bluuebunny/crossref_metadata_2025_split huggingface dataset:
Actin and Actin Filaments
Authors: Tondeleir Davina , Vandekerckhove Joël , Ampe Christophe 
Published: April 2013

AbstractActin is an evolutionary conserved molecule that self assembles into long polymers. These filaments form the building block of the actin cytoskeleton. This system is one of the main engines enabling cell motility processes. In muscle cells stable actin filaments participate in contraction. In nonmuscle cells, however, the filaments are more dynamic and polymerisation of actin generates the force for the formation of cellular protrusions required for cell migration. Various actin‐binding proteins orchestrate this dynamic turnover of actin filaments and thereby contribute to the different migration modes possible for nonmuscle cells. Next to its role in the cytoplasm actin also resides in the nucleus where it may regulate transcription in multiple ways. Because of its complexity, impaired regulation of the actin cytoskeleton disturbs cell function and deregulations of the actin machinery are associated with an increasing number of diseases such as myopathies and cancer.Key Concepts:Actins are conserved proteins with important functions during development and in adult life.Actin self‐assembles into structurally and kinetically polarised filaments.Numerous actin‐binding proteins regulate (dis)assembly and organise filaments in higher order structures.Dynamic actin polymerisation drives multiple types of nonmuscle cell migration via formation of specific subcellular structures.Actin cytoskeletal diseases are caused by mutations in actins or via disturbed regulation of the cytoskeleton.In addition to its cytoplasmic function in cell motility processes, actin has a nuclear role in transcription.
Cell Junctions
Authors: Wegener Joachim 
Published: April 2013

Abstract

For any multicellular organism to function, it is a prerequisite that its individual cells interact with each other. These interactions are realised by cell‐to‐cell junctions that provide mechanical stability, information exchange or occlusion of extracellular diffusion pathways between neighbouring cells. The latter is an unconditional prerequisite for the formation of interfaces within the organism or between organism and environment. In order to provide these different physiological functions the corresponding cell junctions have their individual molecular architecture but share some common construction principles. For all of them transmembrane proteins are required that interact with corresponding structures on the surface of the opposing cell to form either mechanically stable interconnections, tight diffusion barriers, aqueous channels or well‐defined nanometre gaps for the fast diffusion of signal molecules. In most cases these transmembrane proteins interact with intracellular adapter proteins or the cytoskeleton, which is critical for their correct functionality.

Key Concepts:

More than 200 different cell types act together in the tissues and organs of the human body.

Cellular cooperation in multicellular organisms is based on various cellular interactions and cell junctions.

From a functional viewpoint cell junctions can be grouped into: (1) occluding junctions, (2) mechanical junctions and (3) communicating junctions.

Barrier‐forming epithelial and endothelial cells, which build up interfacial tissues between two fluid compartments, express tight junctions that occlude the diffusion pathway between adjacent cells.

Tight junctions are mainly composed of different transmembrane proteins (
occludin
, members of the claudin family, etc.) that use their extracellular domains to interact with the corresponding protein domains on the adjacent cell surface to block the intercellular cleft.

Mechanical stability of epithelial cell layers is based on adherens junctions and desmosomes that both provide a stable mechanical linkage between the intracellular cytoskeletons of adjacent cells.

Exchange of signalling molecules or metabolites smaller than 1000 g mol
−1
is provided by gap junctions (electrical synapses) who form aqueous channels between neighbouring cells.

Plant cells show a special kind of communicating junctions, the plasmodesmata.

