bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical heterogeneity in cell death: Combined synchrotron IR and fluorescence microscopy studies of single apoptotic and necrotic cells
Authors: Jamin Nadège , Miller Lisa , Moncuit Janine , Fridman Wolf‐Herman , Dumas Paul , Teillaud Jean‐Luc 
Published: August 2003

AbstractThe combination of synchrotron IR microspectroscopy and fluorescence microscopy has led to the identification of specific IR signatures of apoptosis and necrosis at a single cell level. Apoptosis was induced by treatment of Fas+ tumor cell lines with anti‐Fas monoclonal antibodies. Detection of the early and late stages of apoptosis was performed using conjugated annexin V‐fluorescein isothiocyanate (AV‐FITC) and propidium iodide. Very early cellular changes were detected by IR before externalization of phosphatidylserine and AV‐FITC labeling, and they were probably linked to DNA unwinding. The IR signals at 1044, 1177, and 1222 cm−1, as well as an intensity variation in the CHx stretching region, are the main signature changes of early and late apoptosis, in line with the hypothesis of DNA fragmentation. The increased intensity of the CHx stretching bands of the lipids was observed only at an early stage of apoptosis. Changes in the relative intensity of CH3 and CH2 stretching accompany this increased intensity, suggesting changes in the relative amount and/or type of lipids concomitant with an increased lipid content. Finally, necrotic cells were characterized by marked changes in their chemical composition because several new vibrational features were observed. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 366–373, 2003
Fourier transform IR attenuated total reflectance spectroscopy studies of cysteine‐induced changes in secondary conformations of bovine serum albumin after UV‐B irradiation
Authors: Wei Yen‐Shan , Lin Shan‐Yang , Wang Shun‐Li , Li Mei‐Jane , Cheng Wen‐Ting 
Published: August 2003

AbstractFourier transform IR spectroscopy equipped with attenuated total reflection was used to investigate the cysteine‐induced alteration of the protein secondary structure of bovine serum albumin (BSA) in aqueous solution before and after UV‐B irradiation. Several amino acids were also studied. The results indicate the unchanged IR spectra of BSA coincubated with amino acids, except cysteine, did not change after 72‐h UV‐B irradiation. There was no difference in the IR spectrum of the unirradiated BSA coincubated with cysteine. A shoulder at 1620 cm−1 attributed to the intermolecular β‐sheet structure was observed for the IR spectrum of BSA coincubated with cysteine after 72‐h UV‐B irradiation. Moreover, the peak intensity at 1303 cm−1 that is due the α‐helix structure was reduced, but the peak intensity at 1247 cm−1 corresponding to β‐sheet structures was increased. Longer UV‐B exposure for a BSA solution coincubated with cysteine changed the BSA solution from clear to viscous to gel form in which a transparent gel and another white gel were simultaneously observed. A gradual IR spectral alteration was found for BSA coincubated with cysteine and subjected to increased UV‐B irradiation. The longer UV‐B irradiation yielded increased intensity at 1620 cm−1. The second‐derivative IR peaks at 1655, 1631, and 1548 cm−1 were shifted to 1650, 1620, and 1544 cm−1, respectively, by the increase of UV‐B irradiation, suggesting a progressive transformation from an α‐helix to an intermolecular β‐sheet structure for BSA coincubated with cysteine. This strongly implies that longer UV‐B exposure time for the BSA solution in the presence of cysteine did alter the protein secondary structures of BSA more, thus inducing gel formation by protein aggregation. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 345–351, 2003
Allophycocyanin: Trimers, monomers, subunits, and homodimers
Authors: MacColl Robert , Eisele Leslie E. , Menikh Abdellah 
Published: August 2003

