bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 at the immunological and T-lymphocytic virological synapse
Authors: Haller Claudia , Fackler Oliver T. 
Published: August 2008

Abstract
Cell-cell transmission of human immunodeficiency virus type 1 (HIV-1) is considered the most effective mode of viral spread in T-lymphocyte cultures. Evidence has accumulated that HIV-1 assembles polarized synaptic-like structures, referred to as virological synapses, as specialized sites of viral transfer. Interestingly, it was recently also discovered that HIV-1 impairs the formation of the structurally similar immunological synapse, thereby modulating exogenous T-lymphocyte stimulation to yield an optimal activation state for productive HIV-1 infection. The careful dissection of these opposing effects will contribute to our understanding of retroviral spread and cellular signal transduction machineries.
Taxonomy and molecular phylogeny of Arthrobotrys mangrovispora, a new marine nematode-trapping fungal species
Authors: Swe Aung , Jeewon Rajesh , Pointing Stephen B. , Hyde Kevin D. 
Published: August 2008

Abstract

Arthrobotrys mangrovispora sp. nov. (fungi) isolated from decaying submerged wood in mangroves of Hong Kong is described and illustrated. The species closely resembles A. scaphoides and A. microscaphoides, but is distinguished by its conidial shape and size and septum number. Conidia vary in shape; they are broadly turbinate to elongate-fusoid, range from 25–(38.9)–50×12– (17.3)–24 μm, and possess 0–3 septa. The proportions of conidia with 0, 1, 2 or 3 septa are 6%, 23.5%, 50% and 20.5%, respectively. The new species forms adhesive network trapping devices. Phylogenetic analyses of nuclear and protein-coding DNA sequences (28S, ITS and a combined ITS+β-tubulin dataset) indicate that the new taxon should be assigned to Arthrobotrys.
Mutagenic and Recombinagenic Responses to Defective DNA Polymerase δ Are Facilitated by the Rev1 Protein in pol3-t Mutants of Saccharomyces cerevisiae
Authors: Mito Erica , Mokhnatkin Janet V , Steele Molly C , Buettner Victoria L , Sommer Steve S , Manthey Glenn M , Bailis Adam M 
Published: August 2008

Abstract
Defective DNA replication can result in substantial increases in the level of genome instability. In the yeast Saccharomyces cerevisiae, the pol3-t allele confers a defect in the catalytic subunit of replicative DNA polymerase δ that results in increased rates of mutagenesis, recombination, and chromosome loss, perhaps by increasing the rate of replicative polymerase failure. The translesion polymerases Pol η, Pol ζ, and Rev1 are part of a suite of factors in yeast that can act at sites of replicative polymerase failure. While mutants defective in the translesion polymerases alone displayed few defects, loss of Rev1 was found to suppress the increased rates of spontaneous mutation, recombination, and chromosome loss observed in pol3-t mutants. These results suggest that Rev1 may be involved in facilitating mutagenic and recombinagenic responses to the failure of Pol δ. Genome stability, therefore, may reflect a dynamic relationship between primary and auxiliary DNA polymerases.
Tilting at Quixotic Trait Loci (QTL): An Evolutionary Perspective on Genetic Causation
Authors: Weiss Kenneth M 
Published: August 2008

Abstract
Recent years have seen great advances in generating and analyzing data to identify the genetic architecture of biological traits. Human disease has understandably received intense research focus, and the genes responsible for most Mendelian diseases have successfully been identified. However, the same advances have shown a consistent if less satisfying pattern, in which complex traits are affected by variation in large numbers of genes, most of which have individually minor or statistically elusive effects, leaving the bulk of genetic etiology unaccounted for. This pattern applies to diverse and unrelated traits, not just disease, in basically all species, and is consistent with evolutionary expectations, raising challenging questions about the best way to approach and understand biological complexity.
Epidemiology of Highly Endemic Multiply Antibiotic-Resistant Shigellosis in Children in the Peruvian Amazon
Authors: Kosek Margaret , Yori Pablo Peñataro , Pan William K. , Olortegui Maribel Paredes , Gilman Robert H. , Perez Juan , Chavez Cesar Banda , Sanchez Graciela Meza , Burga Rosa , Hall Eric 
Published: August 2008

