bluuebunny/crossref_metadata_2025 huggingface dataset:
A dual-functional paramyxovirus F protein regulatory switch segment
Authors: Russell Charles J. , Kantor Karen L. , Jardetzky Theodore S. , Lamb Robert A.
Published: October 2003

Many viral fusion–mediating glycoproteins couple α-helical bundle formation to membrane merger, but have different methods for fusion activation. To study paramyxovirus-mediated fusion, we mutated the SV5 fusion (F) protein at conserved residues L447 and I449, which are adjacent to heptad repeat (HR) B and bind to a prominent cavity in the HRA trimeric coiled coil in the fusogenic six-helix bundle (6HB) structure. These analyses on residues L447 and I449, both in intact F protein and in 6HB, suggest a metamorphic region around these residues with dual structural roles. Mutation of L447 and I449 to aliphatic residues destabilizes the 6HB structure and attenuates fusion activity. Mutation of L447 and I449 to aromatic residues also destabilizes the 6HB structure despite promoting hyperactive fusion, indicating that 6HB stability alone does not dictate fusogenicity. Thus, residues L447 and I449 adjacent to HRB in paramyxovirus F have distinct roles in fusion activation and 6HB formation, suggesting this region is involved in a conformational switch.
Regulation of TrkB receptor tyrosine kinase and its internalization by neuronal activity and Ca2+ influx
Authors: Du Jing , Feng Linyin , Zaitsev Eugene , Je Hyun-Soo , Liu Xu-wen , Lu Bai
Published: October 2003

Internalization of the neurotrophin–Trk receptor complex is critical for many aspects of neurotrophin functions. The mechanisms governing the internalization process are unknown. Here, we report that neuronal activity facilitates the internalization of the receptor for brain-derived neurotrophic factor, TrkB, by potentiating its tyrosine kinase activity. Using three independent approaches, we show that electric stimulation of hippocampal neurons markedly enhances TrkB internalization. Electric stimulation also potentiates TrkB tyrosine kinase activity. The activity-dependent enhancement of TrkB internalization and its tyrosine kinase requires Ca2+ influx through N-methyl-d-aspartate receptors and Ca2+ channels. Inhibition of internalization had no effect on TrkB kinase, but inhibition of TrkB kinase prevents the modulation of TrkB internalization, suggesting a critical role of the tyrosine kinase in the activity-dependent receptor endocytosis. These results demonstrate an activity- and Ca2+-dependent modulation of TrkB tyrosine kinase and its internalization, and they provide new insights into the cell biology of tyrosine kinase receptors.
DNA damage-induced replication arrest in Xenopus egg extracts
Authors: Stokes Matthew P. , Michael W. Matthew
Published: October 2003

Chromosomal replication is sensitive to the presence of DNA-damaging alkylating agents, such as methyl methanesulfonate (MMS). MMS is known to inhibit replication though activation of the DNA damage checkpoint and through checkpoint-independent slowing of replication fork progression. Using Xenopus egg extracts, we now report an additional pathway that is stimulated by MMS-induced damage. We show that, upon incubation in egg extracts, MMS-treated DNA activates a diffusible inhibitor that blocks, in trans, chromosomal replication. The downstream effect of the inhibitor is a failure to recruit proliferating cell nuclear antigen, but not DNA polymerase α, to the nascent replication fork. Thus, alkylation damage activates an inhibitor that intercepts the replication pathway at a point between the polymerase α and proliferating cell nuclear antigen execution steps. We also show that activation of the inhibitor does not require the DNA damage checkpoint; rather, stimulation of the pathway described here results in checkpoint activation. These data describe a novel replication arrest pathway, and they also provide an example of how subpathways within the DNA damage response network are integrated to promote efficient cell cycle arrest in response to damaged DNA.
BPAG1n4 is essential for retrograde axonal transport in sensory neurons
Authors: Liu Jia-Jia , Ding Jianqing , Kowal Anthony S. , Nardine Timothy , Allen Elizabeth , Delcroix Jean-Dominique , Wu Chengbiao , Mobley William , Fuchs Elaine , Yang Yanmin
Published: October 2003

Disruption of the BPAG1 (bullous pemphigoid antigen 1) gene results in progressive deterioration in motor function and devastating sensory neurodegeneration in the null mice. We have previously demonstrated that BPAG1n1 and BPAG1n3 play important roles in organizing cytoskeletal networks in vivo. Here, we characterize functions of a novel BPAG1 neuronal isoform, BPAG1n4. Results obtained from yeast two-hybrid screening, blot overlay binding assays, and coimmunoprecipitations demonstrate that BPAG1n4 interacts directly with dynactin p150Glued through its unique ezrin/radixin/moesin domain. Studies using double immunofluorescent microscopy and ultrastructural analysis reveal physiological colocalization of BPAG1n4 with dynactin/dynein. Disruption of the interaction between BPAG1n4 and dynactin results in severe defects in retrograde axonal transport. We conclude that BPAG1n4 plays an essential role in retrograde axonal transport in sensory neurons. These findings might advance our understanding of pathogenesis of axonal degeneration and neuronal death.
Plasticity of Repetitive DNA Sequences within a Bacterial (Type IV) Secretion System Component
Authors: Aras Rahul A. , Fischer Wolfgang , Perez-Perez Guillermo I. , Crosatti MariaLuisa , Ando Takafumi , Haas Rainer , Blaser Martin J.
Published: October 2003

