bluuebunny/crossref_metadata_2025 huggingface dataset:
Behaviour: Role of Genes
Authors: Järvilehto Timo , Lickliter Robert
Published: September 2009

Much effort in behavioural genetics has been motivated by the hope that one day human behaviour will be explicable in genetic terms. This hope is based on the assumption that the contribution of genetic and environmental factors to behaviour can somehow be partitioned. However, recent advances in genomics, cellular and developmental biology, and developmental psychology have made it clear that such partitioning is biologically implausible. The functional significance of genes or any other influence on phenotypic development can be understood only in relation to the organism–environment system of which they are a part. Genes and environments are neither alternative nor independent causes for phenotypic traits.

Key Concepts:

Gene activity is involved in the production of all phenotypic traits.

Partitioning behaviours into those specified by the genes and those that are the result of the environment is not possible.

The causes of behaviour are always relational and distributed across internal and external factors and events.

The influence of any single factor on behaviour (genes, hormones, diet, social interaction) is contingent on the organization of the entire organism–environment system.

Genes do not have a privileged position in the development of behaviour, because they are themselves regulated participants in the developmental process.

Modern developmental theory rejects attempts to separate the organism and environment.
Macrophytes: Ecology of Aquatic Plants
Authors: Bornette Gudrun , Puijalon Sara
Published: September 2009

Aquatic plants contribute to maintaining key functions and related biodiversity in freshwater ecosystems, and to provide the needs of human societies. The way the ecological niches of macrophytes are determined by abiotic filters and biotic ones is considered. A simple, broadly applicable model of the distribution of growth forms according to abiotic filters is proposed. The consequence for the dynamics of plant communities and the main threats to macrophyte occurrence and diversity are discussed.

Key concepts:

Macrophytes contribute to maintaining key functions and related biodiversity in freshwater ecosystems, and to provide the needs of human societies.

Most aquatic species are phylogenetically descended from terrestrial plants that have later adapted to aquatic life.

Water plants are usually poorly lignified, as water preserves plants from gravitational stress, and are characterized by the presence of aerenchyma, which increases oxygen flux from shoots to roots, and by a large leaf surface, together with a thin cuticle, which increase contact with water and carbon uptake.

Macrophyte dispersal relies partly on water drift, and thus on seed buoyancy and on the ability of plants to break themselves up and regrow from broken dispersed fragments, and partly on endozoochory by animals (mainly birds).

In freshwater ecosystems, the production, community composition and life‐history traits of macrophytes are governed by the availability of carbon, nitrogen and phosphorous.

Water movements (waves, flow velocity) tend to select streamlined or prostrate growth forms, and contribute to the dispersal of seeds and vegetative propagules.

Moderate disturbances (by floods or drawdowns) decrease biotic interactions in aquatic plant communities and as a consequence favour biodiversity and decrease successional rate.

Free‐floating and tall species with floating leaves are the most competitive for light, and usually dominate macrophyte communities when nutrient levels in the water are sufficiently high.

In the framework of global change, eutrophication of freshwaters, together with decreases in natural disturbance regimes in river floodplains, increases in groundwater abstraction and the increase of temperature may all contribute in decreasing macrophyte biodiversity by favouring competitive and invasive species, to the detriment of ruderal, stress‐tolerant poorly competitive ones.
Chemolithotrophy
Authors: Oren Aharon
Published: September 2009

Many prokaryotes,
Bacteria
as well as
Archaea
, obtain their energy from the oxidation of reduced inorganic compounds such as hydrogen, ammonia, nitrite, sulfide, elemental sulfur, hydrogen and Fe(II) ions. These organisms can derive all their cellular carbon from carbon dioxide, and they are thus able to grow without any organic compounds and without light. Such microorganisms are called chemolithotrophs or chemoautotrophs. Chemolithotrophic life is possible in the presence as well as in the absence of molecular oxygen. Processes mediated by chemolithotrophic prokaryotes include nitrification (the formation of nitrate from ammonia), production of sulfuric acid from sulfide and elemental sulfur, and the formation of methane from hydrogen and carbon dioxide. Some ecosystems, for example those that develop around deep‐sea hot vents, are entirely driven by carbon fixed by chemolithotrophic microorganisms.

Key concepts

Certain groups of prokaryotes obtain their energy from the oxidation of reduced inorganic compounds such as sulfide, ammonia and hydrogen, and use carbon dioxide as carbon source. These organisms are called chemolithotrophs or chemoautotrophs.

Chemolithotrophy is widespread in the two domains of prokaryotes: the
Bacteria
and the
Archaea
.

Many chemolithotrophs use molecular oxygen as electron acceptor, but chemolithotrophy is also possible in the absence of oxygen. Nitrate, sulfate, elemental sulfur or carbon dioxide serves as electron acceptors for certain groups of chemolithotrophs.

Nitrification, or the oxidation of ammonia via nitrite to nitrate by chemolithotrophic bacteria, is a key process in the global nitrogen cycle.

Two types of anaerobic chemolithotrophs oxidize hydrogen with carbon dioxide as electron acceptor: methanogens and homoacetogens, producing methane and acetate, respectively.

Chemolithotrophs participate in the biogeochemical cycles of certain metals (iron, manganese) and metalloids (arsenic).

