bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoglycosidase and Glycoamidase Release of N‐Linked Glycans
Authors: Freeze Hudson H. , Kranz Christian 
Published: January 2010

AbstractNearly all proteins entering the lumen of the endoplasmic reticulum (ER) become glycosylated en route to a cellular organelle, the plasma membrane, or the extracellular space. Many glycans can be attached to proteins, but the most common are the N‐linked glycans (oligosaccharides). These chains are added very soon after a protein enters the ER, but they undergo extensive remodeling (processing), especially in the Golgi. Processing changes the sensitivity of the N‐glycan to enzymes that cleave entire sugar chains or individual monosaccharides, which also changes the migration of the protein on SDS gels. These changes can be used to indicate when a protein has passed a particular subcellular location. This unit details some of the methods used to track a protein as it trafficks from the ER to the Golgi toward its final location. Curr. Protoc. Mol. Biol. 89:17.13A.1‐17.13A.25. © 2010 by John Wiley & Sons, Inc.
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
Authors: Blankenberg Daniel , Kuster Gregory Von , Coraor Nathaniel , Ananda Guruprasad , Lazarus Ross , Mangan Mary , Nekrutenko Anton , Taylor James 
Published: January 2010

AbstractHigh‐throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high‐throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large‐scale analysis with just a Web browser. Curr. Protoc. Mol. Biol. 89:19.10.1‐19.10.21. © 2010 by John Wiley & Sons, Inc.
Chromatin Interaction Analysis Using Paired‐End Tag Sequencing
Authors: Fullwood Melissa J. , Han Yuyuan , Wei Chia‐Lin , Ruan Xiaoan , Ruan Yijun 
Published: January 2010

AbstractChromatin Interaction Analysis using Paired‐End Tag sequencing (ChIA‐PET) is a technique developed for large‐scale, de novo analysis of higher‐order chromatin structures. Cells are treated with formaldehyde to cross‐link chromatin interactions, DNA segments bound by protein factors are enriched by chromatin immunoprecipitation, and interacting DNA fragments are then captured by proximity ligation. The Paired‐End Tag (PET) strategy is applied to the construction of ChIA‐PET libraries, which are sequenced by high‐throughput next‐generation sequencing technologies. Finally, raw PET sequences are subjected to bioinformatics analysis, resulting in a genome‐wide map of binding sites and chromatin interactions mediated by the protein factor under study. This unit describes ChIA‐PET for genome‐wide analysis of chromatin interactions in mammalian cells, with the application of Roche/454 and Illumina sequencing technologies. Curr. Protoc. Mol. Biol. 89:21.15.1‐21.15.25. © 2010 by John Wiley & Sons, Inc.
Mapping Networks of Protein‐Mediated Physical Interactions Between Chromatin Elements
Authors: Tiwari Vijay K. , Baylin Stephen B. 
Published: January 2010

AbstractUnderstanding of transcriptional regulation has advanced in recent years in part due to development of technologies which allow determination of physical proximities between interacting chromatin regions at a resolution beyond that offered by conventional microscopy techniques. However, these methods do not specifically identify the protein component(s) that might mediate such interactions. This unit provides a detailed protocol for Combined 3C‐ChIP‐Cloning (6C) technology, which combines multiple techniques to simultaneously identify physical proximities between chromatin elements as well as the proteins that mediate these interactions. The unit further explores how the 6C assay can be combined with other techniques for a complete, cell‐type‐specific mapping of all inter‐ and intrachromosomal interactions mediated by specific proteins. Thus, the 6C assay provides a useful tool to address the role of specific proteins in nuclear organization and to advance our understanding about the relation of chromatin higher‐order organization and transcriptional regulation. Curr. Protoc. Mol. Biol. 89:21.16.1‐21.16.13. © 2010 by John Wiley & Sons, Inc.
Methylation‐Sensitive Single‐Molecule Analysis of Chromatin Structure
Authors: Miranda Tina B. , Kelly Theresa K. , Bouazoune Karim , Jones Peter A. 
Published: January 2010