DNA rearrangement permits bacteria to regulate gene content and expression. In Helicobacter pylori, cagY, which contains an extraordinary number of direct DNA repeats, encodes a surface-exposed subunit of a (type IV) bacterial secretory system. Examining potential DNA rearrangements involving the cagY repeats indicated that recombination events invariably yield in-frame open reading frames, producing alternatively expressed genes. In individual hosts, H. pylori cell populations include strains that produce CagY proteins that differ in size, due to the predicted in-frame deletions or duplications, and elicit minimal or no host antibody recognition. Using repetitive DNA, H. pylori rearrangements in a host-exposed subunit of a conserved bacterial secretion system may permit a novel form of antigenic evasion.
Immune Evasion by Murine Melanoma Mediated through CC Chemokine Receptor-10
Authors: Murakami Takashi , Cardones Adela R. , Finkelstein Steven E. , Restifo Nicholas P. , Klaunberg Brenda A. , Nestle Frank O. , Castillo S. Sianna , Dennis Phillip A. , Hwang Sam T.
Published: October 2003

Human melanoma cells frequently express CC chemokine receptor (CCR)10, a receptor whose ligand (CCL27) is constitutively produced by keratinocytes. Compared with B16 murine melanoma, cells rendered more immunogenic via overexpression of luciferase, B16 cells that overexpressed both luciferase and CCR10 resisted host immune responses and readily formed tumors. In vitro, exposure of tumor cells to CCL27 led to rapid activation of Akt, resistance to cell death induced by melanoma antigen-specific cytotoxic T cells, and phosphatidylinositol-3-kinase (PI3K)–dependent protection from apoptosis induced by Fas cross-linking. In vivo, cutaneous injection of neutralizing antibodies to endogenous CCL27 blocked growth of CCR10-expressing melanoma cells. We propose that CCR10 engagement by locally produced CCL27 allows melanoma cells to escape host immune antitumor killing mechanisms (possibly through activation of PI3K/Akt), thereby providing a means for tumor progression.
Impaired V(D)J Recombination and Lymphocyte Development in Core RAG1-expressing Mice
Authors: Dudley Darryll D. , Sekiguchi JoAnn , Zhu Chengming , Sadofsky Moshe J. , Whitlow Scott , DeVido Jeffrey , Monroe Robert J. , Bassing Craig H. , Alt Frederick W.
Published: October 2003

RAG1 and RAG2 are the lymphocyte-specific components of the V(D)J recombinase. In vitro analyses of RAG function have relied on soluble, highly truncated “core” RAG proteins. To identify potential functions for noncore regions and assess functionality of core RAG1 in vivo, we generated core RAG1 knockin (RAG1c/c) mice. Significant B and T cell numbers are generated in RAG1c/c mice, showing that core RAG1, despite missing ∼40% of the RAG1 sequence, retains significant in vivo function. However, lymphocyte development and the overall level of V(D)J recombination are impaired at the progenitor stage in RAG1c/c mice. Correspondingly, there are reduced numbers of peripheral RAG1c/c B and T lymphocytes. Whereas normal B lymphocytes undergo rearrangement of both JH loci, substantial levels of germline JH loci persist in mature B cells of RAG1c/c mice, demonstrating that DJH rearrangement on both IgH alleles is not required for developmental progression to the stage of VH to DJH recombination. Whereas VH to DJH rearrangements occur, albeit at reduced levels, on the nonselected alleles of RAG1c/c B cells that have undergone D to JH rearrangements, we do not detect VH to DH rearrangements in RAG1c/c B cells that retain germline JH alleles. We discuss the potential implications of these findings for noncore RAG1 functions and for the ordered assembly of VH, DH, and JH segments.
The Balance Between Pax5 and Id2 Activities Is the Key to AID Gene Expression
Authors: Gonda Hiroyuki , Sugai Manabu , Nambu Yukiko , Katakai Tomoya , Agata Yasutoshi , Mori Kazuhiro J. , Yokota Yoshifumi , Shimizu Akira
Published: October 2003

Pax5 activity is enhanced in activated B cells and is essential for class switch recombination (CSR). We show that inhibitor of differentiation (Id)2 suppresses CSR by repressing the gene expression of activation-induced cytidine deaminase (AID), which has been shown to be indispensable for CSR. Furthermore, a putative regulatory region of AID contains E2A- and Pax5-binding sites, and the latter site is indispensable for AID gene expression. Moreover, the DNA-binding activity of Pax5 is decreased in Id2-overexpressing B cells and enhanced in Id2−/− B cells. The kinetics of Pax5, but not E2A, occupancy to AID locus is the same as AID expression in primary B cells. Finally, enforced expression of Pax5 induces AID transcription in pro–B cell lines. Our results provide evidence that the balance between Pax5 and Id2 activities has a key role in AID gene expression.
Novel Regulation of Calcium Inhibition of the Inositol 1,4,5-trisphosphate Receptor Calcium-release Channel
Authors: Mak Don-On Daniel , McBride Sean M.J. , Petrenko Nataliya B. , Foskett J. Kevin
Published: October 2003

The inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R), a Ca2+-release channel localized to the endoplasmic reticulum, plays a critical role in generating complex cytoplasmic Ca2+ signals in many cell types. Three InsP3R isoforms are expressed in different subcellular locations, at variable relative levels with heteromultimer formation in different cell types. A proposed reason for this diversity of InsP3R expression is that the isoforms are differentially inhibited by high cytoplasmic free Ca2+ concentrations ([Ca2+]i), possibly due to their different interactions with calmodulin. Here, we have investigated the possible roles of calmodulin and bath [Ca2+] in mediating high [Ca2+]i inhibition of InsP3R gating by studying single endogenous type 1 InsP3R channels through patch clamp electrophysiology of the outer membrane of isolated Xenopus oocyte nuclei. Neither high concentrations of a calmodulin antagonist nor overexpression of a dominant-negative Ca2+-insensitive mutant calmodulin affected inhibition of gating by high [Ca2+]i. However, a novel, calmodulin-independent regulation of [Ca2+]i inhibition of gating was revealed: whereas channels recorded from nuclei kept in the regular bathing solution with [Ca2+] ∼400 nM were inhibited by 290 μM [Ca2+]i, exposure of the isolated nuclei to a bath solution with ultra-low [Ca2+] (<5 nM, for ∼300 s) before the patch-clamp experiments reversibly relieved Ca2+ inhibition, with channel activities observed in [Ca2+]i up to 1.5 mM. Although InsP3 activates gating by relieving high [Ca2+]i inhibition, it was nevertheless still required to activate channels that lacked high [Ca2+]i inhibition. Our observations suggest that high [Ca2+]i inhibition of InsP3R channel gating is not regulated by calmodulin, whereas it can be disrupted by environmental conditions experienced by the channel, raising the possibility that presence or absence of high [Ca2+]i inhibition may not be an immutable property of different InsP3R isoforms. Furthermore, these observations support an allosteric model in which Ca2+ inhibition of the InsP3R is mediated by two Ca2+ binding sites, only one of which is sensitive to InsP3.
Spontaneous Channel Activity of the Inositol 1,4,5-Trisphosphate (InsP3) Receptor (InsP3R). Application of Allosteric Modeling to Calcium and InsP3 Regulation of InsP3R Single-channel Gating
Authors: Mak Don-On Daniel , McBride Sean M.J. , Foskett J. Kevin
Published: October 2003

The InsP3R Ca2+ release channel has a biphasic dependence on cytoplasmic free Ca2+ concentration ([Ca2+]i). InsP3 activates gating primarily by reducing the sensitivity of the channel to inhibition by high [Ca2+]i. To determine if relieving Ca2+ inhibition is sufficient for channel activation, we examined single-channel activities in low [Ca2+]i in the absence of InsP3, by patch clamping isolated Xenopus oocyte nuclei. For both endogenous Xenopus type 1 and recombinant rat type 3 InsP3R channels, spontaneous InsP3-independent channel activities with low open probability Po (∼0.03) were observed in [Ca2+]i < 5 nM with the same frequency as in the presence of InsP3, whereas no activities were observed in 25 nM Ca2+. These results establish the half-maximal inhibitory [Ca2+]i of the channel to be 1.2–4.0 nM in the absence of InsP3, and demonstrate that the channel can be active when all of its ligand-binding sites (including InsP3) are unoccupied. In the simplest allosteric model that fits all observations in nuclear patch-clamp studies of [Ca2+]i and InsP3 regulation of steady-state channel gating behavior of types 1 and 3 InsP3R isoforms, including spontaneous InsP3-independent channel activities, the tetrameric channel can adopt six different conformations, the equilibria among which are controlled by two inhibitory and one activating Ca2+-binding and one InsP3-binding sites in a manner outlined in the Monod-Wyman-Changeux model. InsP3 binding activates gating by affecting the Ca2+ affinities of the high-affinity inhibitory sites in different conformations, transforming it into an activating site. Ca2+ inhibition of InsP3-liganded channels is mediated by an InsP3-independent low-affinity inhibitory site. The model also suggests that besides the ligand-regulated gating mechanism, the channel has a ligand-independent gating mechanism responsible for maximum channel Po being less than unity. The validity of this model was established by its successful quantitative prediction of channel behavior after it had been exposed to ultra-low bath [Ca2+].
Electrostatic Control and Chloride Regulation of the Fast Gating of ClC-0 Chloride Channels
Authors: Chen Tsung-Yu , Chen Mei-Fang , Lin Chia-Wei
Published: October 2003

