bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional Characterization of the Genomic Promoter of Borna Disease Virus (BDV): Implications of 3′-Terminal Sequence Heterogeneity for BDV Persistence
Authors: Rosario Debralee , Perez Mar , de la Torre Juan Carlos
Published: April 2005

Borna disease virus (BDV) is an enveloped virus with a genome organization characteristic ofMononegavirales. However, based on its unique features, BDV is considered the prototypic member of a new virus family,Bornaviridae, within the orderMononegavirales. We have described the establishment of a reverse genetics system for the rescue of BDV RNA analogues, or minigenomes, that is based on the use of polymerase I/polymerase II. Using this BDV minigenome rescue system, we have examined the functional implications of the reported sequence heterogeneity found at the 5′ and 3′ termini of the BDV genome and also defined the minimal BDV genomic promoter within the 3′-terminal 25 nucleotides. Our results suggest that the accumulation of RNA genome species containing truncations of one to three nucleotides at their 3′ termini may contribute to modulate BDV RNA replication and gene expression during long-term persistence.
Low Levels of Human Immunodeficiency Virus Type 1 DNA in High-Risk Seronegative Men
Authors: Koning Fransje A. , van der Vorst Teun J. K. , Schuitemaker Hanneke
Published: April 2005

We detected human immunodeficiency virus type 1 (HIV-1) DNA at very low levels in sequential peripheral blood mononuclear cell samples of five out of six high-risk, seronegative, homosexual men and five out of five individuals 7.8 to 1.6 years prior to seroconversion. These data indicate a high prevalence of low-level HIV-1 DNA in exposed seronegative individuals.
Residues in the Murine Leukemia Virus Capsid That Differentially Govern Resistance to Mouse
Fv1
and Human
Ref1
Restrictions
Authors: Lassaux Adeline , Sitbon Marc , Battini Jean-Luc
Published: April 2005

We identified new residues within a 101-amino-acid stretch of the murine leukemia virus capsid that differentially modulate resistance and susceptibility to the mouse
Fv1
and human
Ref1
genes. Among these residues, aspartate 92 and histidine 117 are both required for
Fv1

b

resistance, whereas the latter is sufficient to confer
Ref1
resistance.
Failure of the Lamivudine-Resistant rtM204I Hepatitis B Virus Mutants To Efficiently Support Hepatitis Delta Virus Secretion
Authors: Vietheer P. T. K. , Netter H. J. , Sozzi T. , Bartholomeusz A.
Published: April 2005

Hepatitis delta virus (HDV) is encapsidated by the envelope proteins of hepatitis B virus (HBV). The major HBV lamivudine (LMV)-resistant mutations in the polymerase gene within the reverse transcriptase (rt) region at rtM204V or rtM204I are associated with changes in the overlapping envelope gene products, in particular, the gene encoding small envelope protein (s) at sI195M or sW196L/S/Stop. We have demonstrated that the LMV resistance mutations corresponding to sW196L/S inhibited secretion of HDV particles, while changes corresponding to sI195M did not affect secretion. Differential efficiencies of HBsAg proteins expressed by LMV-resistant HBV to support HDV secretion may have consequences for clinical prognosis as coinfected patients are treated with antiviral agents.
Raman Optical Activity of the Central Part of Hinge Peptide
Authors: Kapitán Josef , Baumruk Vladimír , Gut Vladimír , Hlaváček Jan , Dlouhá Helena , Urbanová Marie , Wünsch Erich , Maloň Petr
Published: April 2005

Central cyclic part of the hinge peptide (a parallel dimer of the pentapeptide Boc-Cys-Pro-Pro-Cys-Pro-NHCH3 with two disulfide bonds) derived from the sequence of human IgG1 is a rather rigid structure having predominantly polyproline II helical conformation as shown by vibrational circular dichroism spectra. It exhibits significant Raman optical activity (ROA) signal due to vibrations associated with the disulfide bridges. We report positive ROA for the S-S stretching vibration at 510 cm-1 and for the C-S stretching vibration at 655 cm-1. These signals can provide means to assess the conformation of disulfide bridges in proteins, otherwise difficult to investigate.
Polyhedral Oxaruthenaborane Chemistry. Characterisation of a [(η6-C6Me6)RuOB9H13] Species of arachno Eleven-Vertex Cluster Character and Other Aspects of Oxaborane Chemistry
Authors: Bould Jonathan , Bown Mark , Kennedy John D.
Published: April 2005

[(η6-C6Me6)RuOB9H13], obtained in trace yield from the reaction between [{RuCl2(η6-C6Me6)}2] and the [arachno-B6H11]- anion, has been shown by DFT calculations of structure and of boron-atom nuclear shielding to be of an arachno eleven-vertex cluster geometry that is derived by the removal of adjacent six-connected and five-connected vertices from a closed thirteen-vertex deltahedral 1:6:5:1 stack. The results lead to further considerations in oxaborane chemistry, which are explored and consolidated by calculation. Additional products from the reaction include [4-(η6-C6Me6)-n-arachno-4-RuB8H14], also substantiated by DFT calculations, and several four-, five-, six-, nine- and ten-vertex ruthenaboranes that are either known compounds or simple variants of known compounds.
Synthesis, Reactions, Conformation Analysis, and NMR Spectra of 5,10-Epoxy-5ξ,10ξ-estrane-3,17-diones
Authors: Buděšínský Miloš , Fajkoš Jan , Günter Jaroslav , Kasal Alexander
Published: April 2005

