bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virulent Toxoplasma gondii Evade Immunity-Related GTPase-Mediated Parasite Vacuole Disruption within Primed Macrophages
Authors: Zhao Yanlin , Ferguson David J. P. , Wilson Douglas C. , Howard Jonathan C. , Sibley L. David , Yap George S. 
Published: March 2009

Abstract
Cytokine-activated macrophages restrain the replication of intracellular parasites and disrupt the integrity of vacuolar pathogens. In this study, we show that inducible nitric oxide synthase and the immunity-related GTPase (IRG) family member Irgm3, respectively, are required for the ability of in vivo primed macrophages to restrain the growth of Toxoplasma gondii and to destroy the parasite’s intracellular niche. Remarkably, virulent Type I strains of T. gondii evade IRG-dependent vacuolar disruption, while remaining susceptible to iNOS-dependent restriction. The ability of virulent T. gondii to escape killing by macrophages is controlled at the level of the individual vacuole and is associated with differential permissiveness for association of the IRG proteins Irga6 (IIGP1) and Irgb6 (TGTP) to the vacuolar membrane. Surprisingly, expression of the Type I ROP-18 virulence determinant in an avirulent strain did not confer the evasive phenotype. These results pinpoint evasion of vacuolar disruption by IRG proteins as a new determinant of pathogen virulence.
Apoptosome and Caspase Activation
Authors: Declercq Wim , Vandenabeele Peter 
Published: March 2009

Abstract
Apoptosis is an evolutionarily conserved form of cell death that executes programmed cell death during development and tissue homeostasis. Insufficient levels of apoptosis can contribute to the development of cancer, whereas excessive apoptosis is implicated in degenerative diseases, such as stroke, cardiac failure, and neurological pathologies. Since the beginning of the 1990s, our knowledge of apoptotic signaling pathways has increased tremendously. The caspase family of aspartate‐specific cysteine proteases is conserved in many species and incorporates key proteases involved in initiation and execution of apoptosis. Together with the discovery and better understanding of their activation complexes, such as the apoptosome, new strategies to modulate cell death in pathological conditions are being developed.
Circular Dichroism (CD) for Natural Products
Authors: Taniguchi Tohru , Nakanishi Koji 
Published: March 2009

AbstractCircular dichroism (CD) spectroscopy is used widely for nonempirical determinations of absolute configuration. The advantages of CD spectroscopy are summarized as follows: 1) CD spectra are measurable in ultra microscale because of high sensitivity, 2) the CD exciton chirality method enables one to determine the absolute configuration in a straightforward and nonambiguous manner, and 3) the recent progress in molecular orbital (MO) computations enhances versatility of CD. The basic aspects of CD and theoretical calculations for assignment of absolute configurations are described first. This analysis is followed by an outline of the exciton chirality method and the selection of chromophores with optimal λmaxand ɛ for use in this method. The additivity relation encountered in molecules in which multiple chromophores are present is a fundamental principle that greatly simplifies the analyses of complex CD spectra that consist of complex CD extrema (i.e., maxima and minima). The examples cited are intended to illustrate the various approaches that lead to determination of absolute configurations by CD.
Fluorescence in Living Systems: Applications in Chemical Biology
Authors: Cornish Virginia W. , Gallagher Sarah S. 
Published: March 2009

AbstractIncreasingly, studies of biomolecules are progressing from understanding how isolated biomolecules workin vitroto asking how macromolecular machines, signaling pathways, and other biological networks function in the complex environment of the living cell. Just as chemical methods greatly impacted fundamental studies of the structure and function of biomoleculesin vitroin the last century, chemical methods are now being developed to study biomolecule functionin vivo. This review focuses on chemical biology tools being developed to provide fluorescent reporters for biomolecules in living cells. The wealth ofin vitrofluorescent reporters is the underpinning of much of this research, but it is beyond the scope of this review. Emphasis is placed on protein tagging, beginning with the fluorescent proteins and more recently moving to chemical tagging methods. In addition, chemical tools for fluorescence imaging of other classes of biomolecules and dynamic modifications to biomolecules in living cells are also overviewed.
Biocatalytic Synthesis of Natural and Non‐Natural α‐Amino Acids
Authors: Harald Gröger , Dietz Friedrich R. 
Published: March 2009

