadata_2025 huggingface dataset:
Tsunami hazard assessment in the southern Colombian Pacific Basin and a proposal to regenerate a previous barrier island as protection
Authors: Otero L. J. , Restrepo J. C. , Gonzalez M.
Published: April 2013

Abstract. In this study, the tsunami hazard posed to 120 000 inhabitants of Tumaco (Colombia) is assessed, and an evaluation and analysis of regenerating the previous El Guano Island for tsunami protection is conducted. El Guano Island was a sandy barrier island in front of the city of Tumaco until its disappearance during the tsunami of 1979; the island is believed to have played a protective role, substantially reducing the scale of the disaster. The analysis is conducted by identifying seismotectonic parameters and focal mechanisms of tsunami generation in the area, determining seven potential generation sources, applying a numerical model for tsunami generation and propagation, and evaluating the effect of tsunamis on Tumaco. The results show that in the current situation, this area is vulnerable to impact and flooding by tsunamis originating nearby. El Guano Island was found to markedly reduce flood levels and the energy flux of tsunami waves in Tumaco during the 1979 tsunami. To reduce the risk of flooding due to tsunamis, the regeneration and morphological modification of El Guano Island would help to protect Tumaco.
Advanced interpretation of land subsidence by validating multi-interferometric SAR data: the case study of the Anthemountas basin (northern Greece)
Authors: Raspini F. , Loupasakis C. , Rozos D. , Moretti S.
Published: April 2013

Abstract. The potential of repeat-pass space borne SAR (Synthetic Aperture Radar) interferometry has been exploited to investigate spatial patterns of land subsidence in the Anthemountas basin, in the northern part of Greece. The PSI (Persistent Scatterer Interferometry) approach, based on the processing of long series of SAR acquisitions, has been applied to forty-two images acquired in 1995–2001 by ERS1/2 satellites. Interferometric results have been analyzed at a basin scale as support for land motion mapping and at local scale for the characterization of ground motion events affecting the village of Perea in the Thermaikos municipality and the "Macedonia" international airport. PSI results revealed a moderate subsidence phenomenon along the wider coastal zone of Anthemountas basin corresponding to intense groundwater extraction. Highest values, exceeding 20 mm yr−1, were measured in the airport area where the thickest sequence of compressible Quaternary sediments occurs. Intense subsidence has been detected also in the Perea village (maximum deformation up to 10–15 mm yr−1), where a series of fractures, causing damages to both buildings and infrastructure, occurred in 2005–2006. Furthermore, a linear pattern of deformation, elongated parallel to the major normal Thermi fault, has been observed, indicating movements with a probable tectonic component.
A glacial systems model configured for large ensemble analysis of Antarctic deglaciation
Authors: Briggs R. , Pollard D. , Tarasov L.
Published: April 2013

Abstract. This article describes the Memorial University of Newfoundland/Penn State University (MUN/PSU) glacial systems model (GSM) that has been developed specifically for large-ensemble data-constrained analysis of past Antarctic Ice Sheet evolution. Our approach emphasizes the introduction of a large set of model parameters to explicitly account for the uncertainties inherent in the modelling of such a complex system. At the core of the GSM is a 3-D thermo-mechanically coupled ice sheet model that solves both the shallow ice and shallow shelf approximations. This enables the different stress regimes of ice sheet, ice shelves, and ice streams to be represented. The grounding line is modelled through an analytical sub-grid flux parametrization. To this dynamical core the following have been added: a heavily parametrized basal drag component; a visco-elastic isostatic adjustment solver; a diverse set of climate forcings (to remove any reliance on any single method); tidewater and ice shelf calving functionality; and a new physically-motivated empirically-derived sub-shelf melt (SSM) component. To assess the accuracy of the latter, we compare predicted SSM values against a compilation of published observations. Within parametric and observational uncertainties, computed SSM for the present day ice sheet is in accord with observations for all but the Filchner ice shelf. The GSM has 31 ensemble parameters that are varied to account (in part) for the uncertainty in the ice-physics, the climate forcing, and the ice-ocean interaction. We document the parameters and parametric sensitivity of the model to motivate the choice of ensemble parameters in a quest to approximately bound reality (within the limits of 31 parameters).
Catheter-induced Brachial Artery Dissection during Transradial Angioplasty
Authors: Ruzsa Zoltán , Molnár Levente , Szabó György , Merkely Béla
Published: April 2013

The transradial approach is becoming a very popular technique in coronary and peripheral interventions because of its low vascular complication rate and improved patient comfort. Reported complications during the transradial approach are radial artery spasm, perforation, occlusion and formation of pseudoaneurysms. The kinking of the diagnostic catheter during catheter manipulation in a severely tortuous subclavian artery can occur very easily, and catheter movements at this point can cause barchial and subclavian artery dissection. We report a case of brachial and subclavian artery dissection during transradial diagnostic angiography, treated by angioplasty and stenting.
Evolution, ovulation and cancer
Authors: VijayRaghavan K , Rath Satyajit
Published: April 2013

Secretions by epithelial cells of the fallopian tube regulate ovulation through conserved pathways, which means that experiments on flies might provide insights into the human reproductive system and, possibly, ovarian cancer.
Cocaine and Amphetamines
Authors: Rebec George V
Published: April 2013

