bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centrifugal Elutriation to Obtain Synchronous	Populations of Cells
Authors: Wahl Alan F. , Donaldson Karen L. 
Published: June 2004

AbstractCounterflow centrifugal elutriation is a noninvasive method for separating large numbers of cells on the basis of their size and mass. For mammalian cells, this method is useful for separating mixed populations of cells, in particular cells at different stages of the cell division cycle without perturbing cell metabolism or using synchronizing agents. This unit describes a method for separating 2 x 108 cells using the standard JE‐6B rotor or larger numbers of cells in the JE‐5.0 rotor. To verify the purity and to characterize the cell cycle positions of cells in the elutriated populations, the unit includes protocols for measuring nascent DNA synthesis by [3H]thymidine incorporation and for detecting DNA synthesis and content by propidium iodide flow cytometry alone or in combination with bromodeoxyuridine incorporation.
Preparation of Extracellular Matrices Produced by Cultured Corneal Endothelial and PF‐HR9 Endodermal Cells
Authors: Vlodavsky Israel 
Published: June 2004

AbstractThe ECM is an organized complex of collagens, proteoglycans, and glycoproteins, all interacting to produce a highly stable structure upon which cells migrate, proliferate, differentiate, and survive in vivo. Cultured bovine corneal endothelial (BCE) cells and PF‐HR9 endodermal cells produce underlying ECMs that adhere strongly to plastic and closely resemble subendothelial and subepithelial basement membranes in vivo in their morphology, molecular composition, and biological activities. This unit describes the methods for preparation of these ECMs, their properties, and their cellular effects.
In Vitro Analysis of Chloroplast Protein Import
Authors: Smith Matthew D. , Schnell Danny J. , Fitzpatrick Lynda , Keegstra Kenneth 
Published: June 2004

AbstractThis unit describes protocols for isolating chloroplasts from pea (Pisum sativum) and Arabidopsis thaliana for the study of nuclear‐encoded plastid precursor proteins. Chloroplasts from both preparations are competent for the in vitro import of recombinant preproteins synthesized using in vitro translation systems derived from reticulocyte or wheat germ lysates. These assays can be used to test whether a particular protein is targeted to chloroplasts, for analyzing the suborganellar location of newly imported preproteins, or to study the mechanism of import itself.
In VitroRNASplicing in Mammalian Cell Extracts
Authors: Rooke Nanette , Underwood Jason 
Published: June 2004

AbstractAlmost every eukaryotic pre‐mRNA generated by RNA polymerase II transcription requires the removal of introns to create mRNA. The correct splicing of constitutive exons is thus critical for normal protein expression and function. Moreover, the removal of many introns by the spliceosome is controlled in a tissue‐specific or developmentally specific manner. In order to study RNA splicing at a biochemical level, it is necessary to employ an in vitro, or cell‐free, system. Cell‐free splicing systems require two main components: (1) an extract made from mammalian cell nuclei and (2) the introns and exons of the eukaryotic gene of interest. This minigene construct allows the synthesis of sufficient quantities of pre‐mRNA substrates in vitro, which are then incubated in the nuclear extract and analyzed for splicing. Nuclear extracts, first developed for studying transcription in vitro, are modified for splicing. This unit describes how to set up an in vitro splicing reaction using a mammalian nuclear extract derived from either cell line or tissue, and how to analyze the splicing reaction products.
Cell Traction
Authors: Galbraith Catherine G. , Sheetz Michael P. 
Published: June 2004

AbstractTraction forces are exerted by cells on their substratum as they migrate. These forces under the entire cell or subcellular regions can be measured. This unit describes several protocols for making silicone sheets to measure traction forces under the entire cell, as well as a protocol for developing a micromachined device to measure forces under subcellular regions.
Labeling Cultured Cells with 32Pi and Preparing Cell Lysates for Immunoprecipitation
Authors: Sefton Bartholomew M. 
Published: June 2004

AbstractSignal transduction pathways may involve protein phosphorylation at one or more residues. Detection of phosphorylation involves labeling with radioactive inorganic phosphate and subsequent immunoprecipitation with appropriate antibodies. This unit describes labeling conditions for adherent and nonadherent cells and preparation of the lysates from these cells for immunoprecipitation. The labeling method is appropriate for labeling other phosphorylated component of cells, but alternate methods are necessary for their detection.
Use of Glycosidases to Study Protein Trafficking
Authors: Freeze Hudson H. 
Published: June 2004