Electrical communication between two neurons or a neuron and muscle cells is provided by chemical synapses, which relay electrochemical signals by a pulse of neurotransmitters.
Immunology: Comparative Immunology of Mammals
Authors: Ellis Shirley A 
Published: April 2013

AbstractThe mammalian immune system comprises a complex, coordinated and finely controlled series of interactions involving cells and molecules which has evolved to protect the host against disease. Mammals consist of a highly diverse group of animals in which the immune system has been subjected to a variety of selective pressures. This is reflected in differences in the organisation and function of their immune systems, and is seen especially in those gene families characterised by complexity and polymorphism, such as those encoding immunoglobulins (Ig), T‐cell receptors (TCR), major histocompatibility complex (MHC) molecules and natural killer (NK) cell receptors. The evolution of these components in a range of mammalian groups and species will be the main focus of this article.Key Concepts:The mammalian immune system has evolved to protect the host against disease.The system is complex, involving specialised tissues, cells, soluble mediators and membrane‐bound molecules.The mammalian adaptive immune response is characterised by extreme specificity in terms of antigen recognition.This specificity is largely determined by genes encoding the major histocompatibility complex (MHC) molecules, immunoglobulins (Igs) and T‐cell receptors (TCRs).Selection pressure by pathogens is believed to drive the generation of polymorphism in functional MHC genes.MHC molecules present antigen to TCR and some additionally interact with NK cell receptors.NK cells act as both effector and regulatory cells of the immune response.Different mammalian groups and species have evolved a wide range of strategies to cope with rapidly changing pathogens, all aimed at protecting the host from disease.
Cell Cycle: Regulation by Cyclins
Authors: Truman Andrew W , Kitazono Ana A , Fitz Gerald Jonathan N , Kron Stephen J 
Published: April 2013

Abstract

The cell cycle is defined as the periodic occurrence of events that result in chromosome duplication (
deoxyribonucleic acid, DNA
replication in S phase) and separation (mitosis). This process is directly regulated by both external stimuli (such as nutrient availability) and internal stimuli (such as cell size and
DNA
integrity). These events are co‐ordinately driven by the
cyclin‐dependent kinases (CDKs)
. Although the expression of CDKs typically remains relatively constant, their activities are highly regulated by
CDK‐binding proteins
known as
Cyclins
.
Cyclins
are structurally related proteins whose levels fluctuate throughout the cell cycle. Cyclin levels in the cell are dynamically regulated through tight control over both their rate of synthesis and degradation via
ubiquitin
‐mediated proteolysis. These
CDK
activators also impart distinct substrate specificity to
CDKs
for the temporal regulation of cell division.

Key Concepts:

Cyclin levels oscillate throughout the cell cycle.

Cyclins bind to CDKs and regulate their kinase activity.

Cyclin‐CDK complexes direct the specificity of appropriate substrate interactions during the cell cycle.

Inappropriate regulation of cyclins can be both the cause and the result of oncogenesis.

As well as controlling normal cell cycle progression, cyclins function also in the exiting of the cell cycle (such as G0 in terminally differentiated cells and the onset of senescence caused by DNA damage).
Group Translocation –
PEP
:
PTS
Authors: Saier Milton H , Shlykov Maksim A 
Published: April 2013

Abstract

The phosphoenolpyruvate:carbohydrate phospho‐transferase system (PEP:PTS) is a prokaryotic enzyme/transport system that phosphorylates its extracellular carbohydrate substrates during transport, leading to intracellular accumulation of the sugar phosphate esters. Several phosphoryl transfer proteins play essential roles in sugar uptake, and they comprise a phosphoryl transfer chain using PEP as the phosphoryl donor, and the incoming sugar as the ultimate phosphoryl acceptor. This phosphoryl transfer chain is: PEP→EI→HPr→IIA→IIB+ IIC→sugar, where E=Enzyme and HPr=a small heat stable, histidine‐containing protein, and only the IIC constituent, the transport protein, is not phosphorylated. In mixtures of carbon sources, preferential growth on PTS substrates often occurs, as the phosphorylation state of PTS proteins coordinates the activities and synthesis of enzymes that initiate sugar metabolism. The mechanisms of regulation are different in representative Gram‐negative and Gram‐positive bacteria, but in both cases the PTS plays a central role. The PTS in

Escherichia coli

accomplishes this goal by regulating both cyclic adenosine monophosphate (AMP) synthesis and the uptake of sugar inducers of enzyme synthesis. It also plays a role in the coordination of nitrogen metabolism with carbon metabolism. In many bacteria, the PTS serves as a chemosensory system, directing movement of bacteria up concentration gradients of PTS sugars. In a few bacteria, the PTS functions in regulation but not in sugar uptake. Although this enzyme system has not been found in eukaryotes, it has been identified in archaea. The PTS is thus a multifunctional enzyme/transport/sensor/regulatory system that coordinates many activities in prokaryotic cells.

