bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endocytic Organelles: Methods for Preparation and Analysis
Authors: Guimaraes de Araujo Mariana Eca , Fialka Irene , Huber Lukas A 
Published: December 2010

AbstractEndocytic organelles can be prepared using a variety of techniques. Methods include the homogenisation of cells, the isolation of endosomes by density centrifugation, electromigratory techniques, immunoisolation and fluorescence‐activated organelle sorting (FAOS). The integration of these biochemical techniques with large‐scale proteomics has lead to the rapid expansion of the organelle proteomes characterised. Unfortunately, several limitations have been uncovered. First, the isolation of pure endosomal compartments is rarely achieved. Second, the constant flux of proteins from and to a specific organelle leads to variations in proteome composition that are often time‐ and signalling‐dependent. Innovative approaches such as protein correlation profiling (PCP) and localisation of organelles by isotype tagging (LOPIT) may, in the near future, bring us closer to our aim: the generation of a detailed and reliable organelle proteome chart that accounts for time‐ and signalling‐dependent fluxes as well as variations in the posttranslational modifications (PTMs) observed.Key Concepts:The quality of subcellular organelle purification depends to a great extent on the homogenisation procedure.Upon homogenisation, several methods can be employed to enrich the organelle of choice (density centrifugation, electromigratory techniques, immunoisolation and FAOS).Subcellular organelle proteomes have been uncovered by the powerful combination of cell biology/biochemistry techniques with large‐scale proteomics.Innovative methodologies are being established to overcome some of the caveats observed on the initial organelle proteome studies.Future organelle proteome studies will focus on the dynamics of protein association with organelles (time and signalling specificity). They will also focus on posttranslational modifications and their direct impact on protein function.
Cell Staining: Fluorescent Labelling of the Golgi Apparatus
Authors: Dejgaard Selma Y , Dejgaard Kurt , Presley John F 
Published: December 2010

Abstract

Immunofluorescence has been the primary method for labelling the Golgi apparatus for light microscopic observation in fixed cells. The Golgi apparatus was initially labelled in living cells by using that the fluorescent ceramide analogue
N
‐6[7‐nitro‐2,1,3‐benzoxadiazol‐4‐yl] aminocaproyl sphingosine or by microinjection of fluorescently conjugated antibodies to exposed Golgi epitopes. With the common availability of the green fluorescent protein (GFP) and advanced fluorescence microscopes including confocal microscopes, imaging of the Golgi apparatus in living cells is now a major experimental approach. Time‐lapse imaging of living cells has also been combined with photobleach techniques in order to study the dynamics of transient protein association with the Golgi apparatus. Similar approaches have been used to study the dynamics of the cargo transport through the exocytic pathway.

Key Concepts:

Immunofluorescence can be used to visualise proteins in the Golgi apparatus or its subdomains.

Live‐cell visualisation of the Golgi apparatus is possible with GFP‐tagged proteins.

Photobleaching and photoactivation techniques permit visualisation of protein dynamics and flux through the Golgi apparatus in living cells.
Nucleolus: Structure and Function
Authors: Olson Mark OJ 
Published: December 2010

Abstract

The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells. The nucleolar organiser regions of chromosomes, which contain the genes for pre‐ribosomal
ribonucleic acid
(rRNA), serve as the foundation for nucleolar structure. The nucleolus disassembles at the beginning of mitosis, its components disperse in various parts of the cell and reassembly occurs during telophase and early G1 phase. Ribosome assembly begins with transcription of pre‐rRNA. During transcription ribosomal and nonribosomal proteins attach to the RNA. Subsequently, there is modification and cleavage of pre‐rRNA and incorporation of more ribosomal proteins and 5S rRNA into maturing pre‐ribosomal complexes. The nucleolus also contains proteins and RNAs that are not related to ribosome assembly and a number of new functions for the nucleolus have been identified. These include assembly of signal recognition particles, sensing cellular stress and transport of human immunodeficiency virus 1 (HIV‐1) messenger RNA.

Key Concepts:

The nucleolus, whose primary function is to assemble ribosomes, is the largest structure in the cell nucleus.

