bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheCaenorhabditis elegans ing-3Gene Regulates Ionizing Radiation-Induced Germ-Cell Apoptosis in a p53-Associated Pathway
Authors: Luo Jingjing , Shah Sitar , Riabowol Karl , Mains Paul E 
Published: November 2008

AbstractThe inhibitor of growth (ING) family of type II tumor suppressors are encoded by five genes in mammals and by three genes in Caenorhabditis elegans. All ING proteins contain a highly conserved plant homeodomain (PHD) zinc finger. ING proteins are activated by stresses, including ionizing radiation, leading to the activation of p53. ING proteins in mammals and yeast have recently been shown to read the histone code in a methylation-sensitive manner to regulate gene expression. Here we identify and characterize ing-3, the C. elegans gene with the highest sequence identity to the human ING3 gene. ING-3 colocalizes with chromatin in embryos, the germline, and somatic cells. The ing-3 gene is part of an operon but is also transcribed from its own promoter. Both ing-3(RNAi) and ing-3 mutant strains demonstrate that the gene likely functions in concert with the C. elegans p53 homolog, cep-1, to induce germ-cell apoptosis in response to ionizing radiation. Somatically, the ing-3 mutant has a weak kinker uncoordinated (kinker Unc) phenotype, indicating a possible neuronal function.
Formation and Longevity of Chimeric and Duplicate Genes inDrosophila melanogaster
Authors: Rogers Rebekah L , Bedford Trevor , Hartl Daniel L 
Published: November 2008

AbstractHistorically, duplicate genes have been regarded as a major source of novel genetic material. However, recent work suggests that chimeric genes formed through the fusion of pieces of different genes may also contribute to the evolution of novel functions. To compare the contribution of chimeric and duplicate genes to genome evolution, we measured their prevalence and persistence within Drosophila melanogaster. We find that ∼80.4 duplicates form per million years, but most are rapidly eliminated from the genome, leaving only 4.1% to be preserved by natural selection. Chimeras form at a comparatively modest rate of ∼11.4 per million years but follow a similar pattern of decay, with ultimately only 1.4% of chimeras preserved. We propose two mechanisms of chimeric gene formation, which rely entirely on local, DNA-based mutations to explain the structure and placement of the youngest chimeric genes observed. One involves imprecise excision of an unpaired duplication during large-loop mismatch repair, while the other invokes a process akin to replication slippage to form a chimeric gene in a single event. Our results paint a dynamic picture of both chimeras and duplicate genes within the genome and suggest that chimeric genes contribute substantially to genomic novelty.
Stm1 Modulates mRNA Decay and Dhh1 Function in Saccharomyces cerevisiae
Authors: Balagopal Vidya , Parker Roy 
Published: November 2008

Abstract
The control of mRNA degradation and translation are important for the regulation of gene expression. mRNA degradation is often initiated by deadenylation, which leads to decapping and 5′–3′ decay. In the budding yeast Saccharomyces cerevisae, decapping is promoted by the Dhh1 and Pat1 proteins, which appear to both inhibit translation initiation and promote decapping. To understand the function of these factors, we identified the ribosome binding protein Stm1 as a multicopy suppressor of the temperature sensitivity of the pat1Δ strain. Stm1 loss-of-function alleles and overexpression strains show several genetic interactions with Pat1 and Dhh1 alleles in a manner consistent with Stm1 working upstream of Dhh1 to promote Dhh1 function. Consistent with Stm1 affecting Dhh1 function, stm1Δ strains are defective in the degradation of the EDC1 and COX17 mRNAs, whose decay is strongly affected by the loss of Dhh1. These results identify Stm1 as an additional component of the mRNA degradation machinery and suggest a possible connection of mRNA decapping to ribosome function.
Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course
Authors: Dymond Jessica S , Scheifele Lisa Z , Richardson Sarah , Lee Pablo , Chandrasegaran Srinivasan , Bader Joel S , Boeke Jef D 
Published: November 2008