Key Concepts:

Biological membranes provide the fundamental barrier that separates the inside of a cell (the cytoplasm) from the extracellular space.

Embedded in these structures are proteins, many of which transport substances across the membrane.

The phosphotransferase system (PTS) serves as a complex transport system.

It consists of energy‐coupling enzymes (Enzymes I, HPr, IIA and IIB) as well as the PTS permeases (Enzymes IIC or IICs).

The IIC components couple phosphoryl transfer from IIB∼P to sugar substrate phosphorylation.

The process of coupled sugar uptake with sugar phosphorylation, involving substrate modification, is called ‘group translocation’.

The PTS serves as a chemoreception system, directing the activity of the bacterial flagellum so that bacteria swim up concentration gradients of nutrient sugars.

The PTS is a complex multifaceted system, regulating the activities of many non‐PTS enzymes and transporters, thereby creating a hierarchical system of carbon sources.

PTS protein domains are incorporated into many transcription factors, enzymes and transporters, allowing it to regulate these determinants of prokaryotic cell physiology and pathology.

A comprehensive understanding of prokaryotic cell biology requires a detailed understanding of the PTS.
Sleep Disorders
Authors: Sinton Christopher M , McCarley Robert W 
Published: April 2013

Abstract

Sleep medicine is an increasingly important specialty as the adverse health consequences of disturbed sleep are recognised by patients and physicians, and the current classification of sleep disorders, as recognised by the American Academy of Sleep Medicine (AASM), is summarised. Two primary sleep disorders, narcolepsy with cataplexy and the disorders of arousal, a symptomatic cluster that includes sleepwalking, confusional arousal and sleep terrors, are reviewed in greater detail. Both disorders can be summarised as being caused by inappropriate switching between the states of vigilance, although they are very different in age of onset, severity and impact on health. In narcolepsy the boundary between sleep and wakefulness is uncontrolled but in the disorders of arousal the boundary between states of sleep is affected. These two disorders also have a genetic predisposition suggesting that advances in knowledge of the relevant mutations could eventually translate into better understanding of the possible mechanisms and hence lead to improved treatments.

Key Concepts:

The disorders of sleep are primary, for example as a result of pathology in the mechanisms of sleep and wakefulness, or secondary, for example resulting from a medical condition.

Apnoea, interruptions of breathing lasting longer than 10 s that result in arousal from sleep, is the principal presenting condition at sleep clinics.

Polysomnography is used to record physiological parameters such as respiration rate, heart rate and blood oxygen level simultaneously with data allowing the stage of sleep or wakefulness to be defined.

Basic research into the neurophysiology, molecular genetics and neurochemistry of sleep and wakefulness has been critical for understanding the causes of many sleep disorders.

The classification of sleep disorders is continuously evolving and being refined as new disorders are recognised in the clinic and neurophysiological and neurochemical pathologies are better understood.
Gnathostomulida (Unsegmented Marine Worms)
Authors: Sterrer Wolfgang 
Published: April 2013