In some environments such as deep‐sea hydrothermal vents and certain underground caves, chemolithotrophic primary production driven by the oxidation of hydrogen sulfide provides the basis for the functioning of the ecosystem.
Seed Dispersal
Authors: Nathan Ran , Bullock James M , Ronce Ophélie , Schurr Frank M
Published: September 2009

The sedentary life of adult plants accentuates the critical importance of the short phase during which individual plants move: the dispersal of seeds, a common, widespread and fascinating phenomenon. Ultimately, selective pressures favouring dispersal include inbreeding avoidance, reduction of competition with kin and nonkin and the tracking of establishment opportunities in time and space. Proximately, dispersal mechanisms include nonrandom release from the mother plant, and transport by multiple dispersal vectors not necessarily those inferred from the seed morphology. The resulting patterns, often described by dispersal kernels, typically show a decline in seed deposition with distance from the source and a tail of long‐distance dispersal events. Yet, environmental heterogeneity may cause more complex dispersal patterns. Dispersal has important consequences for the fate of individuals, populations, communities and ecosystems, enabling metapopulations and metacommunities to persist and playing a critical role in shaping the evolutionary and plastic response of plants to changing environments.

Key concepts

Dispersal is a widespread phenomenon among plants, selected to avoid inbreeding, to reduce competition with kin and nonkin and to cope with spatiotemporally variable environments.

Causes for dispersal evolution act in concert, interact and may affect differently the evolution of short‐ and long‐distance dispersal.

Seeds typically depart from the source plant in a nonrandom fashion, suggesting selection to coordinate seed release with favourable conditions for dispersal and/or establishment.

Seeds of a given plant species are typically dispersed by multiple vectors, including ‘nonstandard’ vectors differing from those inferred from the seed morphology.

Dispersal kernels describe how seed deposition varies – in one, two or three spatial dimensions – in relation to the distance from the seed source.

One‐dimensional dispersal kernels generally show a decline in seed number (or density) with distance, and a ‘fat’ tail implying more long‐distance dispersal events than expected from a negative exponential distribution.

Complex dispersal kernels arise because seed deposition often varies not only with distance but also with direction and environmental heterogeneity.

Dispersal plays a key role in allowing plants to adapt to climate changes, to spread within and outside their native range and to maintain metapopulations and metacommunities.

New methods to model the underlying mechanisms, to analyze gene flow and genetic structure and to quantify dispersal patterns increase our understanding and predictability of seed dispersal in general, and long‐distance dispersal in particular.
Plant Actin Biology
Authors: Deeks Michael J , Hussey Patrick J
Published: September 2009

Actin is a major component of the plant cytoskeleton. Filamentous actin (F‐actin) contributes to the maintenance of the internal architecture of the cell, drives cytoplasmic streaming (the movement of components around the cytosol) and contributes to the process of cell division. The biochemistry of plant actin has many similarities to that of yeast and animals, but has developed its own strategies and molecular machinery to organize actin filaments. F‐actin provides tracks for myosin molecular motors to transport organelles at high velocities and actin is required for specific stages of vesicle trafficking that underpin cell growth and development. The means by which plant cells control the nucleation of new actin filaments from G‐actin have diverged considerably from yeast and metazoans. The unique aspects of the plant actin cytoskeleton are likely to have arisen from a combination of the environmental challenges to a sessile multicellular existence and a complex evolutionary history.

Key concepts

The basic principles of actin biochemistry applicable to animals, fungi and protists are conserved in plants but there are a number of specific modifications as plants do not possess the full complement of animal actin‐binding proteins.

Actin filaments in plants have to fulfil unique functions. Actin focuses on the expansion of tip growing cells, maintains cytoarchitecture and responds to the environment (e.g. polarizing in response to pathogen stimulation). During cell division actin filaments participate in all major plant‐specific arrays.

A stationary cell is NOT a physically inactive cell. Actin cables are exploited for organelle transport. Actin‐based transport tends to dominate over microtubule‐based movement. Plants utilize the fastest known type V myosin (known in plants as type XI) within the eukaryote kingdom. Polymerization dynamics are thought to add to trafficking capabilities as low levels of antiactin drugs disrupt vesicle delivery and fusion during cell growth yet preserve myosin‐mediated transport.

New proteins and new domain combinations have become established in plants to regulate the actin cytoskeleton in accordance with the unusual demands placed on them. Importantly, these radical adaptations should not be considered purely in terms of a response to a sedentary way of life as the fungal kingdom has achieved such a conversion using arguably less radical cytoskeletal solutions. Consequently the impact of other unique facets of plant evolutionary history and niches must be considered.
The Rust Fungi
Authors: Kolmer James A , Ordonez Maria E , Groth James V
Published: September 2009

The rust fungi are a monophyletic group of approximately 7000 species in the basidiomycota and are highly specialized obligate parasites of plants. The life cycle of rusts can be complex. Some rusts have up to five spore stages that alternate between haploid and dikaryotic nuclear conditions and that can occur on two taxonomically unrelated host plants. The rusts have evolved specialized structures that allow them to penetrate and obtain nutrients from living host cells. Biologic forms of a single rust species may differ in ability to attack different genera of host plants. Furthermore, within a single rust species they can be highly variable in ability to attack different genotypes of one host species. At the species level, genes that condition avirulence/virulence in rusts interact in a specific relationship with rust‐resistance genes in plants. Many of the most important plant diseases in the world are caused by rust fungi.