Abstract
A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ∼750-bp fragments. Once trained in assembly of such DNA “building blocks” by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular “lab meeting” sessions help prepare them for future roles in laboratory science.
Physicians' Contact With Families After the Death of Pediatric Patients: A Survey of Pediatric Critical Care Practitioners' Beliefs and Self-Reported Practices
Authors: Borasino Santiago , Morrison Wynne , Silberman Jordan , Nelson Robert M. , Feudtner Chris 
Published: November 2008

OBJECTIVES. Although research with bereaved families has shown that they appreciate contact with clinicians after the child's death, this realm of clinical practice remains empirically uncharted. The objective of this study was to describe pediatric critical care practitioners' attitudes and self-reported practices regarding contacting families after a patient's death.
METHODS. A total of 376 board-certified members of the American Academy of Pediatrics Section of Critical Care received e-mail invitations to complete a Web-based questionnaire; 204 members responded (effective response rate: 54.3%).
RESULTS. Most (95%) participants reported 0 to 1 patient deaths per week. A total of 79% of the respondents reported contacting families at least sometimes, 71.9% had attended funerals, and only 2.5% thought that it was inappropriate for clinicians to attend funerals. A total of 75.9% agreed that follow-up contact helps the family, whereas 47.3% agreed that follow-up contact helps the physicians. The most common methods of follow-up contact included the passive measures of providing contact information; active methods such as meeting with the family, calling them by telephone, or writing a letter or note were used less often. In multivariable analysis, respondents were more likely to report contact with a family after the death of a child when they affirmed the belief that such contact was useful to the family or to the physician or when they were female physicians. Regarding reported funeral attendance after the death of a patient, multivariable analysis revealed similar patterns of association but to an attenuated and nonstatistically significant degree.
CONCLUSIONS. A high proportion of pediatric critical care physicians have contacted bereaved families and attended funerals after the death of a child patient. These practices were consistently associated with the belief that such follow-up contact helps the family or the practitioner.
Mapping of Oxygen Concentration in Biological Samples Using EPR Imaging
Authors: Vikram Deepti S. , Ahmad Rizwan , Rivera Brian K. , Kuppusamy Periannan 
Published: November 2008

AbstractElectron paramagnetic resonance (EPR) spectroscopy is widely used for measurement and imaging of oxygen and free radicals in biological systems. EPR oximetry is non‐invasive, capable of providing local, reproducible, and repetitive measurements of oxygen concentration or partial pressure of oxygen (pO2) in tissues. Although EPR oximetry is used primarily as a research tool, it has the potential to be useful in the clinic. This review provides a brief overview of the technique and its application to selected biological systems.
Critical Evaluations of Additives Used in Shale Slickwater Fracs
Authors: Kaufman P. , Penny G. S. , Paktinat J. 
Published: November 2008

Abstract
Slickwater fracturing has increased over the past decade with the advent of shale gas plays. Horizontal wells are now the standard with up to 1 million gallons of water in as many as 6 to 9 frac stages per well. The objective is to create as much contact with the reservoir as possible and many times a secondary goal is to prop open the created fractures. Additive packages have been minimized to save money. Due to environmental concerns and fresh water availability, the flowback and produced water is collected and used for subsequent fracture treatments. The purpose of this work is to examine water treatment techniques and critically evaluate the performance of additives that are employed in slickwater fracs of shale reservoirs and give guidelines for selecting additives that will optimize performance during pumping, fluid recovery and production. Comments will be made on the topic of proppant selection. Following the proppant, the major additive in most jobs will be the friction reducer which is required to reduce the friction pressure while pumping at the extreme rates of 50 to 120 barrels per minute (bpm). The second concern should be additives to treat bacteriological activity. The injection of water will ultimately result in the cultivation of sulfate reducing bacteria which produce Hydrogen sulfide (H2S) and biproducts such as black iron sulfide on the surface if not treated properly. Scale inhibitors become vitally important as water dissolves salts from the formation. Shales have sub microDarcy matrix permeability with natural fractures and cleats providing avenues for gas desorption and flow to the wellbore. Shales can have as much as 50% clays. Are additives necessary to stabilize clays? Finally, the use of surfactants can be beneficial in promoting the flowback of injected fluids to restore the relative permeability to gas. Which surfactant types are the most beneficial?
Photoconductivity and photoluminescence in chemically deposited films of CdSSe:CdCl2,Ho
Authors: Bhushan S. , Oudhia A. 
Published: November 2008