Abstract

First described in 1956, Gnathostomulida is a phylum of microscopic, free‐living, unsegmented and hermaphroditic marine worms. Uniquely distinguished by a monociliated epidermis (that is, a body surface where each cell carries only one cilium) and possession of complex cuticular mouthparts consisting of paired jaws and an unpaired basal plate, they are most likely related to Rotifera, Acanthocephala and Micrognathozoa. There are two orders, Filospermoidea (with a pointed anterior devoid of compound sensory bristles; without a bursa copulatrix; and filiform sperm, with one flagellum) and Bursovaginoidea (with a rounded anterior with compound sensory bristles; with a bursa; and rounded or cone‐shaped sperm, aflagellate). Approximately 100 species have been recorded to date, of which many are with global or circumtropical distribution. Gnathostomulids may numerically dominate the invertebrate meiobenthos in detritus‐rich, sulfide‐rich and oxygen‐poor shallow sandy bottoms (0–25 m, rarely to 400 m) where they typically occur, seemingly feeding on microbes that they scrape off sand grains.

Key Concepts:

Gnathostomulida is a small phylum of microscopic, free‐living, unsegmented and hermaphroditic marine worms.

Gnathostomulids are unique among animals in having an entirely monociliated epidermis.

Gnathostomulids have complex cuticular mouthparts consisting of paired jaws and an unpaired basal plate.

Gnathostomulids are most likely related to Rotifera, Acanthocephala and Micrognathozoa, with which they can be united in the superphylum Gnathozoa.

Gnathostomulids typically occur interstitially in detritus‐ and sulfide‐rich but oxygen‐poor shallow sandy bottoms.
Post‐Permian Radiation
Authors: Twitchett Richard J , Foster William J 
Published: April 2013

AbstractEvents at the close of the Permian Period, led to the most severe mass extinction of the Phanerozoic. Sepkoski's ‘Palaeozoic Fauna’ suffered most; the surviving groups, more ‘modern’ in aspect, were those that would seed the post‐Permian radiation. This radiation has long been identified as a ‘delayed’ radiation, being apparently of longer duration than other post‐extinction radiations, although recent advances in radiometric dating have shortened the Early Triassic. Comparing rates of recovery between different groups or regions is not straightforward because the quality of the fossil record is rather poor during the Early Triassic. The analysis of trace fossils provides one approach to assessing ecological recovery in the absence of well‐preserved shells. Groups that radiated into vacant or largely vacated ecospace include the bivalves, which colonised deeper infaunal habitats; the Scleractinia which replaced the Palaeozoic reef‐building metazoans; and the reptiles that became top marine predators.Key Concepts:The Late Permian mass extinction event is the most severe extinction event known from the fossil record.Late Permian global warming led to a reduction in ocean circulation, increased ocean stratification and expansion of low‐oxygen ‘dead zones’.The Palaeozoic fauna is dominated by sessile, epifaunal filter‐feeders such as corals, crinoids and brachiopods, whereas the Modern fauna is dominated by motile, epifaunal and infaunal organisms such as bivalves, echinoids and gastropods.The best‐preserved fossil remains usually require an absence of scavenging animals, rapid burial and rapid mineralisation.The quality of the fossil record is not constant through time and is affected by a number of different sampling and preservational factors.Trace fossils provide evidence of the activities of benthic organisms that may not be preserved as body fossils, and are the only records of the responses of these animals to past extinction events.
Extinction: K–Pg Mass Extinction
Authors: MacLeod Norman 
Published: April 2013