Key concepts:

The rust fungi are a monophyletic group of approximately 7000 species within the basidiomycota, the group of fungi that includes mushrooms and shelf fungi.

Rust fungi have complex life cycles with up to five spore stages that alternate between haploid and dikaryotic nuclear condition on two unrelated host plants.

The rust fungi are obligate parasites of plants and have evolved specialized structures to infect and obtain nutrients from plants.

Rusts have a highly specific host range. Genes in rust that express avirulence or virulence interact with rust‐resistance genes in host plants to condition a compatible or incompatible interaction. Some rust species are highly variable for biologic forms that vary in their ability to attack host genotypes with different rust‐resistance genes.

Many of the most important plant diseases worldwide are caused by rust fungi.
Sleep and Memory
Authors: Aton SJ , Seibt J , Frank MG
Published: September 2009

Current behavioural evidence indicates that sleep plays a central role in memory consolidation. Neural events during post‐learning sleep share key features with both early and late stages of memory consolidation. For example, recent studies have shown neuronal changes during post‐learning sleep which reflect early synaptic changes associated with consolidation, including activation of shared intracellular pathways and modifications of synaptic strength. Sleep may also play a role in later stages of consolidation involving propagation of memory traces throughout the brain. However, to date the precise molecular and physiological aspects of sleep required for this process remain unknown. The behavioural effects of sleep may be mediated by the large‐scale, global changes in neuronal activity, synchrony and intracellular communication that accompany this vigilance state, or by synapse‐specific ‘replay’ of activity patterns associated with prior learning.

Key concepts

Memory consolidation involves plastic changes at the synaptic and brain systems levels; these changes occur over timescales of minutes (synaptic consolidation) to days or months (systems consolidation).

Cellular changes occurring during early post‐learning sleep suggest that synaptic consolidation may occur preferentially during sleep.

Brain‐imaging and gene‐expression studies have provided limited evidence that sleep may facilitate the gradual redistribution of memory traces throughout the brain.

Sleep may facilitate consolidation through large‐scale changes in neural activity, neurotransmission or gene expression associated with rapid eye movement (REM) and non‐REM (NREM) vigilance states.

It remains unclear whether sleep‐dependent consolidation is mediated by permissive (global) or instructive (synapse‐specific) mechanisms.
Memory: Mechanisms Other than
LTP
Authors: Debanne Dominique , Campanac Emilie
Published: September 2009

Synaptic plasticity is not the exclusive mode of memory storage, and persistent regulation of voltage‐gated ionic channels also participates in information storage. Long‐term changes in neuronal excitability have been reported in several brain areas following learning. Synaptic activation of glutamate receptors initiates long‐lasting modification in neuronal excitability at the pre‐ or postsynaptic side. Intrinsic plasticity is mediated by changes in the expression level or biophysical properties of ion channels in the membrane and can affect many different neuronal operations such as dendritic integration and action potential generation and propagation. Similarly to synaptic plasticity, long‐lasting intrinsic plasticity is bidirectional and expresses a certain level of input or cell specificity. Synaptic and intrinsic plasticities not only share common learning rules and induction pathways but also contribute in synergy with these synaptic changes to the formation of a coherent mnesic engram.

Key concepts:

Synaptic plasticity is not the exclusive mode of memory storage, and persistent regulation of voltage‐gated ionic channels also participates in information storage following learning. Synaptic activation of glutamate receptors initiates long‐lasting modification in neuronal excitability at the pre‐ or postsynaptic side. Intrinsic plasticity is mediated by changes in the expression level or biophysical properties of ion channels in the membrane and can affect many different neuronal operations such as dendritic integration and action potential generation and propagation. Synaptic and intrinsic plasticities not only share common learning rules and induction pathways but also contribute in synergy with these synaptic changes to the formation of a coherent mnesic engram.
Learning Disorders: Beyond Dyslexia
Authors: Banai Karen , Yifat Rachel
Published: September 2009

Learning disabilities (LD) – the unexpected academic difficulties experienced by many otherwise typically developing persons – are highly heterogeneous in nature. Thus, while at the academic level 80–90% of individuals with LD suffer from poor reading fluency and/or accuracy, at the cognitive level multiple processes are implicated including language, attention, perception and memory. Similarly, at the biological level many brain systems and processes are affected. In the auditory system alone, individuals with LD were shown to process sound abnormally at all levels of the auditory pathway from the brainstem to high level cortical areas. Taken together, current research suggests that a single core deficit model is unlikely to account for the aetiology of LD and furthermore, that the observed pattern of academic strengths and weaknesses is affected little by differences in underlying processes. Therefore, it appears that different underlying vulnerabilities result in similar academic outcomes.

Key Concepts

Physiological and perceptual processing of the acoustic elements of sound such as its duration, frequency, rate of presentation, etc.

The concurrent occurrence of two disorders. In the present context, an individual diagnosed with LD is more likely to be diagnosed with another form of learning or attention disorder compared to an undiagnosed individual.

Disorders that involve the processing of linguistic information such as phonology, grammar and semantics. May reflect difficulties in expression, comprehension or both.