As stimulants, cocaine and amphetamines activate both the sympathetic and central nervous systems to heighten arousal, increase behavioural activation, and, when delivered rapidly to the brain, create the so‐called flash or rush followed by a long‐lasting state of euphoria. Cocaine, derived from coca leaves, and amphetamines, a group of synthetic compounds whose molecular structure resembles adrenalin, increase the level of norepinephrine (noradrenalin) and dopamine in the synapse. As part of the brain's reward circuit, dopamine neurons play a critical role in drug craving. The stimulant properties of cocaine and amphetamines have been known for centuries, but illicit manufacturing techniques now produce versions of these drugs that can be smoked or injected to enhance their pleasurable effects. Repeated drug use changes the way that neurons in the reward circuit process information. The end result is a fundamental change in brain circuitry that increases the likelihood of addiction.

Key Concepts:

Cocaine occurs naturally in coca leaves, which have been chewed for centuries to increase feelings of energy.

The amphetamines were modelled after ephedrine, a plant‐derived alkaloid that improves breathing and has stimulating effects on behaviour.

Cocaine and amphetamines activate the sympathetic nervous system by increasing the synaptic level of norepinephrine.

The rewarding or pleasurable effects of these drugs involve an increase in dopamine, a transmitter released in key areas of the forebrain.

Cocaine increases synaptic norepinephrine and dopamine by blocking the transporter proteins that removes these catecholamine transmitters from the synapse.

The amphetamines increase synaptic norepinephrine and dopamine by forcing the transporters to operate in reverse.

A direct increase in dopamine transmission in the nucleus accumbens, a part of the limbic forebrain, is common to many drugs of abuse and appears to be a key mechanism leading to addiction.

With repeated use of these drugs, long‐lasting changes occur in the accumbens and other key forebrain nuclei to promote drug craving and relapse.

Medically, cocaine is used as a local anaesthetic, whereas some amphetamines are used as treatment for narcolepsy and attention‐deficit‐hyperactivity disorder.

Caffeine and other xanthines are not as powerful in stimulating behaviour and act by blocking receptors for adenosine, a purine nucleotide.
Peptide Neurotransmitters and Hormones
Authors: Li Ka Wan
Published: April 2013

Neuropeptides are structurally diverse class of chemical messengers that play important roles in the coordination of many physiological and behavioural events. Neuropeptides are derived from the cleavage of the larger precursor proteins at the dibasic amino acid sites by prohormone convertases. They are synthesised in the cell body, packaged in the large dense core vesicles and released in a neuronal activity‐dependent manner. The neuropeptides may function as blood‐borne hormones, or as mediators/transmitters affecting neuronal activity in the nervous system. In the target cells, neuropeptides activate the complementary G protein‐coupled receptors and elicit responses that are specific to these cells. The released peptide is subsequently inactivated by the actions of several nonspecific extracellular peptidases.

Key Concepts:

Neuropeptides are structurally diverse class of chemical messengers produced by nerve cells to coordinate many physiological and behavioural processes.

The major neuroendocrine centre in the brain is the pituitary gland.

Neuropeptides are derived from the cleavage of the larger precursor proteins by specific endoproteases that are co‐packaged in the dense core secretory granules.

Receptors for neuropeptides belong mainly to the family of G protein‐coupled receptor.
Autonomic Nervous System
Authors: Gabella Giorgio
Published: April 2013

The autonomic nervous system (ANS) is a set of nerves and nerve cells that provide the innervation of blood vessels and the airways, heart, intestines and urogenital organs. These nerves regulate and coordinate bodily functions based on secretory activity of glands, on contraction and relaxation of smooth muscle and cardiac muscle, and on sensations arising from deep viscera.

Motor activity is a crucial function in hollow organs: muscle contraction propels fluids or solid bodies into tubes and ducts. Autonomic nerves control the motility of viscera, but there is also myogenic activity, generated spontaneously by the muscle itself. Myogenic and neurogenic controls are well balanced in the heart; myogenic control predominates in the muscles of intestine or uterus; neurogenic control predominates in the urinary bladder or the ductus deferens.

The sensory nerves provide ill‐localized but deep sensation about the state of the body, and can convey the sensation of pain (visceral pain).

Key Concepts:

A large array of nerves reaches the viscera and the vessels of the body from the central nervous system, and signals pass continuously in both directions.

Autonomic nerves control the motility (contraction, dilatation, tension) of cardiac muscle and of smooth muscle, both in viscera (visceral smooth muscle) and in blood vessels (vascular smooth muscle).

The musculature of viscera is under control of autonomic nerves, but, in some organs, it can also contract myogenically, that is, independently of external influences.

Autonomic pathways are chains of neurons and nerves linking brainstem and spinal cord to the peripheral organs.

Autonomic pathways contain nerve ganglia where nerve fibres synapse onto ganglion neurons and new nerve fibres are issues and travel peripherally.

Nerve fibres of the autonomic nerves are thin and often without a myelin sheath, and their conduction velocity is slower than in somatic nerves.

The autonomic nervous system (ANS) comprises sensory fibres, emerging from ganglion neurons in the dorsal root ganglia, which provide deep sensation about the state of the viscera and can convey the sensation of pain.

