bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring ice-capped active Volcán Villarrica, southern Chile, using terrestrial photography combined with automatic weather stations and global positioning systems
Authors: Rivera Andrés , Corripio Javier G. , Brock Ben , Clavero Jorge , Wendt Jens 
Published: March 2009

AbstractVolcán Villarrica (39°25′12″ S, 71°56′27″ W; 2847 m a.s.l.) is an active ice-capped volcano located in the Chilean lake district. The surface energy balance and glacier frontal variations have been monitored for several years, using automatic weather stations and satellite imagery. In recent field campaigns, surface topography was measured using Javad GPS receivers. Daily changes in snow-, ice-and tephra-covered areas were recorded using an automatic digital camera installed on a rock outcrop. In spite of frequently damaging weather conditions, two series of consecutive images were obtained, in 2006 and 2007. These photographs were georeferenced to a resampled 90 m pixel size SRTM digital elevation model and the reflectance values normalized according to several geometric and atmospheric parameters. The resulting daily maps of surface albedo are used as input to a distributed glacier-melt model during a 12 day mid-summer period. The spatial pattern of cumulative melt is complex and controlled by the distribution of airfall and wind-blown tephra, with extremely high melt rates occurring downwind of the crater and exposed ash banks. The camera images are also used to visualize the pattern of glacier crevassing. The results demonstrate the value of terrestrial photography in understanding the energy and mass balance of the glacier, including the generation of meltwater, and the potential value of the technique for monitoring volcanic activity and potential hazards associated with ice–volcano interactions during eruptive activity.
Cyclic Nucleotide‐gated Ion Channels
Authors: Zheng Jie , Matulef Kimberly 
Published: March 2009

Abstract

Cyclic nucleotide‐gated (CNG) ion channels are activated by cAMP or cGMP, crucial intracellular messenger molecules that regulate a wide variety of physiological activities. In photoreceptors and olfactory neurons, CNG channels play an essential role in transducing sensory stimuli into electrical and chemical responses. CNG channels are also found in other tissues including brain and sperm, where they may contribute to physiological functions including pacemaking, synaptic transmission and chemosensation. The exquisite regulation of different CNG channels by divalent cations, calmodulin, phosphorylation and phospholipids allows these proteins to carry out disparate physiological functions with high precision. Our understanding of the structure of these channels has been greatly enhanced by the recent determination of the structures of domains of related ion channels. The powerful combination of electrophysiology, biochemistry, patch‐clamp fluorometry and X‐ray crystallography has begun to unravel the mystery of how CNG channels are regulated and how the binding of cyclic nucleotides lead to channel opening.

Key concepts

Ion channels are membrane proteins that allow ions to diffuse across cellular membranes in a regulated manner.

CNG channels are ion channels regulated by the direct binding of cyclic nucleotides.

Photoreceptors are retinal cells that contain a high density of ion channels regulated by the binding of cyclic nucleotides.

Olfaction is the process of odour sensation, also regulated by the binding of cyclic nucleotides.

Permeation describes the ability of ion channels to selectively determine which ions can move through them.

Gating is the process by which ion channels open and close to control the flow of ions.

Structure/function describes the relationship between the 3D structure of an ion channel and its function.

Cyclic nucleotides are small ligands used to control the gating of CNG channels.
Extremophiles and Biotechnology
Authors: Antranikian G 
Published: March 2009

Abstract
Microbial diversity in extreme habitats, e.g. the deep subsurface, polar regions, salt lakes, hot springs, solfataric field and alklaine lakes, is very broad and delivers a valuable resource of unique enzymes (extremozymes) and chemical compounds. The study of these extremophiles will provide new keys to the understanding of life processes under stress conditions and will unravel the mechanisms developed by biological systems to cope to harsh conditions. This gained knowledge will be used to develop new biobased products and bioprocesses in various fields such as fine chemicals, feed, food, cosmetics, textile, paper and pharmaceutical industries.
Geminiviridae
Authors: Briddon Rob W , Stanley John 
Published: March 2009