On epoxidation of estr-5(10)-ene-3,17-dione, the 5β,10β-epoxide is the major product. The mixture of epoxides was converted into 5,10β-dihydroxy-5α-estrane-3,17-dione, 10α- and 10β-hydroxyestr-4-ene-3,17-dione, and estrone. Due to the sensitivity of the products, 1H NMR was the best way to monitor the reaction pathway.
Synthesis of Novel Conformationally Locked Carbocyclic Nucleosides Derived from 5,5- and 6,6-Bis(hydroxymethyl)bicyclo[2.2.1]heptan-2-ol
Authors: Hřebabecký Hubert , Masojídková Milena , Holý Antonín
Published: April 2005

(1R*,2R*,3R*,4S*)-3-Amino-6,6-bis(hydroxymethyl)bicyclo[2.2.1]heptan-2-ol (13) was prepared from (bicyclo[2.2.1]hept-5-ene-2,2-diyl)dimethyl dibenzoate (7) viacis-diol8, cyclic sulfate10, and azide12. (1R*,2R*,3S*,4S*)-3-Amino-6,6-bis(hydroxymethyl)bicyclo[2.2.1]-heptan-2-ol (18) and (1R*,2S*,3S*,4S*)-3-amino-5,5-bis(hydroxymethyl)bicyclo[2.2.1]heptan-2-ol (19) were obtained by addition of chromyl azide to double bond of7, chromatographic separation, debenzoylation and hydrogenation of resulting azides14and16. The amines13,18, and19were used to build (1R*,2R*,3R*,4S*)- (21a), (1R*,2R*,3S*,4S*)-3-(6-chloro-9H-purin-9-yl)-6,6-bis(hydroxymethyl)bicyclo[2.2.1]heptan-2-ol (21b), and (1R*,2S*,3S*,4S*)-3-(6-chloro-9H-purin-9-yl)-5,5-bis(hydroxymethyl)bicyclo[2.2.1]heptan-2-ol (21c), respectively. Ammonolysis of these compounds led to 6-amino-9H-purine derivatives22a-22c. 6-(Dimethylamino)-9H-purine analogues23a-23cand 6-(cyclopropylamino)-9H-purine analogues24a-24cwere prepared by aminolysis of21a-21c. Reaction of amines13,18, and19with ethylN-((2E)-3-ethoxymethacryloyl)carbamate afforded thymine derivatives28a-28c.
The importance of cyclopentadienyl substituent effects in group 4 metallocene dinitrogen chemistry
Authors: Pool Jaime A , Chirik Paul J
Published: April 2005

This article highlights some of our recent efforts and presents new data on the importance of cyclopentadienyl substituent effects on group 4 metallocene dinitrogen chemistry. Reactions such as the coordination of N2 to an isolated titanium sandwich complex, alkali-metal reductions of zirconocene dihalide complexes, alkane reductive elimination reactions, and the hydrogenation of zirconium dinitrogen complexes are all extremely sensitive to the groups present on the cyclopentadienyl rings. These results are promising for the future of N2 fixation, as the reactivity of a specific metallocene can be dramatically altered by subtle manipulations in ligand substituents.Key words: cyclopentadienyl, zirconium, dinitrogen, ammonia, sandwich.
Ligand-assisted reduction of Co(II) to Co(I) and subsequent coordination of dinitrogen
Authors: Scott Jennifer , Gambarotta Sandro , Korobkov Ilia
Published: April 2005

Reaction of the bis-aminopyridine dianion {[2,6-[2,6-(i-Pr)2PhN-C=(CH2)]2(C5H3N)]Li(THF)}{Li(THF)4} with CoCl2(THF)1.5under Ar afforded the dinuclear complex {[2,6-(i-Pr)2PhN-C=(CH2)](C5H3N)[2,6-(i-Pr)2PhN=C(CH2)]}2[Co(µ-Cl)Li(THF)3]2·4(THF) (1) in which the ligand is coupled to a second identical unit at a terminal methylene carbon. In turn, the CC bond formation caused reduction of the Co(II) center to the monovalent state. The same reaction performed under a nitrogen atmosphere afforded the double dinitrogen complex {[2,6-(i-Pr)2PhN-C=(CH2)](C5H3N)[2,6-(i-Pr)2PhN=C(CH2)]}2[Co(N2)]2·2(toluene) (2). Key words: low-valent Co, diiminopyridinato, dinitrogen fixation.
Bonding, activation, and protonation of dinitrogen on a molybdenum pentaphosphine complex  Comparison to trans-bis(dinitrogen) and -nitrile  dinitrogen complexes with tetraphosphine coordination
Authors: Stephan Gerald C , Peters Gerhard , Lehnert Nicolai , Habeck Carsten M , Näther Christian , Tuczek F
Published: April 2005

The molybdenum-N2 pentaphosphine complex [Mo(N2)(dpepp)(dppm)] (1) containing a bi- and a tridentate phosphine ligand (dpepp = PhP(CH2CH2PPh2)2, dppm = Ph2PCH2PPh2) has been prepared and characterized. By protonation of 1 with triflic acid the NNH2 complex [Mo(NNH2)(dpepp)(dppm)](CF3SO3)2 (2) is formed without loss of the pentaphosphine coordination. The electronic properties of 1 and 2 and their 15N and (or) 2H counterparts are investigated by NMR, IR, and Raman spectroscopy coupled to DFT frequency and NMR shift calculations. Force constants are evaluated from experimental frequencies and isotope shifts by the quantum chemistry based normal coordinate analysis procedure (QCB-NCA). The results for the N2 complex 1 are compared with those obtained earlier for bis(dinitrogen) and trans-nitrile dinitrogen systems. Importantly, the N2 in the pentaphosphine complex is more strongly activated compared to corresponding bis(dinitrogen) compounds and more weakly activated compared to trans-nitrile N2 systems. The activation of the NNH2 ligand in complex 2 is similar to trans-nitrile systems and weaker compared to corresponding NNH2 complexes with coordinated anions like [MoF(NNH2)(dppe)2](BF4). These results are discussed based on the relative donoracceptor properties of the respective trans ligands, demonstrating the influence of σ donation and π acceptance on the activation of N2 in transition metal complexes.Key words: nitrogen fixation, phosphine complexes, NMR shifts, DFT calculations, normal coordinate analysis.
Synthesis and characterization of cationic iron complexes supported by the neutral ligands NPi-Pr3, NArPi-Pr3, and NSt-Bu3
Authors: MacBeth Cora E , Harkins Seth B , Peters Jonas C
Published: April 2005