OBJECTIVE. Our goal was to estimate the impact of a Shigella vaccine in an area where shigellosis is endemic by characterizing the disease burden and antibiotic-resistance profiles of isolates and by determining the prevalence of Shigella flexneri serotypes.
PATIENTS AND METHODS. We conducted a 43-month-long prospective, community-based diarrheal disease surveillance in 442 children &lt;72 months of age in the Peruvian Amazon between October 1, 2002, and April 15, 2006.
RESULTS. The incidence of diarrheal disease was 4.38 episodes per child-year. The incidence rate for shigellosis was 0.34 episodes per child-year in children &lt;72 months of age and peaked in children between 12 and 23 months at 0.43 episodes per child-year. Maternal education at or beyond the primary grade level, piped water supply, weight-for-age z score, and improved water-storage practices were the most significant determinants of disease in this community with living conditions comparable to many rural areas in the developing world.
CONCLUSIONS. Children living in this region had a 20-fold higher rate of disease incidence detected by active surveillance as those recently estimated by passive detection. Most symptomatic disease was caused by S flexneri, although the diversity of serotypes will require a multivalent vaccine to have a significant impact on the burden of disease caused by shigellosis. Several other public health disease-control interventions targeted at water source and improved storage, nutritional interventions, and improved maternal education seem to have a greater impact than a univalent S flexneri 2a vaccine.
Cofactor Biosynthesis
Authors: Haase Ilka , Fischer Markus , Bacher Adelbert , Eisenreich Wolfgang , Rohdich Felix 
Published: August 2008

AbstractWhereas plants and certain microorganisms can generate all required coenzymes from CO2or simple organic precursors, animals must obtain precursors (designated as vitamins) for a major fraction of their coenzymes from nutritional sources. Still, most vitamins must be converted into the actual coenzymes by reactions catalyzed by animal enzymes. The structures and biosynthetic pathways of some coenzymes are characterized by extraordinary complexity. Enzymes for coenzyme biosynthesis have frequently low catalytic rates, and some of them catalyze reactions with highly unusual mechanisms.
DNA
Helicases: Chemistry and Mechanisms
Authors: Pugh Robert A. , Spies Maria 
Published: August 2008

Abstract
DNA helicases are members of a larger class of enzymes composed of molecular motors that couple the energy of NTP binding and hydrolysis to directional translocation along a nucleic acid lattice. Structurally and mechanistically related helicases perform drastically different roles in DNA metabolism by associating with various macromolecular machineries that orchestrate DNA processing events. Within these macromolecular ensembles, DNA helicase translocation is coupled to separation of duplex DNA into two single strands, which is necessary for DNA replication, repair, recombination and transcription. Translocation by DNA helicases can also result in the disassembly of protein–nucleic acid complexes formed during DNA metabolism. One major consequence of cellular dependence on DNA helicases is that defects in these enzymes result in a broad spectrum of disorders usually characterized by premature aging, susceptibility to cancer, and other diseases normally associated with aging.
Fluorescence to Study Nucleic Acids
Authors: Asseline Ulysse 
Published: August 2008

AbstractThe power of fluorescence spectroscopy in the study of nucleic acids relies on the availability of hundreds of different fluorophores that span the visible spectrum of light and the possibility of using them to label oligonucleotides (short fragments of DNA or RNA obtained by chemical synthesis) specifically. Any sequence can be obtained with one or more fluorophores and fluorophore quenchers attached at preselected positions by linkages with suitable parameters to ensure the optimal properties for the fluorescent oligonucleotides. Fluorescent labeling of long DNA or RNA fragments is also possible by enzymatic methods. Fluorescence‐based studies of nucleic acids are widely used in different areas such as basic research, molecular and clinical diagnostics, disease monitoring, therapeutic development, food technology, environmental sciences, and biotechnology. After a few words on biological and fluorescence backgrounds, the main labeling strategies will be developed and examples of biological questions that can be addressed with fluorescent oligonucleotides and the major types of fluorescence spectroscopy techniques will be reported.
Starch Biosynthesis in Plants
Authors: Preiss Jack 
Published: August 2008