AbstractMethylation‐sensitive single‐molecule analysis of chromatin structure is a high‐resolution method for studying nucleosome positioning. As described in this unit, this method allows for the analysis of the chromatin structure of unmethylated CpG islands or in vitro–remodeled nucleosomes by treatment with the CpG‐specific DNA methyltransferase SssI (M.SssI), followed by bisulfite sequencing of individual progeny DNA molecules. Unlike nuclease‐based approaches, this method allows each molecule to be viewed as an individual entity instead of an average population. Curr. Protoc. Mol. Biol. 89:21.17.1‐21.17.16. © 2010 by John Wiley & Sons, Inc.
Overview of Very Small Embryonic‐Like Stem Cells (VSELs) and Methodology of Their Identification and Isolation by Flow Cytometric Methods
Authors: Zuba‐Surma Ewa K. , Ratajczak Mariusz Z. 
Published: January 2010

AbstractThe protocols presented here describe the procedures employed to identify and isolate very small embryonic‐like stem cells (VSELs) using flow cytometric technologies including fluorescence‐activated cell sorting (FACS). We describe the recommended steps in detail for their successful identification and isolation from adult tissues. These protocols were initially established to isolate such cells from murine bone marrow (BM) and human cord blood (CB) and may also be employed to isolate these primitive cells from other adult organs and embryonic tissues. Here, we focus on some critical parameters/key points required for the successful identification and purification of these rare cells by employing classical flow cytometry. In the last part of this unit, we also discuss a novel flow cytometric tool, ImageStream, an imaging flow cytometer, which allows better identification and morphological analysis of sorted cells. Curr. Protoc. Cytom. 51:9.29.1‐9.29.15. © 2010 by John Wiley & Sons, Inc.
Use of Flow Cytometric Methods to Quantify Protein‐Protein Interactions
Authors: Blazer Levi L. , Roman David L. , Muxlow Molly R. , Neubig Richard R. 
Published: January 2010

AbstractA method is described for the quantitative analysis of protein‐protein interactions using the flow cytometry protein interaction assay (FCPIA). This method is based upon immobilizing protein on a polystyrene bead, incubating these beads with a fluorescently labeled binding partner, and assessing the sample for bead‐associated fluorescence in a flow cytometer. This method can be used to calculate protein‐protein interaction affinities or to perform competition experiments with unlabeled binding partners or small molecules. Examples described in this protocol highlight the use of this assay in the quantification of the affinity of binding partners of the regulator of G‐protein signaling protein, RGS19, in either a saturation or a competition format. An adaptation of this method that is compatible for high‐throughput screening is also provided. Curr. Protoc. Cytom. 51:13.11.1‐13.11.15. © 2010 by John Wiley & Sons, Inc.
Real‐Time Embedded Software
Authors: Edwards Stephen A. 
Published: January 2010

AbstractReal‐time embedded software is responsible for observing and controlling systems in the physical world. Because of this role, it has timeliness requirements above and beyond that of traditional software: when it produces results is often as important the results themselves. The real‐time challenge, compounded with the usual difficulties of producing correct, complex software systems, makes producing real‐time embedded software all the more difficult.Such software runs on digital computing hardware, is usually structured following principles from real‐time scheduling, and often implements algorithms derived from control theory. Effective development of such software requires knowledge of these three fields.Low‐level concerns such as memory‐mapped I/O, polling, and interrupts are discussed first, followed by a discussion of how to simulate concurrency and PThreads. An introduction to real‐time scheduling theory follows, including a discussion of the rate‐monotonic approach. The article ends with a discussion of real‐time operating systems and the future of real‐time embedded software.
Hair Cells
Authors: Marcotti Walter , Masetto Sergio 
Published: January 2010

Abstract

Hair cells are the sensory receptors in the inner ear that detect sound and head motion to begin the processes of hearing and balance control. The defining feature of hair cells is the hair bundle, the transduction organelle protruding from their apical surface composed of ordered arrays of stereocilia. Mechanical deflection of the hair bundle, normally induced by physiological stimuli, increases the open probability of mechanically gated cation channels located at the tip of stereocilia. The resulting depolarizing inward current generates a receptor potential. The information encoded in this electrical response is transmitted to the auditory or vestibular afferent nerve fibres via the Ca
2+
‐induced release of neurotransmitter from the hair cell's basal pole. In this way sensory information is relayed to the brain enabling us to perceive sound and maintain balance. In mammals, hair cell loss causes irreversible balance and hearing impairment because these sensory cells show very little or no regenerative ability.