AbstractResults of the scanning electron microscopy (SEM), X-ray diffraction (XRD), optical absorption, photoconductivity (PC), and photoluminescence (PL) studies for the CdSSe:CdCl2,Ho films are presented in this paper. The SEM studies of different CdSSe films show a layered growth structure. A crystalline nature of the films is observed in the XRD studies. The regions with stacking fault were also observed in the X-ray diffractograms. The optical absorption spectra of these films show variations corresponding to the band gaps and the grain-sizes obtained under various deposition conditions and also with annealing. The effect of flux, impurities and annealing on the saturated photo to dark current ratio Ipc/Idc is observed in the PC rise and decay studies. The maximum value of Ipc/Idc ∼107 is obtained for the impurity doped annealed films. The PL emission spectra of CdSSe films show two emission peaks associated with the annihilation of free excitons and the transitions between shallow donor and deep acceptor states. In CdSSe:CdCl2,Ho films, two PL emission peaks are observed at 495 nm and 545 nm corresponding to the transitions 5S2→5I8 and 5F3→5I8, respectively, in Ho. The effect of pH on PL and grain size is also included in the present studies.
Multimodal biometric authentication based on score level fusion using support vector machine
Authors: Wang F. , Han J. 
Published: November 2008

AbstractFusion of multiple biometrics for human authentication performance improvement has received considerable attention. This paper presents a novel multimodal biometric authentication method integrating face and iris based on score level fusion. For score level fusion, support vector machine (SVM) based fusion rule is applied to combine two matching scores, respectively from Laplacianface based face verifier and phase information based iris verifier, to generate a single scalar score which is used to make the final decision. Experimental results show that the performance of the proposed method can bring obvious improvement comparing to the unimodal biometric identification methods and the previous fused face-iris methods.
Assays for S‐Adenosylmethionine (AdoMet/SAM)‐Dependent Methyltransferases
Authors: Wooderchak Whitney L. , Zhou Zhaohui Sunny , Hevel Joan 
Published: November 2008

AbstractModification of small molecules and proteins by methyltransferases impacts a wide range of biological processes. Here we report two methods for measuring methyltransferase activity. First we describe an enzyme‐coupled continuous spectrophotometric assay used to quantitatively characterize S‐adenosyl‐L‐methionine (AdoMet or SAM)–dependent methyltransferase activity. In this assay, S‐adenosyl‐L‐homocysteine (AdoHcy or SAH), the transmethylation product of AdoMet‐dependent methyltransferase, is hydrolyzed to S‐ribohomocysteine and adenine by recombinant AdoHcy nucleosidase. Subsequently, the adenine generated from AdoHcy is further hydrolyzed to homoxanthine and ammonia by recombinant adenine deaminase. This deamination is associated with a decrease in absorbance at 265 nm that can be monitored continuously. Secondly, we describe a discontinuous assay that follows radiolabel incorporation into the methyl receptor. An advantage of both assays is the destruction of AdoHcy by AdoHcy nucleosidase, which alleviates AdoHcy product feedback inhibition of S‐adenosylmethionine‐dependent methyltransferases. Importantly both methods are inexpensive, robust, and amenable to high throughput. Curr. Protoc. Toxicol. 38:4.26.1‐4.26.12. © 2008 by John Wiley & Sons, Inc.
A Bacterial Cell‐Free Expression System to Produce Membrane Proteins and Proteoliposomes: From cDNA to Functional Assay
Authors: Liguori Lavinia , Marques Bruno , Lenormand Jean‐Luc 
Published: November 2008