AbstractAs proteins transit through the cell secretory pathway, modification of their substituent sugar chains occurs in a stepwise fashion. In the course of this processing (maturation) of oligosaccharide chains, the chains acquire sensitivity or resistance to highly specific glycosidases. Thus it is possible to identify processing mileposts by analyzing the general structure of the carbohydrate chains. This unit describes reaction conditions for the family of glycosidases and analysis of the results of digestion reactions.
Endocytosis: Biochemical Analyses
Authors: McGraw Timothy E. , Subtil Agathe 
Published: June 2004

AbstractMany integral membrane proteins synthesized in the endoplasmic reticulum ultimately arrive at the cell surface to contact the cell environment. During transit through the Golgi and trans‐Golgi network, proteins acquire post‐translational modifications that can be used to track the appearance of such modified proteins at the cell surface. Cellular proteins can be treated with enzymes‐‐e.g., sialidase or protease‐‐or antibodies, or biotinylated to identify molecules that have reached the cell surface. Some proteins first enter the endocytic pathway before appearing at the cell surface; this is detected by treating the cells at 4o and 37oC. Analysis of the number of sialic acids on proteins of cells treated at 4oC identifies proteins resident at the cell surface, while cells treated at 37oC internalize the sialidase, which can then act with proteins in the endocytic compartments.
Current Concepts in Cell Death
Authors: Zhivotovsky Boris , Orrenius Sten 
Published: June 2004

AbstractThis unit attempts to define cell toxicity that leads to cellular demise, with a strong emphasis on cell death via both apoptosis and necrosis, by summarizing some of the more recent developments in cellular, molecular, and biochemical studies of the events that govern the induction and execution of cell death. Specific topics pertaining to cell death include structural changes, macromolecular degradation, cellular signaling, the role of mitochondria, and genetic modulation of apoptotic cell death.
Nonisotopic Methods for Determination of Poly(ADP‐Ribose) Levels and Detection of Poly(ADP‐Ribose) Polymerase
Authors: Haince Jean François , Poirier Guy G. , Kirkland Jim B. 
Published: June 2004

AbstractPoly(ADP‐ribosyl)ation is a post‐translational modification catalyzed mostly by the 116‐kDa enzyme poly(ADP‐ribose) polymerase‐1 (PARP‐1), a nuclear enzyme that transfers an ADP‐ribose moiety onto a limited number of nuclear proteins, including itself. When cells are exposed to environmental stresses such as alkylating agents or free radicals, there is up to a 500‐fold increase in net poly(ADP‐ribose) synthesis in response to DNA strand breaks. The enzyme responsible for 80% to 90% of this stimulated poly(ADP‐ribose) synthesis is PARP‐1, while other PARPs are responsible for the remaining 10% to 20%. The physiological meaning of these phenomena is not clear; however, it can be interpreted as a way of translating an event occurring on DNA to the nucleus by protein modification and finally to the cytoplasm via NAD+ depletion. It has also been proposed that the presence of negatively charged poly(ADP‐ribose) at the site of DNA damage may play several roles in regulation of base excision repair, p53 functions, and apoptosis. This unit describes protocols for measuring the levels of poly(ADP‐ribose) in cells using nonisotopic reagents and for identifying the poly(ADP‐ribose) polymerase enzymes present in cells.
Sequence File Format Conversion with Command‐Line Readseq
Authors: Gilbert Don 
Published: June 2004

AbstractOne of the major challenges in using bioinformatics software is that there are a wide variety of sequence formats, e.g., GenBank, EMBL, and FASTA. It is often the case that a sequence or a set of sequences is in one format but is needed in another. This unit offers a solution to this problem ‐ Readseq. Readseq is a program that can read and write 18 different formats
Low‐temperature controllable calcination syntheses of potassium dititanate
Authors: Bao Ningzhong , Feng Xin , Lu Xiaohua , Shen Liming , Yanagisawa Kazumichi 
Published: June 2004