Abstract

The
Geminiviridae
comprise a group of plant viruses with small, circular, single‐stranded
deoxyribonucleic acid
(DNA) genomes encapsidated in particles that have a twinned quasi‐icosahedral (geminate) shape, from which the family derives its name. They are among the smallest of viruses known and are transmitted exclusively by specific insect vectors. Some are associated with highly diverse circular, single‐stranded DNA betasatellites that are essential for disease progression. Their association with alphasatellites provides evidence of the interaction of geminiviruses with other families of plant‐infecting viruses. Collectively, geminiviruses are pathogens of cereals, vegetable and fibre crops, posing a serious threat to agriculture worldwide. Efforts to control these viruses by conventional means, such as using insecticides against their insect vectors and by breeding resistance, have either proven unsuccessful or have not been durable. For this reason, researchers are increasingly looking to engineered resistance as a means to control these important diseases.

Key Concepts:

Geminiviruses are important insect‐transmitted pathogens of cereal, vegetable and fibre crops in tropical and temperate regions throughout the World, including developed and developing countries.

Geminiviruses often cause striking symptoms in plants, indeed the earliest description of virus symptoms in plants is believed to relate to those caused by a geminivirus, and such symptoms occasionally are considered to be horticulturally desirable.

All geminiviruses have single‐stranded DNA genomes and a twinned particle morphology that is unique to this family of plant viruses.

Some geminiviruses are associated with single‐stranded DNA satellites, referred to as alphasatellites and betasatellites, the latter playing an essential role in maintenance of the disease.

Because their small DNA genomes encode only a limited number of genes, geminiviruses manipulate the metabolism of the infected cell to produce conditions suitable for their proliferation.

Geminiviruses are proving invaluable in the investigation of fundamental biological processes such as DNA replication, cell cycle regulation, gene expression and pathogen resistance in plants.

Geminiviruses are highly recombinogenic, and the derivation of a large number of geminivirus and satellite DNA sequences is providing important insights into their diversity, adaptability and evolution.

Conventional control strategies, such as the use of chemicals to eliminate their insect vectors and breeding natural host plant resistance, have proven ineffective in reducing crop losses to geminivirus infection, leading to the development of promising alternative (genetically engineered) strategies.

Sequences derived from geminiviruses are being used to develop systems for high‐level expression of valuable proteins in plants.
Haematopoietic Growth Factors
Authors: Thomas Daniel , Lopez Angel F 
Published: March 2009

Abstract
Haematopoietic growth factors regulate the production of all the cellular elements of blood by stimulating the proliferation, survival and differentiation of haematopoietic cells in various stages of maturation and also enhancing certain mature cell functions. Recombinant growth factors are used in the clinic to stimulate cell production as part of treatment for anaemia, neutropenia and thrombocytopenia and to aid in the collection of bone marrow stem cells.
Melanoma
Authors: Villanueva Jessie , Herlyn Meenhard 
Published: March 2009

Abstract

Melanoma is a form of skin cancer that originates from specialized cells in the skin called melanocytes. Environmental, biochemical, molecular and genetic factors are all involved in the genesis of melanoma. Although the incidence of melanoma continues to rise worldwide, no current effective treatment is available for metastatic disease. Thus, development of new and efficacious strategies to treat this aggressive disease is urgently needed. Understanding the molecular and cellular basis of melanoma initiation, progression and metastasis is critical to identify new targets for novel therapeutic approaches that would improve survival and offer hope to patients coping with this aggressive neoplasm.

Key Concepts:

Melanoma is a serious form of skin cancer that originates from pigment‐producing cells called melanocytes.

The incidence of melanoma continues to rise worldwide, constituting a serious public health problem.

Major risk factors for melanoma include exposure to UV radiation, fair skin, large number of dysplastic nevi and a family history of melanoma.

Multiple factors, including genetic, molecular and environmental contribute to the development of melanoma.