AbstractLimitations in the production of folded membrane proteins represent the major bottleneck for functional and structural studies of this huge category of macromolecules. Cell‐free expression systems provide an attractive alternative to the classical overexpression systems for producing membrane proteins. However, optimization of these systems remains a challenging task, considering the hydrophobic properties of these molecules. This unit describes the production of eukaryotic membrane proteins either in soluble form or integrated into liposomes using a bacterial cell‐free expression system. Liposomes in the reaction mixture induce the direct insertion of freshly produced membrane proteins into the bilayer and allow the formation of functional proteoliposomes in which the membrane proteins are correctly folded. Curr. Protoc. Protein Sci. 54:5.22.1‐5.22.30. © 2008 by John Wiley & Sons, Inc.
Expression and Purification of ZEBRA Fusion Proteins and Applications for the Delivery of Macromolecules into Mammalian Cells
Authors: Rothe Romy , Lenormand Jean‐Luc 
Published: November 2008

AbstractThe recent development of peptide carriers for efficient and specific delivery of biologically active molecules into mammalian cells represents a major advance in the study of both normal and uncontrolled cell growth. In the past few years, this technology has been successfully applied to the delivery of therapeutic molecules in animal models, and now some of these carriers are available in the clinic for the treatment of some human diseases. This unit describes the production, in a bacterial expression system, of reporter proteins (EGFP and β‐galactosidase) fused to a transduction domain of the Epstein‐Barr virus ZEBRA protein, as well as purification of the fusion proteins. The purified fusion proteins can be added to any of a large spectrum of mammalian cells and the internalization process measured by flow cytometry and fluorescence microscopy on live cells. Fluorescence microscopy on fixed cells is used to study their intracellular distribution. Curr. Protoc. Protein Sci. 54:18.11.1‐18.11.29. © 2008 by John Wiley & Sons, Inc.
Detection of Proteins on Blot Transfer Membranes
Authors: Sasse Joachim , Gallagher Sean R. 
Published: November 2008

AbstractStaining of blot transfer membranes permits visualization of proteins and allows the extent of transfer to be monitored. In the protocols described in this unit, proteins are stained after electroblotting from one‐dimensional or two‐dimensional polyacrylamide gels to blot membranes such as polyvinylidene difluoride (PVDF), nitrocellulose, or nylon membranes. Protocols are provided for the use of six general protein stains: Amido black, Coomassie blue, Ponceau S, colloidal gold, colloidal silver, and India ink. In addition, the fluorescent stains fluorescamine and IAEDANS, which covalently react with bound proteins, are described. Approximate detection limits for each nonfluorescent stain are indicated along with membrane compatibilities. Curr. Protoc. Immunol. 83:8.10B.1‐8.10B.6. © 2008 by John Wiley & Sons, Inc.
Laboratory Maintenance of Rickettsia rickettsii
Authors: Ammerman Nicole C. , Beier‐Sexton Magda , Azad Abdu F. 
Published: November 2008

AbstractThis unit includes protocols for the laboratory maintenance of the obligate intracellular bacterium Rickettsia rickettsii, including propagation in mammalian cell cultures, as well as isolation, counting, and storage procedures. Regulations for working with R. rickettsii in biosafety level 3 containment are also discussed. Curr. Protoc. Microbiol. 11:3A.5.1‐3A.5.21. © 2008 by John Wiley & Sons, Inc.
What US prosecutors and defence attorneys know and believe about eyewitness testimony
Authors: Wise Richard A. , Pawlenko Nell B. , Safer Martin A. , Meyer David 
Published: November 2008

AbstractThe present study compared what prosecutors and defence attorneys know about eyewitness testimony, what they believe jurors know about eyewitness testimony, and what legal safeguards they think are necessary to educate jurors about eyewitness factors. A total of 73 prosecutors and 1184 defence attorneys completed a survey about eyewitness testimony. Both groups of attorneys had extensive experience practicing law and trying criminal cases. Prosecutors were significantly less knowledgeable than the defence attorneys on almost every issue including the weak relationship between eyewitness confidence and accuracy at trial, jurors' inability to distinguish between accurate and inaccurate eyewitnesses and the benefits of sequential lineups. The prosecutors were less willing than the defence attorneys to permit eyewitness expert testimony and were less sceptical of jurors' knowledge of eyewitness testimony. We highlight issues from the survey that are relevant to the training of prosecutors and defence attorneys about eyewitness testimony. Copyright © 2008 John Wiley & Sons, Ltd.
Quantum Dots Decorated with Magnetic Bionanoparticles
Authors: Fernández Belén , Gálvez Natividad , Cuesta Rafael , Hungría Ana B. , Calvino José J. , Domínguez‐Vera José M. 
Published: November 2008