AbstractThe synthesis of enantiomerically pure α‐amino acids has attracted the attention of generations of organic chemists, and a broad range of efficient synthetic methods is already known. The developed synthetic approaches are based on different concepts such as 1) “classic” chemical resolution (by means of diastereomeric salt pair formation), 2) chiral pool syntheses making use of easily accessible chiral products, 3) chemocatalytic syntheses, and 4) the use of biotechnological methodologies. With respect to the latter one, one can apply enzymatic approaches such as enzymatic resolution (including dynamic kinetic resolution processes) and biocatalytic asymmetric syntheses as well as fermentation. Notably, many of those biotechnological α‐amino acid syntheses have made it up to industrially applied process technologies. The focus of this review is on synthetically widely applied and highly applicable biocatalytic concepts for natural and non‐natural α‐amino acids with one and two stereogenic center(s). Industrial α‐amino acid products as well as their highly efficient process technologies are covered therein as well.
Protein Folding: Energetics
Authors: Baldwin Robert L. 
Published: March 2009

AbstractThe energetics of protein folding determine how the amino acid sequence of a protein is constrained to fold into its correct three‐dimensional structure. Thus, knowledge of the folding energetics is needed to predict protein structure from sequence or to modify sequence and structure by protein engineering. The traditional approach to folding energetics, which emphasizes major factors, is followed here. This article discusses chiefly three major factors: the hydrophobic factor, peptide hydrogen bonds/peptide solvation, and backbone conformational entropy. Auxiliary factors, such as van der Waals interactions, disulfide bonds, salt bridges, and helix propensities, are discussed briefly.
Ribosome, Chemistry of
Authors: Karbstein Katrin 
Published: March 2009

AbstractRibosomes are the most complex, ancient, and important RNA‐protein complexes present in every cell. A large body of previous data shows that their function is carefully regulated and quality controlled, which leads to a remarkably low rate of amino‐acid misincorporation. A prerequisite to this exquisitely accurate function is correctly assembled ribosomes. Here, I consider mechanisms that may help in regulating ribosome assembly and in ensuring that ribosomes are faithfully assembled. Evidence for the existence of these mechanisms is then presented based on data in the literature. Future experiments will be required to test the importance of these events in quality control.
HIV
: Small Molecule Approaches
Authors: Vacca Joseph P. 
Published: March 2009

Abstract
The human immunodeficiency retrovirus (HIV), recognized widely as the causative agent of AIDS, was discovered over 25 years ago and is one of the most highly studied viruses of all time. In the 1980s through the mid 1990s, only a few treatment options were available and contracting this virus usually resulted in death. Since the introduction in the mid‐1990s of HAART (Highly Active Anti‐Retroviral Therapy), the disease has become manageable for many people who can tolerate the new drugs (1, 2). This review article will describe the way that the virus works and will highlight the many points of intervention and the small molecules that have been developed to stop the virus from replicating.
Iron–Sulfur Clusters: Properties and Functions
Authors: Noodleman Louis , Pique Michael E. , Roberts Victoria A. 
Published: March 2009

AbstractIron–sulfur clusters reside at the active sites of iron–sulfur proteins and are intimately involved in many critical biological functions. The active sites are usually redox active, and the most common functions include simple electron transfer, proton‐coupled electron transfer, and oxidation or reduction of substrates. Some nonredox functions that involve cluster electronic polarization have also been established. The redox active character of iron–sulfur clusters and iron atom lability are also used for essential biological regulatory functions both in bacteria and eukaryotic cells. The versatility of sulfur ligation and iron–sulfur covalency (partial charge transfer) lie at the heart of iron–sulfur cluster functionality. Iron–sulfur proteins are among the most ancient biological catalysts, and iron–sulfur clusters may have had important prebiotic functions as well. In this review, we summarize the wide variety of iron–sulfur catalytic and regulatory functions. We show how many spectroscopic and physical methods contribute to our current understanding of catalytic and regulatory states and energetic pathways. Quantum mechanical [largely density functional theory (DFT)] methods link electronic structures to energetics and spectroscopic data, and provide a unifying framework for additional progress on many open questions. The active site transition metal complexes also interact with the protein and solvent environment. The main theoretical/computational tools for studying these interactions are Poisson‐Boltzmann electrostatics methods and combined quantum mechanics/molecular mechanics (QM/MM) methods. The principal experimental tools for examining cluster‐protein interactions include comparisons of synthetic complexes with corresponding proteins, the use of alternative substrates or inhibitors for enzymes, redox energetics, reaction kinetics studies, and spectroscopic observations.
De Novo Sequencing of Peptides Using Mass Spectrometry
Authors: Dass Chhabil 
Published: March 2009