Mutations in genes critical for proliferation (e.g. BRAF) and survival (e.g. AKT) contribute to melanomagenesis.

Metastatic melanoma is highly resistant to current therapies.

Targeting signalling pathways that are essential for tumour progression and maintenance, such as BRAF/MAPK and PI3K/AKT, offer a rational approach for the development of effective antimelanoma therapies
Macrophage Function Disorders
Authors: Bowdish Dawn ME , Gordon Siamon 
Published: March 2009

Abstract
Macrophages respond to alterations in their microenvironment by producing a wide variety of products that mediate inflammation, immunity and tissue homeostasis or injury. Macrophage recognize pathogen‐associated molecular patterns (e.g. bacterial products) and endogenous ligands (e.g. apoptotic cells) through a broad and adaptable range of pattern‐recognition receptors. The consequence of this recognition is generally effective clearance via phagocytosis; however, when this is not effective macrophages may become inappropriately activated and initiate an inappropriate inflammatory response. Although primary deficiencies of macrophage function in human disease are relatively uncommon, there is increasing evidence that even subtle genetic changes in macrophage function contribute to altered responses to both acute infections and in many major acquired disease processes such as autoimmunity, inflammatory diseases and cancer.
Disorders with Synuclein Pathology and Parkinsonism
Authors: Kilarski Laura L , Buchman Vladimir L , Morris Huw R 
Published: March 2009

Abstract

A variety of neurodegenerative disorders are classified as synucleinopathies based on the presence of prominent
α‐synuclein
pathology. These diseases include Parkinson disease (PD) and dementia with Lewy bodies (with neuronal Lewy body formation) and multiple system atrophy (with glial cytoplasmic inclusions). The normal function of
α‐synuclein
includes regulation of pre‐synaptic vesicles. Autosomal dominant PD can be due to coding mutations or multiplications of the
α‐synuclein
gene (
SNCA
). The coding mutations are thought to lead to a gain of function, in particular acceleration of the formation of proto‐fibrils. Duplications and triplications of
SNCA
lead to autosomal dominant PD with a gene dosage effect on age of onset and clinical severity; variants in the
SNCA
promoter which lead to an upregulation of
SNCA
expression are associated with an increased risk of sporadic PD.

Key concepts

αhyphen;Synuclein is deposited in the common neurodegenerative conditions Parkinson disease (PD), and dementia with Lewy bodies as neuronal cytoplasmic inclusions (Lewy bodies).

The normal function of αhyphen;synuclein is incompletely understood but is likely to involve interaction with, and regulation of synaptic vesicles.

There is some evidence that αhyphen;synuclein may have a role as a cellular chaperone and in interacting with the proteasome.

Mendelian coding mutations in the αhyphen;synuclein gene (SNCA) can lead to autosomal dominant PD and dementia with Lewy bodies (DLB).

SNCA mutations lead to an enhancement of protofibril formation as well as affecting normal
αhyphen;synuclein
function.

SNCA duplications and triplications lead to autosomal dominant PD: an increase in the transcription of normal sequence SNCA can lead to disease.

Promoter variation at the SNCA is associated with PD; in vitro evidence suggests that protective promoter alleles lead to a downregulation of SNCA expression.
Modelling of Plant Growth and Development
Authors: Rolland‐Lagan Anne‐Gaëlle 
Published: March 2009

