bluuebunny/crossref_metadata_2025 huggingface dataset:
Geminivirus C3 Protein: Replication Enhancement and Protein Interactions
Authors: Settlage Sharon B. , See Renee G. , Hanley-Bowdoin Linda
Published: July 2005

Most dicot-infecting geminiviruses encode a replication enhancer protein (C3, AL3, or REn) that is required for optimal replication of their small, single-stranded DNA genomes. C3 interacts with C1, the essential viral replication protein that initiates rolling circle replication. C3 also homo-oligomerizes and interacts with at least two host-encoded proteins, proliferating cell nuclear antigen (PCNA) and the retinoblastoma-related protein (pRBR). It has been proposed that protein interactions contribute to C3 function. Using the C3 protein of
Tomato yellow leaf curl virus
, we examined the impact of mutations to amino acids that are conserved across the C3 protein family on replication enhancement and protein interactions. Surprisingly, many of the mutations did not affect replication enhancement activity of C3 in tobacco protoplasts. Other mutations either enhanced or were detrimental to C3 replication activity. Analysis of mutated proteins in yeast two-hybrid assays indicated that mutations that inactivate C3 replication enhancement activity also reduce or inactivate C3 oligomerization and interaction with C1 and PCNA. In contrast, mutated C3 proteins impaired for pRBR binding are fully functional in replication assays. Hydrophobic residues in the middle of the C3 protein were implicated in C3 interaction with itself, C1, and PCNA, while polar resides at both the N and C termini of the protein are important for C3-pRBR interaction. These experiments established the importance of C3-C3, C3-C1, and C3-PCNA interactions in geminivirus replication. While C3-pRBR interaction is not required for viral replication in cycling cells, it may play a role during infection of differentiated cells in intact plants.
Viral Diversity in Hot Springs of Pozzuoli, Italy, and Characterization of a Unique Archaeal Virus,
Acidianus
Bottle-Shaped Virus, from a New Family, the
Ampullaviridae
Authors: Häring Monika , Rachel Reinhard , Peng Xu , Garrett Roger A. , Prangishvili David
Published: July 2005

Virus-like particles with five different morphotypes were observed in an enriched environmental sample from a hot, acidic spring (87 to 93°C, pH 1.5) in Pozzuoli, Italy. The morphotypes included rigid rods, flexible filaments, and novel, exceptional forms. Particles of each type were isolated, and they were shown to represent viable virions of five novel viruses which infect members of the hyperthermophilic archaeal genus
Acidianus
. One of these, named the
Acidianus
bottle-shaped virus, ABV, exhibits a previously unreported morphotype. The bottle-shaped virion carries an envelope which encases a funnel-shaped core. The pointed end of the virion is likely to be involved in adsorption and channeling of viral DNA into host cells. The broad end exhibits 20 (± 2) thin filaments which appear to be inserted into a disk, or ring, and are interconnected at their bases. These filaments are apparently not involved in adsorption. ABV virions contain six proteins in the size range 15 to 80 kDa and a 23.9-kb linear, double-stranded DNA genome. Virus replication does not cause lysis of host cells. On the basis of its unique morphotype and structure, we propose to assign ABV to a new viral family, the
Ampullaviridae
.
Characterization of a Human H5N1 Influenza A Virus Isolated in 2003
Authors: Shinya Kyoko , Hatta Masato , Yamada Shinya , Takada Ayato , Watanabe Shinji , Halfmann Peter , Horimoto Taisuke , Neumann Gabriele , Kim Jin Hyun , Lim Wilina , Guan Yi , Peiris Malik , Kiso Makoto , Suzuki Takashi , Suzuki Yasuo , Kawaoka Yoshihiro
Published: July 2005

In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.
Chlorella Virus-Encoded Deoxyuridine Triphosphatases Exhibit Different Temperature Optima
Authors: Zhang Yuanzheng , Moriyama Hideaki , Homma Kohei , Van Etten James L.
Published: July 2005

A putative deoxyuridine triphosphatase (dUTPase) gene from chlorella virus PBCV-1 was cloned, and the recombinant protein was expressed in
Escherichia coli
. The recombinant protein has dUTPase activity and requires Mg
2+
for optimal activity, while it retains some activity in the presence of other divalent cations. Kinetic studies of the enzyme revealed a