The opening and closing of chloride (Cl−) channels in the ClC family are thought to tightly couple to ion permeation through the channel pore. In the prototype channel of the family, the ClC-0 channel from the Torpedo electric organ, the opening-closing of the pore in the millisecond time range known as “fast gating” is regulated by both external and internal Cl− ions. Although the external Cl− effect on the fast-gate opening has been extensively studied at a quantitative level, the internal Cl− regulation remains to be characterized. In this study, we examine the internal Cl− effects and the electrostatic controls of the fast-gating mechanism. While having little effect on the opening rate, raising [Cl−]i reduces the closing rate (or increases the open time) of the fast gate, with an apparent affinity of >1 M, a value very different from the one observed in the external Cl− regulation on the opening rate. Mutating charged residues in the pore also changes the fast-gating properties—the effects are more prominent on the closing rate than on the opening rate, a phenomenon similar to the effect of [Cl−]i on the fast gating. Thus, the alteration of fast-gate closing by charge mutations may come from a combination of two effects: a direct electrostatic interaction between the manipulated charge and the negatively charged glutamate gate and a repulsive force on the gate mediated by the permeant ion. Likewise, the regulations of internal Cl− on the fast gating may also be due to the competition of Cl− with the glutamate gate as well as the overall more negative potential brought to the pore by the binding of Cl−. In contrast, the opening rate of the fast gate is only minimally affected by manipulations of [Cl−]i and charges in the inner pore region. The very different nature of external and internal Cl− regulations on the fast gating thus may suggest that the opening and the closing of the fast gate are not microscopically reversible processes, but form a nonequilibrium cycle in the ClC-0 fast-gating mechanism.
Interaction Mechanisms between Polyamines and IRK1 Inward Rectifier K+ Channels
Authors: Guo Donglin , Lu Zhe
Published: October 2003

Rectification of macroscopic current through inward-rectifier K+ (Kir) channels reflects strong voltage dependence of channel block by intracellular cations such as polyamines. The voltage dependence results primarily from the movement of K+ ions across the transmembrane electric field, which accompanies the binding–unbinding of a blocker. Residues D172, E224, and E299 in IRK1 are critical for high-affinity binding of blockers. D172 appears to be located somewhat internal to the narrow K+ selectivity filter, whereas E224 and E299 form a ring at a more intracellular site. Using a series of alkyl-bis-amines of varying length as calibration, we investigated how the acidic residues in IRK1 interact with amine groups in the natural polyamines (putrescine, spermidine, and spermine) that cause rectification in cells. To block the pore, the leading amine of bis-amines of increasing length penetrates ever deeper into the pore toward D172, while the trailing amine in every bis-amine binds near a more intracellular site and interacts with E224 and E299. The leading amine in nonamethylene-bis-amine (bis-C9) makes the closest approach to D172, displacing the maximal number of K+ ions and exhibiting the strongest voltage dependence. Cells do not synthesize bis-amines longer than putrescine (bis-C4) but generate the polyamines spermidine and spermine by attaching an amino-propyl group to one or both ends of putrescine. Voltage dependence of channel block by the tetra-amine spermine is comparable to that of block by the bis-amines bis-C9 (shorter) or bis-C12 (equally long), but spermine binds to IRK1 with much higher affinity than either bis-amine does. Thus, counterintuitively, the multiple amines in spermine primarily confer the high affinity but not the strong voltage dependence of channel block. Tetravalent spermine achieves a stronger interaction with the pore by effectively behaving like a pair of tethered divalent cations, two amine groups in its leading half interacting primarily with D172, whereas the other two in the trailing half interact primarily with E224 and E299. Thus, nature has optimized not only the blocker but also, in a complementary manner, the channel for producing rapid, high-affinity, and strongly voltage-dependent channel block, giving rise to exceedingly sharp rectification.
Allosteric Activation of Sodium–Calcium Exchange Activity by Calcium
Authors: Reeves John P. , Condrescu Madalina
Published: October 2003

The activity of the cardiac Na+/Ca2+ exchanger is stimulated allosterically by Ca2+, but estimates of the half-maximal activating concentration have varied over a wide range. In Chinese hamster ovary cells expressing the cardiac Na+/Ca2+ exchanger, the time course of exchange-mediated Ca2+ influx showed a pronounced lag period followed by an acceleration of Ca2+ uptake. Lag periods were absent in cells expressing an exchanger mutant that was not dependent on regulatory Ca2+ activation. We assumed that the rate of Ca2+ uptake during the acceleration phase reflected the degree of allosteric activation of the exchanger and determined the value of cytosolic Ca2+ ([Ca2+]i) at which the rate of Ca2+ influx was half-maximal (Kh). After correcting for the effects of mitochondrial Ca2+ uptake and fura-2 buffering, Kh values of ∼300 nM were obtained. After an increase in [Ca2+]i, the activated state of the exchanger persisted following a subsequent reduction in [Ca2+]i to values <100 nM. Thus, within 30 s after termination of a transient increase in [Ca2+]i, exchange-mediated Ca2+ entry began without a lag period and displayed a linear rate of Ca2+ uptake in most cells; a sigmoidal time course of Ca2+ uptake returned 60–90 s after the transient increase in [Ca2+]i was terminated. Relaxation of the activated state was accelerated by the activity of the endoplasmic reticulum Ca2+ pump, suggesting that local Ca2+ gradients contribute to maintaining exchanger activation after the return of global [Ca2+]i to low values.
Karl Barth's Critically Realistic Dialectical Theology
Authors: McCormack Bruce L.
Published: October 2003