AbstractStarch is a major storage compound in plants that is present both in leaves and in storage tissues. Biochemical and molecular biological data show that ADP‐glucose is the glucosyl donor for plant starch synthesis, and its synthesis is catalyzed by ADP‐glucose pyrophosphorylase. Subsequently, starch synthases catalyze the transfer of the glucosyl residue from ADP‐glucose to the oligosaccharide chains of the starch components amylose and amylopectin to form new α‐1,4‐glucosidic residues. After elongation of these α‐1,4‐glucosidic chains, the branching enzyme catalyzes a cleavage of the elongated chain and transfers the cleaved portion of the oligosaccharide chain to either another region in the amylopectin molecule or to a new amylopectin and forms a new α‐1,6‐glucosidic linkage. Amylose synthesis is catalyzed by the granule‐bound starch synthase. Regulation of starch synthesis occurs at the ADP‐glucose pyrophosphorylase step. The enzyme from higher plants, green algae, and cyanobacteria is activated allosterically by 3‐phosphoglycerate and inhibited by inorganic phosphate. Isolation of mutants and control analyses indicate that the allosteric activation and inhibition are of physiological and functional importance in the regulation of starch synthesis. Furthermore, evidence indicates that ADP‐glucose pyrophosphorylases can also be regulated by a redox mechanism. The current knowledge of the enzyme structures and critical amino acids necessary for substrate binding, allosteric effector binding, regulation, and catalysis for the ADP‐glucose pyrophosphorylase is reviewed.
High Throughput Screening (HTS) Techniques: Applications in Chemical Biology
Authors: Inglese James , Auld Douglas S. 
Published: August 2008

AbstractThe rapid testing of chemical libraries for biological activity is the primary aim of high throughput screening (HTS). Advances in HTS have paralleled those in molecular biology, instrumentation and automation, and informatics, and the increased availability of arrayed compound libraries. Sophisticated high sensitivity assays and the associated technologies required to implement these assays in HTS have been largely developed within the pharmaceutical industry for the identification of new chemical matter for drug development. However, HTS approaches are now widely applied to the broader questions within biological research. By way of introduction, we will describe the components of HTS and provide examples of strategies used to identify novel chemtypes for specific biological targets using large chemical libraries. We then will illustrate how more narrowly defined compound collections (e.g., targeted libraries or bioactive compounds) have been profiled against related targets or cell types for the purpose of discovering or defining, compound class/gene family selectivity, off‐target activity or “hidden phenotypes”, toxic fingerprints, or any other relationship between chemical structure and bioactivity. In this way, HTS systems can expand the scope of an experimental hypothesis to address questions of chemical biology, be they at the level of an isolated enzymatic activity or that of a complex cellular phenotype.
Membrane Compartments in Immune Cell Signaling and Trafficking
Authors: Hammond Stephanie , Holowka David , Baird Barbara 
Published: August 2008

Abstract
Cells of the immune system detect and respond to the presence of foreign antigens by signaling through an array of receptors, which include the multichain immune recognition receptor (MIRR) family. Stimulated changes in membrane architecture, which includes protein and lipid segregation within membranes as well as membrane trafficking, regulate these cellular responses. We provide a brief overview of MIRR signaling, which focuses on signaling through the IgE receptor in mast cells, and we highlight specific examples in which membrane compartmentalization plays a role in this signaling pathway. We summarize biochemical methods used to isolate and characterize membrane subdomains. Finally, we discuss cross‐correlation microscopy methods, application of antigen‐patterned surfaces, and fluorescence‐based trafficking assays to study dynamics of stimulated proteins interactions and membrane trafficking.
Membrane Potentials in Living Systems
Authors: O'Shea Paul 
Published: August 2008