K
m

of 11.7 μM, a turnover
k
cat
of 6.8 s
−1
, and a catalytic efficiency of
k
cat
/

K
m

= 5.8 × 10
5
M
−1
s
−1
. dUTPase genes were cloned and expressed from two other chlorella viruses IL-3A and SH-6A. The two dUTPases have similar properties to PBCV-1 dUTPase except that IL-3A dUTPase has a lower temperature optimum (37°C) than PBCV-1 dUTPase (50°C). The IL-3A dUTPase differs from the PBCV-1 enzyme by nine amino acids, including two amino acid substitutions, Glu81→Ser81 and Thr84→Arg84, in the highly conserved motif III of the proteins. To investigate the difference in temperature optima between the two enzymes, homology modeling and docking simulations were conducted. The results of the simulation and comparisons of amino acid sequence suggest that adjacent amino acids are important in the temperature optima. To confirm this suggestion, three site-directed amino acid substitutions were made in the IL-3A enzyme: Thr84→Arg84, Glu81→Ser81, and Glu81→Ser81 plus Thr84→Arg84. The single substitutions affected the optimal temperature for enzyme activity. The temperature optimum increased from 37 to 55°C for the enzyme containing the two amino acid substitutions. We postulate that the change in temperature optimum is due to reduction in charge and balkiness in the active cavity that allows more movement of the ligand and protein before the enzyme and substrate complex is formed.
Soluble Mimetics of Human Immunodeficiency Virus Type 1 Viral Spikes Produced by Replacement of the Native Trimerization Domain with aHeterologous Trimerization Motif: Characterization and Ligand Binding Analysis
Authors: Pancera Marie , Lebowitz Jacob , Schön Arne , Zhu Ping , Freire Ernesto , Kwong Peter D. , Roux Kenneth H. , Sodroski Joseph , Wyatt Richard
Published: July 2005

The human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein, gp120, mediates binding to the viral receptors and, along with the transmembrane glycoprotein gp41, is a major target for neutralizing antibodies. We asked whether replacing the gp41 fusion/trimerization domain with a stable trimerization motif might lead to a more stable gp120 trimer that would be amenable to structural and immunologic analysis. To obtain stable gp120 trimers, a heterologous trimerization motif, GCN4, was appended to the C terminus of YU2gp120. Biochemical analysis indicated that the gp120-GCN4 trimers were superior to gp140 molecules in their initial homogeneity, and trilobed structures were observable by electron microscopy. Biophysical analysis of gp120-GCN4 trimers by isothermal titration calorimetry (ITC) and ultracentrifugation analyses indicated that most likely two molecules of soluble CD4 could bind to one gp120-GCN4 trimer. To further examine restricted CD4 stoichiometric binding to the gp120-GCN4 trimers, we generated a low-affinity CD4 binding trimer by introducing a D457V change in the CD4 binding site of each gp120 monomeric subunit. The mutant trimers could definitively bind only one soluble CD4 molecule, as determined by ITC and sedimentation equilibrium centrifugation. These data indicate that there are weak interactions between the gp120 monomeric subunits of the GCN4-stabilized trimers that can be detected by low-affinity ligand sensing. By similar analysis, we also determined that removal of the variable loops V1, V2, and V3 in the context of the gp120-GCN4 proteins allowed the binding of three CD4 molecules per trimer. Interestingly, both the gp120-GCN4 variants displayed a restricted stoichiometry for the CD4-induced antibody 17b of one antibody molecule binding per trimer. This restriction was not evident upon removal of the variable loops V1 and V2 loops, consistent with conformational constraints in the wild-type gp120 trimers and similar to those inherent in the functional Env spike. Thus, the gp120-GCN4 trimers demonstrate several properties that are consistent with some of those anticipated for gp120 in the context of the viral spike.
Herpes Simplex Virus Type 1 Strain HSV1716 Grown in Baby Hamster Kidney Cells Has Altered Tropism for Nonpermissive Chinese Hamster Ovary Cells Compared to HSV1716 Grown in Vero Cells
Authors: Conner Joe , Rixon Frazer J. , Brown S. Moira
Published: July 2005

Chinese hamster ovary (CHO) cells are traditionally regarded as nonpermissive cells for herpes simplex virus type 1 (HSV-1) infection as they lack the specific entry receptors, and modified CHO cells have been instrumental in the identification of HSV-1 receptors in numerous studies. In this report we demonstrate that the HSV-1 strain 17+ variant HSV1716 is able to infect unmodified CHO cells but only if the virus is propagated in baby hamster kidney (BHK) cells. Infection of CHO cells by BHK-propagated HSV1716 results in expression of immediate-early, early, and late viral genes, and infectious progeny virions are produced. In normally cultured CHO cells, up to a maximum of 50% of cells were permissive for BHK-propagated HSV1716 infection, with 24 h of serum starvation increasing this to 100% of CHO cells, suggesting that the mechanism used by BHK-propagated virus to infect CHO cells was cell cycle dependent. The altered tropism of HSV1716 was also evident in another nonpermissive mouse melanoma cell line and is an exclusive property resulting from propagation of the virus using BHK cells, as viruses propagated on Vero, C8161 (a human melanoma cell line), or indeed, CHO cells were completely unable to infect either CHO or mouse melanoma cells.
Molecular Basis for Mitochondrial Localization of Viral Particles during
Beet Necrotic Yellow Vein Virus
Infection
Authors: Valentin Clarisse , Dunoyer Patrice , Vetter Guillaume , Schalk Catherine , Dietrich André , Bouzoubaa Salah
Published: July 2005