This book, the first of two volumes, seeks to challenge the prevailing view in the historiography of 20th century theology — that Karl Barth was a leading representative of a “neo-orthodoxy” which was dominant between 1930 and 1960. It lays the foundation for a revision through a genetic-historical interpretation of Barth’s theological development. It argues that the “turn” to a “neo-orthodox” form of theology that was believed to have occurred with the Church Dogmatics in 1931-32 never took place. Subsequent to his break with “liberalism” in 1915, Barth became and remained a critically realistic dialectical theologian.
The Von Balthasar Thesis and the Myth of the Neo‐Orthodox Barth
Authors: McCormack Bruce L.
Published: October 2003

This introductory chapter begins with a discussion on how the interpretation of Karl Barth’s theological development has been dominated by Hans Urs von Balthasar’s book, Karl Barth: Darstellung und Deutung seiner Theologie (1951) for over forty years. It identifies three studies that have challenged von Balthasar’s thesis: Eberhard Jüngel’s ‘Von der Dialektik zur Analogie’, Ingrid Spieckermann’s Gotteserkenntnis, and Michael Beintker’s Die Dialektik in der’dialektischen Theologie. A new paradigm for interpreting Barth’s development is then presented.
Prologue
Authors: McCormack Bruce L.
Published: October 2003

This section presents several lines from a sermon by Karl Barth dated December 28, 1913.
The Marburg Background
Authors: McCormack Bruce L.
Published: October 2003

This chapter explores Karl Barth’s theological and political writings prior to the First World War. It begins with a discussion on his upbringing and student years, and the theological situation at the turn of the century. Barth’s earliest writings showed him to be a very dedicated follower of Wilhelm Herrmann’s theology. These also reflected his strong attachment to the general epistemological theory of Cohen and Natorp.
Socialism and Religious Socialism in Safenwil
Authors: McCormack Bruce L.
Published: October 2003

Karl Barth was a dedicated theological liberal prior to the outbreak of the First World War. In August 1914, 93 German intellectuals, among which were Barth’s theological teachers, declared their support for the war policy of Wilhelm II. This precipitated his break with liberal theology. Barth adopted a new Ansatz — a new starting point for theological reflection, which placed knowledge of God the central question.
The Righteousness of God
Authors: McCormack Bruce L.
Published: October 2003

Barth’s critique of Romans marked his first major effort to explain his new theology. He sought to establish an eschatologically conditioned theological realism which would overcome every attempt to ground theology in the human subject. He wanted to speak of a knowledge of God grounded in itself alone, place God’s reconciling activity in Christ beyond the reach of historical investigation, and faith beyond the reach of psychological investigation.
Theology in a Revolutionary Age
Authors: McCormack Bruce L.
Published: October 2003

Barth’s theology underwent further change between November 1918 and October 1920, in that his process eschatology gave way to the consistent eschatology which would stamp the second edition of his commentary on Romans. The turbulent social-political upheavals during this period such as the Russian Revolution did not have a significant influence on his theological development. More decisive was his reaction to reviews of his commentary, which showed how easily his organological model of eschatology could be misunderstood.
Shift to a Consistent Eschatology
Authors: McCormack Bruce L.
Published: October 2003

This chapter explores the factors that influenced Karl Barth’s shift from the process eschatological model which stamped Romans I to the consistent eschatology of Romans II. The influence of his philosopher brother Heinrich Barth and Franz Overbeck was more important than that of Søren Kierkegaard. From Kierkegaard, Barth learned a style of communication, an attitude, and the Kierkegaardian understanding of the paradoxicality of the incarnation.
Clearing the Ground: The Theology of Romans II
Authors: McCormack Bruce L.
Published: October 2003

This chapter explores the theology of Romans II. It covers Barth’s theological epistemology, the source of the charge of scepticism, dialectics, emergence of a critically realistic ethic, and political action. Barth’s later critique of Romans II is also presented.
Honorary Professor of Reformed Theology
Authors: McCormack Bruce L.
Published: October 2003

This chapter chronicles Karl Barth’s teaching career in Göttingen, Germany in the 1920s. During his first five semesters in Göttingen, his attitude towards doctrine became more positive, and he came to view the Church as a locus of authority in theology rather than the locus of judgement. Aside from the transformation of his esteem for the Church, Barth began analysing the problem of the contingency of revelation, i.e., what it means to affirm that one piece of history has been qualified by revelation as the site of the salvation history. This sets the stage for a thorough reconsideration of the doctrine of incarnation.
The Göttingen Dogmatics
Authors: McCormack Bruce L.
Published: October 2003

Karl Barth’s theology entered a new phase when he adopted the anhypostatic-enhypostatic model of Christology. However, his basic orientation was towards the revelation-event which occurs in the here and now basis of God’s Self-revelation in Christ. Thus, though the ground of his theology was now Christological, his theology was largely pneumatocentric. This is most evident in his doctrine of election, which was centred in the concrete situation of the person who is addressed by revelation in the here and now.
Professor of Dogmatics and New Testament Exegesis in Münster
Authors: McCormack Bruce L.
Published: October 2003