A special set of nerves forms the enteric nervous system, self‐contained and independent from other nerves.

In many parts of the ANS, at the surface of ganglion neurons, nerve endings and muscle cells there are receptors that are sensitive to neurotransmitters, to other neurochemicals, to hormones, to signalling molecules and to exogenously administered substances (pharmacological agents or drugs).
Dendrites
Authors: Ross William N , Larkum Matthew
Published: April 2013

Dendrites are highly branched neuronal structures that form the main synaptic target of other nerve cells. They are studded with small spines that are the contact points for excitatory inputs. Dendrites integrate these excitatory inputs, along with inhibitory inputs, in the form of brief depolarising or hyperpolarizing synaptic potentials, and generate the output of the neuron. This signal is usually in the form of an action potential initiated near the soma. Although early models assumed that the dendrites were passive, we now know that they have many voltage dependent conductances distributed heterogeneously over the surface of the arbours. These conductances lead to various forms of signal modulation and localised regenerative activity that greatly expand the computational complexity of CNS neurons.

Key Concepts:

Dendrites comprise approximately 95% of the neuronal surface and are the main place where synaptic contacts are made.

Dendritic architecture is stereotypical for different neurons types and probably relates to the integrative function of these cells.

Synaptic potentials originate in the dendrites and propagate decrementally to the axon hillock where the output sodium spike is usually generated.

Dendrites contain voltage‐dependent channels distributed in ways characteristic to each cell type, which modulate the propagation of synaptic potentials.

These voltage‐dependent channels can also support regenerative action potentials, which either back‐propagate over the dendrites from the somatic region, or are initiated locally in the dendrites.

These dendritic action potentials are complex. They are primarily sodium dependent, calcium dependent, or, in some cases, involve the ligand‐gated NMDA receptor.

The function of these dendritic action potentials is not always clear. One possibility is to control the calcium concentration in different parts of the cell, which can then regulate synaptic plasticity or other signalling mechanisms. Another possibility is to influence the integration of synaptic potentials and ultimately determine the output of the neuron.
Glutamate as a Neurotransmitter
Authors: Mennerick Steven , Zorumski Charles F
Published: April 2013

Glutamate is a major excitatory neurotransmitter in the vertebrate central nervous system (CNS). Glutamate is released from vesicles that reside at axon terminals of neurons that use this amino acid as a neurotransmitter. Vesicular release is triggered by the arrival of a brief electrical signal (the action potential) at the presynaptic terminal. Most neurons in the vertebrate CNS, even if they themselves do not use glutamate as a neurotransmitter, are contacted by glutamate presynaptic terminals. Glutamate receptors mediate signalling initiated by glutamate release and are involved in plastic changes in the nervous system. These receptors fall into two classes: G protein coupled (metabotropic) and ligand‐gated ion channels (ionotropic). Ionotropic glutamate receptor activation on the target cell initiates a brief electrical depolarisation, which if large enough, causes an action potential in the target cell, and the cycle of signalling begins again. Excessive activation of glutamate receptors can cause neurotoxicity.

Key Concepts:

Glutamate is used as a neurotransmitter at the majority of synapses in the vertebrate CNS.

Glutamate generally has an excitatory action on target neurons, increasing the probability of action potential firing in the target.

Glutamate acts through G protein coupled receptors and through ligand‐gated ion channels.

Glutamate synapses exhibit remarkable plasticity (malleability) that may play an important role in memory formation.

In excess glutamate can be neurotoxic, acting through the same glutamate receptors that mediate normal signalling.
Motor Output from the Brain and Spinal Cord
Authors: Berkowitz Ari
Published: April 2013

All skeletal muscles are controlled by activation and inhibition of motor neurons in the spinal cord and brainstem. Motor neurons integrate information from a wide variety of sources in the brain and spinal cord. Simple limb reflexes and basic patterns of limb movements, including locomotion, are coordinated by spinal cord interneurons and sensory neurons. Descending inputs from the reticular formation, the vestibular nuclei and the superior colliculus in the brainstem are important in the control of automatic, axial, postural and locomotor movements. Descending inputs from several areas of the cerebral cortex and from the red nucleus are important in the control of voluntary, distal limb and fine movements. The basal ganglia in the basal forebrain and the cerebellum in the hindbrain are involved in the modification and learning of movements. These structures act indirectly on motor output, via outputs through the thalamus to widespread areas of the cerebral cortex.

Key Concepts:

All voluntary movement involves motor neurons in the spinal cord and brainstem that cause contraction of skeletal muscles.

Neurons in many areas of the brain and spinal cord are active at overlapping times to control voluntary movements.

The spinal cord can produce coordinated movements of the limbs, such as locomotion, as well as simple reflexes.

The superior colliculus can trigger orienting movements, especially of the eyes and head.

Voluntary limb movements involve neurons in several parts of the cerebral cortex, including especially the frontal lobe, which project axons to the spinal cord.

Cortical movement control signals are modified by loops to and from the basal ganglia and the cerebellum, going through the thalamus.

The basal ganglia modify the speed and amplitude of movements and contribute to learning new movement sequences.