The nucleolus organiser regions of chromosomes, which contain the genes for pre‐rRNA, are the foundation for the nucleolus.

All active nucleoli contain at least two ultrastructural components, the nucleolar dense fibrillar component representing early pre‐ribosomal complexes and the granular component containing more mature pre‐ribosomal particles.

Most nucleoli in higher eukaryotes also contain fibrillar centres, which are the interphase equivalents of the nucleolus organiser regions.

The nucleolus disassembles at the beginning of mitosis and begins to reassemble in telophase.

Ribosome assembly begins with the transcription of pre‐rRNA by RNA polymerase I.

Ribosomal and nonribosomal proteins and 5S RNA associate with the pre‐rRNA during and after transcription.

The pre‐rRNA is modified and processed into rRNA with the aid of nonribosomal proteins and small nucleolar RNAs.

The nucleolus has numerous other functions including assembly of signal recognition particles, modification of transfer RNAs and sensing cellular stress.
Desminopathy
Authors: Goldfarb Lev G , Olivé Montse , Vicart Patrick , Goebel Hans H 
Published: December 2010

Abstract

Desminopathy is one of the newly identified myopathies caused by mutations in
desmin
(
DES
), an intermediate filament, or
αB‐crystallin
(
CRYAB
), a chaperone for

DES

. The condition is defined as skeletal and cardiac myopathy characterised by the presence of chimeric aggregates in muscle fibre areas that consist of

DES

,

CRYAB

and other proteins. Identification of pathogenic mutations, analysis of underlying disease phenotypes and successful modelling of these conditions in cell cultures and transgenic mice specified critical pathogenic events. As the range of desminopathy clinical manifestations is extremely wide and myopathology not specific, diagnostic criteria need to be reliably outlined and molecular testing readily available to ensure prevention of sudden death from cardiac arrhythmias and other complications.

Key Concepts:

Desminopathy is associated with mutations in desmin (
DES
) and αB‐crystallin (
CRYAB
) genes.

DES
is a muscle‐specific type III intermediate filament; most of the known disease‐associated
DES
mutations affect domains that are crucial for filament assembly.

CRYAB
serves as a chaperone for
DES
and, if mutated, causes a disease identical to desminopathy.

In humans and transgenic mice,
DES
and
CRYAB
mutants invoke accumulation of chimeric intracellular aggregates containing
DES
,
CRYAB
and other cytoskeletal proteins.

DES
mutations show diverse pathogenic effects depending on the structural relationships these mutations disrupt and the type of inheritance.

Desminopathy is a skeletal and cardiac myopathy. Muscle imaging (CT and MRI) is helpful in identifying characteristic patterns of skeletal muscle involvement.

Atrioventricular conduction abnormalities and arrhythmias are regularly present in desminopathy patients; they require urgent implantation of a permanent pacemaker or an implantable cardioverter defibrillator (ICD).

Respiratory insufficiency can be a major cause of disability and death and may require continuous positive airway pressure (CPAP).

Molecular testing of patients for
DES
and
CRYAB
mutations is available and should be used to ensure prevention of sudden death from cardiac arrhythmias and other complications.
Genetics of Glaucoma
Authors: Liu Yutao , Allingham R Rand 
Published: December 2010

Abstract

Glaucoma is the major cause of blindness worldwide. Primary open‐angle glaucoma (POAG) and angle closure glaucoma (ACG) are the most prevalent forms of glaucoma and are the most common causes of glaucoma‐related blindness worldwide. It has become increasingly clear that a host of genetic and environmental factors contribute to the glaucoma phenotype. The genetic discussion covered in this review includes POAG, pigment dispersion glaucoma (PDG), exfoliation glaucoma (XFG), childhood glaucomas and angle closure glaucoma. Numerous chromosomal loci and genetic associations have been reported for different types of glaucoma. This article examines the current status of investigations into the genetic architecture of the glaucomas and how this evolving understanding may contribute to the clinical management of patients with this disease.

Key Concepts:

Glaucoma is characterised by the progressive loss of retinal ganglion cells that is associated with a characteristic optic neuropathy and visual field loss.