AbstractThermodynamic calculations were used to estimate the free energy for reactions of anatase and TiO2·nH2O with K2CO3 to generate potassium dititanate at 25–1200°C, and the results showed that amorphous TiO2·nH2O with reaction activity higher than that of anatase can decrease the lowest generation temperature of potassium dititanate. The precise temperatures of 300°C for TiO2·nH2O and 500°C for anatase were determined by experiments. The crystal growth of potassium dititanate was studied experimentally. It was found that potassium dititanate hydrate is first formed from TiO2·nH2O at 300°C, and converts into K2Ti2O5·0.35H2O at 640°C. The dehydration of K2Ti2O5·0.35H2O occurs at 660–820°C, ending with the generation of K2Ti2O5 single crystals at 820°C. Potassium dititanates with a diversity of morphologies, sizes, water contents, and crystallinities, showing various abilities for optical absorption/reflex, were fabricated from TiO2·nH2O under control, whereas only K2Ti2O5 was prepared from anatase at 500–850°C, which indicate that reaction processes and properties of products are determined according to the type of reactants and the reaction temperature. © 2004 American Institute of Chemical Engineers AIChE J, 50: 1568–1577, 2004
Extinction deficits in male rhesus macaques with a history of self‐injurious behavior
Authors: Lutz Corrine , Tiefenbacher Stefan , Meyer Jerrold , Novak Melinda 
Published: June 2004

AbstractSelf‐injurious behavior (SIB) occurs in both human and nonhuman primate populations. Despite the potential for harm, SIB may persist in part because of an inability to inhibit behavior that results in wounding. A lever‐pressing task was used to test the prediction that monkeys with SIB would show greater persistence in lever‐pressing on extinction trials than monkeys without the disorder. The subjects were 15 individually‐housed adult male rhesus macaques, 10 of which (the SIB group) had a veterinary record of self‐inflicted wounding. All of the monkeys were trained to lever‐press for food rewards to a criterion of 400 total responses. The test procedures consisted of five daily 30‐min sessions divided into six 5‐min intervals. On day 1, the subjects received continuous reinforcement. On days 2–4, testing consisted of alternating reinforced/unreinforced 5‐min intervals, beginning with reinforcement. Reinforced intervals were cued with a buzzer. On day 5, the subjects received no reinforcement. The number of lever‐presses and behavioral responses were recorded during each session. Saliva samples were collected for cortisol measurement before and after test sessions on days 1, 2, and 5. As predicted, monkeys with SIB lever‐pressed more than controls during extinction intervals on days 2–4. There was no difference on day 1 or day 5. The frequency of scratching, yawning, and abnormal behavior increased when reinforcement was intermittent (days 2–4) or absent (day 5). Cortisol levels were highest with continuous reinforcement (day 1), and may reflect differential levels of food intake rather than stress. The presence of extinction deficits suggests that SIB may persist in some monkeys because they lack the ability to regulate the intensity of their biting behavior. Am. J. Primatol. 63:41–48, 2004. © 2004 Wiley‐Liss, Inc.
Transmission of STLV in a closed colony of macaques
Authors: Parrish Stephanie W.K. , Brown Arthur E. , Chanbancherd Penprapa , Gettayacamin Montip , Parrish John H. 
Published: June 2004

AbstractA 3.3% seroprevalence of simian T‐lymphotropic virus (STLV) was found in a closed breeding and research colony of rhesus and cynomolgus macaques in Thailand. Epidemiology of STLV within the colony was assessed by means of a retrospective analysis of banked and freshly collected serum samples, and a review of the animals' medical records. Evidence was found that the virus had been imported into the colony by some of the original animals, and was subsequently transmitted both vertically and horizontally. The cell‐associated nature of STLV was demonstrated by iatrogenic transmission of the virus following a whole blood transfusion, but there was no transmission to animals that received only serum from the same infected donor. Transmission by all routes was infrequent, as indicated by the overall seroprevalence of 3.3% (14 of 420 samples) after the colony had been closed for 11 years. Maternal–infant transmission appeared to be <12%. Am. J. Primatol. 63:103–109, 2004. © 2004 Wiley‐Liss, Inc.
Studies on dimensional stability and thermal properties of rubber wood chemically modified with styrene and glycidyl methacrylate
Authors: Devi Rashmi R. , Maji T. K. , Banerjee A. N. 
Published: June 2004