A mental representation of recently perceived stimuli that can be used to ease the perception of ongoing stimuli.

Processes related to the linguistic analysis of the basic units of speech such as the ability to segment words to syllables, phonemes or units that are thought to structure sound to convey linguistic meaning, or to remember a string of speech sounds in short‐term memory.

The ability to perform cognitive operations (e.g. repeating in backwards order) on items held in short‐term memory.
Gaucher Disease
Authors: Germain Dominique P
Published: September 2009

Gaucher disease (GD) is a lysosomal storage disorder due to deficiency in acid β‐glucosidase. Partial enzyme deficiency is associated with parenchymal disease of the liver, spleen and bone marrow in non‐neuronopathic, type 1 GD, while complete deficiency, caused by severe mutations in the

GBA

gene, is additionally associated with neurological manifestations in type 2 and type 3 GD. Specific therapy is available for GD: enzyme replacement therapy has proven safe and effective and is the current standard of care for type 1 GD but cannot reverse the neurological deficits in type 2 or type 3. New recombinant enzymes are currently in clinical trials. Small‐molecule inhibitors of
glucosylceramide synthase
are both available and being developed for substrate reduction therapy. Active‐site‐specific pharmacological chaperones and gene therapy are being explored as other potential therapeutic options.

Key concepts:

Gaucher disease (GD) is an autosomal recessive inborn error of sphingolipid metabolism due to the deficient activity of the lysosomal enzyme acid β‐glucosidase.

Three phenotypes of GD are conventionally distinguished on the basis of the absence (type 1) or presence and severity (types 2 and 3) of central nervous system involvement.

Patients with type 1 GD may present with splenomegaly, hepatomegaly, radiologic bone disease, thrombocytopaenia, anaemia and bone pain.

A higher incidence of multiple myeloma in GD has been reported and patients should have their immunoglobulin profile determined at diagnosis and monitored every 2 years.

The natural course of GD varies widely, with some subjects remaining asymptomatic up to the age of 70 or 80 years, in contrast to the sometimes fatal progression in childhood. This emphasizes the need for a regular follow‐up to enable timely initiation of enzyme therapy.

The demonstration of a deficient activity of acid β‐glucosidase activity in leukocytes is the reference laboratory method which should be used to confirm the clinical diagnosis of GD.

Enzyme replacement therapy (ERT) with imiglucerase is central to modern management of GD. The aim of ERT is to achieve reversal of the symptomatic clinical manifestations and prevent irreversible lesions of the various organs.

Over 3500 patients are receiving treatment worldwide, with a maximum follow‐up of 15 years. The therapeutic results have been the subject of several analyses. The response to ERT is generally excellent, although marked inter‐individual variability exists. ERT is safe and well tolerated.

Substrate reduction therapy (miglustat) reduces tissue glycosphingolipid storage by limiting the amount of the precursor synthesized to a level that can be cleared by the mutant enzyme with residual hydrolytic activity.

Since the neurological forms of GD do not respond to ERT, further research on other therapeutic strategies including gene therapy, substrate reduction therapy and chaperone therapy is warranted.
The
BCL
‐2 Family Proteins – Key Regulators and Effectors of Apoptosis
Authors: Vaux David L
Published: September 2009

BCL‐2 was the first cloned component of the mechanism for apoptosis – the process by which metazoan cells commit suicide – to be recognized. Mammals are now known to carry genes for a large number of BCL‐2 like proteins, some of which, like BCL‐2 itself, inhibit apoptosis, and others that promote or are required for apoptosis. Direct interactions between BCL‐2 family members are essential for the proper regulation and implementation of apoptosis during development and for homoeostasis. Abnormalities to the regulation of cell death, such as those caused by mutations to genes for BCL‐2 family members prevent apoptosis occurring when it should, and can lead to diseases including cancer. Understanding the roles of BCL‐2 family members, their structures and how they interact, has allowed the development of novel agents for the treatment of cancer that are now in clinical trials.

Key concepts

A major mechanism by which mammalian cells kill themselves involves members of the BCL‐2 family of proteins, some of which promote cell death, and others which inhibit cell death.

BCL‐2 family proteins interact with each other to regulate and implement the cell death programme.

Abnormalities to the regulation of this cell death process, including mutations to genes for BCL‐2 family members, can lead to a disease, such as cancer.
Mitochondrial Outer Membrane Permeabilization
Authors: Parsons Melissa J , Green Douglas R
Published: September 2009

Defects in apoptosis have dire consequences and can contribute to the development of autoimmune disorders, neurological diseases and cancer. At the centre of the intrinsic apoptotic signalling pathway lies the mitochondrion, which is not only the bioenergetic centre of the cell, but also the cell's reservoir of pro‐death factors such as cytochrome
c
. These proteins reside in the mitochondrial intermembrane space (IMS), and their release from the IMS induces a signalling cascade that leads to the demise of the cell. The critical event governing the release of pro‐apoptotic molecules from the IMS is mitochondrial outer membrane permiabilization (MOMP). Although two models exist to explain the execution of MOMP, both models incorporate the widely accepted idea that MOMP is achieved through the coordinated actions of pro‐ and antiapoptotic members of the Bcl‐2 (B‐cell lymphoma) family of proteins. In addition, non‐Bcl‐2 family proteins, mitochondrial dynamics and mitochondrial bioenergetics are also involved in MOMP.