During infection,
Beet necrotic yellow vein virus
(BNYVV) particles localize transiently to the cytosolic surfaces of mitochondria. To understand the molecular basis and significance of this localization, we analyzed the targeting and membrane insertion properties of the viral proteins. ORF1 of BNYVV RNA-2 encodes the 21-kDa major coat protein, while ORF2 codes for a 75-kDa minor coat protein (P75) by readthrough of the ORF1 stop codon. Bioinformatic analysis highlighted a putative mitochondrial targeting sequence (MTS) as well as a major (TM1) and two minor (TM3 and TM4) transmembrane regions in the N-terminal part of the P75 readthrough domain. Deletion and gain-of-function analyses based on the localization of green fluorescent protein (GFP) fusions showed that the MTS was able to direct a reporter protein to mitochondria but that the protein was not persistently anchored to the organelles. GFP fused either to MTS and TM1 or to MTS and TM3-TM4 efficiently and specifically associated with mitochondria in vivo. The actual role of the individual domains in the interaction with the mitochondria seemed to be determined by the folding of P75. Anchoring assays to the outer membranes of isolated mitochondria, together with in vivo data, suggest that the TM3-TM4 domain is the membrane anchor in the context of full-length P75. All of the domains involved in mitochondrial targeting and anchoring were also indispensable for encapsidation, suggesting that the assembly of BNYVV particles occurs on mitochondria. Further data show that virions are subsequently released from mitochondria and accumulate in the cytosol.
A SYSTEMATIC STUDY ON NONRELATIVISTIC QUARK–ANTIQUARK INTERACTIONS
Authors: ABOU-SALEM L. I.
Published: July 2005

A simple phenomenological potential model is suggested to describe the interaction between the constituent quarks of meson systems. Taking the spin-dependence terms in consideration modifies some previous potential models. The resonance masses and the leptonic decay widths of [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] mesons are calculated using the nonrelativistic wave equation. A comparison between the present calculations and the available experimental results are given.
SPECTATOR EFFECTS IN THE DECAY B→Kγγ
Authors: IGNATIEV A. YU. , JOSHI G. C. , MCKELLAR B. H. J.
Published: July 2005

We report the results of the first computation related to the study of the spectator effects in the rare decay mode B→Kγγ within the framework of Standard Model. It is found that the account of these effects results in the enhancement factor for the short-distance reducible contribution to the branching ratio.
MAXWELL FIELD ON THE POINCARÉ GROUP
Authors: VARLAMOV V. V.
Published: July 2005

The massless field of spin 1 is defined on the eight-dimensional configuration space; this space is a direct product of Minkowski space and of a two-dimensional complex sphere. Field equations for the spin-one field are derived from a Dirac-like Lagrangian separately for the translation group and Lorentz group parts. It is shown that a Dirac form of Maxwell equations (the so-called Majorana–Oppenheimer formulation of electrodynamics) follows directly from the field equations of translation group part. The photon field is realized via Biedenharn type functions on the Poincaré group. This allows us to consider both Dirac and Maxwell fields on an equal footing, as the functions on the Poincaré group.
DYNAMICAL ORIGIN OF LOW-MASS FERMIONS IN RANDALL–SUNDRUM BACKGROUND
Authors: FUKAZAWA KENJI , INAGAKI TOMOHIRO , KATSUKI YASUHIKO , MUTA TAIZO , OHKURA KENSAKU
Published: July 2005

We investigate a dynamical mechanism to generate fermion mass in the Randall–Sundrum background. We consider four-fermion interaction models where the fermion field propagates in an extra-dimension, i.e. the bulk four-fermion interaction model. It is assumed that two types of fermions with opposite parity exist in the bulk. We show that electroweak-scale mass is dynamically generated for a specific fermion–antifermion condensation, even if all the scale parameters in the Lagrangian are set to the Planck scale.
Mitochondrial function and mitochondria-induced apoptosis in an overstimulated rat ovarian cycle
Authors: Navarro Ana , Torrejón Rafael , Bández Manuel J. , López-Cepero José M. , Boveris Alberto
Published: July 2005