AbstractRubber wood (Hevea brasiliensis) was impregnated with styrene and glycidyl methacrylate (GMA) as the crosslinking monomer. After impregnation, the polymerization was accomplished by catalyst heat treatment. Water uptake (%) and water vapor exclusion (%) of the rubber wood were found to be improved on treatment. Dimensional stability expressed in terms of volumetric swelling in water vapor (90% relative humidity) as well as in liquid water and water repellent effectiveness (WRE) of the treated samples were determined and also found to be improved. The wood–polymer interaction was confirmed by FTIR spectroscopy. Thermal properties of untreated and treated wood samples were evaluated by thermogravimetric analysis (TGA) and differential scanning calorimetery (DSC) and an improvement in thermal stability was observed for the wood–polymer composites. The improvement in properties observed as more with styrene–GMA (1:1) combination. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1938–1945, 2004
Effects of process conditions and mixing protocols on structure of extruded polypropylene nanocomposites
Authors: Zhu Linjie , Xanthos M. 
Published: June 2004

AbstractPolymer melt‐direct intercalation or exfoliation is a promising approach for the preparation of nanocomposites. The structure of nanoclay platelets in the nanocomposites depends not only on the properties of polymer matrix and nanoclay, but also on the operating conditions during processing. The objective of the present work is to investigate the effects of clay chemical modifiers, mixing protocols, and operating conditions upon the clay structure in nanocomposites prepared with a corotating twin‐screw extruder. Two mixing methods were used for the nanocomposite preparation: two‐step mixing and one‐step mixing. Experimental results obtained from melt flow index and complex viscosity measurements suggest that nanoclay C15A is more exfoliated than C30B in a polypropylene homopolymer containing a maleic anhydride grafted PP (PB) as compatibilizer. The two‐step mixing method results in better exfoliation for the nanofillers than the one‐step mixing method. A numerical simulation has been carried out to evaluate the mean residence time and shear rate in different screw configurations under various process conditions. X‐ray diffraction experiments indicate that the residence time is a dominant factor in producing satisfactory nanocomposites in extruders. However, high shear rate coupled with long residence time might result in poor exfoliation of clay. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1891–1899, 2004
Effect of temperature on aggregation/dissociation behavior of interpolymer complexes stabilized by hydrogen bonds
Authors: Khutoryanskiy Vitaliy V. , Nurkeeva Zauresh S. , Mun Grigoriy A. , Dubolazov Artem V. 
Published: June 2004

AbstractThe effect of temperature on the aggregation/dissociation behavior of interpolymer complexes based on poly(acrylic acid) and various nonionic polymers—poly(vinyl pyrrolidone), poly(ethylene oxide), poly(acrylamide), hydroxypropylcellulose, hydroxyethylcellulose, poly(vinyl methyl ether), poly(vinyl ether of ethyleneglycol), and vinyl ether of ethyleneglycol‐co‐vinyl butyl ether—has been studied in aqueous solutions. It was shown that nonionic polymers could be classified into two groups according to the stability of their polycomplexes with respect to temperature. The first group of nonionic polymers forms interpolymer complexes, which are stable and undergo further aggregation upon increase in temperature. The second group forms polycomplexes, which dissociate at higher temperatures. The nature of forces stabilizing different interpolymer complexes in aqueous solutions is discussed. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1946–1950, 2004
Sorption equilibrium of Cr(VI) ions by strong base anion exchangers with pyridine structures
Authors: Neagu Violeta , Untea I. , Tudorache Elena , Orbeci Cristina 
Published: June 2004

AbstractChromate sorption on pyridine strong base anion exchangers with different functional groups (methyl, ethyl, and butyl groups), at the quaternary nitrogen atoms, was studied as a function of various initial concentrations (100–1500 mg Cr/L) and counterion type. The studied resins in the Cl−[ form have higher Cr(VI)‐retention capacities than those in the SO form. The pyridine strong base anion exchangers showed a selectivity reversal for the sulfate and chromate anions compared to that of the commercial resins. The alkyl substituent length of the quaternary nitrogen atoms exerted a substantial influence on the Cr(VI)‐retention capacity values for the resins in the Cl− form; the chromate anions preferred resins with methyl functional groups, that is, resins with a greater hydrophilic structure. For the resins in the SO form the length of the substituent at the quaternary nitrogen atom had only a negligible influence on their Cr(VI)‐retention values. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1957–1963, 2004
Effect of montmorillonite on the properties of thermosensitive poly(N‐isopropylacrylamide) composite hydrogels
Authors: Bignotti Fabio , Sartore Luciana , Penco Maurizio , Ramorino Giorgio , Peroni Isabella 
Published: June 2004