Abstract
Membrane potentials are a ubiquitous feature of all living cells and play different roles in manifold cellular processes. Three different membrane potentials are known to exist that include the transmembrane potential difference, the surface electrostatic potential and the membrane dipole potential. Each of these are discussed in terms of their different physical origins and characteristics together with representative examples of how they feature in cell biology as well as some examples in physiology. Techniques for the quantitative measurement of each of these potentials are described in both model systems as well as with living systems. As many of these practices involve the use of spectroscopic technologies (particularly fluorescence) they lend themselves to spatial (single cell) imaging applications and examples of the biological roles that spatial variation or localisation of each of these potentials are also outlined.
Neurotransmission: Measuring Chemical Events
Authors: Jacobs Christopher B. , Vickrey Trisha L. , Venton B. Jill 
Published: August 2008

Abstract
Measuring chemical events in neurotransmission is challenging because fast measurements of small amounts of neurotransmitters and neuromodulators are needed to track the dynamics of chemical changes accurately. In this article, we outline the basics of three popular methods for measuring neurochemical changes: electrophysiology, microdialysis, and electrochemistry. Electrophysiological techniques measure changes in membrane potentials associated with neurotransmission. These methods are often used to measure receptor‐gated ion channel currents and are popular for neuropharmacology studies. Microdialysis is a sampling technique that can be used to monitor basal levels of neurotransmitters directly. When coupled to a separation technique, microdialysis is advantageous because it can be used to detect virtually any compound in the brain. Electrochemical techniques are popular because microelectrodes allow rapid, direct detection of neurotransmitters with minimal tissue disturbance. Although the analytes must be electroactive, electrochemistry has been used successfully to monitor neurochemical changes in various preparations, from single cells to behaving animals. Future research in monitoring neurochemical events will include improving the temporal resolution, spatial resolution, and selectivity of measurements.
Combinatorial Libraries: Applications in Chemical Biology
Authors: Nestler H. Peter 
Published: August 2008

Abstract
The sequencing of genomes gave access to the complete set of building blocks for organisms of various species. A plethora of “‐omics” technologies has been developed to investigate the dynamic interactions of the building blocks to understand the functioning of living organisms. Synthetic molecules have proven to be powerful tools to modulate that states of biological systems, but the challenges to find suitable probes are tremendous. Combinatorial libraries allow preparing and testing diverse sets of molecules with high efficiency. In this article, we will discuss how combinatorial chemistry enables to investigate and modulate biochemical function in the quest to chart chemical and biological spaces.
Origins of Life: Emergence of the
RNA
World
Authors: Robertson Michael P. 
Published: August 2008

Abstract
The RNA World hypothesis refers to a period during the evolution of life on Earth, preceding the DNA/RNA/protein‐based systems of modern biology, during which RNA alone directed and catalyzed the chemistry of life. The concept is an elegant solution to the problem of devolving our intertwined 3‐biopolymer biochemistry toward its origins as the simplest system imaginable. In support of this idea, a scattering of molecular clues within our cells point suggestively toward an RNA‐only period leading up to the ribozyme‐mediated invention of protein synthesis. Indeed, the RNA World hypothesis is a very sensible scenario when considered from the perspective of trying to simplify life's complexity. The alternative perspective, however, imagining a sterile, primordial Earth and trying to assemble abiotically produced precursors into the RNA World is an extremely difficult problem. Certain steps along the logical chemical pathway to the RNA World have been demonstrated in the laboratory, but many others remain problematic. The exploration of RNA's catalytic properties has been encouraging, but complex ribozymes are extremely scarce in RNA populations. If the RNA World did once exist, it came about by a mechanism that has not yet been adequately elucidated, including the possibility that a different, unknown, biopolymer system may have preceded the RNA World.
Polyketide Biosynthesis: Fungi
Authors: Simpson Thomas J. , Cox Russell J. 
Published: August 2008

Abstract
Fungi produce a wide variety of biologically active compounds. Among these compounds, the polyketides form a large and structurally diverse group. These compounds are synthesized by highly programmed, large iterative multifunctional proteins, which are called the polyketide synthases. This review describes the structure and biosynthesis of polyketide fungal metabolites and highlights recent work on the links between gene sequence, protein architecture, and biosynthetic programming for fungal polyketide synthases.
Serine Proteases and Serine Protease Inhibitors
Authors: Page Michael J. , Cera Enrico Di 
Published: August 2008