The cerebellum adapts movements to altered sensory feedback and may also contribute to a wide variety of other functions, including memory, language and emotion.

Patients with movement disorders may in the future be able to control a limb or prosthetic device with ‘their thoughts’, via a brain–machine interface that monitors the activity of some of their cortical neurons.
Opiates and Opioids
Authors: Dickenson Tony
Published: April 2013

Morphine and the opiates, drugs found in the opium poppy or their chemical derivatives, are some of the most valuable drugs in medicine due to their ability to suppress pain. They act on systems in the brain, spinal cord and body that are more weakly regulated by endogenous opioids, natural transmitters. The effects of opioids can now be explained in terms of their acting as agonists at one of the four opiate receptors found in the brain, spinal cord and peripheral nervous system. All four receptors are inhibitory but the major one is the μ‐opioid receptor which mediates the wanted (analgesia and relief of anxiety) and unwanted effects of opioids (respiratory depression, nausea, constipation and the potential for dependence). These receptor events underlie the medical and nonmedical use of opioid drugs.

Key Concepts:

Opiates and opioids refer to drugs that are based on the structure or actions of morphine and codeine found naturally in the opium poppy.

These exogenous agents modulate the function of the central nervous system and body systems through activation of inhibitory opioid receptors, of which there are four.

The most important is the μ‐opioid receptor, named after morphine.

The receptors are not present just in case we wander into a poppy field but because there are endogenous opioid peptides that function as inhibitory neurotransmitters through activation of these receptors.

Opioids are valuable medical drugs – the analgesia and relief of anxiety are important effects but there are side‐effects that include respiratory depression, nausea, constipation, sedation and the potential for dependence.

Drugs such as heroin have dangers due to these side‐effects.
Bacterial and Archaeal Inclusions
Authors: Shively Jessup M , Cannon Gordon C , Heinhorst Sabine , Bryant Donald A , DasSarma Shiladitya , Bazylinski Dennis , Preiss Jack , Steinbüchel Alexander , Docampo Roberto , Dahl Christiane
Published: April 2013

Bacterial inclusions can be defined as discrete structures seen within the confines of prokaryotic cells, generally intracytoplasmic, but in some instances in the periplasmic region of the cell. Inclusions function as metabolic reserves, cell positioners, or as metabolic organelles. Some inclusions may contribute to more than one of these functions. Those that function as metabolic reserves are glycogen, polyhydroxyalkanoate, wax ester, triacylglycerol, cyanophycin, and polyphosphate granules, and sulfur globules. These reserves are commonly accumulated in response to a nutrient imbalance, for example, under conditions of excess carbon/energy. Magnetosomes and gas vesicles contribute to cell mobility thereby assisting the cells in attaining nutrient and/or redox needs. Carboxysomes, containing the enzyme ribulose bisphosphate carboxylase/oxygenase, and chlorosomes, sacs of self‐aggregated bacterriochlorophyll are carbon‐fixing and light‐harvesting organelles, respectively.

Key Concepts:

The cytoplasmic region of prokaryotic cells can be much more complex than originally thought.

In addition to flagella, many prokaryotes have developed mechanisms whereby they are capable of positioning/orienting themselves in an aqueous environment.

Although not as complex as the well‐known eukaryotic organelles, many prokaryotes possess simple organelles.

Many of the inclusions may have useful properties for applications in biotechnology
Ultramicrobacteria
Authors: Duda Vitaly I
Published: April 2013

Ultramicrobacteria (UMB) are species of the domain Bacteria, whose cells possess a volume of less than 0.1 μm
3
and a small size of genome (from 3.2 to 0.58 Mb). UMB feature a combination of such determining characters as ultrasmall size of proliferating cells and small size of genome. As a synonym for UMB, some authors use the term ‘nanobacteria’ (NB). Several dozens of UMB species have been isolated from various habitats, such as aquatic and soil environments, sediments, silts, Greenland ice, permafrost, human intestines and insects; and are cultured under laboratory conditions on various nutritive media. The term ‘nan(n)obacteria’ is also used to designate ultrasmall bacterium‐like particles occurring in rocks, sands, soils, in deep subsurface, meteorite and clinical samples. UMB include species of free‐living and parasitic bacteria. They are characterised by a great diversity of morphology, ultrastructural organisation, physiology, biochemistry and ecology. Unique processes UMB perform are dehalorespiration, epibiont obligate and facultative parasitism, synthesis of organic compounds in oceanic waters involving bacteriorhodopsin. UMB have been found among organisms of six large phylogenetic branches of prokaryotes, where their nearest relatives are organisms with larger, typical‐of‐bacteria, cells; this is indicative of the polyphyletic origin of the currently known UMB species by reductive evolution.

Key Concepts:

Formation of a minimal autoreplicating microbial cell is the prerogative of the prokaryotes.

Ultrasmall size of cells enables parasitism (predation) of UMB on ‘large‐cell’ species of prokaryotes.

UMB are important model objects for studies of genome evolution in prokaryotes.

UMB studies are of vital importance for solving issues of the origin and evolution of primeval living objects.

UMB research opens new vistas for biotechnology.

Use of UMB representatives, mycoplasms, played a crucial role in epochal works by J Craig Venter and collaborators for experimentally creating a new living being (cells with chemically synthesised genome) and a new bacterial species.