Key Concepts:

Apoptosis is one mechanism of cell death, which is characterized by distinct morphological features and occurs in response to specific physiological cues.

Apoptosis is a signalling cascade that leads to the demise of the cell.

The intrinsic apoptotic signalling cascade is one of the two main apoptotic pathways.

Mitochondrial outer membrane permeabilization (MOMP) is the key step in apoptosis that involves the mitochondria.

Bcl‐2 family proteins are both pro‐ and antiapoptotic in nature, and are the main regulators of MOMP.

Bak or Bax is necessary for MOMP.

MOMP leads to the release of pro‐death factors from the intermembrane space (IMS), which engage caspases to carry out the apoptotic signalling cascade.

Mitochondrial bioenergetics are disrupted during MOMP.
Evolution of the p53 and p63/p73 Gene Families
Authors: Pintus Sergey S
Published: September 2009

The tumour suppressor protein p53 is one of the most studied eukaryote proteins. The finding of its paralogues – p63 and p73 – inspired investigations of the whole family. p73 and p63 appeared to have functions distinct from p53 and to be involved in complex regulation of the latter. Evolutionary studies revealed distant homologues of the family not only in vertebrates but also in protostomes and even in nonmetazoans. The evolutionary history of the p53 family and its relatives is complex, controversial and its intensive study goes on.

Key concepts:

The p53 and p63/p73 gene families evolve from the common p63‐like ancestor via specialization through gene duplications and domain gains and losses.
Comparative Analysis of mi
RNA
‐mediated Gene Regulation in Mammals
Authors: Zhang Yaou , Lv Qing
Published: September 2009

Micro
ribonucleic acids
(miRNAs) are a class of small noncoding RNAs, which are involved in a range of physiological and pathological processes. All animal miRNAs share common genomic structure, biosynthetic pathways and reaction mechanisms but mammals seem to have more miRNAs to match their organism complexity and longer 3′‐UTR (untranslated region) to evaluate more miRNA target sites. During the episode of miRNA innovation observed at the vertebrates to the placental mammals, multiple unique miRNAs have emerged only in primates as compared with other mammals. The dramatically expanding of mammalian miRNAs and their targets suggest that miRNAs play important roles in mammalian evolution.

Key concepts

MicroRNAs (miRNAs) are group of small noncoding RNAs with approximately 22 nucleotides.

miRNAs play important roles in many physiological and pathological processes in almost all eukaryotes, including development, cell proliferation, apoptosis, differentiation, tumours and many others.

Compared with other animals, mammalians seem to have more miRNAs.

The sequence of many miRNAs is conserved, like lin‐4 and let‐7 family, indicating strong functional constraint on miRNA evolution.

However, nonconserved miRNAs represent a potentially important source of functional novelties during evolution.

There is a rapid evolution of the miRNA cluster in primates, including frequent tandem duplications and nucleotide substitutions.

All animal miRNAs share common genomic structure, biosynthetic pathways and reaction mechanisms.

Each mammalian miRNA regulates on average 200 target genes whereas many genes have multiple target sites for either one miRNA or many different miRNAs.

The avoidance of miRNA targeting might be as important as conservation of miRNA target sites in the evolution of tissue‐specific gene expression patterns.

Some miRNAs are similarly expressed in mammals and most metazoans, indicating an evolutionarily conserved function, but others seem to be more ubiquitously expressed and only detected in specific cell types.
Molecular Evolution of The Keratin‐associated Protein Gene Family
Authors: Wu Dong‐Dong , Zhang Ya‐Ping
Published: September 2009

Hair, unique to mammals, plays a profound role in the heat retention within homoiotherms and presumably contributes significantly to the rapid radiation of mammals to become the dominant terrestrial vertebrate on earth. Keratin‐associated protein (KRTAP) is one of the major component of hair. Phylogenetic analysis of the KRTAP gene family could illuminate the origin and evolution of mammalian hair to some extent. Furthermore, study of

KRTAP

gene family will provide important information on the hair‐related disorders.

Key concepts

KRTAP is one of the major components of mammalian hair. To some extent, a relation lies between the molecular evolution of KRTAP gene family and evolution of hair. Comparative genomic and polymorphism data of the KRTAP gene family will provide important information on the hair disorders in the human populations.
Single Particle
EM
Authors: Fernández José‐Jesús , Valpuesta José‐María
Published: September 2009

Single particle electron microscopy (EM) plays an important role in structural biology because it allows derivation of biologically relevant information about proteins and macromolecular complexes. A large amount of randomly oriented images of the specimen under study (so‐called particles) are collected from micrographs taken with an electron microscope. These particles are then computationally aligned and combined to yield the three‐dimensional structure, which is subsequently subjected to visualization and interpretation. The resolution attained with this technique still precludes tracing of the polypeptide chain or the clear visualization of the secondary structure elements in most cases. Nevertheless, the integrative combination of the information provided by the different structural techniques (X‐ray crystallography, EM and so on) at different resolution levels provides a comprehensive interpretation of the structure.

Key concepts

Single particle electron microscopy (EM) allows the structural determination of proteins and macromolecular complexes.

The combination of the structure obtained by single particle EM and the high‐resolution information obtained by other structural techniques allows the derivation of biologically relevant information.