AbstractThe K–Pg mass extinction event occurred at the end of the Cretaceous System (K, for kreta or chalk, a common Cretaceous rock type) and the beginning of the Paleogene System (Pg). During the last million years of the Cretaceous, just prior to the K–Pg boundary, between 40% and 75% of marine invertebrate and terrestrial vertebrate species disappear from the fossil record. Included in this extinction are such well‐known groups as dinosaurs (but not birds), pterosaurs, mosasaurs, ammonites and many species of marine plankton. Although there is broad consensus that these extinctions were driven by climate/oceanographic change, the potential causes of these changes remain topics of controversy. What is known is that the Earth was subjected to a substantial fall in sea‐level (c. 100 m), widespread volcanism, and a large comet/meteor impact during the extinction interval.Key Concepts:Mass extinctions occur when atypically high numbers of organismal extinctions take place within geologically short intervals of time.Stratigraphic successions are characterised by stacked intervals of net sediment accumulation and discontinuities that mark intervals of no sediment accumulation or active erosion.Molecular phylogenetic data indicate that many groups originally thought to have radiated after the K–Pg extinction (e.g. mammals and birds) have deeper histories than is indicated by the fossil record and should be regarded as K–Pg survivors.Sea‐level changes across the K–Pg boundary indicate that more complete records of the biotic change will be found in shallow marine environments rather than in terrestrial or deep‐marine settings.Patterns of species extinction in complete K–Pg successions indicate that this event occurred over a prolonged interval (e.g. tens to hundreds of thousands of years) prior to the K–Pg boundary rather than suddenly and coincident with the K–Pg boundary.Of the three main K–Pg extinction mechanisms – sea‐level change, volcanism, asteroid/comet impact – all affect the environment in remarkably similar ways.Flood basalt volcanism is the only extinction mechanism that exhibits a consistent association with intervals of mass extinction.The multiple‐cause model – in which a geologically unusual juxtaposition of sea‐level change, volcanism and asteroid/comet impact seems the most likely candidate for the cause of this extinction event.
Evolution of Development
Authors: Bickel Ryan D , Brisson Jennifer A 
Published: April 2013

Abstract

Research in the field of evolutionary developmental biology, or “evo‐devo”, addresses how genetic changes result in developmental changes, causing phenotypic differences between species over evolutionary time. Evo‐devo has its roots in comparative embryology of the late nineteenth and early twentieth centuries, but the fields of evolution and development diverged soon thereafter. Advances in developmental genetics in the 1970s and 1980s, combined with the discovery that distantly related organisms share key regulatory genes and processes, provided new avenues of research in evo‐devo. Today the strong interest in this field illustrates that evolutionary biologists increasingly wish to understand mechanistically how genotypic differences are translated into phenotypic diversity. Current studies compare developmental processes across many taxonomic scales, from between phyla to between closely related species. The combination of traditional developmental biology techniques and modern approaches such as genomics has made evo‐devo studies possible in a wide range of organisms.

Key Concepts:

Evolutionary developmental biology is the study of how developmental differences result in phenotypic diversity.

Homologues of regulatory genes often have similar functions in even distantly related species.

Enhancer modularity allows regulatory genes to evolve new functions while maintaining previously established functions.

Studies between closely related species increase the power of detecting nucleotide changes that cause phenotypic differences.
Speciation: Introduction
Authors: Hvala John A , Wood Troy E 
Published: April 2013

Abstract

Speciation is the formation of two or more new species from one ancestral species. How new species form is a complex process and a fundamental biological question. Answering this question provides insights into patterns of biodiversity and informs conservation strategies. Research on the causes and patterns of speciation is heavily influenced by species concepts – how we define species. The biological species concept is perhaps the most influential, and it groups individuals into species on the basis of the ability to interbreed. Consequently, most research on the process of speciation is driven by the search for mechanisms that affect reproductive compatibility among closely related lineages. Once formed, a new species can maintain its identity by sharing advantageous genes among dispersed and reproductively compatible populations. Conversely, distinguishing traits can be maintained between species via isolating mechanisms. These contrasting mechanisms produce discrete clusters of phenotypic variation rather than a continuum of forms.

Key Concepts:

Speciation tends to form clusters of biodiversity rather than continuous gradients.

Species concepts heavily influence conclusions about how speciation occurs.

Choice of species concept depends on the goal of the research and the organisms being studied.

Species remain distinct from each other because of various isolating mechanisms, which prevent gene flow between species.

Isolating mechanisms have a genetic basis.

Hybridisation between species pairs often occurs in nature and can yield insights into the causes of speciation.

Hybridisation can lead to the fusion of two species into one, to reinforcement of reproductive barriers, or even to the formation of new ‘hybrid species’ that are ecologically distinct and genetically isolated from their parent species.