bluuebunny/crossref_metadata_2025 huggingface dataset:
Role for Mismatch Repair Proteins Msh2, Mlh1, and Pms2 in Immunoglobulin Class Switching Shown by Sequence Analysis of Recombination Junctions
Authors: Schrader Carol E. , Vardo Joycelyn , Stavnezer Janet
Published: July 2002

B cells from mice deficient in mismatch repair (MMR) proteins show decreased ability to undergo class switch recombination in vitro and in vivo. The deficit is not accompanied by any reduction in cell viability or alterations in the cell cycle in B cells cultured in vitro. To assess the role of MMR in switching we examined the nucleotide sequences of Sμ-Sγ3 recombination junctions in splenic B cells induced in culture to switch to IgG3. The data demonstrate clear differences in the sequences of switch junctions in wild-type B cells in comparison with Msh2-, Mlh1-, and Pms2-deficient B cells. Sequences of switch junctions from Msh2-deficient cells showed decreased lengths of microhomology between Sμ and Sγ3 relative to junctions from wild-type cells and an increase in insertions, i.e., nucleotides which do not appear to be derived from either the Sμ or Sγ3 parental sequence. By contrast, 23% of junctions from Mlh1- and Pms2-deficient cells occurred at unusually long stretches of microhomology. The data indicate that MMR proteins are directly involved in class switching and that the role of Msh2 differs from that of Mlh1 and Pms2.
Inward Rectification in ClC-0 Chloride Channels Caused by Mutations in Several Protein Regions
Authors: Ludewig Uwe , Jentsch Thomas J. , Pusch Michael
Published: July 2002

Several cloned ClC-type Cl− channels open and close in a voltage-dependent manner. The Torpedo electric organ Cl− channel, ClC-0, is the best studied member of this gene family. ClC-0 is gated by a fast and a slow gating mechanism of opposite voltage direction. Fast gating is dependent on voltage and on the external and internal Cl− concentration, and it has been proposed that the permeant anion serves as the gating charge in ClC-0 (Pusch, M., U. Ludewig, A. Rehfeldt, and T.J. Jentsch. 1995. Nature (Lond.). 373:527–531). The deactivation at negative voltages of the muscular ClC-1 channel is similar but not identical to ClC-0. Different from the extrinsic voltage dependence suggested for ClC-0, an intrinsic voltage sensor had been proposed to underlie the voltage dependence in ClC-1 (Fahlke, C., R. Rüdel, N. Mitrovic, M. Zhou, and A.L. George. 1995. Neuron. 15:463–472; Fahlke, C., A. Rosenbohm, N. Mitrovic, A.L. George, and R. Rüdel. 1996. Biophys. J. 71:695–706). The gating model for ClC-1 was partially based on the properties of a point-mutation found in recessice myotonia (D136G). Here we investigate the functional effects of mutating the corresponding residue in ClC-0 (D70). Both the corresponding charge neutralization (D70G) and a charge conserving mutation (D70E) led to an inwardly rectifying phenotype resembling that of ClC-1 (D136G). Several other mutations at very different positions in ClC-0 (K165R, H472K, S475T, E482D, T484S, T484Q), however, also led to a similar phenotype. In one of these mutants (T484S) the typical wild-type gating, characterized by a deactivation at negative voltages, can be partially restored by using external perchlorate (ClO4−) solutions. We conclude that gating in ClC-0 and ClC-1 is due to similar mechanisms. The negative charge at position 70 in ClC-0 does not specifically confer the voltage sensitivity in ClC-channels, and there is no need to postulate an intrinsic voltage sensor in ClC-channels.
Effect of Membrane Tension on Gap Junctional Conductance of Supporting Cells in Corti's Organ
Authors: Zhao Hong-Bo , Santos-Sacchi J.
Published: July 2002

The effects of turgor pressure-induced membrane tension on junctional coupling of Hensen cell isolates from the inner ear were evaluated by input capacitance or transjunctional conductance measurement techniques. Turgor pressure was altered by changing either pipette pressure or the osmolarities of extracellular solutions. Both positive pipette pressure and extracellular applications of hypotonic solutions, which caused cell size to concomitantly increase, uncoupled the cells as indicated by reduced input capacitance and transjunctional conductance. These changes were, in many cases, reversible and repeatable. Intracellular application of 50 μM H-7, a broad-based protein kinase inhibitor, and 10 mM BAPTA did not block the uncoupling effect of positive turgor pressure on inner ear gap junctions. The transjunctional conductance at a holding potential of −80 mV was 53.6 ± 5.8 nS (mean ± SEM, n = 9) and decreased ∼40% at a turgor pressure of 1.41 ± 0.05 kPa. Considering the coincident kinetics of cell deformation and uncoupling, we speculate that mechanical forces work directly on gap junctions of the inner ear. These results suggest that pathologies that induce imbalances in cochlear osmotic pressure regulation may compromise normal cochlear homeostasis.
Functional Coupling of Ryanodine Receptors to KCa Channels in Smooth Muscle Cells from Rat Cerebral Arteries
Authors: Pérez Guillermo J. , Bonev Adrian D. , Patlak Joseph B. , Nelson Mark T.
Published: July 2002