AbstractSerine proteases are among the largest group of proteolytic enzymes in the human genome that play vital roles in health and disease. Regulation of their activityin vivois mediated by a diverse group of serine protease inhibitors. An overview of the interplay between serine proteases and their inhibitors is provided. In addition, approaches to characterize this relationship are discussed with subsequent emphasis on how such measures apply to pathologies that result from defect of serine proteases or their inhibitors.
Protein Misfolding and Disease
Authors: Scheinost Johanna C. , Boldt Grant E. , Wentworth Paul 
Published: August 2008

Abstract
The amyloidoses are a class of conformational diseases that arise from the conversion of normally unfolded or globular proteins into fibrillar aggregates that are either pathogenic or non‐functional. At present there are more than 20 proteins that are associated with human amyloid diseases. This review focuses on three natively unfolded proteins that form fibrillar aggregates; amyloid‐β, islet amyloid polypeptide (‘amylin’), and α‐synuclein, the diseases they contribute to and chemical and biophysical approaches that are used to investigate these proteins' aggregation.
Chromosome Formation
Authors: Potts Patrick Ryan , Yu Hongtao 
Published: August 2008

Abstract
Chromosomes are large molecules of DNA that organize genetic materials of an organism. Chromosomes need to be properly organized, packaged, and compacted to ensure their integrity and segregation to daughter cells during mitosis. In eukaryotic cells, chromosomes associate with histones and other proteins to form chromatin within the nucleus. The basic packaging unit of chromatin is the nucleosome. The nucleosome core particle consists of 147 base pairs of DNA that wrap around a core histone octamer. A linear array of nucleosomes is further folded into high‐order chromatin structures. In addition, chromosomes are regulated during mitosis by the structural maintenance of chromosomes (SMC) family of proteins. Sister chromatids are physically tethered during DNA replication by the SMC1/3 cohesin complex to ensure equal segregation of chromosomes to daughter cells. These sister chromatids are compacted by the SMC2/4 condensin complex to form metaphase chromosomes.
Membrane Protein Structure: Techniques
Authors: King Gavin , Dixon Ann M. 
Published: August 2008

Abstract
The biological importance of membrane proteins has been recognized worldwide for many years, but historically these proteins have proved difficult to characterize structurally because of a variety of experimental challenges. Recently, technological advances across several disciplines have prompted considerable progress in three‐dimensional structure determination of membrane proteins. This review describes the state‐of‐the‐art methods that have successfully produced high‐resolution membrane protein structures to date. Most notably, X‐ray crystallography will be discussed, as this technique has made by far the largest contribution to our current knowledge of membrane protein structure. This is followed by discussion of nuclear magnetic resonance spectroscopy and cryo‐electron microscopy, both techniques that have also been successful in producing high‐resolution structures for membrane proteins, albeit to a lesser degree than X‐ray crystallography. Finally, we will discuss atomic force microscopy. Although this technique cannot be used for atomic level structural determination, it offers distinct advantages for investigation of membrane protein oligomerization, dynamics, and large‐scale conformational changes. Recent notable membrane protein structures are included throughout to illustrate progress in the field as well as the strengths and weaknesses of each method.
Metabolome
Authors: Griffin Julian L. , Atherton Helen J. , Pears Michael R. 
Published: August 2008

Abstract
With the development of systems biology, several approaches have been developed to profile a tier of organization in a cell, tissue, or organism globally. Metabolomics, also referred to as metabonomics, is an approach that attempts to profile all the small‐molecule metabolites in a biological matrix. One major challenge of this approach, as with other “‐omic” technologies, is that the metabolome is context dependent and varies with developmental stage/age, genetic modification, disease, and environment. Thus, by definition, the metabolome of an organism must take into consideration all the effects of these manipulations. Despite these challenges, the approach has already been applied to understand metabolism in a range of animal models and has more recently started to be applied to clinical studies. In this article, we will discuss some common approaches currently used in metabolomics and the results that they have produced. In particular, we will focus on the two most common analytical approaches, nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry, and some biological problems they have been used to address.