A great deal of attention is given to the revised version of Barth’s prolegomena lectures published in 1927 under the title Die christliche Dogmatik im Entwurf in treatments of Barth’s development. However, a synchronic comparison, section by section, of all three versions of the prolegomena (the Göttingen and Münster versions together with Church Dogmatics I/I and I/2) shows the extent of which the fundamental decisions which control even the Church Dogmatics I/I and I/2 were already made in 1924-25 in Göttingen. This chapter discusses the events and works which influenced decisions made by Barth.
Fides Quaerens Intellectum
Authors: McCormack Bruce L.
Published: October 2003

This chapter explores Karl Barth’s writing of a book on Anselm, Fides quaerens intellectum. Barth’s main goal was to treat the ‘problematic Anselm’ of Proslogion 2-4 in a new way. He wanted to show that the so-called “ontological proof” set forth by Anselm was not a proof at all. The existence of anything new in the Anselm book, which would have compelled Barth to view Die christliche Dogmatik as a ‘false start’ is discussed.
The Eternal Will of God in the Election of Jesus Christ
Authors: McCormack Bruce L.
Published: October 2003

This chapter explores the “christocentrism” in Barth’s theology. For Barth, “christocentrism” refers to the attempt to understand every doctrine from a centre in God’s Self-revelation in Jesus Christ. “Christocentrism” was a methodological rule, and not a priori principle. It is shown that a lecture by Parisian pastor Pierre Maury on the subject of election paved the way for a form of “christocentrism” synonymous with the name of Karl Barth.
Conclusion
Authors: McCormack Bruce L.
Published: October 2003

This chapter presents a synthesis of the preceding discussions on the theological development of Karl Barth. Through all the phases of his development, Barth was a critically realistic dialectical theologian. All of his efforts in theology may be considered as an attempt to overcome Kant by means of Kant; not retreating behind him and seeking to go around him, but through him. It is important to note that however critical Barth may have been of modern theology, the form in which he taught dialectical theology was a thoroughly modern option.
The Kosovo Report
Authors: Independent International Commission on Kosovo
Published: October 2003

The Kosovo Report is a final product of the work by the Independent International Commission on Kosovo, established to examine key developments prior to, during, and after the Kosovo war, including systematic violations of human rights in the region. The report assesses effectiveness of diplomatic efforts to prevent the war, legality of the NATO bombing campaign against Yugoslavia, and the progress of the United Nations in post‐conflict reconstruction. The Report makes a recommendation for the future status of Kosovo and proposes a new general framework for humanitarian intervention based on principles of legitimacy. It argues that the intervention by the international community in the Kosovo conflict did not so much create a precedent for intervention elsewhere as raise vital question about the legitimacy and practicability of the use of military force to defend human rights. The intervention, the Report concludes, exposed the limitations of the current international law on the balance between the rights of citizens and the rights of states; it demonstrated the difficulties that ensue when even the most sophisticated and professional military forces are deployed to achieve humanitarian goals; and it showed the immense obstacles that lie in the path of creating multi‐ethnic cooperation in societies torn apart by ethnic war.
Executive Summary
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Presents the main findings of the report. It outlines the nature of the armed conflict in Kosovo, the early diplomatic efforts, the NATO intervention, the ensuing humanitarian crisis and the establishment of UNMIK as an interim administration. The importance of early prevention measures is emphasized.
Address by Former President Nelson Mandela
Authors:   The Independent International Commission on Kosovo
Published: October 2003