This paper compares the local geometries, spin states, and redox properties of a series of iron complexes supported by neutral, tetradentate NP3(tris(phosphine)amine) and NS3(tris(thioether)amine) ligands. Our consideration of an Fe-mediated N2fixation scheme similar to that proposed by Chatt for molybdenum motivates our interest in systems of these types. This report specifically describes the synthesis and characterization of cationic Fe(II) chloride complexes supported by the neutral ligands NPi-Pr3(NPi-Pr3 = [N(CH2CH2P-i-Pr2)3]), NArPi-Pr3(NArPi-Pr3 = [N(2-diisopropylphosphine-4-methylphenyl)3]), and NSt-Bu3(NSt-Bu3 = [N(CH2CH2S-t-Bu)3]). The solid-state structures, electrochemistry, and magnetic properties of these complexes are reported. Whereas the NPi-Pr3and NArPi-Pr3ligands provide pseudotetrahedral S = 2 ferrous cations [Fe(NPi-Pr3)Cl]PF6(1[PF6]) and [Fe(NArPi-Pr3)Cl]BPh4(2[BPh4]) featuring a long FeN bond distance, the NSt-Bu3ligand gives rise to a trigonal bipyramidal structure with a S = 1 ground state and a much shorter FeN interaction. The complexes 1[BPh4] and 2[BPh4] can be reduced under CO to give rise to the five-coordinate Fe(I) monocarbonyls [Fe(NPi-Pr3)CO]BPh4(4[BPh4]) and [Fe(NArPi-Pr3)CO]BPh4(5[BPh4]). The solid-state structures and electrochemistry of 4[BPh4] and 5[BPh4] are described, as is the EPR spectrum of 4[BPh4]. The synthesis and characterization of the hydridedinitrogen complex [Fe(NPi-Pr3)(N2)(H)]PF6(6[PF6]) has also been accomplished and its properties are also reported.Key words: nitrogenase, iron, polydentate phosphines, thioether ligands, N2chemistry, nitrogen, Fe(I).
Portability of the RNNMo(3+) core  Application to the synthesis of dinitrogen-derived trialkoxymolybdenum organodiazenido complexes
Authors: Cherry John-Paul F , Diaconescu Paula L , Cummins Christopher C
Published: April 2005

An alcoholysis strategy has been employed in the synthesis of new oligo- or polymeric trialkoxymolybdenum diazenido complexes [R1NNMo(O-1-Ad)3]x (R1 = Me or C(O)OMe) as well as their mononuclear THF solvates R1NNMo(O-1-Ad)3(THF). Dinitrogen-derived diazenido precursor complexes R1NNMo(N[R]Ar)3 (R = i-Pr, Ar = 3,5-C6H3Me2) react smoothly with 3 equiv. 1-adamantanol to liberate 3 equiv. HN(R)Ar without disruption of the diazenidomolybdenum(3+) core. X-ray structural investigations were carried out for diazenido complex MeNNMo(O-1-Ad)3(THF) and for the corresponding cationic dimethyldiazenido complex [Me2NNMo(O-1-Ad)3(THF)]+, obtained as its triflate salt. The latter cation was found upon cobaltocene reduction to undergo NN bond cleavage, producing nitride NMo(O-1-Ad)3 (synthesized independently) and dimethylamine. Key words: molybdenum, dinitrogen, bond cleavage, hydrazido, diazenido.
NETWORK MODELING ISSUES FOR GRID APPLICATION SCHEDULING
Authors: CASANOVA HENRI
Published: April 2005

The dominant trend in scientific computing today is the establishment of platforms that span multiple institutions to support applications at unprecedented scales. On most distributed computing platforms a requirement to achieve high performance is the careful scheduling of distributed application components onto the available resources. While scheduling has been an active area of research for many decades most of the platform models traditionally used in scheduling research, and in particular network models, break down for platforms spanning wide-area networks. In this paper we examine network modeling issues for large-scale platforms from the perspective of scheduling. The main challenge we address is the development of models that are sophisticated enough to be more realistic than those traditionally used in the field, but simple enough that they are still amenable to analysis. In particular, we discuss issues of bandwidth sharing and topology modeling. Also, while these models can be used to define and reason about realistic scheduling problems, we show that they also provide a good basis for fast simulation, which is the typical method to evaluate scheduling algorithms, as demonstrated in our implementation of the SIMGRID simulation framework.
STEADY-STATE SCHEDULING ON HETEROGENEOUS CLUSTERS
Authors: BEAUMONT OLIVIER , LEGRAND ARNAUD , MARCHAL LORIS , ROBERT YVES
Published: April 2005