POAG (primary open‐angle glaucoma) is the most common type of glaucoma and is characterised by the presence of glaucomatous optic neuropathy without an identifiable secondary cause.

XFG (exfoliation glaucoma) is the most common identifiable form of open‐angle glaucoma.

PCG (primary congenital glaucoma) is the most common childhood glaucoma with a developmental abnormality of the anterior chamber angle.

Genetic linkage analysis has been widely used to search for genes that account for Mendelian diseases inherited as either autosomal dominant or recessive traits.

Genetic admixture mapping is widely used to localise disease‐associated genetic variants that differ in prevalence across populations.

Genome‐wide association study (GWAS) is a powerful method used to identify common genetic variants that are associated with the specific diseases or trait.

Genetic association analysis has been widely used to determine whether a genetic variant is associated with a disease or trait.
Pathogenesis of Polyglutamine Diseases
Authors: Pennuto Maria , Sambataro Fabio 
Published: December 2010

Abstract

Polyglutamine (polyQ) diseases are neurodegenerative disorders caused by expansion in specific genes of a trinucleotide repeat, cytosine–adenine–guanine (CAG), which encodes glutamine. In 1991, CAG repeat expansion in the androgen receptor was linked to spinal and bulbar muscular atrophy (SBMA), thus indicating for the first time a causative role of polyQ expansion in neurodegenerative disorders. Subsequently, polyQ expansions in eight other genes were shown to be responsible for different neurodegenerative diseases, including Huntington disease, dentatorubral‐pallidoluysian atrophy and six types of spinocerebellar ataxia. PolyQ diseases share several features, such as the phenomenon of genetic anticipation, and that to be late‐onset and progressive disorders. Despite these and other common features, specific populations of neurons are vulnerable in each disease. Approximately 20 years after the discovery of expanded polyQ as a leading cause of neurodegeneration, why selective neuronal populations degenerate in each disorder is still an enigma.

Key Concepts:

Polyglutamine diseases are a family of late onset, genetically inherited neurodegenerative disorders.

Polyglutamine diseases are caused by expansion of the CAG trinucleotide repeat encoding glutamine in nine different genes.

Expansion of polyglutamine confers a novel, toxic gain of function to the mutant protein.

The length of the polyglutamine tract correlates with disease onset and dictates disease severity.

Polyglutamine proteins are ubiquitous. None the less, expansion of polyglutamine tracts causes selective neuronal dysfunction and degeneration.

Specific populations of neurons degenerate in each polyglutamine disease, giving rise to different clinical disease manifestations.
Ecological Role of Viruses in Aquatic Ecosystems
Authors: Hewson Ian , Chow Cheryl , Fuhrman Jed A 
Published: December 2010

Abstract

Over two decades of research have indicated that viruses play crucial roles in aquatic food webs as active constituents of the microbial loop and in the population ecology of both prokaryotic and eukaryotic microorganisms. Over the past 5 years, there has been a sharp increase in reported aquatic virus research, notably in the areas of freshwater viral ecology, viruses of eukaryotic microorganisms and viral genetic diversity. Recent studies of the interactions between viral infection, bacterivory and grazing have demonstrated the complex dynamics of viral infection within aquatic ecosystems. These reports have helped solidify our understanding of the environmental controls on viral abundance, impacts of viral infection upon host community structure and have elucidated new roles of viruses in biogeochemical cycles – such as photosystem gene expression. Previously unrecognised groups of viruses (
ribonucleic acid
viruses and single‐stranded
deoxyribonucleic acid
viruses) have also been revealed as diverse and active components of marine virioplankton assemblages.

Key Concepts:

Viruses are the most numerically dominant organisms on earth, and their abundance varies between habitats, often according to local primary productivity.

Both viral activity and bacterivory contribute significantly to bacterial mortality in aquatic ecosystems, which in turn influence global‐scale biogeochemical cycles.

Methodological advances, such as metagenomics and genomics, have greatly facilitated studies of marine viruses and resulted in key discoveries on viral diversity, viral–host gene transfer and viral influence on host cell physiology.

Photosystem genes are common in cyanophage and are hypothesised to enhance viral production rates.