Abstract

Peptides are important biomolecules that play a variety of functional roles. Knowledge of the specific sequence of amino acids in peptides is essential to understand their biological functions, to identify them in target tissues, to map changes in their metabolic profile, to assess the purity of newly synthesized peptides and to characterize their precursor proteins. Currently, mass spectrometry has assumed a pivotal role in determining the sequence of peptides. The procedure involves conversion of peptide molecules into gas‐phase ions, fragmentation of these species into the sequence‐specific ions, and deciphering the mass spectral data into the sequence of the target peptide. This procedure, known as “
de novo
sequencing”, requires understanding of the peptide fragmentation rules and guidelines for interpretation of a mass spectrum. These aspects are discussed in detail in this chapter.
The $300,000/Year Architect
Authors: Gauchet Urs 
Published: March 2009

AbstractCould building information modelling (BIM) shake up not only design and delivery processes, but also be set to redefine the construction hierarchy? Could it shift the architect's position from near the bottom of the current food chain to one nearer the top? Urs Gauchat, Professor and Dean of the School of Architecture at the New Jersey Institute of Technology, outlines the architect's place in a complex future where there is an increasing demand for buildings but a demise in available materials and conventional energy sources. Copyright © 2009 John Wiley & Sons, Ltd.
Information Modelling as a Paradigm Shift
Authors: Shelden Dennis 
Published: March 2009

AbstractBuilding information modelling (BIM) is not just a change in software or skills sets, it requires a paradigm shift. Dennis Shelden, Chief Technology Officer of Gehry Technologies, outlines the more ‘fundamental, subtle and profound decisions’ on the road to BIM. It is necessary to fully consider not only the impacts both ‘upstream’ and ‘downstream’ from the conventional design phase, but also the possible creative restrictions as there is a potential trade‐off that comes with the emphasis on collaborative processes. Copyright © 2009 John Wiley & Sons, Ltd.
Carlos Zapata and Antonio Citterio's Cooper Square Hotel, New York
Authors: Merkel Jayne 
Published: March 2009

AbstractUnlike most glamorous new high‐rise apartment buildings in downtown Manhattan, this thin, tilted white glass tower provides homes away from home for chic out‐of‐towners. And what ‘homes’ they are. Upstairs are astounding long‐range views; on the lower floors, a series of glass‐walled lounges, restaurants, balconies, a garden and even a library with a wood‐burning fireplace. And, as Jayne Merkel explains, these sensual pleasures are mixed with intellectual ones. There are art and travel books in every room and guests can enjoy ‘movie nights’ in the screening room.
Herbert Art Gallery and Museum, Coventry
Authors: Littlefield David 
Published: March 2009

AbstractDespite being ‘assembled from fragments’, like the Midlands city in which it is located, the new extension to the Herbert Art Gallery provides a new refinement and logic to the previously eclectic museum and its environs. David Littlefield describes how Pringle Richards Sharratt have realised this new coherency through artful layering, reorientation and rationalisation. Copyright © 2009 John Wiley & Sons, Ltd.
Computational Spring Systems: Open Design Processes for Complex Structural Systems
Authors: Ahlquist Sean , Fleischmann Moritz 
Published: March 2009

AbstractSean Ahlquist and Moritz Fleischmann are both former graduates of the Emergent Technologies and Design Programme at the Architectural Association (AA) in London, who have now established their own innovative research and design practice, morse. Here they describe their work with computational spring algorithms that has enabled iterative investigations of tension active systems and structures. Copyright © 2009 John Wiley & Sons, Ltd.
Complex Systems Architecture
Authors: Spiller Neil 
Published: March 2009