AbstractThe development of an organism results from complex interactions between biophysical and biochemical processes and is very dynamic. Therefore the mechanisms at play are best studied using computer simulations. The large amount of molecular data on multiple aspects of plant development and advances in plant imaging make it possible to use simulation modelling as a tool to complement experimental studies. For instance, models of gene regulation networks can predict genetic interactions, which can later be tested experimentally. Models of pattern formation in the root and the shoot based on the transport of the plant hormone auxin can simulate the localization of proteins involved in auxin efflux as well as generating realistic profiles of auxin distribution. Models are also starting to incorporate growth and the role of mechanical forces in development, which should provide a link between molecular biology studies and biophysics.Key conceptsPlant development is highly dynamic as pattern formation and growth occur concurrently.Modelling studies which can account for observed experimental data suggest genetic interactions in space can generate spatial patterns during plant development in a similar way to reaction‐diffusion mechanisms initially postulated in the middle of the twentieth century.Models of the relation between auxin gradient and root growth suggests the plant hormone auxin acts similarly to a morphogen. In the case of auxin the response to the morphogen may affect the morphogen gradient. This feedback mechanism can generate patterns similar to reaction diffusion and may account for phyllotaxis and leaf vein pattern formation. Experimental data is still needed to link models of auxin‐regulated pattern formation with gene regulatory networks.Mechanical forces affect growth and pattern formation. Methodologies are being developed to model the biomechanics of growth and integrate patterning through chemical and physical processes at various scales of organization.
Plant Innate Immunity
Authors: Staal Jens , Dixelius Christina 
Published: March 2009

Abstract
The ability to discriminate between self‐ and nonself‐molecules is characteristic of all living organisms. This feature forms the basis for the activation of innate immune responses upon microbial attack. If microbes bypass the external physical barrier, plants have evolved two classes of immune receptors to detect nonself‐molecules to prevent further pathogen progress. One class consists of membrane‐resident pattern‐recognition receptors that sense molecules from microbes, the so‐called microbe‐associated molecular patterns (MAMPs). The second class consists of plant resistance (R) proteins that have capacity to detect directly or indirectly isolate‐specific pathogen effectors encoded by avirulence genes. These receptors are mainly intracellular. An alternative route is effector molecules that act as transcription factors. Signal transduction cascades link recognition and defence responses through second messengers, transcription factors and crosstalk between plant hormones to fine‐tune the overall response.
Biological Impacts of Climate Change
Authors: McCarty John P , Wolfenbarger L LaReesa , Wilson James A 
Published: March 2009

Abstract

Climate has far reaching impacts on biological systems. Survival and reproduction depend on how well adapted individuals are to local climate patterns. Climate change can disrupt the match between organisms and their local environment, reducing survival and reproduction and causing subsequent impacts on populations or species’ distributions across geographic regions. Climate change may benefit some species and cause extinction for others. Cumulatively, it will alter biological communities and the functioning of ecosystems. The Earth is already experiencing sufficient climate change to affect biological systems; well‐documented changes in plant and animal populations are related to recent climate change. Predicting future biological impacts of climate change remains a formidable challenge for science.

Key concepts

Climate has a pervasive influence on individual plants and animals, populations, communities and entire ecosystems.

Changes in climate will have far reaching effects on all aspects of biology.

Changes in climate over the past several decades have already produced measurable changes in biological systems worldwide.

Species can respond to climate change by moving to areas where climate is favourable, by evolving to cope with the challenges posed by new environmental conditions, or, if climate changes too rapidly, by going extinct.

Analysing recent trends give us certainty that changes will occur in biological systems valued by humans. Many of those changes will have negative impacts on human well‐being but there will also be changes that benefit people.

Scientists try to predict how biological systems will change by analysing past changes in response to climate change, by conducting experiments and by constructing models.

Uncertainty in predictions of biological change comes both from uncertainty about the rate of future climate change and from uncertainty about the direct and indirect effects of climate change on biological systems.
Mitochondria as a Key Determinant of Aging
Authors: Walter Ludivine , Lee Siu Sylvia 
Published: March 2009

Abstract
For a long time, mitochondria have been considered as primary targets of the aging process, notably through accumulation of oxidative damage and mitochondrial deoxyribonucleic acid (DNA) mutations that lead to gradual decline of mitochondrial function. Recent investigations in various model organisms have revealed conserved molecular pathways that can impact longevity. Intriguingly, some of these longevity pathways involve proteins with key functions in the mitochondria. Furthermore, a growing number of studies indicate that signals emanated from mitochondria can directly impact the longevity of the whole organism. Thus, the mitochondrion organelle likely plays an active and causal role in longevity determination. This renders mitochondria a key determinant in the complex network of physiological signals that modulates longevity.
Phylogenetic Methods in Ecology
Authors: Ackerly David D 
Published: March 2009