Description of new UMB cell structures expands the diversity pattern of the ultrastructural and molecular organisation of the prokaryotic cell.

Gram‐negative, Gram‐positive or archaeal type of cell organisation are not the prohibitive factors for UMB or UMA to form.
Algal Carbon Dioxide Concentrating Mechanisms
Authors: Mukherjee Bratati , Moroney James V
Published: April 2013

Photosynthetic microorganisms like cyanobacteria and many eukaryotic algae acclimate to a limited availability of carbon dioxide (CO
2
) in their environment by inducing a process called the carbon dioxide concentrating mechanism. This process uses an active inorganic carbon (C
i
; CO
2
and/or HCO
3
−
) uptake system that leads to the internal accumulation of C
i
to levels significantly higher than extracellular levels. Carbonic anhydrase activity converts much of the accumulated hydrogen carbonate to CO
2
, concentrating this substrate around Rubisco and thereby optimising photosynthetic efficiency even under low CO
2
conditions. The efficiency of the process is further improved by the sequestration of Rubisco into specialised structures like the cyanobacterial carboxysome or the pyrenoid in eukaryotic algae. The carbon dioxide concentrating mechanism enhances carbon dioxide fixation and growth in algae. With the increasing demands for sustainable energy sources, algae with efficient carbon dioxide concentrating mechanisms are attractive models for biotechnological and transgenic applications for biofuel and biomass production.

Key Concepts:

The carbon dioxide concentrating mechanism helps photosynthetic algae optimise photosynthesis under limiting CO
2
conditions.

Rubisco uses both carbon dioxide and oxygen as substrates.

Rubisco is localised in the carboxysome in cyanobacteria and the pyrenoid in the green alga,
Chlamydomonas reinhardtii.

The charged hydrogen carbonate needs transporters to enter the cell and cross organellar membranes.

Carbonic anhydrase is an efficient enzyme that carries out the reversible interconversion of carbon dioxide and hydrogen carbonate and this reaction proceeds at a much faster rate than the uncatalysed reaction.

At higher pH levels most of the inorganic carbon is in the form of hydrogen carbonate.

Most algae with carbon dioxide concentrating mechanisms can take up both carbon dioxide and hydrogen carbonate.

Carbon dioxide can diffuse out of the cell so algae trap carbon dioxide in the form of the charged hydrogen carbonate anion.

Algae are used for large‐scale biomass production and are currently being explored as sources of bio‐fuel.
Algal Cell Walls
Authors: Domozych David S
Published: April 2013

Algal cell walls are composed of a diverse array of fibrillar, matrix and crystalline polymers interacting with various ions and water. The diverse array of cell walls exhibited in the various algal groups is a manifestation of ancient evolutionary origins and ecological pressures of modern earth habitats. Cell walls often represent the dominant component of the extracellular matrix and represent the largest or a significant percentage of the photosynthetically fixed carbon of the algae. Walls are typically fibrous composites of microfibrillar polysaccharides embedded in matrix polysaccharides and proteoglycans. Scales and extracellular polymeric substances may also constitute the algal extracellular matrix. The production of the cell walls requires the highly coordinated interaction of several subcellular systems and is controlled by complex gene expression programmes. Modern technologies employed from immunology, molecular genetics, biochemistry and microscopy‐based imaging are transforming our understanding of the cell structure, functions and development.

Key Concepts:

Algae represent a diverse group of photosynthetic eukaryotes with a wide range of cell wall types.

New technologies derived from immunology, microscopy‐based imaging, molecular genetics and biochemistry are greatly enhancing our understanding of algal cell walls.

Primitive green algae of the Prasinophyceae produce layers of multishaped scales.

The Charophycean green algae produce cell walls containing polymers similar to land plants.

The red algae possess complex composite cell walls made of cellulose, xylan or mannan fibrils and extensive matrix polysaccharides including the economically important carrageenan and agar.

Diatoms produce highly sculpted frustules made of silica‐based composites and often produce extensive stalks and other extracellular polymeric substances.

Brown algae produce cell walls containing cellulose, matrix polysaccharides and in some cases, phenolics.
Algal Eyes
Authors: Hegemann Peter , Dieckmann Carol
Published: April 2013

‘Vision’ is defined in a very general sense as recognition of the ambient light pattern by a motile organism and its use for orientation in a local environment. The ‘eye’ is the organ or organelle in which the light absorption and transformation into a transient intracellular signal occurs. The pigmented eyespot is functioning as the optical system that operates in most motile green algae as an interference reflecting device (quarter wave stack). In Chlorophyceae the light sensors are light‐gated ion channels (Channelrhodopsin (ChR)), whereas in Euglenoida photo‐activated adenylyl cyclases (PAC) fulfil this function. ChR is located within the eyespot overlaying part of the plasma membrane whereas PAC is found as a paraflagellar swelling at the basis of the long flagalla.

Key Concepts:

Motile green algae are able to detect the light direction by means of a pigmented eye.

Algal eyes are designed for detection of defuse light.

Chlorophyceae use light‐gated ion channels (Channelrhodopsins) for fast depolarisation of the plasma membrane.