The relationship between Ca2+ release (“Ca2+ sparks”) through ryanodine-sensitive Ca2+ release channels in the sarcoplasmic reticulum and KCa channels was examined in smooth muscle cells from rat cerebral arteries. Whole cell potassium currents at physiological membrane potentials (−40 mV) and intracellular Ca2+ were measured simultaneously, using the perforated patch clamp technique and a laser two-dimensional (x–y) scanning confocal microscope and the fluorescent Ca2+ indicator, fluo-3. Virtually all (96%) detectable Ca2+ sparks were associated with the activation of a spontaneous transient outward current (STOC) through KCa channels. A small number of sparks (5 of 128) were associated with currents smaller than 6 pA (mean amplitude, 4.7 pA, at −40 mV). Approximately 41% of STOCs occurred without a detectable Ca2+ spark. The amplitudes of the Ca2+ sparks correlated with the amplitudes of the STOCs (regression coefficient 0.8; P < 0.05). The half time of decay of Ca2+ sparks (56 ms) was longer than the associated STOCs (9 ms). The mean amplitude of the STOCs, which were associated with Ca2+ sparks, was 33 pA at −40 mV. The mean amplitude of the “sparkless” STOCs was smaller, 16 pA. The very significant increase in KCa channel open probability (>104-fold) during a Ca2+ spark is consistent with local Ca2+ during a spark being in the order of 1–100 μM. Therefore, the increase in fractional fluorescence (F/Fo) measured during a Ca2+ spark (mean 2.04 F/Fo or ∼310 nM Ca2+) appears to significantly underestimate the local Ca2+ that activates KCa channels. These results indicate that the majority of ryanodine receptors that cause Ca2+ sparks are functionally coupled to KCa channels in the surface membrane, providing direct support for the idea that Ca2+ sparks cause STOCs.
Going beyond the buzzword: what exactly is CRM?
Authors: Fletcher Lloyd Alan
Published: July 2002

Customer Relationship Management (CRM) is a business strategy for improving profitability by focusing on customer needs and creating an attentive relationship with the customer. It involves a personalized and interactive approach for the entire customer lifecycle. Successful implementation of a CRM approach requires changes in organization structure, culture, and skills, as well as front‐ and back‐office information systems. CRM is a hot topic at the moment, and the marketplace of ‘CRM solutions’ is rife with confusing jargon, grandiose claims, and marketing hyperbole. This article attempts to explain what CRM actually is (and isn't), and provides some suggestions for how you should approach CRM for your business.
Linear systems of plane curves with base points of equal multiplicity
Authors: Ciliberto Ciro , Miranda Rick
Published: July 2002

In this article we address the problem of computing the dimension of the space of plane curves of degree

d
d

with

n
n

general points of multiplicity

m
m

. A conjecture of Harbourne and Hirschowitz implies that when

d
≥
3
m

d \geq 3m

, the dimension is equal to the expected dimension given by the Riemann-Roch Theorem. Also, systems for which the dimension is larger than expected should have a fixed part containing a multiple

(
−
1
)

(-1)

-curve. We reformulate this conjecture by explicitly listing those systems which have unexpected dimension. Then we use a degeneration technique developed to show that the conjecture holds for all

m
≤
12

m \leq 12

.
Novel Mechanism for Regulation of Epidermal Growth Factor Receptor Endocytosis Revealed by Protein Kinase A Inhibition
Authors: Salazar Gloria , González Alfonso
Published: July 2002