Female rats were treated with FSH (40 IU/kg) on the first and second diestrus days (D1 and D2) and with LH (40 IU/kg) on the proestrus (P) day to synchronize and maximize ovarian changes. Follicle area increased by 50% from D1 to P, and the estrus (E) phase showed multiple corpora lutea and massive apoptosis. Increased oxygen uptakes (42–102%) were determined in ovary slices and in isolated mitochondria in active state 3 along the proliferation phase (D1-D2-P) that returned to initial values in the E phase. Mitochondrial content and the electron transfer activities of complexes I and IV were also maximal in the P phase (20–79% higher than in D1). Production of NO by mitochondrial nitric oxide synthase (mtNOS), biochemically determined, and the mtNOS functional activity in regulating state 3 oxygen uptake were also maximal at P and 79–88% higher than at D1. The moderately increased rate of NO in the proliferative phase is associated with mitochondrial biogenesis, whereas the high rate of NO generation by mtNOS at phase P appears to trigger mitochondria-dependent apoptosis. The calculated fraction of ovary mitochondria in state 3 was at a minimal value at the P phase. Mitochondrial oxidative damage, with increased thiobarbituric acid-reactive substances and protein carbonyls, indicates progressive mitochondrial dysfunction between phases P and E. The roles of mitochondria as ATP provider, as a source of NO to signal for mitochondrial proliferation and mitochondria-dependent apoptosis, and as a source of O2−and H2O2appear well adapted to serve the proliferation-apoptosis sequence of the ovarian cycle.
Rapid fluctuations in atrial fibrillatory electrophysiology detected during controlled respiration
Authors: Holmqvist Fredrik , Stridh Martin , Waktare Johan E. P. , Brandt Johan , Sörnmo Leif , Roijer Anders , Meurling Carl J.
Published: July 2005

Heart rate during sinus rhythm is modulated through the autonomic nervous system, which generates short-term oscillations. The high-frequency components in these oscillations are associated with respiration, causing sinus arrhythmia, mediated by the parasympathetic nervous system. In this study, we evaluated whether slow, controlled respiration causes cyclic fluctuations in the frequency of the fibrillating atria. Eight patients (four women; median age 63 yr, range 53–68 yr) with chronic atrial fibrillation (AF) and third-degree atrioventricular block treated by permanent pacemaker were studied. ECG was recorded during baseline rest, during 0.125-Hz frequency controlled respiration, and finally during controlled respiration after full vagal blockade. We calculated fibrillatory frequency using frequency analysis of the fibrillatory ECG for overlapping 2.5-s segments; spectral analysis of the resulting frequency trend was performed to determine the spectrum of variations of fibrillatory frequency. Normalized spectral power at respiration frequency increased significantly during controlled respiration from 1.4 (0.76–2.0) (median and range) at baseline to 2.7 (1.2–5.8) ( P = 0.01). After vagal blockade, the power at respiration frequency decreased to 1.2 (0.23–2.8) ( P = 0.01). Controlled respiration causes cyclic fluctuations in the AF frequency in patients with long-duration AF. This phenomenon seems to be related to parasympathetic modulations of the AF refractory period.
Gene transfer of extracellular superoxide dismutase improves endothelial function in rats with heart failure
Authors: Iida Shinichiro , Chu Yi , Francis Joseph , Weiss Robert M. , Gunnett Carol A. , Faraci Frank M. , Heistad Donald D.
Published: July 2005

Oxidative stress is associated with endothelial dysfunction in heart failure. The goals of this study were to determine whether 1) gene transfer of extracellular superoxide dismutase (ecSOD) reduces levels of superoxide and improves endothelial function in the aorta and mesenteric artery in rats with heart failure, and 2) the heparin-binding domain (HBD) of ecSOD, by which ecSOD binds to cells, is required for protective effects of ecSOD. Seven weeks after coronary ligation, in rats with heart failure and sham-operated rats, we injected adenoviral vectors intravenously that express ecSOD, ecSOD with deletion of the HBD (ecSODΔHBD), or a control vector. Four days after injection of viruses, responses to acetylcholine, ADP, and sodium nitroprusside were examined in rings of the aorta and mesenteric artery. ecSOD bound to endothelium and increased SOD activity in the aorta after gene transfer of ecSOD, not ecSODΔHBD. Gene transfer of ecSOD, but not ecSODΔHBD, reduced levels of superoxide and improved relaxation to acetylcholine and ADP in the aorta and mesenteric artery from rats with heart failure. Improvement of relaxation to acetylcholine in the mesenteric artery from rats with heart failure after gene transfer of ecSOD was mediated in part by hydrogen peroxide. The major finding of this study is that the HBD of ecSOD is necessary for protection against endothelial dysfunction in rats with heart failure. We speculate that a common gene variant in the HBD of ecSOD, which is a risk factor for ischemic heart disease, may be a risk factor for vascular maladaptation and endothelial dysfunction in heart failure.
Assessment of systolic and diastolic ventricular properties via pressure-volume analysis: a guide for clinical, translational, and basic researchers
Authors: Burkhoff Daniel , Mirsky Israel , Suga Hiroyuki
Published: July 2005

Assessment of left ventricular systolic and diastolic pump properties is fundamental to advancing the understanding of cardiovascular pathophysiology and therapeutics, especially for heart failure. The use of end-systolic and end-diastolic pressure-volume relationships derived from measurements of instantaneous left ventricular pressure-volume loops emerged in the 1970s as a comprehensive approach for this purpose. As invasive and noninvasive techniques for measuring ventricular volume improved over the past decades, these relations have become commonly used by basic, translational, and clinical researchers. This review summarizes 1) the basic concepts underlying pressure-volume analysis of ventricular and myocardial systolic and diastolic properties, 2) deviations from ideal conditions typically encountered in real-life applications, 3) how these relationships are appropriately analyzed, including statistical analyses, and 4) the most common problems encountered by investigators and the appropriate remedies. The goal is to provide practical information and simple guidelines for accurate application and interpretation of pressure-volume data as they pertain to characterization of ventricular and myocardial properties in health and disease.
Actin cytoskeleton regulates extracellular matrix-dependent survival signals in glomerular epithelial cells
Authors: Bijian Krikor , Takano Tomoko , Papillon Joan , Le Berre Ludmilla , Michaud Jean-Louis , Kennedy Chris R. J. , Cybulsky Andrey V.
Published: July 2005