AbstractAllophycocyanin is a photosynthetic light‐harvesting pigment–protein complex located in the phycobilisomes of cyanobacteria and red algae. Using dynamic light scattering and circular dichroism, solutions of purified allophycocyanin were shown to consist of homogeneous trimers (α3β3) with a nonspherical shape over a very wide range of protein concentrations at pH 6.0 and 20°C. Deconvolutions of the visible circular dichroism spectrum of the trimer were carried out for the first determination of the individual spectra of all six‐component chromophores. The chromophores were shown to be in different microenvironments that helped determine the spectrum of the trimer. Monomers (αβ) that were formed in either the presence of 0.50M NaSCN or at 45°C were shown to be completely reversible to trimers. However, subunits (α and β) that were formed in either the presence of 8M urea or at 60°C, using spectroscopy and gel‐filtration column chromatography, were observed to only partially reconstitute trimers. Homodimers (α2 and/or β2) formed during the regeneration of trimers. The homodimer, which was detected for the first time when both subunits were present, was shown to be in equilibrium with its subunits. Unlike the trimer situation, subunits were found to fully reconstitute monomers in the presence of 0.50M NaSCN. These results suggest a route to trimer assembly from subunits with monomers serving as intermediaries and the homodimers forming in a nonproductive step that did not interfere with the overall assembly scheme. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy), 72: 352–365, 2003
Optical properties of Erwinia herbicola bacteria at 0.190–2.50 μm
Authors: Arakawa E. T. , Tuminello P. S. , Khare B. N. , Milham M. E. 
Published: August 2003

AbstractWe measure the complex index of refraction of Erwina herbicola (also known as Enterobacter agglomerans or Pantoea agglomerans) bacteria (ATTC 33243) over the spectral region from 0.190 to 2.50 μm (4000–52,632 cm−1). Transmission measurements are made on solid films of E. herbicola and on suspensions of the bacteria in water. These measurements, combined with spectral reflectance and Kramers–Krönig analysis, allow the determination of the real and imaginary parts over the entire wavelength interval. Accurate and consistent results are obtained for this complex and difficult to measure material. This is part of a continuing series of measurements of the optical constants of representative biological materials that are applicable to the development of methods for detection of airborne biological contaminants, where the material under study is used as a surrogate for a pathogenic agent. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 391–398, 2003
Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions
Authors: Andrushchenko V. , Van De Sande J. H. , Wieser H. 
Published: August 2003

AbstractVibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0–0.4M (a Cu2+/phosphate molar ratio [Cu]/[P] of 0–0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine‐cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine‐thymine (AT) base pairs, which favors a “sandwich” complex in which a Cu2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B‐form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A‐ or Z‐form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3‐dimensional structure of the DNA–metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 374–390, 2003
Raman structural markers of tryptophan and histidine side chains in proteins
Authors: Takeuchi Hideo 
Published: August 2003

AbstractThe Raman spectrum of a protein contains a wealth of information on the structure and interaction of the protein. To extract the structural information from the Raman spectrum, it is necessary to identify and interpret the marker bands that reflect the structure and interaction in the protein. Recently, new Raman structural markers have been proposed for the tryptophan and histidine side chains by examining the spectra–structure correlations of model compounds. Raman structural markers are now available for the conformation, hydrogen bonding, hydrophobic interaction, and cation–π interaction of the indole ring of Trp. For His, protonation, tautomerism, and metal coordination of the imidazole ring can be studied by using Raman markers. The high‐resolution X‐ray crystal structures of proteins provide the basis for testing and modifying the Raman structural markers of Trp and His. The structures derived from Raman spectra are generally consistent with the X‐ray crystal structures, giving support for the applicability of most Raman structural makers. Possible modifications and limitations to some marker bands are also discussed. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 305–317, 2003
Die Winogradsky‐Säule: Modellversuch zur Mikrobiologie
Authors: Telgmann Gisela 
Published: August 2003

AbstractIn einer Winogradsky‐Säule entwickeln sich unterschiedliche Schwefel— und Sauerstoffgradienten. Die im Schlamm und Wasser vorhandenen Mikroorganismen siedeln sich entsprechend ihrer Ansprüche an ihre ökologische Nische in „Etagen”︁ an und vermehren sich im Verlauf der folgenden Wochen derart stark, dass sie als farbige Banden sichtbar werden. Mit Hilfe einfacher Identifizierungsmöglichkeiten können diese Banden bekannten Mikroorganismen zugeordnet werden. Die Kenntnis ihrer Stoffwechselleistungen und Lebensansprüche ermöglicht die Deutung der zeitlichen Abfolge bei der Bandenbildung und die Zuordnung wichtiger Vorgänge zu wesentlichen Teilprozessen des Kohlenstoff‐, Schwefel‐ und Stickstoffkreislaufes. Die Beobachtung über mehrere Wochen ermöglicht die Unterscheidung von Sukzession und Klimaxstadium und lässt so das Prozesshafte ökologischer Vorgänge erkennen.
Auf der Suche nach alten Bekannten: Sequenzvergleich durch Alignments
Authors: Haubold Bernhard 
Published: August 2003