The depolarisation changes of the plasma membrane (PM) follow intensity changes recorded by the photoreceptor according to the orientation of the cells respective to the direction of the light source.

Depolarisation of the PM is continued to the flagellar membrane.

Flagallar membrane depolarisation causes activation of voltage gated Ca‐channel and influx of Ca2+.

Intraflagellar Ca2+changes modulate the flagellar beating pattern resulting in directional changes of the swimming.

As a sensor, Euglenoids use a photo‐activated adenylyl cyclases (PAC) that produces cAMP in the light.

Since the PAC is attached to the long flagella, the produced cAMP is immediately sensed by the cAMP‐regulated ion channels at the flagaller base.

The intraflagallar Ca2+changes alter the flagellar bending and the swimming direction accordingly.
Algal Flagella
Authors: Wirschell Maureen , Dutcher Susan K
Published: April 2013

Flagella are highly conserved organelles comprised of several hundred proteins that are assembled using the equally conserved mechanism called intraflagellar transport (IFT). The molecular motors dynein and kinesin drive IFT‐mediated flagellar assembly. In addition, flagellar movement is powered by the flagellar dynein motors. The outer and inner dynein arms function in generating flagellar beat frequency and flagellar waveform that are the two main features of flagellar bending. The biflagellate algae

Chlamydomonas reinhardtii

is a powerful model organism for the study of flagellar assembly and function. Recent advances have revealed that cilia and flagella play vital motile and sensory roles in the developing human embryo and in adult tissue function. Defects in assembly or function of mammalian cilia/flagella underlie an expanding set of human diseases and syndromes, collectively called ‘the ciliopathies’. Much of our current understanding of flagellar assembly, motility and the ciliopathies has come from studies in
Chlamydomonas
.

Key Concepts:

Cilia and flagella are highly conserved organelles.

Dynein motors drive flagellar movement.

Chlamydomonas reinhardtii
is a powerful model experimental system for studying flagella.

Defects in assembly or function of cilia/flagella result in multiple pathologies called ‘the ciliopathies’.
Green Algae
Authors: Lewis Louise A , Hall John D , Zechman Frederick W
Published: April 2013

The green algae are a large and diverse group of photosynthetic eukaryotes. They comprise many ancient and diverse lineages, including land plants. Through evolutionary time, green algae have formed a number of symbiotic associations with fungi and animals and their chloroplasts have been incorporated into other eukaryotic organisms through secondary endosymbioses. Green algae display many degrees of organismal complexity: from microscopic unicells to macroscopic, multicellular thalli more than a metre in length. They are critical components of almost all aquatic ecosystems and many terrestrial ecosystems as well. Green algae are commercially important as feed and as a source of many industrial and pharmaceutical chemicals. Available chloroplast, mitochondrial and nuclear genomic data have contributed greatly to our understanding of their biology and evolutionary history. Scientists are still discovering new species and lineages of green algae as well as novel biological and chemical characteristics.

Key Concepts:

Green algae are extraordinarily diverse morphologically and are separated taxonomically into two phyla, Chlorophyta and Charophyta.

Embryophyte land plants evolved from green algae in Charophyta.

Similar morphological forms of vegetative cells evolved in independent lineages of green algae.

As primary producers, green algae are important components of marine, freshwater and terrestrial ecosystems.

Green algae are important model organisms.

Green algae are important symbionts with fungi, bacteria, animals and plants.

Green algae are economically important as sources of industrial products, biofuels and food.

Most groups of green algae are poorly studied and many new species are being discovered.
Chytridiomycota
Authors: Longcore Joyce E , Simmons D Rabern
Published: April 2013

The Chytridiomycota is a phylum in the kingdom Fungi, whose members produce unwalled, asexual spores that swim by means of a single, posteriorly directed flagellum. Members are microscopic saprobes or parasites found in fresh and saline water and soils. The phylum contains two classes, the Monoblepharidomycetes with one order and the Chytridiomycetes with seven orders and several undescribed groups. Orders are based on molecular and ultrastructural characters. Many species of chytrids were described without these characters and need to be re‐examined to place them in the proper orders and genera. Chytrids are important as degraders of cellulose, keratin and chitin and also as algal pathogens, sometimes controlling algal blooms. A few are plant pathogens withSynchytrium endobioticumcausing black wart of potatoes. The rhizophydialean chytridBatrachochytrium dendrobatidisgrows in keratinised skin cells of amphibians and is pathogenic to many species, causing amphibian population declines on several continents and extirpation of some species.

Key Concepts:

Members of the Chytridiomycota are ubiquitous in aquatic and terrestrial habitats and can be found by microscopically examining baits placed with aquatic debris or with soil plus water.

Chytridiomycota reproduce primarily by zoospores, which are mitotically produced, contained by a membrane and motile via a posteriorly directed flagellum.

Because of convergent evolution of light microscopic characters, many genera described before the molecular era are polyphyletic and may not be placed in the correct order.

Systematics in the Chytridiomycota relies on transmission electron microscopic features of zoospores and on DNA sequence information.

Algal parasites are usually species specific and are capable of affecting population levels of planktonic algae.