Viral‐induced mortality may be a key factor in controlling or terminating algal blooms.
Genome‐wide Association Studies of Cancers
Authors: Ku Chee Seng , Naidoo Nasheen , Hartman Mikael , Pawitan Yudi 
Published: December 2010

Abstract

Advances in high‐throughput genotyping technologies have enabled the efficient systematic screening of single‐nucleotide polymorphisms (SNPs) throughout the human genome for disease associations in genome‐wide association studies (GWAS). Many human complex diseases have been interrogated by GWAS; these include autoimmune and chronic inflammatory diseases, neurological and neuropsychiatric diseases, cardiovascular diseases and cancers among others. Presently, more than 60 cancer GWAS have been published and numerous novel SNPs and genetic loci were found to be associated with various cancers such as breast, prostate and colorectal cancers. These SNP associations were supported by robust statistical evidence. The GWAS of cancers have so far focused only on SNPs. Other germline genetic variations such as small insertions and deletions (indels), copy number variations (CNVs) and tandem repeat polymorphisms should also be investigated for their associations with cancers in the future.

Key Concepts:

Cancer is similar to other complex diseases in that it is a consequence of complex interactions between multiple genetic factors and environmental exposures.

The genetic susceptibility of cancer has been previously established by epidemiological, twin and familial aggregation studies.

The implication of a genetic component in the aetiology of cancer has driven enormous research endeavours to identify the genetic risk factors.

The candidate gene association and linkage analysis approaches to identifying these genetic risk factors has, however, generated inconsistent results in the past.

Notable advances have been achieved in recent years by genome‐wide association studies (GWAS) – where several hundred–thousand single nucleotide polymorphisms (SNPs) throughout the human genome are interrogated for disease associations.

Numerous novel genetic loci or genes have been implicated in a variety of cancers by GWAS.

This significant progress in dissecting the germline genetic component of cancers is credited to the development of high‐throughput genotyping technologies, which has enabled GWAS to be done more efficiently on thousands of samples.

Similar to other complex diseases, most of the GWAS‐identified SNPs for cancers have small effect sizes (OR <1.5) and collectively only account for a small fraction of the heritability of cancers.

Several practical steps to further uncover additional genetic loci for cancers include (a) extending GWAS in different populations, (b) meta‐analysis, (c) subgroup analysis and (d) a second tier of replication.

In addition, other approaches should also be considered such as investigating rare variants or less common SNPs, targeted resequencing of the GWAS‐identified loci, copy number variations and homozygosity mapping analysis.
Prochlorococcusand Other Photosynthetic Picoplankton
Authors: Moore Lisa R 
Published: December 2010

AbstractThe smallest yet most abundant photosynthetic organism on earth is the marine cyanobacterium,Prochlorococcus, which represent a key component in marine ecology and global biogeochemical cycles. This tiny cell is extremely successful, dominating throughout the surface photic zone of the subtropical and tropical low nutrient, oligotrophic regions of the world's oceans from ∼45 °N to 40 °S. It has evolved to be an oligotrophic specialist, through a reduction in cell size, a streamlined genome and a reduced cellular requirement for the limited resources available in this environment. The ability to examine the abundance and distribution ofProchlorococcusin the wild, and measure its genomic and metabolic properties in the lab and field, has madeProchlorococcusa model system for advancing our understanding of the ecology of marine microbes.Key Concepts:The smallest photosynthetic cells in the oceans (picophytoplankton) dominate numerically and contribute significantly to primary production on a global scale.Prochlorococcusis a cyanobacterium with a reduced cell size and streamlined genome providing it with advantages over other phytoplankton in oligotrophic oceans around the world.The ability to measure genomic and metabolic properties in natural populations and isolates, and the ability to follow population dynamics, makesProchlorococcusan excellent model system for studying microbial ecology on all scales.
Remipedia and the Evolution of Hexapods
Authors: von Reumont Björn M , Burmester Thorsten 
Published: December 2010