The biological material has to be specially prepared prior to be imaged in the electron microscope.

The three‐dimensional structure of the specimen is determined by collecting, aligning and combining a large number of randomly oriented particles of the specimen that are extracted from the microscope images.
Structure and Function of
IAP
and Bcl‐2 Proteins
Authors: Hinds Mark G , Mace Peter D , Day Catherine L
Published: September 2009

Interactions between pro‐apoptotic and pro‐survival proteins control the apoptotic programme in cells. Regulation of caspases, the proteolytic enzymes that destroy the cell, is critical and the actions of the inhibitor of apoptosis (IAP) and B‐cell lymphoma‐2 (Bcl‐2) proteins control the life–death switch. IAP proteins can inhibit caspases and signal the destruction of regulatory molecules. In contrast, in mammals, the Bcl‐2 family controls mitochondrial integrity and the release of factors that activate caspases or block the action of IAPs. Structures of many of these proteins, and the complexes they form, are now available and underpin current models of apoptosis. Here we review key features of these structures and highlight how these studies have led to the development of antagonist compounds that allow the pro‐survival effects of IAP and Bcl‐2 proteins to be negated.

Key Concepts

Caspases are kept inactive in healthy cells by the actions of molecules that inhibit their oligomerization and processing.

Pro‐survival Bcl‐2 proteins have a hydrophobic BH3‐binding groove that is required for binding both pro‐apoptotic BH3‐only and Bax‐like proteins.

Bcl‐2 proteins exhibit conformational plasticity and can adopt distinct conformations that are required for their activity.

The IBM‐binding site on the BIR domains is required for direct inhibition of caspases by IAPs.

The RING domain of IAP proteins mediates their ubiquitin E3‐ligase activity, and is required for the pro‐apoptotic activity of IAP‐antagonist molecules.

Structures of molecules that prevent caspase activation, in complex with their inhibitors, have guided the development of antagonist compounds that have therapeutic potential.
Replication of Viruses Infecting Eukaryotes
Authors: Gutierrez Crisanto , Martínez‐Salas Encarnacion
Published: September 2009

Viruses are biological entities incapable of existing in a cell‐independent manner. Viruses infecting eukaryotic cells offer all possibilities of genome composition, being either DNA or RNA, single‐stranded or double‐stranded, circular or linear, segmented or non‐segmented. Therefore, viruses have evolved a variety of replication strategies to convert viral genome information into infectious viral particles. Furthermore, gene expression strategies affecting replication, transcription, translation, signalling or macromolecular trafficking, have evolved to exploit and subvert the cellular machinery. The cellular response to virus infection is dependent on the gene expression strategies exploited by the different type of viruses. Conversely, to counteract the cellular antiviral response, viruses have developed sophisticated mechanisms leading to a large heterogeneity in the nature of virus‐host interactions. Their study is providing key information for designing strategies of virus control. At the same time, viruses are useful molecular tools to delineate the mechanisms behind basic cellular processes.

Key Concepts:

Capsid: A protein shell comprising the main structural unit of a virus particle.

Matrix protein: A structural protein of a virus particle that underlies the envelope and links it to the core.

Monocistronic: A messenger RNA that encodes a single protein.

Negative strand: The group of RNA viruses whose genome contains the reverse polarity of the messenger RNA.

Nucleocapsid: The core of a virus particle consisting of the genome plus a complex of proteins.

Polyprotein: A long polypeptide encoding several mature proteins that are subsequently released by protease cleavage.

Positive strand: The group of RNA viruses whose genome contains the same polarity as the messenger RNA.

Receptor: A molecule on the surface of a cell that is used by a virus for attachment.

Segmented genome: The group of viruses with the genome packaged in the capsid split into two or more molecules.

Uncoating: The stage of viral replication at which structural proteins are disassembled and the virus genome is exposed to the replication machinery.
Thermomechanical Models
Authors: Luong Minh P.
Published: September 2009

The thermal effects due to thermomechanical coupling in solids have been identified within the context of the thermodynamics of irreversible processes. This article aims to illustrate the use of infrared thermography as a nondestructive, real‐time, and noncontact technique to detect, observe, and evaluate the evolution of temperature changes caused by the diverse physical processes occurring in solids under loading. The results obtained highlight the advantages of differential infrared thermography. This technique minimizes the thermal noise in real or industrial environments and thus facilitates the detection, discrimination, and interpretation of the diverse dissipative phenomena involved in these nonlinear coupled thermomechanical effects. Stress and strain concentrations occurring in loaded materials and structural components result in localized forces that are sufficient to promote plasticity. In addition to traditional techniques of mechanical strength evaluation, it provides under service loading a ready evaluation of a limit of acceptable damage, beyond which the material will be destroyed, or of fatigue resistance under cyclic excitations or dynamic solicitations. The work suggests various potential applications of this thermal technique in diverse engineering fields: nondestructive testing using thermal conduction phenomena, elastic stress measurements, localization of dissipative phenomena, and rapid evaluation of endurance limit for industrial materials.
Failure Modes of Aerospace Materials
Authors: Jata Kumar V. , Roy Ajit , Parthasarathy Triplicane A.
Published: September 2009