Current models put forward that the epidermal growth factor receptor (EGFR) is efficiently internalized via clathrin-coated pits only in response to ligand-induced activation of its intrinsic tyrosine kinase and is subsequently directed into a lysosomal-proteasomal degradation pathway by mechanisms that include receptor tyrosine phosphorylation and ubiquitylation. Herein, we report a novel mechanism of EGFR internalization that does not require ligand binding, receptor kinase activity, or ubiquitylation and does not direct the receptor into a degradative pathway. Inhibition of basal protein kinase A (PKA) activity by H89 and the cell-permeable substrate peptide Myr-PKI induced internalization of 40–60% unoccupied, inactive EGFR, and its accumulation into early endosomes without affecting endocytosis of transferrin and μ-opioid receptors. This effect was abrogated by interfering with clathrin function. Thus, the predominant distribution of inactive EGFR at the plasma membrane is not simply by default but involves a PKA-dependent restrictive condition resulting in receptor avoidance of endocytosis until it is stimulated by ligand. Furthermore, PKA inhibition may contribute to ligand-induced EGFR endocytosis because epidermal growth factor inhibited 26% of PKA basal activity. On the other hand, H89 did not alter ligand-induced internalization of EGFR but doubled its half-time of down-regulation by retarding its segregation into degradative compartments, seemingly due to a delay in the receptor tyrosine phosphorylation and ubiquitylation. Our results reveal that PKA basal activity controls EGFR function at two levels: 1) residence time of inactive EGFR at the cell surface by a process of “endocytic evasion,” modulating the accessibility of receptors to stimuli; and 2) sorting events leading to the down-regulation pathway of ligand-activated EGFR, determining the length of its intracellular signaling. They add a new dimension to the fine-tuning of EGFR function in response to cellular demands and cross talk with other signaling receptors.
Incidence of and Risk Factors for Asymptomatic Peripheral Arterial Occlusive Disease: A Longitudinal Study
Authors: Hooi Jurenne D. , Kester Arnold D. M. , Stoffers Henri E. J. H. , Overdijk Marjori M. , van Ree Jan W. , Knottnerus J. André
Published: July 2002

The current study describes the age- and sex-specific incidence rates and risk factors for asymptomatic and symptomatic peripheral arterial occlusive disease (PAOD) among 2,327 subjects and the incidence of intermittent claudication in asymptomatic PAOD subjects. The study population was selected from 18 general practice centers in the Netherlands. PAOD was assessed with the ankle-brachial blood pressure index, and intermittent claudication was assessed with a modified version of the Rose questionnaire. After 7.2 years, the overall incidence rate for asymptomatic PAOD, using the person-years method, was 9.9 (95% confidence interval (CI): 7.3, 18.8) per 1,000 person-years at risk. The rate was 7.8 (95% CI: 4.9, 20.3) for men and 12.4 (95% CI: 7.7, 24.8) for women. For symptomatic PAOD, the incidence rate was 1.0 (95% CI: 0.7, 7.5) overall, 0.4 (95% CI: 0.3, 10.0) for men, and 1.8 (95% CI: 1.0, 10.3) for women. Multivariate analyses showed that increasing age, smoking, hypertension, and diabetes mellitus were the most important risk factors. The overall incidence rate for intermittent claudication among PAOD subjects who were asymptomatic at baseline was 90.5 per 1,000 person-years at risk (95% CI: 36.4, 378.3). The incidence of asymptomatic PAOD was higher than the incidence of symptomatic PAOD, with women developing PAOD more often than men. In the development of preventive strategies, modification of atherosclerotic risk factors, such as smoking, hypertension, and diabetes, should be the main goals.
Representing metabolic pathway information: an object-oriented approach.
Authors: Ellis L B , Speedie S M , McLeish R
Published: July 2002

MOTIVATION: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. RESULTS: CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. AVAILABILITY: CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.
Genome rearrangement with gene families
Authors: Sankoff David
Published: July 2002

Motivation: The theory and practice of genome rearrangement analysis breaks down in the biologically widespread contexts where each gene may be present in a number of copies, not necessarily contiguous. In some of these contexts it is, however, appropriate to ask which members of each gene family in two genomes G and H, lengths lG and lH, are its true exemplars , i.e. which best reflect the original position of the ancestral gene in the common ancestor genome. This entails a search for the two exemplar strings of same length n (= number of gene families, including singletons), having the smallest possible rearrangement distance: the exemplar distance .

Results: A branch and bound algorithm calculates these distances efficiently when based on easily calculated traditional rearrangement distances, such as signed reversals distance or breakpoint distance, which also satisfy a property of monotonicity in the number of genes. Simulations show that in two random genomes, the expected exemplar distance/n is sensitive to the number and size of gene families, but approaches 1 as the number of singleton families increases. When the basic rearrangement distance is just the number of breakpoints, the expected cost of computing the exemplar breakpoints distance (EBD), as measured by total calls to the underlying breakpoint distance routine, is highly dependent on both n and the configuration of gene families. On the other hand, basing exemplar distance on exemplar reversals distance (ERD), the expected computing cost depends on the configuration of gene families but is not sensitive to n.