AbstractPhylogenetic comparative methods, incorporating patterns of similarity among close relatives, are an important tool in the ecological research. In tests of adaptive hypotheses, examining interspecific correlations between traits and environmental conditions, independent contrasts and related methods address the statistical nonindependence among species due to common ancestry. In community ecology, patterns of co‐occurence among related species provide insights into community assembly processes. In conservation biology, phylogenetic diversity can be an important assessment tool to prioritize species assemblages. Developments in phyloinformatics and improved phylogenies for different groups will promote expanded use of comparative methods in many areas of ecology.Key conceptsComparative biology focuses on similarities and differences among species to test hypotheses in ecology, evolutionary biology and related fields.Closely related species tend to be ecologically similar, reflecting their descent from a common ancestor. This similarity must be considered in tests of adaptive correlations between organismal traits and environmental conditions, as it can create statistical nonindependence among species.The method of phylogenetic independent contrasts, which compares trait values of related species across a phylogeny, provides a robust method to address the nonindependence of species and is widely used in ecology.A variety of processes influence the assembly of ecological communities. Communities may be composed of species that are ecologically similar, reflecting shared adaptations to the environment (known as environmental filtering), or species that are ecologically distinct, as predicted if biotic interactions such as competition or facilitation play an important role.The study of phylogenetic community structure – the degree of relatedness of co‐occurring species – provides insight into the processes influencing community assembly. Co‐occurrence of close relatives is likely caused by environmental filtering, whereas a variety of processes may lead to co‐occurrence of more distant relatives, including competition, facilitation and convergent evolution.Phylogenetic diversity – which can be measured as the sum of the branch lengths in a phylogeny – provides a valuable tool in conservation biology. Targeting areas with high phylogenetic diversity may be an efficient means to maximize conservation of taxa with high diversity of ecological and economic features.Phylogenetic approaches are an important tool to integrate ecological and evolutionary processes across a range of temporal and spatial scales.
Population Genetics of Plant Pathogens
Authors: Zhan Jiasui 
Published: March 2009

AbstractPopulation genetics of plant pathogens considers the origin, maintenance and distribution of genetic variation under the influence of mutation, gene flow, recombination, genetic drift and selection. Intensive monoculture in modern agriculture creates a best environment for pathogens to colonize, reproduce and transmit. Global trade of agricultural products and germplasm exchange for breeding programme may also facilitate the evolution of plant pathogens. Sustainable disease management programmes need to integrate host resistance, fungicide application, resistance gene deployment and other strategies, such as good sanitation and efficient quarantine.
Fungicides for Plant Diseases
Authors: Hollomon Derek W 
Published: March 2009

AbstractFungicides are essential for maintaining healthy crops, and consistent yields of high quality produce. This is unlikely to change in the foreseeable future. Protectant fungicides prevent infection, are phytotoxic so remain on leaf surfaces protecting only foliage existing when treatments are applied. Eradicant (curative) fungicides control existing infections, are not phytotoxic and xylem mobile so protect new foliage appearing after treatment. Protectant fungicides are usually multi‐site inhibitors whereas eradicants only inhibit one step in a metabolic pathway. A major constraint is loss of fungicides through resistance. Mixtures or alternation of low‐risk multi‐site inhibitors and high‐risk single‐site inhibitors underpins resistance management strategies. Examples are given for modes of action and resistance mechanisms for key active ingredients. Fungicide chemistry has provided increasingly active, but environmentally safe, compounds allowing lower dose rates. This trend is likely to continue through inhibition of regulatory rather than metabolic pathways.Key concepts:Differences between protectant and eradicant fungicides.Differences between multi‐site and single‐site inhibitors.Fungicide modes of action.Management of fungicide resistance.