This paper considers steady-state scheduling techniques for heterogeneous systems, such as clusters and grids. The use of steady-state scheduling is advocated to solve a variety of important problems, which would be too difficult to tackle with the objective of makespan minimization. Several examples are given, namely master-slave tasking, mixed task and data parallelism, and pipelined macro-communications (scatter, broadcast, multicast). For each example, both the advantages and the limitations of the approach are discussed.
CROSS-POLLINATING PARALLEL GENETIC ALGORITHMS FOR MULTI-OBJECTIVE SEARCH AND OPTIMIZATION
Authors: WILSON LUCAS A. , MOORE MICHELLE D.
Published: April 2005

This paper discusses the design of a parallel genetic algorithm to generate solutions to multi-objective problems. The algorithm uses multiple optimization criteria, independent cross-pollinating populations, and handles multiple hard constraints. Individuals in the population consist of multiple chromosomes. The complexity of the algorithm is the number of generations processed times O(N2) where N is the total number of individuals used for path generation on any of the optimizations. The results of initial empirical studies on the effects of pollination and recommendations for possible future work are presented.
Activation of the extracellular signal-regulated kinase by complement C5b-9
Authors: Cybulsky Andrey V. , Takano Tomoko , Papillon Joan , Bijian Krikor , Guillemette Julie
Published: April 2005

Extracellular signals may be transmitted to nuclear or cytoplasmic effectors via the mitogen-activated protein kinases. In the passive Heymann nephritis (PHN) model of membranous nephropathy, complement C5b-9 induces glomerular epithelial cell (GEC) injury, proteinuria, and activation of phospholipases and protein kinases. This study addresses the complement-mediated activation of the extracellular signal-regulated kinase (ERK). C5b-9 induced ERK threonine202/tyrosine204phosphorylation (which correlates with activation) in GEC in culture and PHN in vivo. Expression of a dominant-inhibitory mutant of Ras reduced complement-mediated activation of ERK, but activation was not affected significantly by downregulation of protein kinase C. Complement-induced ERK activation resulted in phosphorylation of cytosolic phospholipase A2and was, in part, responsible for phosphorylation of mitogen-activated protein kinase-associated protein kinase-2, but did not induce phosphorylation of the transcription factor, Elk-1. Activation of ERK was attenuated by drugs that disassemble the actin cytoskeleton (cytochalasin D, latrunculin B), and these compounds interfered with the activation of ERK by mitogen-activated protein kinase kinase (MEK). Overexpression of a constitutively active RhoA as well as inhibition of Rho-associated kinase blocked complement-mediated ERK activation. Complement cytotoxicity was enhanced after disassembly of the actin cytoskeleton but was unaffected after inhibition of complement-induced ERK activation. However, complement cytotoxicity was enhanced in GEC that stably express constitutively active MEK. Thus complement-induced ERK activation depends on cytoskeletal remodelling and affects the regulation of distinct downstream substrates, while chronic, constitutive ERK activation exacerbates complement-mediated GEC injury.
Disability and Mortality in a Cohort of Multiple Sclerosis Patients: A Reappraisal
Authors: Bergamaschi Roberto , Montomoli Cristina , Candeloro Elisa , Fratti Cesare , Citterio Antonietta , Cosi Vittorio
Published: April 2005

The aim of the study was to evaluate how the natural history of multiple sclerosis (MS) had changed over a 15-year period. We compared disability and mortality in a cohort of 83 MS patients hospitalised in the Neurological Institute of Pavia, northern Italy, from January 1, 1990, to December 31, 1991, with a similar cohort of 52 patients analysed in the past. After the follow-up, an unfavourable course (death or relevant disability) was observed in 41% of the patients in the new cohort, compared to 63.5% of the patients in the old one. The percentage of deceased patients was reduced from 25 to 6%. The analysis of the pooled data of the two cohorts indicates a recent tendency of firstly hospitalised patients having a shorter disease duration and a lower disability level, which could explain the relevant decrease both in mortality and disability. Finally, our findings confirmed that age at onset, early disability and a short interval between onset and secondary progression increase the risk of an unfavourable course.
Interferon Therapy in Hemodialysis Patients with Chronic Hepatitis C: Study of Tolerance, Efficacy and Post-Transplantation Course
Authors: Mahmoud Ihab M. , Sobh Mohamed A. , El-Habashi Ahmed F. , Sally Samir T. , El-Baz Mahmoud , El-Sawy Essam , Ghoneim Mohamed A.
Published: April 2005

Background: The potential benefit of pre-transplant treatment of chronic hepatitis C on long-term evolution after renal transplantation is not clear. Methods: Fifty successive renal transplant candidates had their sera positive for HCV RNA and a biopsy-proven chronic hepatitis. Out of these, 18 patients received a standard course of interferon-α2b (IFN; 3 MU three times weekly after hemodialysis sessions for 6 months). Results: IFN was discontinued in 2 patients (11%) due to persistent leukopenia. HCV RNA turned negative in 10 patients of the treatment group and in none of the control group. Two patients of the IFN group had a virological relapse post-transplantation. Post-transplant follow-up periods were 41.5 ± 15 and 50 ± 16 months for the treated and control groups respectively. Transaminases remained normal in all patients of the IFN group after transplantation. In contrast, biochemical evidence of acute and chronic hepatitis was observed in 5 (p = 0.03) and 13 (p = 0.002) patients, respectively, of the control group. Logistic regression analysis identified non-receiving IFN before transplantation as a risk factor for post-transplant hepatic dysfunction (odds ratio = 11.7, p = 0.003) and for chronic allograft nephropathy (odds ratio = 11.6, p = 0.02). Conclusions: IFN-treated patients had a significantly better post-transplant hepatic function and significantly lower rates of chronic allograft nephropathy.
The "nations" in the salvific racles of Isaiah
Authors: Croatto Severino J.
Published: April 2005

The purpose of this study is to deconstruct the exegetical tradition that emphasizes the promise of universal salvation for the foreign nations in the book of Isaiah. The real message—scattered all along the book by its final author or Fourth Isaiah—is to affirm the liberation and return of the different Judean diasporas. The nations as such, on the contrary, will receive the negative lot of the reversal of fortunes.
Scoredist: A simple and robust protein sequence distance estimator
Authors: Sonnhammer Erik LL , Hollich Volker
Published: April 2005

Background

Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used.