Availability: Code for EBD and ERD is available from the author or may be accessed at http://www.crm.umontreal.ca/~viart/exemplar˙dis.html

Contact: sankoff@ere.umontreal.ca
DNA binding sites: representation and discovery
Authors: Stormo Gary D.
Published: July 2002

The purpose of this article is to provide a brief history of the development and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be conveniently divided into two subproblems. The first is, given a collection of known binding sites, develop a representation of those sites that can be used to search new sequences and reliably predict where additional binding sites occur. The second is, given a set of sequences known to contain binding sites for a common factor, but not knowing where the sites are, discover the location of the sites in each sequence and a representation for the specificity of the protein.

Contact: stormo@ural.wustl.edu
Support vector machine classification and validation of cancer
tissue samples using microarray expression data
Authors: Furey Terrence S. , Cristianini Nello , Duffy Nigel , Bednarski David W. , Schummer Michèl , Haussler David
Published: July 2002

Motivation: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and an exploration of the data for mis-labeled or questionable tissue results.

Results: We demonstrate the method in detail on samples consisting of ovarian cancer tissues, normal ovarian tissues, and other normal tissues. The dataset consists of expression experiment results for 97802 cDNAs for each tissue. As a result of computational analysis, a tissue sample is discovered and confirmed to be wrongly labeled. Upon correction of this mistake and the removal of an outlier, perfect classification of tissues is achieved, but not with high confidence. We identify and analyse a subset of genes from the ovarian dataset whose expression is highly differentiated between the types of tissues. To show robustness of the SVM method, two previously published datasets from other types of tissues or cells are analysed. The results are comparable to those previously obtained. We show that other machine learning methods also perform comparably to the SVM on many of those datasets.

Availability: The SVM software is available at http://www.cs.columbia.edu/~bgrundy/svm.

Contact: booch@cse.ucsc.edu

To whom correspondence should be addressed.
TAMBIS: Transparent Access to Multiple Bioinformatics
Information Sources
Authors: Stevens Robert , Baker Patricia , Bechhofer Sean , Ng Gary , Jacoby Alex , Paton Norman W. , Goble Carole A. , Brass Andy
Published: July 2002

Summary: TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics resources. It is based on a model of the knowledge of the concepts and their relationships in molecular biology and bioinformatics.

Availability: TAMBIS is available as an applet from http://img.cs.man.ac.uk/tambis

Supplementary Information: A full user manual, tutorial and videos can be found at http://img.cs.man.ac.uk/tambis.

Contact: tambis@cs.man.ac.uk
Sister-Scanning: a Monte Carlo procedure for assessing signals
in recombinant sequences
Authors: Gibbs Mark J. , Armstrong John S. , Gibbs Adrian J.
Published: July 2002

Motivation: To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals.

Results: We have developed a method, that we call ‘sister-scanning’, for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. A Monte Carlo randomization is done for all columns (positions) within a window and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(Z\) \end{document}-scores are obtained for four real sequences or three real sequences with an outlier that is also randomized. The usefulness of the approach is demonstrated using tobamovirus and luteovirus sequences. Contradictory phylogenetic signals were distinguished in both datasets, as were regions of sequence that contained no clear signal or potentially misleading signals related to compositional similarities. In the tobamovirus dataset, contradictory phylogenetic signals were separated by coding sequences up to a kilobase long that contained no clear signal. Our re-analysis of this dataset using sister-scanning also yielded the first evidence known to us of an inter-species recombination site within a viral RNA-dependent RNA polymerase gene together with evidence of an unusual pattern of conservation in the three codon positions.

Availability: A program package, SiScan, for use under MS-DOS can be downloaded from http://life.anu.edu.au/with test data and instructions.

Contact: mgibbs@rsbs.anu.edu.au; johna@rsbs.anu.edu.au; gibbs@rsbs.anu.edu.au

* To whom correspondence should be addressed.
How to reconstruct a large genetic network from
n gene perturbations in fewer than
n2 easy steps
Authors: Wagner Andreas
Published: July 2002

Motivation: The reconstruction of genetic networks is the holy grail of functional genomics. Its core task is to identify the causal structure of a gene network, that is, to distinguish direct from indirect regulatory interactions among gene products. In other words, to reconstruct a genetic network is to identify, for each network gene, which other genes and their activity the gene influences directly. Crucial to this task are perturbations of gene activity. Genomic technology permits large-scale experiments perturbing the activity of many genes and assessing the effect of each perturbation on all other genes in a genome. However, such experiments cannot distinguish between direct and indirect effects of a genetic perturbation.