AbstractDie laufenden Genomprojekte bescheren den Molekularbiologen einen phantastischen, allgemein zugänglichen Datenreichtum. Sowohl die Erhebung dieser Daten als auch ihre Interpretation stützt sich auf ein in der Biologie althergebrachtes Verfahren, dem Vergleich. Relativ neu ist jedoch der starke Einsatz bioinformatischer Methoden zum genomweiten Sequenzvergleich. Dieser Aufsatz gibt eine Einführung in die Genomik und die sie unterstützende Bioinformatik.
Physikalische Uhren zur Frühzeit des Menschen: Archäochronometrie
Authors: Wagner Günther A. , Glasmacher Ulrich A. 
Published: August 2003

AbstractPhysikalische Datierungsverfahren basieren auf dem natürlichen Zerfall radioaktiver Mutternuklide in Tochternuklide. Für den Altersbereich seit dem Auftreten des Menschen (zwei bis drei Millionen Jahre) werden vor allem die K‐Ar, die Lumineszenz, die Kernspaltspuren, die Uranreihen und die Radiokohlenstoffmethode angewandt. Ständige Weiterentwicklungen dieser verschiedenen Methoden führen zu einer präziseren Altersbestimmung und ermöglichen die zeitliche Zuordnung von Funden und Prozessen, die bisher nicht datierbar waren. So konnte mit der 14C‐Datierung von Knochen und der TL‐Datierung von gebrannten Feuersteinen im Geißenklösterle bei Blaubeuren das erste Auftreten des Homo sapiens in Europa auf die Zeit um 40.000 Jahre vor heute festgelegt werden.
Schlüsselenzym der Nitratassimilation: Nitratreduktase
Authors: Appenroth Klaus‐J. , Lillo Cathrine 
Published: August 2003

AbstractDas Schlüsselenzym der Nitratassimilation ist Nitratreduktase (NR). Über drei Redox‐Domänen werden Elektronen von NADH auf Nitrat übertragen, das zu Nitrit reduziert wird. Nitratassimilation ist sehr energieaufwendig, das Reaktionsprodukt Nitrit ist ein Zellgift. Nitratreduktase ist deshalb hochgradig reguliert: Die Expression des NR‐Gens ist lichtabhängig. In dunkelgewachsenen Pflanzen wird dieser Prozess durch Phytochrome kontrolliert, in lichtgewachsenen Pflanzen durch Photosynthese. Nach erfolgter Biosynthese wird die Aktivität der NR im Dunkeln verringert, indem das Enzym phosphoryliert wird und danach an ein inaktivierendes Protein (14‐3‐3) bindet. Auch im Tagesverlauf wird NR reguliert: Durch zirkadiane Steuerung kann die Erhöhung der Enzymaktivität schon vor Tagesbeginn vorbereitet werden. Man spricht von einer „Stickstoff‐Uhr”︁, weil alle notwendigen Komponenten einer biologischen Uhr bei der Nitratassimilation vorhanden sind. Biotechnologische Forschung zur Erzeugung von Pflanzen mit verbesserter Stickstoff‐Assimilation hat bisher noch nicht zu praktischen Ergebnissen geführt.
Strategien gegen die Schwerkraft: Marines Zooplankton
Authors: Schneider Gerald 
Published: August 2003