AbstractThermosensitive composite hydrogels containing various amounts of sodium montmorillonite (NaMM) and poly(N‐isopropylacrylamide) (pNIPAAm) were synthesized. Their equilibrium degree of swelling (DS) was measured in NaCl solutions of different ionic strength and at various temperatures. The DS decreased when increasing the clay content and no substantial shift in the phase transition temperature was noticed. The composite hydrogels investigated had a NaMM content ranging between 1.0 and 5.7 wt % (in 0.1M NaCl at 25°C). A considerable enhancement in the response to thermal stimuli was observed for NaMM contents >2–3 wt %. It is suggested that when the NaMM concentration approaches a critical value, the clay platelets can inhibit the formation of the hydrophobic skin layer that hinders shrinking in conventional pNIPAAm hydrogels. The effect of montmorillonite on the mechanical properties of the hydrogels was investigated by uniaxial compression tests, which showed that the modulus increases with the NaMM content. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1964–1971, 2004
Effects of Nigella sativa on oxidative stress and β‐cell damage in streptozotocin‐induced diabetic rats
Authors: Kanter Mehmet , Coskun Omer , Korkmaz Ahmet , Oter Sukru 
Published: June 2004

AbstractThe aim of the present study was to evaluate the possible protective effects of Nigella sativa L. (NS) against β‐cell damage from streptozotocin (STZ)‐induced diabetes in rats. STZ was injected intraperitoneally at a single dose of 50 mg/kg to induce diabetes. NS (0.2 ml/kg/day, i.p.) was injected for 3 days prior to STZ administration, and these injections were continued throughout the 4‐week study. Oxidative stress is believed to play a role in the pathogenesis of diabetes mellitus (DM). To assess changes in the cellular antioxidant defense system, we measured the activities of antioxidant enzymes (such as glutathione peroxidase (GSHPx), superoxide dismutase (SOD), and catalase (CAT)) in pancreatic homogenates. We also measured serum nitric oxide (NO) and erythrocyte and pancreatic tissue malondialdehyde (MDA) levels, a marker of lipid peroxidation, to determine whether there is an imbalance between oxidant and antioxidant status. Pancreatic β‐cells were examined by immunohistochemical methods. STZ induced a significant increase in lipid peroxidation and serum NO concentrations, and decreased antioxidant enzyme activity. NS treatment has been shown to provide a protective effect by decreasing lipid peroxidation and serum NO, and increasing antioxidant enzyme activity. Islet cell degeneration and weak insulin immunohistochemical staining was observed in rats with STZ‐induced diabetes. Increased intensity of staining for insulin, and preservation of β‐cell numbers were apparent in the NS‐treated diabetic rats. These findings suggest that NS treatment exerts a therapeutic protective effect in diabetes by decreasing oxidative stress and preserving pancreatic β‐cell integrity. Consequently, NS may be clinically useful for protecting β‐cells against oxidative stress. © 2004 Wiley‐Liss, Inc.
Improving judgement with prepaid expert advice
Authors: Sniezek Janet A. , Schrah Gunnar E. , Dalal Reeshad S. 
Published: June 2004

AbstractDecision makers (“Judges”) often make decisions after obtaining advice from an Advisor. The two parties often share a psychological “contract” about what each contributes in expertise to the decision and receives in monetary outcomes from it. In a laboratory experiment, we varied Advisor Experitise and the opportunity for monetary rewards. As expected, these manipulations influenced advice quality, advice taking, and Judge post‐advice decision quality. The main contribution of the study, however, was the manipulation of the timing of monetary rewards (before or after the advising interaction). We found, as predicted, that committing money for expert—but not novice—advice increases Judges' use of advice and their subsequent estimation accuracy. Implications for advice giving and taking are discussed. Copyright © 2004 John Wiley & Sons, Ltd.