Adhesion of rat glomerular epithelial cells (GEC) to collagen activates focal adhesion kinase (FAK) and the Ras-extracellular signal-regulated kinase (ERK) pathway and supports survival (prevents apoptosis). The present study addresses the relationship between actin organization and the survival phenotype. Parental GEC (adherent to collagen) and GEC stably transfected with constitutively active mutants of mitogen-activated protein kinase kinase (R4F-MEK) or FAK (CD2-FAK) (on plastic) showed ERK activation, low levels of apoptosis, and a cortical distribution of F-actin. Parental GEC adherent to plastic showed increased apoptosis, disorganization of cortical F-actin, and formation of prominent stress fibers. Assembly of cortical F-actin was, at least in part, mediated via ERK. However, disruption of the actin cytoskeleton with cytochalasin D or latrunculin B in parental GEC (on collagen) and in GEC that express R4F-MEK or CD2-FAK (on plastic) decreased ERK activation and increased apoptosis. Expression of a constitutively active RhoA (L63RhoA) induced assembly of cortical F-actin, promoted ERK activation, and supplanted the requirement of collagen for survival. Adhesion of GEC to collagen increased phosphatidylinositol-4,5-bisphosphate (PIP2). Downregulation or sequestration of PIP2by transfection with an inositol 5′-phosphatase or the plextrin-homology domain of phospholipase C-δ1 decreased F-actin content and survival. Moreover, overexpression of wild-type or K256E mutant α-actinin-4 with increased affinity for F-actin increased apoptosis. These results demonstrate a reciprocal relationship between collagen-induced cortical F-actin assembly and collagen-dependent survival signaling, including ERK activation. Appropriate remodeling of the actin cytoskeleton may be necessary for facilitating survival, as both disassembly and excessive crosslinking affect survival adversely.
Vibratory Adaptation of Cutaneous Mechanoreceptive Afferents
Authors: Bensmaïa S. J. , Leung Y. Y. , Hsiao S. S. , Johnson K. O.
Published: July 2005

The objective of this study was to investigate the effects of extended suprathreshold vibratory stimulation on the sensitivity of slowly adapting type 1 (SA1), rapidly adapting (RA), and Pacinian (PC) afferents. To that end, an algorithm was developed to track afferent absolute ( I0) and entrainment ( I1) thresholds as they change over time. We recorded afferent responses to periliminal vibratory test stimuli, which were interleaved with intense vibratory conditioning stimuli during the adaptation period of each experimental run. From these measurements, the algorithm allowed us to infer changes in the afferents' sensitivity. We investigated the stimulus parameters that affect adaptation by assessing the degree to which adaptation depends on the amplitude and frequency of the adapting stimulus. For all three afferent types, I0 and I1 increased with increasing adaptation frequency and amplitude. The degree of adaptation seems to be independent of the firing rate evoked in the afferent by the conditioning stimulus. In the analysis, we distinguished between additive adaptation (in which I0 and I1 shift equally) and multiplicative effects (in which the ratio I1/ I0 remains constant). RA threshold shifts are almost perfectly additive. SA1 threshold shifts are close to additive and far from multiplicative ( I1 threshold shifts are twice the I0 shifts). PC shifts are more difficult to classify. We used an integrate-and-fire model to study the possible neural mechanisms. A change in transducer gain predicts a multiplicative change in I0 and I1 and is thus ruled out as a mechanism underlying SA1 and RA adaptation. A change in the resting action potential threshold predicts equal, additive change in I0 and I1 and thus accounts well for RA adaptation. A change in the degree of refractoriness during the relative refractory period predicts an additional change in I1 such as that observed for SA1 fibers. We infer that adaptation is caused by an increase in spiking thresholds produced by ion flow through transducer channels in the receptor membrane. In a companion paper, we describe the time-course of vibratory adaptation and recovery for SA1, RA, and PC fibers.
Marx's “Truly Social” Labour Theory of Value: Part I, Abstract Labour in Marxian Value Theory
Authors: Murray Patrick
Published: July 2005

To make abstractions hold good in actuality means to destroy actuality.
Marx's ‘Truly Social’ Labour Theory of Value: Part II, How Is Labour that Is Under the Sway of Capital Actually Abstract?
Authors: Murray Patrick
Published: July 2005