Results: I present an algorithm to reconstruct direct regulatory interactions in gene networks from the results of gene perturbation experiments. The algorithm is based on a graph representation of genetic networks and applies to networks of arbitrary size and complexity. Algorithmic complexity in both storage and time is low, less than O(n2). In practice, the algorithm can reconstruct networks of several thousand genes in mere CPU seconds on a desktop workstation.

Availability: A perl implementation of the algorithm is given in the Appendix.

Contact: wagnera@unm.edu
Aligning gene expression time series with time warping

algorithms
Authors: Aach John , Church George M.
Published: July 2002

Motivation: Increasingly, biological processes are being studied through time series of RNA expression data collected for large numbers of genes. Because common processes may unfold at varying rates in different experiments or individuals, methods are needed that will allow corresponding expression states in different time series to be mapped to one another.

Results: We present implementations of time warping algorithms applicable to RNA and protein expression data and demonstrate their application to published yeast RNA expression time series. Programs executing two warping algorithms are described, a simple warping algorithm and an interpolative algorithm, along with programs that generate graphics that visually present alignment information. We show time warping to be superior to simple clustering at mapping corresponding time states. We document the impact of statistical measurement noise and sample size on the quality of time alignments, and present issues related to statistical assessment of alignment quality through alignment scores. We also discuss directions for algorithm improvement including development of multiple time series alignments and possible applications to causality searches and non-temporal processes (‘concentration warping’).

Availability: Academic implementations of alignment programs genewarp and genewarpi and the graphics generation programs grphwarp and grphwarpi are available as Win32 system DOS box executables on our web site along with documentation on their use. The publicly available data on which they were demonstrated may be found at http://genome-www.stanford.edu/cellcycle/. Postscript files generated by grphwarp and grphwarpi may be directly printed or viewed using GhostView software available at http://www.cs.wisc.edu/~ghost/.

Contact: church@arep.med.harvard.edu

Supplementary information: http://arep.med.harvard.edu/timewarp/supplement.htm.

* To whom correspondence should be addressed.
PROMO: detection of known transcription regulatory elements
using species-tailored searches
Authors: Messeguer Xavier , Escudero Ruth , Farré Domènec , Núñez Oscar , Martı́nez Javier , Albà M.Mar
Published: July 2002

Summary: We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences.

Availability: PROMO can be accessed online at http://www.lsi.upc.es/~alggen under the research link.

Supplementary information: An example of the graphic interface (Figure 1) can be visualized at http://www.lsi.upc.es/~alggen/recerca/promo/figuraBioinformatics.html.

Contact: peypoch@lsi.upc.es; m.alba@ucl.ac.uk

* To whom correspondence should be addressed.
A redox‐dependent interaction between two electron‐transfer partners involved in photosynthesis
Authors: Morales Renaud , Charon Marie‐Hélène , Kachalova Galina , Serre Laurence , Medina Milagros , Gómez‐Moreno Carlos , Frey Michel
Published: July 2002

Ferredoxin:NADP+:reductase (FNR) catalyzes one terminal step of the conversion of light energy into chemical energy during photosynthesis. FNR uses two high energy electrons photoproduced by photosystem I (PSI) and conveyed, one by one, by a ferredoxin (Fd), to reduce NADP+ to NADPH. The reducing power of NADPH is finally involved in carbon assimilation. The interaction between oxidized FNR and Fd was studied by crystallography at 2.4 Å resolution leading to a three‐dimensional picture of an Fd–FNR biologically relevant complex. This complex suggests that FNR and Fd specifically interact prior to each electron transfer and disassemble upon a redox‐linked conformational change of the Fd.
Finding nuclear localization signals
Authors: Cokol Murat , Nair Rajesh , Rost Burkhard
Published: July 2002