Results

We propose a correction-based protein sequence estimator called Scoredist. It uses a logarithmic correction of observed divergence based on the alignment score according to the BLOSUM62 score matrix. We evaluated Scoredist and a number of optimal matrix methods using three evolutionary models for both training and testing Dayhoff, Jones-Taylor-Thornton, and Müller-Vingron, as well as Whelan and Goldman solely for testing. Test alignments with known distances between 0.01 and 2 substitutions per position (1–200 PAM) were simulated using ROSE. Scoredist proved as accurate as the optimal matrix methods, yet substantially more robust. When trained on one model but tested on another one, Scoredist was nearly always more accurate. The Jukes-Cantor and Kimura correction methods were also tested, but were substantially less accurate.

Conclusion

The Scoredist distance estimator is fast to implement and run, and combines robustness with accuracy. Scoredist has been incorporated into the Belvu alignment viewer, which is available at ftp://ftp.cgb.ki.se/pub/prog/belvu/.
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR – how well do they correlate?
Authors: Dallas Peter B , Gottardo Nicholas G , Firth Martin J , Beesley Alex H , Hoffmann Katrin , Terry Philippa A , Freitas Joseph R , Boag Joanne M , Cummings Aaron J , Kees Ursula R
Published: April 2005

Background

The use of microarray technology to assess gene expression levels is now widespread in biology. The validation of microarray results using independent mRNA quantitation techniques remains a desirable element of any microarray experiment. To facilitate the comparison of microarray expression data between laboratories it is essential that validation methodologies be critically examined. We have assessed the correlation between expression scores obtained for 48 human genes using oligonucleotide microarrays and the expression levels for the same genes measured by quantitative real-time RT-PCR (qRT-PCR).

Results

Correlations with qRT-PCR data were obtained using microarray data that were processed using robust multi-array analysis (RMA) and the MAS 5.0 algorithm. Our results indicate that when identical transcripts are targeted by the two methods, correlations between qRT-PCR and microarray data are generally strong (r = 0.89). However, we observed poor correlations between qRT-PCR and RMA or MAS 5.0 normalized microarray data for 13% or 16% of genes, respectively.

Conclusion

These results highlight the complementarity of oligonucleotide microarray and qRT-PCR technologies for validation of gene expression measurements, while emphasizing the continuing requirement for caution in interpreting gene expression data.
Novel brain wiring functions for classical morphogens: a role as graded positional cues in axon guidance
Authors: Charron Frédéric , Tessier-Lavigne Marc
Published: April 2005

During embryonic development, morphogens act as graded positional cues to dictate cell fate specification and tissue patterning. Recent findings indicate that morphogen gradients also serve to guide axonal pathfinding during development of the nervous system. These findings challenge our previous notions about morphogens and axon guidance molecules, and suggest that these proteins, rather than having sharply divergent functions, act more globally to provide graded positional information that can be interpreted by responding cells either to specify cell fate or to direct axonal pathfinding. This review presents the roles identified for members of three prominent morphogen families – the Hedgehog, Wnt and TGFβ/BMP families– in axon guidance, and discusses potential implications for the molecular mechanisms underlying their guidance functions.
Cellular invasion byStaphylococcus aureusreveals a functional link between focal adhesion kinase and cortactin in integrin-mediated internalisation
Authors: Agerer Franziska , Lux Sigrid , Michel Antje , Rohde Manfred , Ohlsen Knut , Hauck Christof R.
Published: April 2005

Nosocomial infections by Staphylococcus aureus, a Gram-positive pathogen colonising human skin and mucosal surfaces, are an increasing health care problem. Clinical isolates almost invariably express fibronectin-binding proteins that, by indirectly linking the bacteria with host integrin α5β1, can promote uptake of the microorganisms by eukaryotic cells. Integrin engagement by pathogenic fibronectin-binding S. aureus, but not by non-pathogenic S. carnosus, triggered the recruitment of focal contact-associated proteins vinculin, tensin, zyxin and FAK to the sites of bacterial attachment. Moreover, dominant-negative versions of FAK-blocked integrin-mediated internalisation and FAK-deficient cells were severely impaired in their ability to internalise S. aureus. Pathogen binding induced tyrosine phosphorylation of several host proteins associated with bacterial attachment sites, including FAK and the Src substrate cortactin. In FAK-deficient cells, local recruitment of cortactin still occurred, whereas the integrin- and Src-dependent tyrosine phosphorylation of cortactin was abolished. As siRNA-mediated gene silencing of cortactin or mutation of critical amino acid residues within cortactin interfered with uptake of S. aureus, our results reveal a novel functional connection between integrin engagement, FAK activation and Src-mediated cortactin phosphorylation. Cooperation between FAK, Src and cortactin in integrin-mediated internalisation of bacteria also suggests a molecular scenario of how engagement of integrins could be coupled to membrane endocytosis.
ZO-1 alters the plasma membrane localization and function of Cx43 in osteoblastic cells
Authors: Laing James G. , Chou Brian C. , Steinberg Thomas H.
Published: April 2005