In the first part of this two-part article, I argued that, unlike the asocial classical (Ricardian) labour theory of value, Marx's labour theory of value is a ‘truly social’ one. In fact, it is a purely social one. Marx's theory of value is nothing but his theory of the social forms distinctive of the capitalist mode of production. Thus, we may speak of those forms as value-forms, the (generalised) commodity, money (in its several forms), capital, wage-labour, surplus-value and its forms of appearance (profit, interest, and rent), and more. The labour that produces value, then, is labour of a peculiar social sort. This thought is entirely foreign to the classical labour theory of value, and, likewise, to Marxist accounts of value theory that mistake it for a radical version of Ricardian value theory. The gulf between the classical and the Marxian labour theories of value is wide.
Debating Mobilisation, Class Struggle and the Left: A Response to a Reply
Authors: Gail Gregor
Published: July 2005

John Kelly has replied to my assessment of his Rethinking Industrial Relations published earlier in this journal in a fraternal and constructive manner. Here, I wish to undertake two tasks. The first is to assess the response of other academics and writers to his book, in terms of reviews and the use of his work by others. The second is to engage with the points he makes to take the debate further forward.
Festschriften in Public International Law: An Annotated Bibliographical Compilation of Titles, 1930–2000/2001
Authors:   Schwietzke,   Macalister-Smith
Published: July 2005

The authors survey the Festschriften within the literature of public international law. The recipients of the works are identified and the details of the volumes are presented in a comprehensive bibliography. A country synopsis and an index of names supply further information about this category of scholarly publications. The survey covers 325 relevant works that could be located from all countries around the world.
The Right to Strike, Labor Market Liberalization and the New Labor Code in Pre-Accession Lithuania
Authors:   Woolfson,   Beck
Published: July 2005

This article examines legal inhibitions on the right to strike which have emerged in the new market economy of Lithuania. It illustrates how legal impediments impact on the right to strike by analyzing a specific episode of industrial conflict. Further to this, the complaint by the employees' trade union to the International Labor Organization is examined together with the legislative responses of Lithuanian authorities to concerns arising from this dispute. The paper suggests that a broader political imperative of labor market liberalization may be compromising the spirit, if not the letter, of both major ILO conventions on Freedom of Association and Collective Bargaining which are endorsed in the new Lithuanian Labor Code, and also the European Union Charter of Fundamental Rights to which Lithuania has subscribed.
A Comparative Study of the Protection of Civil Rights: The Civil Codes of CIS Countries
Authors:   Korableva
Published: July 2005

This article is devoted to an examination of the civil law means for protecting subjective civil rights. The subject matter of this study are the provisions of the several civil codes that have been promulgated in the countries of the CIS in the post-Soviet period. The effort to harmonize private law in the region has given rise inter alia to several pieces of model legislation, perhaps the most notable of which is the CIS Model Civil Code.The use of the comparative method allows the author to trace the progressive development of the civil codes—and the model code—of countries in the CIS; this also enables the author to consider whether there are any gaps or codification hiatuses in the Civil Code of the Russian Federation. In doing so, the author points to those issues that, in her view, are relevant for court practice. As part of her consideration of this subject, the author has compiled a comparative table of relevant provisions of most of the civil codes in CIS countries.
International Organizations and Foreign States: Participants in Civil Law Relations in Russia
Authors: Kanachevskii Vladimir
Published: July 2005

The author examines the legal status of international organizations and foreign states in trade and commerce in the Russian Federation. The specifi c issues which are touched upon by the author include general problems of the participation of public entities—such as international organizations as legal persons and the immunity of foreign states and international organizations—in civil law relations. The author concludes that domestic legislation should not be considered to be the only source of law for regulating private international relations involving states; practice illustrates that international treaties are also a source of such rules and regulations. Special attention in this article is devoted to characteristic features of the legal personality of international organizations, the sources of law regulating relations in which international organizations participate, the role of domestic law and internal rules of international organization itself, the various aspects of the legal capacity of international organizations as subjects of Russian civil law including agreements involving international organizations, the legal status of their separate divisions, issues relating to the property rights of international organization, and the civil law status of representatives of foreign states attached to international organizations (and their civil servants). The legal base for this research is formed by international treaties, the charters and internal rules of international organizations, and rules of Russian civil legislation as well as decisions of Russian and international judicial bodies. By way of conclusion, the author postulates that it is wise for domestic (and foreign) natural and legal persons, which enter into relations with the international organizations and foreign states, to take into consideration the specifi c nature of the above-mentioned subjects. In practice, this may result in dismissal of a plaintiff 's claim in a RF court where the defendant is an international organization or foreign state. It may thereby be impossible to hold such an organization or state civilly liable (without its consent) for breaching a contractual undertaking.
Migration matters: regulatory T-cell compartmentalization determines suppressive activity in vivo
Authors: Siegmund Kerstin , Feuerer Markus , Siewert Christiane , Ghani Saeed , Haubold Uta , Dankof Anja , Krenn Veit , Schön Michael P. , Scheffold Alexander , Lowe John B. , Hamann Alf , Syrbe Uta , Huehn Jochen
Published: July 2005