Understanding and interpreting aircraft structural and engine failure modes at a material level is important from the standpoint of employing superior fracture‐resistant materials and predicting remaining useful life based on the micromechanics of materials. Failure modes can be understood by observing the fracture surface of a component from a low magnification to several orders of magnitude of magnification. It is also important to know the chemical composition of the material, primary, and secondary processing methods used to fabricate the product form. To predict the fracture modes, knowledge of operational environment and loads is required. Recently, there has been an increasing interest and need to design structural health monitoring systems to maintain systems based on the system condition. Instead of time‐based maintenance, the new paradigm is to perform condition‐based maintenance. Therefore, knowledge of material and structural failure modes is essential to incorporate this new approach. To perform the system health diagnosis, collaborative work between nondestructive evaluation (NDE) and structural health monitoring researchers is critical to build new health monitoring systems in the future. This article broadly discusses and summarizes failure modes of a few structural metallic alloys and polymer‐based composites used in aerospace structures.
Sensor Placement Optimization
Authors: Barthorpe Robert J. , Worden Keith
Published: September 2009

Structural health monitoring (SHM) systems depend critically on using the correct number of sensors and on positioning them appropriately on the structure. A rigorous approach to this problem requires an optimization methodology as described in this article. The article begins with a definition of the problem and provides a literature review covering relevant methodologies. The basic theories of the main approaches are then discussed in more detail. Finally, the article provides an illustrative case study of a combinatorial optimization method based on the problem of impact location on a composite panel.
Operational Loads Monitoring in Military Transport Aircraft and Military Derivatives of Civil Aircraft
Authors: Meadows Len , Reed Steve , Duffield Mike
Published: September 2009

Major military airworthiness authorities have developed complex constructs for aircraft type certification and ongoing airworthiness management. Central to their requirements is the need for structural usage monitoring and operational loads monitoring (OLM). Manufacturers and maintainers of modern military transports have, by necessity, embraced these requirements and are developing expertise in these fields. Most military organizations operate fleets, which contain purpose‐built military aircraft, as well as a number of civilian derivatives adapted for military use. Differing requirements between the civilian and military sector pose a number of challenges for those involved in the aircraft type certification and ongoing airworthiness management of these fleets. Within this article, the regulatory basis of structural usage monitoring and OLM are described and examples of the application of OLM for military transport aircraft and military derivatives of civil aircraft across several air forces are presented.
Management of hematological malignancies during pregnancy
Authors: Rizack Tina , Mega Anthony , Legare Robert , Castillo Jorge
Published: September 2009

The management of hematological malignancies during pregnancy is a challenging endeavor, which not only requires technical skills and knowledge by the clinicians but also requires sound clinical judgment and compassion, keeping in mind the patient and family preferences and, ultimately, the wellbeing of the neonate. The incidence of hematological malignancies during pregnancy is rare, ranging from 1 in 1,000 to 1 in 10,000 deliveries, impeding the design and execution of large prospective studies. The purpose of this review is to evaluate the limited existing data and make useful suggestions in the management of acute and chronic leukemias, Hodgkin and non‐Hodgkin lymphomas, plasma cell myeloma, and other hematological malignancies, such as myelodysplastic syndromes and hairy cell leukemia, during pregnancy. Am. J. Hematol. 2009. © 2009 Wiley‐Liss, Inc.
Empfehlungen des Arbeitskreises 6.1 “Geotechnik der Deponiebauwerke” der Deutschen Gesellschaft für Geotechnik e. V. (DGGT)
Authors: Witt Karl Josef , Ramke Hans‐Günter
Published: September 2009

Der Arbeitskreis “Geotechnik der Deponiebauwerke” hat in 5 Themengruppen bisher 76 Empfehlungen zur Planung, zum Bau und zur Qualitätsüberwachung von Abfalldeponien veröffentlicht. Der diesjährige Bericht zu den Arbeitsergebnissen stellt den Bezug zwischen der im Juli in Kraft getretenen Verordnung zur Vereinfachung des Deponierechts und den GDA‐Empfehlungen her.

Recommendations of the DGGT Committee “Geotechnics of Landfill Structures”.

The Technical Committee “Geotechnics of Landfill Structures” of the German Geotechnical Society published up to now 76 recommendations (GDA‐Geotechnical Landfill Recommendations) structured in 5 main issues. This report on the recent results of the working group delivers the link between the requirements of the new German Directive on the Landfilling of Waste and the detailed technical standard described in the GDA‐Recommendations.
Eu3+ (orange/red) luminescence in LiXSO4Cl (X = Mg, Zn) halosulfate phosphor
Authors: Nagpure I. M. , Dhoble S. J. , Pode R. B.
Published: September 2009

The wet chemical synthesis, X‐ray diffraction and photoluminescence characteristics in alkaline halosulfate phosphors such as LiMgSO4Cl:Eu and LiZnSO4Cl:Eu are reported in this paper. The effect of Li ion on Eu3+ luminescence (5D0 → 7F2 electronic transition) and incorporation of Eu3+ ion in lithium base alkaline halosulfate phosphor has been studied. Copyright © 2009 John Wiley & Sons, Ltd.
Electrochemiluminescence detection of methamphetamine based on a Ru(bpy)32+‐doped silica nanoparticles/Nafion composite film modified electrode
Authors: Cai Zhimin , Lin Zhijie , Chen Xiaomei , Jia Tiantian , Yu Ping , Chen Xi
Published: September 2009