AbstractNeil Spiller reveals the complexity of architectural systems to us, or is it the complexity of the architectural mind? For Spiller, the potential of a single notation as a seed for a truly ecological architecture provides an essential catalyst, triggering a multifaceted musing that takes in diagrams, Paul Preissner's new competition entry for the Taiwan Centre of Disease Control and his future work with Dr Rachel Armstrong on complex biological systems. Copyright © 2009 John Wiley & Sons, Ltd.
The Sustainable Disco
Authors: Croci Valentina 
Published: March 2009

AbstractValentina Croci describes how Dutch artist Daan Roosegaarde's Sustainable Dance Floor (SDF) provides the centrepiece for an eco‐club in Rotterdam that builds low energy consumption into the attraction. The square dance floor uses ‘mechatronic’ sensors to convert kinetic movement into electricity when people dance. Movement is not only part of the thrill, but is literally electrifying. Copyright © 2009 John Wiley & Sons, Ltd.
Replacing a Beloved Building with a Hybrid: Paresky Student Center, Williams College
Authors: Horwitz Jamie 
Published: March 2009

AbstractJamie Horwitz describes how Polshek Partnership's design for a new student centre at Williams College, a small liberal arts college in Williamstown, Massachusetts, has successfully integrated ‘environmentally sensitive practices into the choreography of life’. Catering not only to students' 24‐hour needs, its dining facilities tap into a network of local food producers within its far‐reaching sustainable programme. Copyright © 2009 John Wiley & Sons, Ltd.
Intercalating Dye Harnessed Cationic Conjugated Polymer for Real‐Time Naked‐Eye Recognition of Double‐Stranded DNA in Serum
Authors: Pu Kan‐Yi , Liu Bin 
Published: March 2009

AbstractThiazole orange (TO), an intercalating dye, is integrated into cationic poly(fluorene‐alt‐phenylene) (PFP) to develop a macromolecular multicolor probe (PFPTO) for double‐stranded DNA (dsDNA) detection. This polymer design not only takes advantage of the high affinity between TO and dsDNA to realize dsDNA recognition in biological media, but also brings into play the light‐harvesting feature of conjugated polymers to amplify the signal output of TO in situ. PFPTO differentiates dsDNA from single‐stranded DNA (ssDNA) more effectively upon excitation of the conjugated backbone relative to that upon direct excitation of TO as a result of efficient fluorescence resonance energy transfer from the polymer backbone to the intercalated TO. In the presence of dsDNA, energy transfer within PFPTO is more efficient as compared to that for free TO/PFP system, which leads to better dsDNA discriminability for PFPTO in contrast to that for TO/PFP. The distinguishable fluorescent color for PFPTO solutions in the presence of dsDNA allows naked‐eye detection of dsDNA with the assistance of a hand‐held UV lamp. The significant advantage of this macromolecular fluorescent probe is that naked‐eye detection of label‐free dsDNA can be performed in biological media in real‐time.
Labeling of Adipose‐Derived Stem Cells by Oleic‐Acid‐Modified Magnetic Nanoparticles
Authors: Cen Lian , Neoh Koon Gee , Sun Jian , Hu Feixiong , Liu Wei , Cui Lei , Cao Yilin 
Published: March 2009

AbstractThe in vivo tracking of adipose derived stem cells (ASCs) is of essential concern when they are used as seed cells in tissue engineering. This study explores the feasibility of using magnetic nanoparticles (MNs), a type of contrast agents in magnetic resonance imaging (MRI), to label ASCs such that the labeled ASCs could be tracked in vivo by MRI non‐invasively and repeatedly. To do this, MNs of <10 nm surface‐coated with oleic acid are synthesized via a high‐temperature solution‐phase reaction. Cytotoxicity of the as‐synthesized MNs at concentrations up to 0.1 mg mL−1 on 104 cells mL−1 ASCs is evaluated by LDH release. Since only minor cytotoxicity is detected, the effects of the labeling technique on cellular behaviors and uptake by labeled cells are investigated. Cell proliferation and differentiation with and without MNs are compared. The results show that proliferation of ASCs (104 cells mL−1) labeled by MNs (0.05 mg mL−1) is significantly enhanced and dependent on the labeling time. The MNs are located in the vesicles within cytoplasm of ASCs. The cellular uptake reaches as high as ∼180 pg/cell. Nevertheless, the labeled ASCs still maintained adipogenic and osteogenic differentiation. Hence, the feasibility of labeling ASCs by oleic acid coated MNs is ascertained and it was better to label the cells during their quiescent stage. The labeled ASCs can also be in vivo detected by MRI in a subcutaneous model in vivo. Further MRI tracking of the labeled ASCs in long‐term follow‐up would thus follow this current study.
Exposure to hazardous workplace noise and use of hearing protection devices among US workers—NHANES, 1999–2004
Authors: Tak SangWoo , Davis Rickie R. , Calvert Geoffrey M. 
Published: March 2009