Regulatory T cells (Tregs) play a fundamental role in the suppression of different immune responses; however, compartments at which they exert suppressive functions in vivo are unknown. Although many groups have described the presence of Tregs within inflammatory sites, it has not been shown that inflamed tissues are, indeed, the sites of active suppression of ongoing immune reactions. Here, by using αE+ effector/memory-like Tregs from fucosyltransferase VII-deficient animals, which lack E/P-selectin ligands and fail to migrate into inflamed sites, we analyzed the functional importance of appropriate Treg localization for in vivo suppressive capacity in an inflammation model. Lack of suppression by Tregs deficient in E/P-selectin ligands demonstrates that immigration into inflamed sites is a prerequisite for the resolution of inflammatory reactions in vivo because these selectin ligands merely regulate entry into inflamed tissues. In contrast, control of proliferation of naive CD4+ T cells during the induction phase of the immune response is more efficiently exerted by the naive-like αE–CD25+ Treg subset preferentially recirculating through lymph nodes when compared with its inflammation-seeking counterpart. Together, these findings provide the first conclusive evidence that appropriate localization is crucial for in vivo activity of Tregs and might have significant implications for anti-inflammatory therapies targeting recruitment mechanisms.
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Authors: Kosinski Jan , Feder Marcin , Bujnicki Janusz M
Published: July 2005

Background

The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches.

Results

The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues.

Conclusion

In this article, we report identification of the PD-(D/E)XK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head completion protein of phage T4) and in proteins for which no function was assigned to date (such as YhcG, various phage proteins, novel candidates for restriction enzymes). Our results contributes to the reduction of "white spaces" on the sequence-structure-function map of the protein universe and will help to jump-start the experimental characterization of new nucleases, of which many may be of importance for the complete understanding of mechanisms that govern the evolution and stability of the genome.
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays
Authors: Rouchka Eric C , Khalyfa Abdelnaby , Cooper Nigel GF
Published: July 2005

Background

Enhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse, human, fruit fly, and zebrafish. The availability of large-scale genomic and genic sequence data coupled with advances in microarray technology have made it possible to study the expression of large numbers of sequence products under several different conditions in days where traditional molecular biology techniques might have taken months, or even years. Therefore, to efficiently study a number of gene products associated with a disease, pathway, or other biological process, it is necessary to be able to design primer pairs or oligonucleotides en masse rather than using a time consuming and laborious gene-by-gene method.

Results

We have developed an integrated system, MPrime, in order to efficiently calculate primer pairs or specific oligonucleotides for multiple genic regions based on a keyword, gene name, accession number, or sequence fasta format within the rat, mouse, human, fruit fly, and zebrafish genomes. A set of products created for mouse housekeeping genes from MPrime-designed primer pairs has been validated using both PCR-amplification and DNA sequencing.

Conclusion

These results indicate MPrime accurately incorporates standard PCR primer design characteristics to produce high scoring primer pairs for genes of interest. In addition, sequence similarity for a set of oligonucleotides constructed for the same set of genes indicates high specificity in oligo design.
Correlation of same-visit HbA1c test with laboratory-based measurements: A MetroNet study
Authors: Schwartz Kendra L , Monsur Joseph C , Bartoces Monina G , West Patricia A , Neale Anne Victoria
Published: July 2005

Background

Glycated hemoglobin (HbA1c) results vary by analytical method. Use of same-visit HbA1c testing methodology holds the promise of more efficient patient care, and improved diabetes management. Our objective was to test the feasibility of introducing a same-visit HbA1c methodology into busy family practice centers (FPC) and to calculate the correlation between the same-visit HbA1c test and the laboratory method that the clinical site was currently using for HbA1c testing.

Methods

Consecutive diabetic patients 18 years of age and older having blood samples drawn for routine laboratory analysis of HbA1c were asked to provide a capillary blood sample for same-visit testing with the BIO-RAD Micromat II. We compared the results of the same-visit test to three different laboratory methods (one FPC used two different laboratories).

Results

147 paired samples were available for analysis (73 from one FPC; 74 from the other). The Pearson correlation of Micromat II and ion-exchange HPLC was 0.713 (p < 0.001). The Micromat II mean HbA1c was 6.91%, which was lower than the 7.23% from the ion-exchange HPLC analysis (p < 0.001). The correlation of Micromat II with boronate-affinity HPLC was 0.773 (p < 0.001); Micromat II mean HbA1c 6.44%, boronate-affinity HPLC mean 7.71% (p < 0.001). Correlation coefficient for Micromat II and immuno-turbidimetric analysis was 0.927 (p < 0.001); Micromat II mean HbA1c was 7.15% and mean HbA1c from the immuno-turbidimetric analysis was 7.99% (p = 0.002). Medical staff found the same-visit measurement difficult to perform due to the amount of dedicated time required for the test.