Key concepts:

Hair cells are the sensory receptors of both the auditory and vestibular systems in vertebrates.

Inner ear hair cells derive their name from the stereocilia that protrude from their apical surface, which are deflected as a result of sound (cochlea) or head movement (vestibular organs) and initiate the sensory transduction process.

Cochlear hair cells convert acoustic stimuli into electrical activity that allows the brain to perceive the sensation of hearing.

Vestibular hair cells inform the central nervous system of head position and movements.

The hair bundle, the defining feature of all hair cells, is the mechano‐receptive organelle directly responsible for mechano‐transduction, i.e. for converting the natural stimulus into a neural signal.

In mammals, hair cell loss due to acoustic over‐stimulation, ototoxic drugs, ageing and genetic defects is irreversible, leading to a permanent loss of function.
Substance P
Authors: Bremer Andrew A , Leeman Susan E 
Published: January 2010

AbstractSubstance P (SP) is an 11 amino acid bioactive peptide that causes diverse biological effects in the central nervous system (CNS), as well as in the cardiovascular, respiratory, gastrointestinal, immune and autonomic nervous systems. The principal actions of SP are mediated through its functional interaction with the neurokinin‐1 (NK‐1) receptor, which exists in two isoforms. Investigators are currently focusing on the structure–activity relationships between SP and the different NK‐1 receptor isoforms, as well as the signal transduction pathways involved in the many SP‐mediated responses. In addition, nonpeptide antagonists of SP have been and are continuing to be developed for clinical use. This article summarizes the basic biology of SP and its interaction with the NK‐1 receptor, highlights the role of SP and the neurokinin receptors in clinical disease states and then concludes with describing new exciting areas of SP‐related research.Key Concepts:Substance P is an 11 amino acid bioactive peptide that induces diverse biological responses.The principal receptor for substance P is the neurokinin‐1 receptor, which exists in two isoforms.Antagonists of substance P and the neurokinin‐1 receptor have been and are continuing to be developed for clinical use.Research in the area of substance P and the neurokinin‐1 receptor continues to provide more insight into the importance of these molecules in states of human health and disease.
Eukaryotic Replication Protein A
Authors: Humphreys Troy D , Wold Marc S 
Published: January 2010

Abstract

Replication protein A
(
RPA
) is a single‐stranded
deoxyribonucleic acid
(DNA)‐binding protein required for cellular DNA metabolism.
RPA
is a heterotrimeric complex composed of 70, 32 and 14 kDa subunits, commonly referred to as
RPA1
,
RPA2
and
RPA3
. Homologous complexes are found in all eukaryotes.
RPA
binds single‐stranded DNA with high‐affinity and low‐sequence specificity. In addition,
RPA
interacts specifically with, and modulates the activity of, many proteins required for DNA metabolism in cells.
RPA
primarily functions in the cell to stabilize single‐stranded DNA.
RPA
activity is essential for DNA replication, DNA repair and recombination. In addition,
RPA
is involved in the cellular DNA damage response. Disruption of
RPA
activity or of the activity of
RPA
‐interacting proteins is associated with many human diseases, including cancer.

Key Concepts:

Replication protein A (RPA) is the major eukaryotic single‐stranded DNA‐binding protein.

RPA is a heterotrimeric protein complex with a flexible structure; each subunit is composed of one or more DNA‐binding domains that are linked or flanked by flexible linkers and regulatory regions.