ZO-1 is the major connexin-interacting protein in ROS 17/2.8 (ROS) osteoblastic cells. We examined the role of ZO-1 in Cx43-mediated gap junction formation and function in ROS cells that expressed the connexin-interacting fragment of ZO-1 (ROS/ZO-1dn) cells. Expression of this ZO-17-444 fusion protein in ROS cells disrupted the Cx43/ZO-1 interaction and decreased dye transfer by 85%, although Cx43 was retained on the plasma membrane as assessed by surface biotinylation. Fractionation of lysates derived from ROS/ZO-1dn cells on a 5-30% sucrose flotation gradient showed that 40% of the Cx43 floated into these sucrose gradients, whereas none of the Cx43 in ROS cell lysates entered the gradients, suggesting that more Cx43 is associated with lipid rafts in the transfected ROS cells than in lysates derived from untransfected ROS cells. In contrast to the ROS/ZO-1dn cells, ROS cells that over-expressed ZO-1 protein (ROS/ZO-1myc cells) exhibited increased gap junctional permeability and appositional membrane staining for Cx43. These data demonstrate that ZO-1 regulates Cx43-mediated gap junctional communication in osteoblastic cells and alters the membrane localization of Cx43. They suggest that ZO-1-mediated delivery of Cx43 from a lipid raft domain to gap junctional plaques may be an important regulatory step in gap junction formation.
Structural and Epistemic Parameters in Communities of Practice
Authors: Thompson Mark
Published: April 2005

If communities of practice (Lave and Wenger 1991) are best understood as fluid social relations, enacted among a self-selected group of participants, then are they best left alone, free from “interference” by organizational managers and policymakers? Or are there ways in which organizations can provide helpful support to such communities, without constraining the delicate dynamic by which they are sustained?

This paper supports the latter position, arguing that organizations should sponsor the creation of certain loose organizational structures, around which it is hoped that communities of practice may then interact. However, some recent empirical research is presented suggesting that attempts to control group interaction by introducing too much structure are likely to result in the demise of the community itself. It is therefore proposed that there are lower and upper parameters for structural intervention in communities of practice.

It is suggested that such communities also have epistemic parameters, where participants’ willingness to express their ideas as conceptual boundary objects around which others may engage and develop ideas is a minimum requirement, but where too much inward communicative focus is likely to result in gradual loss of meaning, with a negative effect on the community. In developing this position, this paper attempts to deepen our theoretical understanding of the interrelationship between organizational structure and the epistemic activity of members of communities of practice. Several practical implications of these insights are discussed for organizations wishing to cultivate and maintain communities of practice within their own working environments.
Characterization of active oxygen species under oxygen-alkali bleaching conditions
Authors: Yokoyama Tomoya , Matsumoto Yuji , Meshitsuka Gyosuke
Published: April 2005

The reactivities of active oxygen species toward a non-phenolic lignin model compound, 1-(3,4-dimethoxyphenyl)-1,2-ethanediol (veratryl glycol, VG), and a carbo-hydrate model compound, methyl β-D-glucopyranoside (MGP), were examined and compared under practical oxygen bleaching conditions. In this study, active oxygen species were generated in situ by subjecting a phenolic compound, 2,4,6-trimethylphenol, to oxygen oxidation to faithfully simulate practical oxygen bleaching. The results indicated that the time-dependent reaction selectivity of active oxygen species between VG and MGP, k
VG(t)/k
MGP(t), in the early stage of the reaction is 2.1 and 0.3–0.7 at initial pH values of 11.8 and 13.1, respectively. By comparing this value with the of hydroxyl radical obtained by Ek et al. [Holzforschung 43 (1989) 391] we conclude that the active oxygen species in the early stage of the reaction are hydroxyl radicals. The reaction selectivity at higher pH was much lower, which is explained by the fact that an oxyl anion radical, the conjugate base of the hydroxyl radical, predominantly abstracts hydrogen from aliphatic substructures. Chain-type reactions could be mainly responsible for degradation of the model compounds after the middle stage of the reaction. We suggest that the operation of chain-type reactions is not greatly dependent on the pH of the medium, but on the structure of the substrate.
Condensed tannins from steamed Acacia mearnsii bark
Authors: Duan Wengui , Ohara Seiji , Hashida Koh , Makino Rei
Published: April 2005

The optimum steaming conditions for extraction of condensed tannins from Acacia mearnsii bark were explored, after which characterization of proanthocyanidins from bark steamed under optimum conditions was carried out. The optimum conditions were as follows: steaming time, 30 min; steaming temperature, 140°C; and water volume, 75 ml. The total phenolics content obtained under these conditions amounted to 25.31%, which was much higher than the 21.70% obtained by conventional hot water extraction. Six proanthocyanidin dimers were isolated from the steamed bark. Analysis revealed them to be fisetinidol-(4β-8)-catechin, fisetinidol-(4α-8)-catechin, robinetinidol-(4β-8)-catechin, robinetinidol-(4α-8)-catechin, robinetinidol-(4β-8)-gallocatechin, and robinetinidol-(4α-8)-gallocatechin. Proanthocyanidin polymers were found to consist mainly of prorobinetinidin extender units, similar to those obtained from the same bark by conventional extraction with 70% acetone aqueous solution. However, nuclear magnetic resonance and gel permeation chromatography analyses suggested that during steaming the polymers undergo condensation reactions, as well as inversion of the configuration of interflavanoid bonds.
Modelling anisotropic maturation strains in wood in relation to fibre boundary conditions, microstructure and maturation kinetics
Authors: Alméras Tancrède , Gril Joseph , Yamamoto Hiroyuki
Published: April 2005