AbstractA new class of water‐soluble, fluorescent, magnetic quantum dots––magnetoferritin bioconjugate––is prepared. The nanostructures are patterned mainly as dimer particles as characterized by high‐angle annular dark‐field scanning transmission electron microscopy and electron energy loss spectroscopy. Magnetic (high spontaneous magnetization values, superparamagnetism) and fluorescent (narrow emission peaks, uniform brightness) properties of both nanoblocks are maintained in the final nanostructure.
Electronic Transport Properties of Ensembles of Perylene‐Substituted Poly‐isocyanopeptide Arrays
Authors: Finlayson Chris E. , Friend Richard H. , Otten Matthijs B. J. , Schwartz Erik , Cornelissen Jeroen J. L. M. , Nolte Roeland J. M. , Rowan Alan E. , Samorì Paolo , Palermo Vicenzo , Liscio Andrea , Peneva Kalina , Müllen Klaus , Trapani Sara , Beljonne David 
Published: November 2008

AbstractThe electronic transport properties of stacks of perylene‐bis(dicarboximide) (PDI) chromophores, covalently fixed to the side arms of rigid, helical polyisocyanopeptides, are studied using thin‐film transistors. In device architectures where the transistor channel lengths are somewhat greater than the average polymer chain length, carrier mobilities of order 10−3 cm2 V−1 s−1 at 350 K are found, which are limited by inter‐chain transport processes. The influence of π–π interactions on the material properties is studied by using PDIs with and without bulky substituents in the bay area. In order to attain a deeper understanding of both the electronic and the electronic‐transport properties of these systems, studies of self‐assembly on surfaces are combined with electronic characterization using Kelvin probe force microscopy, and also a theoretical study of electronic coupling. The use of a rigid polymer backbone as a scaffold to achieve a full control over the position and orientation of functional groups is of general applicability and interest in the design of building blocks for technologically important functional materials, as well as in more fundamental studies of chromophoric interactions.
Western lowland gorillas (Gorilla gorilla gorilla) change their activity patterns in response to frugivory
Authors: Masi Shelly , Cipolletta Chloé , Robbins Martha M. 
Published: November 2008

AbstractThe most important environmental factor explaining interspecies variation in ecology and sociality of the great apes is likely to be variation in resource availability. Relatively little is known about the activity patterns of western lowland gorillas (Gorilla gorilla gorilla), which inhabit a dramatically different environment from the well‐studied mountain gorillas (G. beringei beringei). This study aims to provide a detailed quantification of western lowland gorillas' activity budgets using direct observations on one habituated group in Bai Hokou, Central African Republic. We examined how activity patterns of both sexes are shaped by seasonal frugivory. Activity was recorded with 5‐min instantaneous sampling between December 2004 and December 2005. During the high‐frugivory period the gorillas spent less time feeding and more time traveling than during the low‐frugivory period. The silverback spent less time feeding but more time resting than both females and immatures, which likely results from a combination of social and physiological factors. When compared with mountain gorillas, western lowland gorillas spend more time feeding (67 vs. 55%) and traveling (12 vs. 6.5%), but less time resting (21 vs. 34%) and engaging in social/other activities (0.5 vs. 3.6%). This disparity in activity budgets of western lowland gorillas and mountain gorillas may be explained by the more frugivorous diet and the greater dispersion of food resources experienced by western lowland gorillas. Like other apes, western lowland gorillas change their activity patterns in response to changes in the diet. Am. J. Primatol. 71:91–100, 2009. © 2008 Wiley‐Liss, Inc.