Batrachochytrium dendrobatidisis a chytrid pathogen of amphibians responsible for some amphibian population declines on at least five continents.
Fungal Metabolites
Authors: Moss Maurice O
Published: April 2013

The fungi are a kingdom of organisms as complex and diverse as plants and animals with an estimated 1.5 million species, of which only about 10% have been named and described. The diversity of fungi is reflected in the diversity of fungal metabolites which are the products of secondary metabolism. The biosynthetic pathways are also diverse including polyketides, sesquiterpenes and diterpenes, diketopiperazines, cyclic peptides, β‐lactams and combinations of these pathways. Many of these compounds have biological activity which may be harmful, such as mycotoxins and phytotoxins, or beneficial such as antibiotics and other pharmaceuticals. The structure of many of these relatively low molecular weight compounds has often been a challenge to the natural products chemist but the continuing development of mass spectroscopy, nuclear magnetic resonance spectrometry with increasingly sophisticated methods of chromatography have led to the continuing discovery of novel fungal metabolites.

Key Concepts:

Fungal secondary metabolism is both diverse and distinct.

Secondary metabolism is linked to primary metabolism by a common pool of intermediates such as acetyl‐CoA, mevalonate and amino acids.

Penicillins, cephalosporins and griseofulvin are widely used antibiotics.

Mycotoxins such as aflatoxin, ochratoxin and patulin are controlled in human foodstuffs by legislation.

The majority of plants have endophytic fungi some of which produce useful metabolites.
Fungi: Ecological Importance and Impact on Humans
Authors: Kendrick Bryce
Published: April 2013

Fungi play vital roles in the biosphere. They are essential to the recycling of nutrients in all terrestrial habitats because they are the dominant decomposers of the complex components of plant debris, such as cellulose and lignin. As opportunistic heterotrophs, they have evolved hyphae to penetrate solid substrates, and spores for long‐range dispersal. They cause many diseases of plants and animals, but they also have established mutualistic symbioses with a wide range of organisms: cyanobacteria and green algae (in lichens), bryophytes, pteridophytes, gymnosperms and angiosperms (in mycorrhizae), and coleopteran, dipteran, homopteran, hymenopteran and isopteran insects. As parasites or pathogens they are well equipped to penetrate host organisms and to liberate spores that will effectively transmit them from one host to the next, and many species produce toxic compounds (mycotoxins). Some fungi affect human health in various ways.

Key concepts:

Many fungi are opportunistic heterotrophs, disposers of, or recyclers of, organic substrates, especially those of plant origin.

Parasitic fungi attack almost all known taxa of plants and animals.

Fungi have established mutualistic symbioses with cyanobacteria and chlorophycota (green algae) to form lichens.

Fungi often form symbiotic associations with the roots of plants (bryophytes, pteridophytes, gymnosperms and angiosperms) in mycorrhizae.

Some fungi live as symbionts with coleoptera, diptera, homoptera and hymenoptera.

Some fungi cause diseases (mycoses) in humans or excrete toxic compounds (mycotoxins).

Fungal spores can cause severe allergies in humans.
Mycotoxins
Authors: Ehrlich Kenneth C , Chang Perng‐Kuang , Bhatnagar Deepak
Published: April 2013

Mycotoxins are a class of natural fungal metabolites that are specifically toxic to mammals and are frequent contaminants of foods and feeds. In this article we describe mycotoxins from Ascomycota or sac fungi, the largest phylum of fungi, which includes penicillia, aspergilli, fusaria, alternaria, claviceps and other non‐Basidiomycota (‘higher fungi’ or mushroom‐producing) genera. We discuss the toxicity and biosynthesis of the most agriculturally important mycotoxins, namely, polyketide toxins (fumonisins, aflatoxins, ochratoxins, patulin and zearalenone), nonribosomal peptide toxins (ergot alkaloids and tremorgenic toxins) and trichothecenes produced via the terpene biosynthesis pathway. The Ascomycota produce mycotoxins in crops both before harvest and during storage. The genes required for biosynthesis are usually clustered. Transcriptional regulation of biosynthesis involves a pathway‐specific Cys6Zn2type protein as well as a secondary metabolite‐specific methyltransferase, LaeA. Both of these transcription factors are unique to fungi. Hypotheses about the evolution of mycotoxin biosynthesis in fungi are discussed.

Key Concepts:

Mycotoxins are produced by ascomycete (‘lower’) fungi in certain agriculturally important crops.

The most common mycotoxins exert a variety of generally nonlethal toxic effects in animals.

Biosynthesis of mycotoxins usually involves a co‐regulated, clustered set of genes on one chromosome.

Co‐regulation involves transcription factors of the Cys6Zn2type and a putative methyltransferase, LaeA.

Mycotoxins can be of several types: polyketides, nonribosomal peptides or terpene‐derived metabolites.