A generalisation of existing mechanical models is proposed to account for the relation between wood macroscopic properties and fibre microstructure and chemical composition. It is applied to understanding of the origin of anisotropic maturation strains measured at the outermost surface of the xylem. Various assumptions are considered for boundary conditions of the fibre during the progressive maturation process and are applied to experimental data from the literature. Assumptions that the fibre is fully restrained in displacement, or fully unrestrained or unrestrained in the transverse direction only are all incompatible with observations. Indeed, within the tree, the fibre is restrained in the longitudinal and tangential directions, but unrestrained in the radial direction towards the bark. Mixed boundary conditions must be introduced to correctly simulate both longitudinal and tangential maturation strains. In the context of an analytical axisymmetric model, this is estimated by considering a parameter of partial release of tangential stress during maturation. Consistence with data and with finite element computation in the case of a square fibre confirmed that, because of the unrestrained radial condition, a large part of the tangential maturation stress is released in situ.
Resistance of thermo-hygro-mechanically densified wood to colonisation and degradation by brown-rot fungi
Authors: Schwarze Francis W.M.R. , Spycher Melanie
Published: April 2005

Colonisation and wood degradation by three brown-rot fungi, Coniophora puteana, Gloeophyllum trabeum and Poria placenta, were studied in wood of Norway spruce (Picea abies) subjected to three different treatments: hygro-thermal (TH) (160 and 180°C), mechanical densification and thermo-hygro-mechanical (THM) treatment including densification and post-treatment under saturated steam conditions at different temperatures (140, 160 and 180°C). The weight loss induced by all three fungi was lowest in THM-densified wood post-treated at 180°C. Highest weight losses were recorded for controls and TH-treated wood. Fungal colonisation varied in its intensity, depending on the treatment applied to the wood. Hyphal growth in controls and TH-treated wood was abundant, whereas in densified and THM-densified wood it was sparse and confined predominantly to the cell lumina of earlywood tracheids. Also, penetration of large-diameter hyphae and associated degradation in THM-densified wood was impeded by occlusion of the lumina, associated with irreversible compression (loss in shape memory). In contrast to C. puteana and P. placenta, which showed typical brown-rot behaviour, G. trabeum frequently showed hyphal tunnelling within the secondary walls of tracheids and xylem ray parenchyma of controls and thermally treated wood. Such growth was never observed in THM-densified wood post-treated at 180°C.
Extracellular Domains of α-Neurexins Participate in Regulating Synaptic Transmission by Selectively Affecting N- and P/Q-Type Ca2+Channels
Authors: Zhang Weiqi , Rohlmann Astrid , Sargsyan Vardanush , Aramuni Gayane , Hammer Robert E. , Südhof Thomas C. , Missler Markus
Published: April 2005

Neurexins constitute a large family of highly variable cell-surface molecules that may function in synaptic transmission and/or synapse formation. Each of the three known neurexin genes encodes two major neurexin variants, α- and β-neurexins, that are composed of distinct extracellular domains linked to identical intracellular sequences. Deletions of one, two, or all three α-neurexins in mice recently demonstrated their essential role at synapses. In multiple α-neurexin knock-outs, neurotransmitter release from excitatory and inhibitory synapses was severely reduced, primarily probably because voltage-dependent Ca2+channels were impaired. It remained unclear, however, which neurexin variants actually influence exocytosis and Ca2+channels, which domain of neurexins is required for this function, and which Ca2+-channel subtypes are regulated. Here, we show by electrophysiological recordings that transgenic neurexin 1α rescues the release and Ca2+-current phenotypes, whereas transgenic neurexin 1β has no effect, indicating the importance of the extracellular sequences for the function of neurexins. Because neurexin 1α rescued the knock-out phenotype independent of the α-neurexin gene deleted, these data are consistent with a redundant function among different α-neurexins. In both knock-out and transgenically rescued mice, α-neurexins selectively affected the component of neurotransmitter release that depended on activation of N- and P/Q-type Ca2+channels, but left L-type Ca2+channels unscathed. Our findings indicate that α-neurexins represent organizer molecules in neurotransmission that regulate N- and P/Q-type Ca2+channels, constituting an essential role at synapses that critically involves the extracellular domains of neurexins.
Mitochondrial Calcium Ion and Membrane Potential Transients Follow the Pattern of Epileptiform Discharges in Hippocampal Slice Cultures
Authors: Kovács Richard , Kardos Julianna , Heinemann Uwe , Kann Oliver
Published: April 2005

Emerging evidence suggests that mitochondrial dysfunction contributes to the pathophysiology of epilepsy. Recurrent mitochondrial Ca2+ion load during seizures might act on mitochondrial membrane potential (ΔΨm) and proton motive force. By using electrophysiology and confocal laser-scanning microscopy, we investigated the effects of epileptiform activity, as induced by low-Mg2+ion perfusion in hippocampal slice cultures, on changes in ΔΨm and in mitochondrial Ca2+ion concentration ([Ca2+]m).

The mitochondrial compartment was identified by monitoring ΔΨm in the soma and dendrites of patched CA3 pyramidal cells using the mitochondria-specific voltage-sensitive dye rhodamine-123 (Rh-123). Interictal activity was accompanied by localized mitochondrial depolarization that was restricted to a few mitochondria in small dendrites. In contrast, robust Rh-123 release into the cytosol was observed during seizure-like events (SLEs), indicating simultaneous depolarization of mitochondria. This was critically dependent on Ca2+ion uptake and extrusion, because inhibition of the mitochondrial Ca2+ion uniporter by Ru360 and the mitochondrial Na+/Ca2+ion exchanger by 7-chloro-5-(2-chlorophenyl)-1,5-dihydro-4,1-benzothiazepin-2(3H)-one but not the inhibitor of mitochondrial permeability transition pore, cyclosporin A, decreased the SLE-associated mitochondrial depolarization.