Conclusion

For each of the laboratory methods, the correlation coefficient was lower than the 0.96 reported by the manufacturer. This might be due to variability introduced by the multiple users of the Micromat II machine. The mean HbA1c results were also consistently lower than those obtained from laboratory analysis. Additionally, the amount of dedicated time required to perform the assay may limit its usefulness in a busy clinical practice. Before introducing a same-visit HbA1c methodology, clinicians should compare the rapid results to their current method of analysis.
Hospitalization and emergency department visits among seniors receiving homecare: a pilot study
Authors: Smith Andrew A , Carusone Soo B Chan , Willison Kathleen , Babineau Tamara J , Smith Stephanie D , Abernathy Tom , Marrie Tom , Loeb Mark
Published: July 2005

Background

Despite the recent growth in home health services, data on clinical outcomes and acute health care utilization among older adults receiving homecare services are sparse. Obtaining such data is particularly relevant in Ontario where an increasing number of frail seniors receiving homecare are awaiting placement in long-term care facilities. In order to determine the feasibility of a large-scale study, we conducted a pilot study to assess utilization of acute health care services among seniors receiving homecare to determine associated clinical outcomes.

Methods

This prospective cohort study followed forty-seven seniors admitted to homecare by two homecare agencies in Hamilton, Ontario over a 12-month period. Demographic information and medical history were collected at baseline, and patients were followed until either termination of homecare services, death, or end of study. The primary outcome was hospitalization. Secondary outcomes included emergency department visits that did not result in hospitalization and death. Rates of hospitalization and emergency department visits without admission were calculated, and univariate analyses were performed to test for potential risk factors. Survival curves for accumulative rates of hospitalization and emergency department visits were created.

Results

312 seniors were eligible for the study, of which 123 (39%) agreed to participate initially. After communicating with the research nurse, of the 123 who agreed to participate initially, 47 (38%) were enrolled in the study. Eleven seniors were hospitalized during 3,660 days of follow-up for a rate of 3.0 incident hospitalizations per 1,000 homecare-days. Eleven seniors had emergency department visits that did not result in hospitalization, for a rate of 3.3 incident emergency department visits per 1,000 homecare-days. There were no factors significantly associated with hospitalization or emergency department visits when adjustment was made for multiple comparisons.

Conclusion

The incidence of hospitalization and visits to the emergency department among seniors receiving homecare services is high. Getting satisfactory levels of enrolment will be a major challenge for larger prospective studies.
A new approach to estimation of the number of central synapse(s) included in the H-reflex
Authors: Ghavanini Mohammadreza Alavian , Ashraf Alireza , Sadeghi Shahram , Emad Mohammadreza
Published: July 2005

Background

Among the main clinical applications of the H-reflex are the evaluation of the S1 nerve root conductivity such as radiculopathy and measurement of the excitability of the spinal motoneurons in neurological conditions. An attempt has been made to reduce the pathway over which H-reflex can be obtained in a hope to localize a lesion to the S1 nerve root, so the S1 central loop has been suggested. The main goal of this study is the estimation of the H-reflex number of synapse(s) for better understanding of the physiology of this practical reflex.

Methods

Forty healthy adult volunteers (22 males, 18 females) with the mean age of (37.7 ± 10.2) years participated in this study. They were positioned comfortably in the prone position, with their feet off the edge of the plinth. Recording electrodes were positioned at the mid point of a line connecting the mid popliteal crease to the proximal flare of the medial malleolus. Stimulation was applied at the tibial nerve in the popliteal fossa and H, F and M waves were recorded. Without any change in the location of the recording electrodes, a monopolar needle was inserted as cathode at a point 1 cm medial to the posterior superior iliac spine, perpendicular to the frontal plane. The anode electrode was placed over the anterior superior iliac spine, and then M and H waves of the central loop were recorded. After processing the data, sacral cord conduction delay was determined by this formula:

* Sacral cord conduction delay = central loop of H-reflex – (delays of the proximal motor and sensory fibers in the central loop).

Results

The central loop of H-reflex was (6.77 ± 0.28) msec and the sacral cord conduction delay was (1.09 ± 0.06) msec.

Conclusion

The sacral cord conduction time was estimated to be about 1.09 msec in this study and because at least 1 msec is required to transmit the signal across the synapse between the sensory ending and the motor cell, so this estimated time was sufficient for only one central synapse in this reflex.
Nh3D: A reference dataset of non-homologous protein structures
Authors: Thiruv B , Quon G , Saldanha SA , Steipe B
Published: July 2005

Background

The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfil minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here we provide a reference dataset of non-homologous protein domains, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. The dataset is based on domains at the Topology level of the CATH database which hierarchically classifies all protein structures. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted.

Results

The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. We observe that even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%.

Conclusion

Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. Regularly updated versions of Nh3D and the corresponding PDB-formatted coordinate sets are accessible from our Web site http://www.schematikon.org.