This section is the text of an address delivered by Nelson Mandela to the Kosovo Commission's final seminar. It focuses on Africa's need for international attention and assistance to fight gross violations of human rights and promote economic development in places of former and on‐going conflict such as Burundi.
Introduction
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Poses the unresolved questions about the Kosovo conflict that motivated the establishment of the Independent International Commission on Kosovo. Among others, the questions include the role of the United Nations and NATO, and the general purpose of international intervention in preventing armed conflicts. The introduction also presents the Commission's mission statement and lists its members. It outlines the contents of the report, dividing it into a narrative and an analysis.
The Origins of the Kosovo Crisis
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Covers the origins of the Kosovo crisis and violations of international human rights standards, with special focus on the period from the abrogation of Kosovo's autonomous status in 1989 to February 1998. The chapter covers post‐World War II history of Serbian policy in Kosovo, Slobodan Milosevic's rise to power in the late 1980s, Albanian resistance under the League for a Democratic Kosovo (LDK), the establishment of a parallel system of Albanian underground self‐governance and the rise of the Kosovo Liberation Army (KLA). In discussing the breakout of violence in 1998–99, the chapterpoints to failures of “early warning” lessons and the missed opportunities by the international community to prevent the conflict.
Internal Armed Conflict
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Describes the fatal spiral of hardening Serb intransigence and growing Kosovar Albanian armament that followed the abolishment of Kosovo's autonomy in 1990 and led to escalation of the conflict. The chapter identifies important military activities and sites of mass murder, most importantly the early Serbian military operation in Drenice/Drenica and the later execution of 45 Albanians in Recak/Racak. The chapter discusses the rise of the Kosovo Liberation Army (KLA), and describes how the efforts by the UN Security Council and the Contact Group led to an agreement between US envoy Richard Holbrooke and Slobodan Milosevic to implement a cease‐fire and introduce the Kosovo Verification Mission. But this agreement was broken and further diplomatic efforts in Rambouillet and Paris failed to bring about cession of hostilities.
International War Supervenes
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Discusses the aims and the conduct of the NATO bombing campaign against the Yugoslavia; the refugee crisis and civilian casualties of the campaign; and the diplomatic events leading to the final peace agreement. The chapter argues that the NATO campaign did not itself provoke Serbian military's attacks on Kosovo civilians, but that the intervention and the removal of ground monitors may have created an internal environment that made Belgrade government's cleansing operation feasible. The chapter concludes that the intervention failed to achieve its avowed aim of preventing massive ethnic cleansing, that the Kosovar Albanian population had to endure tremendous suffering before finally achieving their freedom and that Milosevic remained in power, however, as an indicted war criminal.
Kosovo Under United Nations Rule
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Traces the establishment of international presence in Kosovo following the signing of the Military‐Technical Agreement (MTA) between NATO and Yugoslavia and the implementation of the UN Security Resolution 1244. The chapter points to the success of the Kosovo International Security Force (KFOR) deployed by NATO to ensure security on ground, and to the mixed record of the civilian United Nations Interim Mission in Kosovo in establishing effective presence. While the return of Albanian refugees was a success for UNMIK, the chapter argues that both KFOR and UNMIK failed to prevent revenge killings and that the poorly deployed UN police force was unprepared to stop inter‐ethnic violence, especially against Kosovo Serbs. Economic assistance and fight against organized crime are identified as some of the major challenges for UNMIK.
The Diplomatic Dimension
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Poses the question of whether diplomacy could have helped avoid a war in Kosovo while protecting the Kosovar Albanians. It argues that the narrative of the international response is inherently inconclusive, with not many clear “lessons” beyond the prudential observations in favour of early engagement and greater attentiveness to non‐violent options. The chapter describes the diplomatic efforts of the Contact Group, the UN Security Council, NATO, the Organization for Security and Cooperation in Europe (OSCE) and individual governments of the US and Russia. Belgrade government's opposition to armed international presence in Kosovo and KLA's refusal to back down from demands for independence are identified as main obstacles to reaching an agreement at Rambouillet.
International Law and Humanitarian Intervention
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Considers the international law controversy provoked by the NATO campaign in Kosovo. The central question addressed is whether the constraints imposed by international law on the non‐defensive use of force are adequate for the maintenance of peace and security. In response, considers the legality of NATO's forceful humanitarian intervention by reference to both jus ad bellum (recourse to war) and jus in bellum (lawfulness of conduct in war), and argues on behalf of legitimacy by way of an emergent framework of principled humanitarian intervention. A pre‐legal proposal is made to move in the direction of establishing a legal doctrine of humanitarian intervention that balances the clams to protect peoples against the importance of restricting discretion to use force in international relations.
Humanitarian Organizations and the Role of Media
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Part 1 argues that when there are large numbers of internally displaced people, humanitarian groups should anticipate and prepare for the risks of a large outflow of refugees. The chapter argues that the United Nations High Commissioner for Refugees (UNHCR) was unprepared to deal with the refugee crisis in Kosovo, and that its ability to coordinate the humanitarian response was hampered by lack of funding and coordination, proliferation of NGOs in the field funded directly by their governments and complex relations with the military. Part 2 of the chapter analyses the relationship between the media on one side and NATO, Yugoslav government, and NGOs on the other side. The second part of the chapter concludes by encouraging development of free press and mass media in post‐war Kosovo.
Kosovo: The Regional Dimension
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Examines past obstacles and presents opportunities for the development of regional cooperation, which, in the long run, remains a necessary precondition for peace and stability in south‐eastern Europe. Three dimensions of regional destabilization are addressed: the final disintegration of Yugoslavia (Serbia, Montenegro, Vojvodina), the direct destabilization of Kosovo's immediate neighbours (Macedonia and Albania) and the negative impact on other regional actors (Bulgaria, Romania, Greece, etc.). The chapter also summarizes the economic impact of the NATO intervention and the mixed record of the Stability Pact designed to foster post‐conflict regional cooperation. It argues that the real test for the moral issues that legitimized the intervention in Kosovo will be the European Union's (EU) ability to sustain a long‐term commitment to help establish a European future for the Balkans.
The Future Status of Kosovo
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Addresses concerns regarding the future status of Kosovo and analyses five possible alternatives: protectorate, partition, full independence, autonomy within a democratic Yugoslavia and conditional independence. The chapter recommends conditional independence as the future status of Kosovo, arguing for a constitutional regime that: (1) ensures respect of all Kosovo citizens’ rights to determine their future, (2) incorporates the role of the international community in providing external security and internal rights protection, (3) ensures full and equal political participation of all Kosovo citizens, (4) guarantees a wide set of internationally protected minority rights and (5) assures minority representation in the police, judiciary, and the government.
Conclusion
Authors:   The Independent International Commission on Kosovo
Published: October 2003