AbstractDie Lebensgemeinschaften des Planktons unterliegen der Gefahr, in für die jeweilige Gruppe lebensfeindliche Wassertiefen abzusinken. Dagegen haben die Organismen verschiedene Strategien entwickelt. Bei marinem Zooplankton sind dies vor allem Dichte reduzierende Mechanismen wie ein möglichst niedriges Protein‐/Lipidverhältnis, ein hoher Wassergehalt und die teilweise Ersetzung von schweren Sulfationen durch leichtere Chloridionen in den Geweben. Neben solchen biochemischen Strategien kennen wir auch aktive und passive Auftriebskörper wie beispielsweise Gasblasen oder extrakorporale Gallertstrukturen, aber auch die Ausnutzung von widerstandsreichen Körpergeometrien und bestimmte Verhaltensweisen, die ein Absinken verhindern. Obwohl seit mehr als hundert Jahren über diese Zusammenhänge nachgedacht wird, erweisen sich neuere Forschungen über dieses Thema als produktiv.
Monarchfalter: Fliegen mit der Sonnenuhr
Authors: Irsch Wilhelm 
Published: August 2003

AbstractJedes Jahr ziehen im Herbst die nordamerikanischen Monarchfalter (Danaus plexippus), Tagschmetterlinge mit einer Flügelspannweite von bis zu zwölf Zentimetern, zu Millionen in ihr Winterquartier im Süden und treten im Frühjahr wieder die Rückreise an. Sie fliegen allein, in Gruppen oder großen Schwärmen und legen bis zu 3500 Kilometer zurück. Die Flugrichtung und der Zeitpunkt dieser Massenwanderung sind so genau vorhersagbar, dass an den Zugstraßen viele Städte das Eintreffen der Falter mit Volksfesten begehen.
Hyänen — sanfte Männchen sind erfolgreicher
Authors: Irsch Wilhelm 
Published: August 2003

AbstractTüpfelhyänen (Crocuta crocuta) leben in hochkomplexen Clans zusammen, bei denen in der Regel die Weibchen das Sagen haben. Verhaltensforscher des Berliner Instituts für Zoo‐ und Wildtierforschung haben nun nachweisen können, dass sanfte Männchen weit mehr Paarungserfolge vorweisen können als ihre aggressiveren Geschlechtsgenossen.
Genome schützen sich vor fremder DNA
Authors: Brennicke Axel 
Published: August 2003

AbstractUnsere kleinsten biologischen Feinde sind DNA‐Stücke, die sich in unserem Erbgut festsetzen und sich von dort aus vermehren. Das Pantoffeltierchen und seine Verwandten liefern jetzt neue Erkenntnisse über Verteidigungsmaßnahmen gegen solche Invasoren. Über den RNA‐Umweg erkennt unser Genom die eingewanderte Fremd‐DNA und schneidet sie heraus.
Giftmörderin mit Appetit
Authors: Tillmann Urban 
Published: August 2003

AbstractFressen und Gefressen werden, dieser tägliche Kampf prägt bekanntermaßen das Leben. Während normalerweise die Rollen von Fressern und Futter klar verteilt sind, gibt es im Plankton offensichtlich bemerkenswerte Ausnahmen — die Alge Prymnesium parvum gehört dazu.
In fremde Haut gehüllt
Authors: Wendler Silke 
Published: August 2003

AbstractParasiten aus der Ordnung der Fächerflügler (Strepsiptera) hüllen sich aktiv in einen Sack aus Hautgewebe des Wirtes und entgehen so dessen Immunabwehr. Die Wirte werden durch diesen Befall mit Tarnkappe sterilisiert, weswegen man über einen Einsatz in der biologischen Schädlingsbekämpfung nachdenkt.
Georg Klebs
Authors: Penzlin Heinz 
Published: August 2003

AbstractVor 100 Jahren begründete Georg Klebs mit seinem Buch „Willkürliche Entwickelungsänderungen bei Pflanzen”︁ die botanische Entwicklungs‐ und Fortpflanzungsphysiologie. Heute ist der Forscher, der schon früh „das Beharrliche im Flusse der Erscheinungen”︁ erkannte, fast in Vergessenheit geraten.
Protein – DNA interactions: the story so far and a new method for prediction
Authors: Jones Susan , Thornton Janet M. 
Published: August 2003