A variety of nuclear localization signals (NLSs) are experimentally known although only one motif was available for database searches through PROSITE. We initially collected a set of 91 experimentally verified NLSs from the literature. Through iterated ‘in silico mutagenesis’ we then extended the set to 214 potential NLSs. This final set matched in 43% of all known nuclear proteins and in no known non‐nuclear protein. We estimated that >17% of all eukaryotic proteins may be imported into the nucleus. Finally, we found an overlap between the NLS and DNA‐binding region for 90% of the proteins for which both the NLS and DNA‐binding regions were known. Thus, evolution seemed to have used part of the existing DNA‐binding mechanism when compartmentalizing DNA‐binding proteins into the nucleus. However, only 56 of our 214 NLS motifs overlapped with DNA‐binding regions. These 56 NLSs enabled a de novo prediction of partial DNA‐binding regions for ∼800 proteins in human, fly, worm and yeast.
ASK1 is required for sustained activations of JNK/p38 MAP kinases and apoptosis
Authors: Tobiume Kei , Matsuzawa Atsushi , Takahashi Takumi , Nishitoh Hideki , Morita Kei‐ichi , Takeda Kohsuke , Minowa Osamu , Miyazono Kohei , Noda Tetsuo , Ichijo Hidenori
Published: July 2002

Apoptosis signal‐regulating kinase (ASK) 1 is activated in response to various cytotoxic stresses including TNF, Fas and reactive oxygen species (ROS) such as H2O2, and activates c‐Jun NH2‐terminal kinase (JNK) and p38. However, the roles of JNK and p38 signaling pathways during apoptosis have been controversial. Here we show that by deleting ASK1 in mice, TNF‐ and H2O2‐induced sustained activations of JNK and p38 are lost in ASK1−/− embryonic fibroblasts, and that ASK1−/− cells are resistant to TNF‐ and H2O2‐induced apoptosis. TNF‐ but not Fas‐induced apoptosis requires ROS‐dependent activation of ASK1–JNK/p38 pathways. Thus, ASK1 is selectively required for TNF‐ and oxidative stress‐induced sustained activations of JNK/p38 and apoptosis.
Histone acetylation: a switch between repressive and permissive chromatin
Authors: Eberharter Anton , Becker Peter B
Published: July 2002

The organization of eukaryotic chromatin has a major impact on all nuclear processes involving DNA substrates. Gene expression is affected by the positioning of individual nucleosomes relative to regulatory sequence elements, by the folding of the nucleosomal fiber into higher‐order structures and by the compartmentalization of functional domains within the nucleus. Because site‐specific acetylation of nucleosomal histones influences all three aspects of chromatin organization, it is central to the switch between permissive and repressive chromatin structure. The targeting of enzymes that modulate the histone acetylation status of chromatin, in synergy with the effects mediated by other chromatin remodeling factors, is central to gene regulation.
Randomized, placebo-controlled studies of inhaled zanamivir in the treatment of influenza
A and B: pooled efficacy analysis
Authors: Monto A. S. , Webster A. , Keene O.
Published: July 2002

Zanamivir, a potent, highly selective inhibitor of influenza virus A and B neuraminidase, has been evaluated in seven, similarly designed, placebo-controlled studies of the treatment of influenza. Patients with typical influenza symptoms were recruited when influenza was known to be circulating in the community. Six of these studies included a zanamivir 10 mg inhaled bd (for 5 days) treatment arm, the dose regimen submitted to regulatory agencies. Pooled analyses were conducted to evaluate efficacy more precisely in terms of the alleviation of symptoms in population subgroups and for secondary endpoints. Median time to alleviation of symptoms, the primary endpoint, was reduced from 6.0 days in the placebo group (n = 1102) to 5.0 days in the zanamivir group (n = 1133), P < 0.001. In febrile, laboratory-confirmed, influenza-positive (IP) patients, time to alleviation was reduced from 6.5 days to 5.0 days, a treatment benefit of 1.5 days (P < 0.001). A larger treatment benefit (3 days) was seen in IP patients who had severe symptoms at entry (n = 474, P < 0.001), compared with 1 day in patients whose symptoms were not severe (n = 1098, P < 0.001). Similarly, a 3 day treatment benefit (P = 0.003) was observed in IP patients aged <50 years (n = 263), compared with 1 day (P < 0.001) in patients aged <50 years. In‘ high-risk’ IP patients (recruited into all treatment studies), there was a treatment benefit of 2.5 days (n = 305, P = 0.006). Pooled analyses of secondary endpoints showed statistically significant reductions in antibiotic use, time to return to normal activities and use of relief medication. In addition, reductions in symptom scores were apparent shortly after commencing zanamivir treatment. By the evening of the second day of treatment, the median total symptom score had fallen by 44% in zanamivir recipients compared with 33% in placebo recipients (P < 0.001). These results highlight the groups likely to show greatest benefit from zanamivir treatment, and confirm the clinical relevance of the treatment benefit.
Formation of Diatexite Migmatite and Granite Magma during Anatexis of Semi-pelitic Metasedimentary Rocks: an Example from St. Malo, France
Authors: MILORD I. , SAWYER E. W. , BROWN M.
Published: July 2002