Abstract

With more than a million species that have already been described, the hexapods (insects and allies) constitute the largest animal group. Still their origin and phylogenetic affinities are matter of intense debate. Although previous morphological work generally considered the millipedes as sister taxon of the hexapods, molecular phylogenetic analyses agree that hexapods are actually closely related to crustaceans. Recent studies have provided evidence that the Remipedia, enigmatic crustaceans that have been discovered only 30 years ago in anchialine cave systems, may be the closest living relatives of hexapods. Support for this hypothesis comes from similar brain architecture, presence of an insect‐type respiratory haemocyanin in remipedes and phylogenomic studies. Thus hexapods may have evolved from a Remipedia‐like marine crustacean. These data evokes doubt on the generally described hypotheses in textbooks that might present an outdated picture of arthropod phylogeny.

Key Concepts:

Hexapods are the most successful animal group, but their relationship to other arthropods and evolutionary origins are matter of debate for more than a century.

Molecular phylogenetic studies have demonstrated that crustaceans are the closest living relatives of hexapods.

Crustaceans are most likely paraphyletic in terms of hexapods, thus one crustacean taxon is more closely related to the hexapods than the other crustaceans.

Brain morphology, haemocyanin structure and evolution, and phylogenomic studies suggest that the crustacean class Remipedia are the closest living relatives of hexapods.

Remipedia live in anchialine caves, which connect the inland ground water body with the salt water from the ocean.

Remipedia harbour a mixture of ancestral and derived morphological characters.

First hexapods may have evolved from marine Remipedia.

Remipedia thus occupy a key position for understanding hexapod evolution.
Nucleic Acid Structural Energetics
Authors: Vieregg Jeffrey R. 
Published: December 2010

AbstractNucleic acids perform many functions essential for life, and exhibit a correspondingly diverse array of structures. This article provides an overview of nucleic acid structure, as well as the forces that govern its formation. The current state of knowledge of nucleic acid thermodynamics is discussed, as well as techniques for predicting and designing structures of interest. Experimental methods used to determine the structure of nucleic acids and the thermodynamics of their reactions are also surveyed.
Electrochemical Detection Methods Following Liquid Chromatography, Capillary Electrophoresis, and Microchip Electrophoresis Separations
Authors: Hulvey Matthew K. , Lunte Susan M. , Fischer David J. , Kuhnline Courtney D. 
Published: December 2010

AbstractElectrochemical detection has proved to be an invaluable tool for analytical applications in a variety of research areas including environmental analysis, materials research, bioanalysis, and neuroscience. While some electrochemical techniques function as stand‐alone methods, a few techniques, including amperometry, conductivity, and voltammetry, have been found to be useful as detectors for separation‐based methods. Electrochemistry (EC) has the ability to provide chemical reduction/oxidation (redox) information about the analytes of interest and can be utilized for direct, quantitative analysis if the number of electrons in the redox process is known. Additional advantages of electrochemical detection include low detection limits, high selectivity, portability, low cost, and the ability to miniaturize the system without a loss in sensitivity. This article focuses on the principles and applications of EC detection in liquid chromatography (LC), capillary electrophoresis (CE), and microchip electrophoresis (ME) systems. Topics include an overview of electrochemical detection schemes and electrode materials, a brief introduction to LC, CE, and ME, and discussions of applications of the above‐mentioned detection schemes to these separation methods.
Matrix Methods in Analytical Spectroscopy
Authors: Roach Carol A. , Neal Sharon L. , Vincent‐Finley Rachel E. 
Published: December 2010

AbstractThe goal of this article is to survey the matrix methods that spectroscopists and data analysts are using to recover chemical information from electronic and vibrational spectral measurements. After an introduction, we review the principles of the spectral measurements at the focus of this article as it defines notation and describes several types of spectral measurements that are either acquired or analyzed in matrix format. These include steady‐state, dynamic, and correlation data. Next, we provide a rigorous mathematical description of the most important numerical methods for matrix analysis. Finally, five classes of matrix analysis methods that have been applied to molecular spectra are surveyed: exploratory data analysis, pattern recognition, spectral calibration, curve resolution, and multiway data methods. Short discussions about software alternatives and future developments are also included. A description of the notational conventions followed and algorithm listings are also provided.