RPA participates in many cellular processes essential for life, including DNA replication and repair by binding to single‐stranded DNA intermediates and interacting with proteins required for these processes.
Stamens
Authors: Smyth David R 
Published: January 2010

Abstract

Stamens are the male reproductive organs of flowers. Typically, a stamen is made up of a pollen‐producing anther borne on a filament. Pollen arises in four sporogenous regions within the anther. The sporogenous cells are surrounded by nutritive support cells, the tapetum. Mature pollen is released from the anther by dehiscence of the anther wall. The developmental identity of the stamen is conferred by the combined action of MADS transcription factors. Subsequent cellular differentiation is under the control of a cascade of other transcription factor and signalling genes now being identified. Male sterility is useful in plant breeding, and may arise by loss‐of‐function of these genes, as well as by defects in mitochondria (cytoplasmic male sterility). Differences in the structure of stamens are associated with the types of pollinators involved. Stamens evolved from the microsporangia‐bearing organs of early seed plants.

Key Concepts:

Pollen is generated in stamens, the male reproductive organs of flowers.

Pollen arises from sporogenous cells within the anthers.

Sporogenous cells are surrounded by the tapetum, a nutritive layer of support cells.

Stamen identity is conferred by the action of MADS transcription factors controlling B, C and SEPALLATA function.

The transcription factor SPOROCYTELESS is required for generation of the sporogenous cells.

Other transcription factors and signalling kinases are required for the entire developmental cascade and are now being identified.

Mature pollen is released by dehiscence of the anther wall through slits called stomia.

The structure of stamens in a species is closely adapted to the specific pollinators involved for that species.

Pollen is also generated in nonflowering seed plants (gymnosperms and various extinct lineages), but it arises in leaf‐like organs (microsporophylls) rather than stamens.
Complement: Deficiency Diseases
Authors: Blom Anna M 
Published: January 2010

AbstractThe complement system is crucial for defence against pathogens, removal of unwanted materials such as dying cells or immune complexes as well as for development of adaptive immune responses. Genetically determined deficiencies of components of the complement system are usually relatively rare but they result in many severe diseases such as an increased susceptibility to recurrent, severe infections, autoimmune disorders (systemic lupus erythematosus), glomerulonephritis including membranoproliferative glomerulonephritis type II, paroxysmal nocturnal haemoglobinuria or angioedema. Recently, mutations and polymorphisms in complement proteins, particularly complement inhibitors, have been associated with atypical haemolytic uremic syndrome and age‐related macular degeneration. The elucidation of the pathophysiological basis for the different clinical presentations of complement‐deficient individuals has contributed to a better understanding of the physiological role of complement in normal individuals as well as to the development of emerging therapies.Key ConceptsThe majority of complement deficiencies are rare but cause severe diseases.Deficiencies of the early components of the classical pathway (C1q/r/s, C4, C2) predispose to systemic lupus erythematosus.The majority of complement deficiencies predispose to infections either withNeisseriaspecies (deficiency of Factor D, Properdin, C5, C6, C7, C8, C9) or Gram‐positive bacteria (C1q/r/s, mannose‐binding lectin, C2, C4, C3, factor I).Mutations in C1q/r/s, C2, C4, C3 and factor I can cause glomerulonephritis.Paroxysmal nocturnal haemoglobinuria is caused by deficiency of complement inhibitors CD55 and CD59.Hereditary angioedema is found in patients with dysfunctional C1‐inhibitor.Atypical haemolytic uremic syndrome is mainly associated with mutations and polymorphisms in complement inhibitors.Age‐related macular degeneration is associated with polymorphisms in complement inhibitor factor H.
Cerebrospinal Fluid and its Abnormalities
Authors: Chan Michael , Amin‐Hanjani Sepideh 
Published: January 2010