Petrological and geochemical variations are used to investigate the formation of granite magma from diatexite migmatites derived from metasedimentary rocks of pelitic to greywacke composition at St. Malo, France. Anatexis occurred at relatively low temperatures and pressures (<800°C, 4–7 kbar), principally through muscovite dehydration melting. Biotite remained stable and serves as a tracer for the solid fraction during melt segregation. The degree of partial melting, calculated from modal mineralogy and reaction stoichiometry, was <40 vol. %. There is a continuous variation in texture, mineralogy and chemical composition in the diatexite migmatites. Mesocratic diatexite formed when metasedimentary rocks melted sufficiently to undergo bulk flow or magma flow, but did not experience significant melt–residuum separation. Mesocratic diatexite that underwent melt segregation during flow generated (1) melanocratic diatexites at the places where the melt fraction was removed, leaving behind a biotite and plagioclase residuum (enriched in TiO2, FeOT, MgO, CaO, Sc, Ni, Cr, V, Zr, Hf, Th, U and REE), and (2) a complementary leucocratic diatexite (enriched in SiO2, K2O and Rb) where the melt fraction accumulated. Leucocratic diatexite still contained 5–15 vol. % residual biotite (mg-number 40–44) and 10–20 vol. % residual plagioclase (An22). Anatectic granite magma developed from the leucodiatexite, first by further melt–residuum separation, then through fractional crystallization. Most biotite in the anatectic granite is magmatic (mg-number 18–22).
Quality control in the secretory assembly line
Authors: Helenius Ari
Published: July 2002

As a rule, only proteins that have reached a native, folded and assembled structure are transported to their target organelles and compartments within the cell. In the secretory pathway of eukaryotic cells, this type of sorting is particularly important. A variety of molecular mechanisms are involved that distinguish between folded and unfolded proteins, modulate their intracellular transport, and induce degradation if they fail to fold. This phenomenon, called quality control, occurs at several levels and involves different types of folding sensors. The quality control system provides a stringent and versatile molecular sorting system that guaranties fidelity of protein expression in the secretory pathway.
Ectopic expression of a Chlamydomonas mt+-specific homeodomain protein in mt− gametes initiates zygote development without gamete fusion
Authors: Zhao Hui , Lu Min , Singh Ritu , Snell William J.
Published: July 2002

The molecular mechanisms that activate expression of zygote genes after fertilization are obscure. In animals, receptor-ligand interactions during sperm–egg membrane fusion as well as delivery of putative regulatory molecules by the sperm into the egg cytoplasm are proposed to activate zygote development and subsequent transcription of zygote genes. The mechanisms of activation of zygote development in higher plants also are mysterious, in part because of the difficulty of isolating female gametes of higher plants. In the unicellular, biflagellated green alga Chlamydomonas, the early steps in zygote development are much more accessible to investigation. Within minutes after mating type plus (mt+) and mating type minus (mt−) gametes fuse, expression of several zygote-specific transcripts is induced independently of protein synthesis. Here, we show that ectopic expression in mt− gametes of an mt+ gamete-specific, homeodomain protein, GSP1, induces a zygote-like phenotype and activates expression of zygote genes. One of the genes, zsp2, expressed in these “haploid zygotes” encodes a zygote cell surface adhesion molecule that promotes formation of multicellular aggregates. In total, expression of six out of seven zygote genes examined was induced by ectopic expression of GSP1. Our experiments show that in addition to contributing their genomes to the zygote cytoplasm, gametes also deliver proteins that can activate gene transcription.
A Gene Expression Screen in Zebrafish Embryogenesis
Authors: Kudoh Tetsuhiro , Tsang Michael , Hukriede Neil A. , Chen Xiongfong , Dedekian Michael , Clarke Christopher J. , Kiang Anne , Schultz Stephanie , Epstein Jonathan A. , Toyama Reiko , Dawid Igor B.
Published: July 2002