Summarizes the goals and the conclusions of the Kosovo Commission's report. It outlines the historical context, summarizes the Report's assessment of human rights abuses and the legality of the NATO campaign and emphasizes the importance of European integration for the future of Kosovo and the entire region. The conclusion also outlines the Kosovo Commission's recommended framework of principles for humanitarian intervention. The first set consists of threshold principles that must be satisfied in order for any claim of humanitarian intervention to be legitimate, and the second set consists of contextual principles that enhance or diminish the degree of legitimacy possessed by forceful intervention.
Heavy-atom derivatization
Authors: Garman Elspeth , Murray James W.
Published: October 2003

Most of the standard methods of solving macromolecular structures involve producing a protein crystal that is derivatized by an anomalous scatterer or heavy atom (MIR, SIRAS, MAD, SAD etc.). The theoretical methodology which underpins the extraction of phase information from such derivatives is widely available in the literature. In addition, there are comprehensive sources of information on the chemistry of heavy-atom compounds and the ligands with which they are known to interact, as well as the Heavy Atom Databank accessible on the World Wide Web. This contribution therefore aims to provide some information on the less well documented practical problems of firstly deciding on an overall strategy for derivatization and secondly performing the physical manipulations involved in producing heavy-atom derivatives from native protein crystals and then cryocooling them. Ways to optimize the chances of isomorphous unit cells are suggested. Methods of determining whether or not the heavy atom is bound are outlined, including the powerful technique of PIXE (particle-induced X-ray emission).
Triiodide derivatization in protein crystallography
Authors: Evans Gwyndaf , Bricogne Gérard
Published: October 2003

Methods for producing protein derivatives using cryosoak techniques with triiodide solutions are described. The methods have been tested using six different proteins. SAD/SIRAS phasing was attempted for each protein using data measured with conventional Cu Kα X-ray equipment and synchrotron radiation. Refinement of all six derivative structures showed that iodine is able to bind as I− (as observed with standard halide soaks) and also as the polyiodide anions I^{-}_{3} and I^{-}_{5}. The various species are able to bind through hydrogen-bond interactions and to more hydrophobic regions of the protein at surface pockets and in intermolecular and intramolecular cavities. On the whole, the derivative agent behaves promiscuously in terms of its binding to proteins and is capable of generating sufficient phasing power from in-house Cu Kα data to permit structure solution by SAD. The results of the phasing experiments and structure refinements are presented.
Introduction to twinning
Authors: Parsons Simon
Published: October 2003

A twinned crystal is an aggregate in which different domains are joined together according to a specific symmetry operation: the twin law. The diffraction patterns derived from different domains are rotated, reflected or inverted with respect to each other, depending on the nature of the relationship between the different domains, and weighted according to the quantity of a particular domain present in the crystal. The diffraction pattern measured during data collection is a superposition of all of these. Reflections from different domains may overlap and twinned crystals fall broadly into two categories in which either all reflections or only certain zones of reflections are affected by overlap. The former occurs when a crystal lattice belongs to a higher point group than the crystal structure itself; the latter frequently occurs when the twin law is a symmetry operation belonging to a higher symmetry supercell.
Phasing the 30S ribosomal subunit structure
Authors: Brodersen D. E. , Clemons W. M. , Carter A. P. , Wimberly B. T. , Ramakrishnan V.
Published: October 2003

The methods involved in determining the 850 kDa structure of the 30S ribosomal subunit from Thermus thermophilus were in many ways identical to those that are generally used in standard protein crystallography. This paper reviews and analyses the methods that can be used in phasing such large structures and shows that the anomalous signal collected from heavy-atom compounds bound to the RNA is both necessary and sufficient for ab initio structure determination at high resolution. In addition, measures to counter problems with non-isomorphism and radiation decay are described.
Optimization of selenium substructures as obtained from SHELXD
Authors: Dall'Antonia Fabio , Baker Patrick J. , Schneider Thomas R.
Published: October 2003

Using the signal of naturally inbuilt or artificially introduced anomalous scatterers to derive initial phases in a macromolecular crystal structure determination has become routine in recent years. In the context of high-throughput crystallography in particular, MAD and SAD (multiple- and single-wavelength anomalous dispersion) methods are central tools. For both techniques, a crucial step is the determination of the substructure of anomalous scatterers; subsequent phasing procedures will profit from a substructure model that is as accurate as possible. The choice of the subset of the diffraction data to be used for the substructure determination has a strong influence on the quality of the substructure and can make the difference between success and failure. The accuracy of selenium substructures obtained using FA
values or various anomalous differences truncated to different resolutions has been investigated by comparing the sites determined by SHELXD with the selenium positions in the refined models. Based on the analysis, some recommendations for obtaining accurate and precise substructures are derived.
Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0
Authors: Bricogne G. , Vonrhein C. , Flensburg C. , Schiltz M. , Paciorek W.
Published: October 2003

The methods for treating experimental data in the isomorphous replacement and anomalous scattering methods of macromolecular phase determination have undergone considerable evolution since their inception 50 years ago. The successive formulations used are reviewed, from the most simplistic viewpoint to the most advanced, including the exploration of some blind alleys. A new treatment is proposed and demonstrated for the improved encoding and subsequent exploitation of phase information in the complex plane. It is concluded that there is still considerable scope for further improvements in the statistical analysis of phase information, which touch upon numerous fundamental issues related to data processing and experimental design.