AbstractThis review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one‐third of DNA‐binding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA‐binding functionality. Copyright © 2003 John Wiley & Sons, Ltd.
The prediction of membrane protein structure and genome structural annotation
Authors: Martelli Pier Luigi , Fariselli Piero , Tasco Gianluca , Casadio Rita 
Published: August 2003

AbstractNew methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β‐barrel and all‐α membrane proteins with high accuracy and a low rate of false positives and false negatives. These methods have been integrated in a suite of programs to filter proteomes of Gram‐negative bacteria, searching for new membrane proteins. Copyright © 2003 John Wiley & Sons, Ltd.
The 4th Bologna Winter School: hot topics in structural genomics
Authors: Casadio Rita 
Published: August 2003

AbstractThe 4th Bologna Winter School on Biotechnologies was held on 9–15 February 2003 at the University of Bologna, Italy, with the specific aim of discussing recent developments in bioinformatics. The school provided an opportunity for students and scientists to debate current problems in computational biology and possible solutions. The course, co‐supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results, recent and promising genome‐wide predictions, protein–protein and protein–DNA interaction predictions and genome functional annotation. The topics were organized into four main sections (http://www.biocomp.unibo.it). Published in 2003 by John Wiley & Sons, Ltd.
Hybrid methods for electromagnetic scattering simulations on overlapping grids
Authors: El Hachemi M. , Hassan O. , Morgan K. , Rowse D. P. , Weatherill N. P. 
Published: August 2003

AbstractThe numerical simulation of practical electromagnetic scattering problems often involves geometries that are complex in shape and that may contain small scale features. The result is a large scale simulation and this requires solution techniques that are efficient, in terms of both computer time and computer memory requirements. In addition, it is advantageous if the method adopted exhibits a high degree of flexibility from the viewpoint of mesh generation. Hybrid methods, based upon the coupling of the structured grid finite difference time domain approach with an unstructured finite element or finite volume time domain procedure, appear ideally suited to meet these requirements. The structured grid method is memory and time efficient, while the unstructured grid methods readily handle general geometries, allowing detailed definition of small scale features. This paper presents the results of an initial investigation into the possibility exploiting these advantages in electromagnetic scattering simulations. Copyright © 2003 John Wiley & Sons, Ltd.
Novel multiparameter flow cytometry assay using Syto16 for the simultaneous detection of early apoptosis and apoptosis‐corrected P‐glycoprotein function in clinical samples
Authors: van der Pol Marjolein A. , Broxterman Henk J. , Westra Guus , Ossenkoppele Gert J. , Schuurhuis Gerrit J. 
Published: August 2003

AbstractBackgroundThe fluorescent probe Syto16 has been used successfully to measure P‐glycoprotein (Pgp) function and, separately, early apoptosis and cell death. The present study was designed to evaluate whether the combined use of Syto16, the Pgp blocker PSC833, and 7‐AAD allows simultaneous detection of all parameters, with emphasis on applications in acute myeloid leukemia (AML).MethodsPgp negative/positive KB cell lines treated with tumor necrosis factor α/hyperthermia and frozen–thawed AML samples were used as apoptosis/Pgp models.ResultsFor the accurate assessment of apoptosis in samples with unknown Pgp status, it was essential to include a sample with PSC833: in such samples, viable cells always show a Syto16high and apoptotic cells a Syto16low fluorescence. Apoptotic cells loose their Pgp activity early on; in Pgp‐positive cells, the Syto16low apoptotic cells then colocalize with the Syto16low viable cells in the situation minus PSC833. We have developed a gating strategy that, apart from quantifying apoptosis, allowed gating out these apoptotic cells for proper Pgp assessment. By using this strategy, no differences in Pgp activity were found in the treated versus the untreated samples (KB cells: P = 0.779, n = 10; AML cells: P = 0.525, n = 45).ConclusionsThe use of the combination Syto16/PSC833/7‐AAD provides a sensitive multiparameter flow cytometry method that enables accurate assessment of both apoptosis, cell death, and Pgp function in clinical samples. Cytometry Part B (Clin. Cytometry) 55B:14–21, 2003. © 2003 Wiley‐Liss, Inc.