The Ca2+ion dependence of simultaneous mitochondrial depolarization suggested enhanced Ca2+ion cycling across mitochondrial membranes during epileptiform activity. Indeed, [Ca2+]mfluctuated during interictal activity in single dendrites, and these fluctuations spread over the entire mitochondrial compartment during SLEs, as revealed using mitochondria-specific dyes (rhod-2 and rhod-ff) and spatial frequency-based image analysis. These findings strengthen the hypothesis that epileptic activity results in Ca2+ion-dependent changes in mitochondrial function that might contribute to the neuronal injury during epilepsy.
Activation of Protease-Activated Receptor-1 Triggers Astrogliosis after Brain Injury
Authors: Nicole Olivier , Goldshmidt Anna , Hamill Cecily E. , Sorensen Scott D. , Sastre Aristide , Lyuboslavsky Polina , Hepler John R. , McKeon Robert J. , Traynelis Stephen F.
Published: April 2005

We have studied the involvement of the thrombin receptor [protease-activated receptor-1 (PAR-1)] in astrogliosis, because extravasation of PAR-1 activators, such as thrombin, into brain parenchyma can occur after blood-brain barrier breakdown in a number of CNS disorders.PAR1-/-animals show a reduced astrocytic response to cortical stab wound, suggesting that PAR-1 activation plays a key role in astrogliosis associated with glial scar formation after brain injury. This interpretation is supported by the finding that the selective activation of PAR-1in vivoinduces astrogliosis. The mechanisms by which PAR-1 stimulates glial proliferation appear to be related to the ability of PAR-1 receptor signaling to induce sustained extracellular receptor kinase (ERK) activation. In contrast to the transient activation of ERK by cytokines and growth factors, PAR-1 stimulation induces a sustained ERK activation through its coupling to multiple G-protein-linked signaling pathways, including Rho kinase. This sustained ERK activation appears to regulate astrocytic cyclin D1 levels and astrocyte proliferationin vitroandin vivo. We propose that this PAR-1-mediated mechanism underlying astrocyte proliferation will operate whenever there is sufficient injury-induced blood-brain barrier breakdown to allow extravasation of PAR-1 activators.
Imagined geographies: Sovereignty, indigenous space, and American Indian struggle
Authors: Biolsi Thomas
Published: April 2005

In this article, I seek to complicate scholars' understanding of the “modular” form of the nation‐state by examining four kinds of indigenous political space that figure in contemporary American Indian struggle in the United States: (1) “tribal” or indigenous‐nation sovereignty on reservation homelands; (2) comanagement of off‐reservation resources and sites shared between tribal, federal, and state governments; (3) national indigenous space in which Indian people exercise portable rights beyond reservations; and (4) hybrid political space in which Indian people exercise dual citizenship and assert rights as tribal citizens under treaty and other federal Indian law, as U.S. citizens under the Constitution, and as social or cultural citizens within a multicultural U.S. society.
Gender, power, and the performance of justice: Muslim women's responses to domestic violence in Kazakhstan
Authors: Snajdr Edward
Published: April 2005

The grassroots assistance that Muslim women activists provide to victims of domestic abuse in Kazakhstan differs significantly from approaches commonly used by service providers in the United States. Yet the activists' informal remedies, which are shaped by discourses of religion and ethnicity and which have attracted women who seek something other than safety or formal justice, are implicitly regulated by cultural politics. By examining particular cases, I show how activists prescribe gender ideologies that guide victims' choices while supporting their own group's broader political goals. These findings may help in understanding the dynamics of women's political agency outside the state.
MICROBIAL COUNTS OF DARK RED LATOSOL SAMPLES STORED AT DIFFERENT TEMPERATURES
Authors: Vieira Francisco Cleber Sousa , Nahas Ely
Published: April 2005

The number of colony forming units (CFU) of different groups of bacteria and fungi in samples stored at temperatures of 5 to -12oC for 0-32 weeks was evaluated. The number of CFU obtained after the different periods of storage of red latossol soil was compared with the number of colonies obtained immediately after removal of soil samples (time zero). The number of total bacteria and actinomycetes in the samples remained practically unchanged throughout the storage period. The number of Gram-negative bacteria decreased by as much as 69% compared to control, while the number of Bacillus spp and of fungi increased 1.9 to 4.9 times starting from the 12th week in samples stored at 5oC. Except for the variations observed in fungal counts, the remaining groups of bacteria practically showed the same variation in number of colonies in soil samples stored at 5oC and -12oC.
EVALUATION OF THE VIABILITY OF PLEUROTUS SPP. STRAINS AFTER LIQUID NITROGEN CRYOPRESERVATION
Authors: Lara-Herrera Isabel , Mata Gerardo , Gaitán-Hernández Rigoberto
Published: April 2005

Viability of 6 mushroom strains of the Pleurotus genus (2 from P. djamor var. djamor, 1 from P. ostreatus var. ostreatus, 2 from P. ostreatus var. columbinus and 1 from P. pulmonarius) after liquid nitrogen cryopreservation (-196º) was evaluated. The contact time for the mycelia of these strains with the cryoprotectant (glycerol) was studied 1, 2 and 3 hours before freezing. We also tested the effect of different times (5, 10 and 15 minutes) and temperatures (30, 45 and 60ºC) of the thawing system for mycelial recovery. The results showed a marked tendency toward faster mycelial recovery when samples were thawed at 30ºC, while at 60ºC no recovery was observed. A change in thawing and contact times with the cryoprotectant did not affect the results significantly, as the thawing temperature and strain employed affected.