An electrochemiluminescence (ECL) approach for methamphetamine determination was developed based on a glassy carbon electrode modified with a Ru(bpy)32+‐doped silica nanoparticles/Nafion composite film. The monodispersed nanoparticles, which were about 50 nm in size, were synthesized using the water‐in‐oil microemulsion method. The ECL results revealed that Ru(bpy)32+ doped in silica nanoparticles retained its original photo‐ and electrochemical properties. The ECL intensity was found to be proportional to methamphetamine concentration over the range from 1.0 × 10−7 to 1.0 × 10−5 mol L−1, and the detection limit was found to be 2.6 × 10−8 mol L−1. The proposed ECL approach was used to analyze the methamphetamine content in drugs. Copyright © 2009 John Wiley & Sons, Ltd.
ESIMS Studies and Calculations on Alkali‐Metal Adduct Ions of Ruthenium Olefin Metathesis Catalysts and Their Catalytic Activity in Metathesis Reactions
Authors: Wang Hao‐Yang , Yim Wai‐Leung , Klüner Thorsten , Metzger Jürgen O.
Published: September 2009

Electrospray ionization mass spectrometry (ESIMS) and subsequent tandem mass spectrometry (MS/MS) analyses were used to study some important metathesis reactions with the first‐generation ruthenium catalyst 1, focusing on the ruthenium complex intermediates in the catalytic cycle. In situ cationization with alkali cations (Li+, Na+, K+, and Cs+) using a microreactor coupled directly to the ESI ion source allowed mass spectrometric detection and characterization of the ruthenium species present in solution and particularly the catalytically active monophosphine–ruthenium intermediates present in equilibrium with the respective bisphosphine–ruthenium species in solution. Moreover, the intrinsic catalytic activity of the cationized monophosphine–ruthenium complex 1 a⋅K+ was directly demonstrated by gas‐phase reactions with 1‐butene or ethene to give the propylidene Ru species 3 a⋅K+ and the methylidene Ru species 4 a⋅K+, respectively. Ring‐closing metathesis (RCM) reactions of 1,6‐heptadiene (5), 1,7‐octadiene (6) and 1,8‐nonadiene (7) were studied in the presence of KCl and the ruthenium alkylidene intermediates 8, 9, and 10, respectively, were detected as cationized monophosphine and bisphosphine ruthenium complexes. Acyclic diene metathesis (ADMET) polymerization of 1,9‐decadiene (14) and ring‐opening metathesis polymerization (ROMP) of cyclooctene (18) were studied analogously, and the expected ruthenium alkylidene intermediates were directly intercepted from reaction solution and characterized unambiguously by their isotopic patterns and ESIMS/MS. ADMET polymerization was not observed for 1,5‐hexadiene (22), but the formation of the intramolecularly stabilized monophosphine ruthenium complex 23 a was seen. The ratio of the signal intensities of the respective with potassium cationized monophosphine and bisphosphine alkylidene Ru species varied from [I4a]/[I4]=0.02 to [I23a]/[I23]=10.2 and proved to be a sensitive and quantitative probe for intramolecular π‐complex formation of the monophosphine–ruthenium species and of double bonds in the alkylidene chain. MS/MS spectra revealed the intrinsic metathesis catalytic activity of the potassium adduct ions of the ruthenium alkylidene intermediates 8 a, 9 a, 10 a, 15 a, and 19 a, but not 23 a by elimination of the respective cycloalkene in the second step of RCM. Computations were performed to provide information about the structures of the alkali metal adduct ions of catalyst 1 and the influence of the alkali metal ions on the energy profile in the catalytic cycle of the metathesis reaction.
Electronic Structure and Redox Properties of Metal Nitride Endohedral Fullerenes M3N@C2n (M=Sc, Y, La, and Gd; 2n=80, 84, 88, 92, 96)
Authors: Valencia Ramón , Rodríguez‐Fortea Antonio , Clotet Anna , de Graaf Coen , Chaur Manuel N. , Echegoyen Luis , Poblet Josep M.
Published: September 2009

An extensive study of the redox properties of metal nitride endohedral fullerenes (MNEFs) based on DFT computational calculations has been performed. The electronic structure of the singly oxidized and reduced MNEFs has been thoroughly analyzed and the first anodic and cathodic potentials, as well as the electrochemical gaps, have been predicted for a large number of M3N@C2n systems (M=Sc, Y, La, and Gd; 2n=80, 84, 88, 92, and 96). In particular, calculations that include thermal and entropic effects correctly predict the different anodic behavior of the two isomers (Ih and D5h) of Sc3N@C80, which is the basis for their electrochemical separation. Important differences were found in the electronic structure of reduced M3N@C80 when M=Sc or when M is a more electropositive metal, such as Y or Gd. Moreover, the changes in the electrochemical gaps within the Gd3N@C2n series (2n=80, 84, and 88) have been rationalized and the use of Y‐based computational models to study the Gd‐based systems has been justified. The redox properties of the largest MNEFs characterized so far, La3N@C2n (2n=92 and 96), were also correctly predicted. Finally, the quality of these predictions and their usefulness in distinguishing the carbon cages for MNEFs with unknown structures is discussed.