AbstractCerebrospinal fluid bathes the central nervous system, providing mechanical support and maintaining a stable environment. Alterations in its production, circulation or absorption result in a pathological condition termed hydrocephalus, characterized by an accumulation of fluid within the cranium, usually in the ventricles of the brain. Similarly, aberrations in the circulation or absorption of cerebrospinal fluid around the spinal cord can create a condition termed syringomyelia. Hydrocephalus can be life‐threatening due to increased intracranial pressure. The most common causes of hydrocephalus are related to obstruction of cerebrospinal fluid flow. In the pediatric population, causes of hydrocephalus include developmental abnormalities, infectious aetiologies, mass lesions, and haemorrhage. Causes of high pressure hydrocephalus in adulthood are primarily related to haemorrhage and tumour, although idiopathic normal pressure hydrocephalus (NPH) is also encountered. The management of hydrocephalus and syringomyelia relies primarily on neurosurgical interventions such as insertion of shunt devices.Key ConceptsCSF provides a mechanical support for the brain and spinal cord.Overproduction of CSF, obstruction to CSF flow or impaired absorption of CSF may lead to disease states such as hydrocephalus or syringomyelia.CSF diversion by means of shunting with catheter implantation or fenestration of anatomic barriers is the primary treatment for diseases of CSF disturbances.
Biological Data Centres
Authors: Stafford Phillip , Lee HoJoon 
Published: January 2010

Abstract

The age of genomics has pushed the cost of sequencing much lower than typical cost/ technology curves would predict. Sanger sequencing, next‐gen sequencing (ABI SOLiD sequencing, Illumina GA, Roche 454) and even whole‐chromosome imaging are providing sequence data faster than most laboratories can analyse or store. The biological data infrastructure that was established in the early 1990s is still in place, mostly because it was very well planned in terms of future needs. The three main biological data centres are NCBI (
http://www.ncbi.nlm.nih.gov/
), DDJB (
http://www.ddbj.nig.ac.jp/
) and EBI/EMBL (
http://www.ebi.ac.uk/embl/
). These centres will be discussed in the context of new types of high‐density biological data, such as microarrays of various sorts. This article will discuss history, the tools that are provided to the public, other biological databases that support and integrate with sequencing databases and a projection of biology in the future.

Key concepts:

Biological data is much denser today than it was even 10 years ago.

Sequencing DNA is faster, cheaper and more accurate today than it was 6 months ago, and far faster than it was 10 years ago. Data repositories have struggled to keep up.

Three main DNA sequence repositories exist: USA, Europe and Japan. These are mirrors of each other, but are also distinct.

Web‐based sequence analysis tools are presented.

Other high‐density databases are listed including GEO, BIND, pdb, HapMap, KEGG and GO.
Neutron Diffraction
Authors: Bradshaw Jeremy P 
Published: January 2010

Abstract

Neutron diffraction, a technique analogous to X‐ray diffraction, is well‐suited to the study of biological materials. By differentiating between hydrogen and its heavier isotope, deuterium, neutron diffraction is able to provide detailed information about the hydrogen atoms within biological macromolecules. It allows biologists to study solvation effects, protonation–deprotonation equilibria and hydrogen bonding, all of which are invisible to X‐ray techniques. Recent years have seen the construction of new neutron research facilities, notably the Spallation Neutron Source in the USA, the World's brightest neutron source. Even with such high‐flux sources, the intensity of neutrons hitting the sample is several orders of magnitude lower than a typical X‐ray experiment. However, the nonionizing nature of neutrons means that beam damage to the specimen is low, even over extended exposure times.

Key Concepts:

Neutron diffraction is closely related to the complementary technique of X‐ray crystallography, a method that led to a revolution in biological sciences.

Hydrogen plays a central role in many biological processes, but is invisible to X‐rays.

Neutrons are able to distinguish between hydrogen and deuterium, so selective deuteration of a single molecule or group can be used to locate it within a complex macromolecular assembly.

The neutron‐scattering contrast of samples can be controlled by changing the deuterium content of the solvent (water‐heavy water exchange).

Neutrons have the ability to discriminate between nitrogen, carbon and oxygen, which can be difficult with X‐rays.

Neutron experiments are carried out at large scale, national or international neutron research centres, because production of the neutrons requires a nuclear reactor or a spallation source.