Mycotoxin biosynthesis has evolved in fungi in the absence of agriculture and is not strictly associated with fungal virulence in contaminated crops.
Fungal Xerophiles (Osmophiles)
Authors: Vinnere Pettersson Olga , Leong Su‐lin L
Published: April 2013

Xerophilic fungi are yeasts and moulds that are capable of growth at or below a water activity (
a
w
) of 0.85. These microorganisms have developed physiological mechanisms that enable their biochemical pathways to function in environments where little water is available. External conditions of low
a
w
are sensed by membrane osmosensors, and xerophiles then accumulate glycerol as a compatible solute to balance the internal and external osmotic pressure. They also modify their membranes to retain this glycerol within the cell. As a group, xerophiles are extremely important in the spoilage of many processed foods and stored commodities, and in indoor environments. Moderate xerophiles include species within
Aspergillus
,
Penicillium
and
Eurotium
. Extreme xerophiles compete poorly at high
a
w
, because they require decreased
a
w
for growth. Some xerophiles have a preference for salt or sugar substrates, whereas other species can be isolated from both jam and salterns. Xerophiles are widely spread on the fungal tree of life.

Key Concepts:

Xerophiles have requirement for reduced water activity; fungi are the most successful xerophilic organisms, and the most extreme xerophiles are found among fungi.

Compatible solutes are accumulated intracellularly to maintain the osmotic balance in response to decreased water availability.

Glycerol is the primary compatible solute among xerophilic fungi.

Membrane composition plays an important role in retaining glycerol within the cells of xerophiles.

Moderate xerophiles of the genera
Aspergillus
,
Eurotium
and
Penicillium
are economically important spoilage organisms.

Some xerophiles are isolated from both high‐salt and high‐sugar environments; others have a preference for either salt or sugar.

Xerophiles can cause spoilage of food and feed: stored commodities, sugary products and salted foods.

Xerophilic species are widely spread on the fungal tree of life.
Fungal Spores
Authors: Moore‐Landecker Elizabeth
Published: April 2013

Many heterotrophic eukaryotic organisms belong to the monophyletic kingdom Fungi. Because of their stationary life style, fungi reproduce by forming spores, cells that are specialised for dispersal to new locations by air, water or animals. Flagellated zoospores are produced by simple aquatic fungi. Most fungi are terrestrial, growing as hyphae and producing thick‐walled nonmotile spores. Asexual spores include sporangiospores and conidia, whereas sexual spores include zygospores, ascospores and basidiospores. Ascospores and basidiospores often are forcibly ejected into the air. Sporulation requires favourable nutritional and environmental conditions such as light and temperature, and involves cellular signalling and metabolic responses. As spores mature, their walls thicken, energy reserves such as lipid are acccumulated, and their metabolism decreases as they prepare for dormancy. Mature spores may undergo either exogenous or constitutive dormancy before germination. Upon germination, metabolic acitivity increases and a germ tube emerges from the spore.

Key Concepts:

Fungal spores have a unique role in fungal life cycles as they provide the genetic link between one generation and another.

Spores can be part of asexual or sexual reproductive cycles, and are sometimes borne by multicellular sporocarps.

Spores in part owe their success to their thick walls, reserve energy source, low metabolic rate and ability to withstand environmental stress that enables them to survive during dispersal.

Some fungi coevolved with insects, establishing mutualistic symbiotic relationships, and depend upon them for spore dispersal.

Sporulation occurs within a narrow range of special nutritional and environmental conditions, and involves signal transduction, gene activation and metabolic turnover.

Sporulation and spore germination of some fungi are coordinated with light and temperature changes marking day and night cycles, the seasons or with life cycles of their hosts.

Conditions required for germination reflect the particular biological adaptations and requirements of the fungus, and ensure that further somatic growth will be successful.

Scientists should understand spore biology so that they may better control animal, plant and human diseases; to better utilise fungi for industrial purposes, or to utilise them more effectively in the laboratory.
Yeasts
Authors: Lachance Marc‐André
Published: April 2013

Yeasts are a group of eukaryotic fungi with a well‐defined cell wall whose growth is either entirely unicellular or a combination of hyphal and unicellular reproduction. The approximately 1500 known yeast species belong to two distinct fungal phyla, the Ascomycota and the Basidiomycota. Within each these phyla, yeasts can be found in several subphyla or classes, reflecting the enormous diversity of their evolutionary origins and biochemical properties. In nature, yeasts are found mainly in association with plants or animals but are also present in soil and aquatic environments. Yeasts grow rapidly and have simple requirements, for which reason they have been used as model systems in biochemistry, genetics and molecular biology. They were the first microorganisms to be domesticated for the production of beer, bread or wine, and they continue to be used for the benefit of humanity in the production of recombinant proteins and other materials.

Key Concepts:

Yeasts share in common a primarily unicellular mode of reproduction.

Yeasts are phylogenetically diverse, being classified in several classes of two fungal phyla.

The concept of yeast is rooted in history and does not always follow logical biological lines.

Yeasts have a rigid cell wall primarily made up of β‐(1–3)‐glucan.

Sexual reproduction in yeasts involves the formation of internally formed ascospores or externally formed basidiospores.

Current yeast classification is based on phylogenetic relationships inferred by gene sequencing.

Yeasts grow in nature primarily in association with the plant–insect interface or with warm‐blooded animals, but also occur in soil and aquatic habitats.

Yeasts serve as important industrial model systems in research.

Yeasts are of great importance in biotechnology. The main products are alcohol, yeast biomass and recombinant proteins.

A few yeast species cause infections in humans and other animals, but most yeasts act in an opportunistic fashion, in individuals that are immunocompromised.