AbstractBackgroundTo estimate the prevalence of workplace noise exposure and use of hearing protection devices (HPDs) at noisy work, NIOSH analyzed 1999–2004 data from the National Health and Nutrition Examination Survey (NHANES).MethodsA total of 9,275 currently employed workers aged ≥16 years were included in the weighted analysis. Hazardous workplace noise exposure was defined as self‐reported exposure to noise at their current job that was so loud that the respondent had to speak in a raised voice to be heard. Industry and occupation were determined based on the respondent's current place and type of work.ResultsTwenty‐two million US workers (17%) reported exposure to hazardous workplace noise. The weighted prevalence of workplace noise exposure was highest for mining (76%, SE = 7.0) followed by lumber/wood product manufacturing (55%, SE = 2.5). High‐risk occupations included repair and maintenance, motor vehicle operators, and construction trades. Overall, 34% of the estimated 22 million US workers reporting hazardous workplace exposure reported non‐use of HPDs. The proportion of noise‐exposed workers who reported non‐use of HPDs was highest for healthcare and social services (73.7%, SE = 8.1), followed by educational services (55.5%).DiscussionHearing loss prevention and intervention programs should be targeted at those industries and occupations identified to have a high prevalence of workplace noise exposure and those industries with the highest proportion of noise‐exposed workers who reported non‐use of HPDs. Am. J. Ind. Med. 52:358–371, 2009. Published 2009 Wiley‐Liss, Inc.
Prosaposin deficiency and saposin B deficiency (activator‐deficient metachromatic leukodystrophy): Report on two patients detected by analysis of urinary sphingolipids and carrying novel PSAP gene mutations
Authors: Kuchař Ladislav , Ledvinová Jana , Hřebíček Martin , Myšková Helena , Dvořáková Lenka , Berná Linda , Chrastina Petr , Asfaw Befekadu , Elleder Milan , Petermöller Margret , Mayrhofer Heidi , Staudt Martin , Krägeloh‐Mann Ingeborg , Paton Barbara C. , Harzer Klaus 
Published: March 2009

AbstractProsaposin deficiency (pSap‐d) and saposin B deficiency (SapB‐d) are both lipid storage disorders caused by mutations in the PSAP gene that codes for the 65–70 kDa prosaposin protein, which is the precursor for four sphingolipid activator proteins, saposins A–D. We report on two new patients with PSAP gene defects; one, with pSap‐d, who had a severe neurovisceral dystrophy and died as a neonate, and the other with SapB‐d, who presented with a metachromatic leukodystrophy‐like disorder but had normal arylsulfatase activity. Screening for urinary sphingolipids was crucial to the diagnosis of both patients, with electrospray ionization tandem mass spectrometry also providing quantification. The pSap‐d patient is the first case with this condition where urinary sphingolipids have been investigated. Multiple sphingolipids were elevated, with globotriaosylceramide showing the greatest increase. Both patients had novel mutations in the PSAP gene. The pSap‐d patient was homozygous for a splice‐acceptor site mutation two bases upstream of exon 10. This mutation led to a premature stop codon and yielded low levels of transcript. The SapB‐d patient was a compound heterozygote with a splice‐acceptor site variant exclusively affecting the SapB domain on one allele, and a 2 bp deletion leading to a null, that is, pSap‐d mutation, on the other allele. Phenotypically, pSap‐d is a relatively uniform disease of the neonate, whereas SapB‐d is heterogeneous with a spectrum similar to that in metachromatic leukodystrophy. The possible existence of genotypes and phenotypes intermediate between those of pSap‐d and the single saposin deficiencies is speculated. © 2009 Wiley‐Liss, Inc.