A screen for developmentally regulated genes was conducted in the zebrafish, a system offering substantial advantages for the study of the molecular genetics of vertebrate embryogenesis. Clones from a normalized cDNA library from early somitogenesis stages were picked randomly and tested by high-throughput in situ hybridization for restricted expression in at least one of four stages of development. Among 2765 clones that were screened, a total of 347 genes with patterns judged to be restricted were selected. These clones were subjected to partial sequence analysis, allowing recognition of functional motifs in 163 among them. In addition, a portion of the clones were mapped with the aid of the LN54 radiation hybrid panel. The usefulness of the in situ hybridization screening approach is illustrated by describing several new markers for the characteristic structure in the fish embryo named the yolk syncytial layer, and for different regions of the developing brain.
Brain Activity During the Encoding, Retention, and Retrieval of Stimulus Representations
Authors: de Zubicaray Greig I. , McMahon Katie , Wilson Stephen J. , Muthiah Santhi
Published: July 2002

Studies of delayed nonmatching-to-sample (DNMS) performance following lesions of the monkey cortex have revealed a critical circuit of brain regions involved in forming memories and retaining and retrieving stimulus representations. Using event-related functional magnetic resonance imaging (fMRI), we measured brain activity in 10 healthy human participants during performance of a trial-unique visual DNMS task using novel barcode stimuli. The event-related design enabled the identification of activity during the different phases of the task (encoding, retention, and retrieval). Several brain regions identified by monkey studies as being important for successful DNMS performance showed selective activity during the different phases, including the mediodorsal thalamic nucleus (encoding), ventrolateral prefrontal cortex (retention), and perirhinal cortex (retrieval). Regions showing sustained activity within trials included the ventromedial and dorsal prefrontal cortices and occipital cortex. The present study shows the utility of investigating performance on tasks derived from animal models to assist in the identification of brain regions involved in human recognition memory.
Effect of Age and Level of Cognitive Function on Spontaneous and Exploratory Behaviors in the Beagle Dog
Authors: Siwak Christina T. , Tapp P. Dwight , Milgram Norton W.
Published: July 2002

Cognitively characterized young and aged beagle dogs were administered six different spontaneous behavior tests, which provided measures of locomotion, exploration, and social interaction. Consistent with our previous findings, we obtained no overall effect of age on locomotion. We did find, however, that for the aged dogs locomotion correlated with level of cognitive function, being lowest in age-unimpaired dogs and highest in impaired dogs. Exploratory behavior, as measured by response to novelty, varied with age, with young dogs scoring the highest. Young dogs spent more time with novel toys and a person, responded more to a silhouette of a dog, and interacted more with a model dog compared to aged dogs. Among the aged dogs, age-unimpaired dogs spent the greatest amount of time sitting or standing beside a person whereas age-impaired dogs spent the most time reacting to a reflection in a mirror. The age-impaired dogs show undirected, stereotypical types of behavioral patterns. These differences in activity patterns may be linked to underlying age-associated neuropathology.
Natively unfolded proteins: A point where biology waits for physics
Authors: Uversky Vladimir N.
Published: July 2002

The experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder–order transition during or prior to their biological function. In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.
ECG‐correlated image reconstruction from subsecond multi‐slice spiral CT scans of the heart
Authors: Kachelrieß Marc , Ulzheimer Stefan , Kalender Willi A.
Published: July 2002

Subsecond spiral computed tomography (CT) offers great potential for improving heart imaging. The new multi‐row detector technology adds significantly to this potential. We therefore developed and validated dedicated cardiac reconstruction algorithms for imaging the heart with subsecond multi‐slice spiral CT utilizing electrocardiogram (ECG) information. The single‐slice cardiacz‐interpolation algorithms 180°CI and 180°CD [Med. Phys.25, 2417–2431 (1998)] were generalized to allow imaging of the heart forM‐slice scanners. Two classes of algorithms were investigated: 180°MCD (multi‐slice cardio delta), a partial scan reconstruction ofdata with(fan angle) resulting in effective scan times of 250 ms (central ray) when a 0.5 s rotation mode is available, and 180°MCI (multi‐slice cardio interpolation), a piecewise weighted interpolation between successive spiral data segments belonging to the same heart phase, potentially providing a relative temporal resolution of 12.5% of the heart cycle when a four‐slice scanner is used and the table increment is chosen to be greater than or equal to the collimated slice thickness. Data segments are selected by correlation with the simultaneously recorded ECG signal. Theoretical studies, computer simulations, as well as patient measurements were carried out for a multi‐slice scanner providingslices to evaluate these new approaches and determine the optimal scan protocol. Both algorithms, 180°MCD and 180°MCI, provide significant improvements in image quality, including extremely arythmic cases. Artifacts in the reconstructed images as well as in 3D displays such as multiplanar reformations were largely reduced as compared to the standardz‐interpolation algorithm 180°MLI (multi‐slice linear interpolation). Image quality appears adequate for precise calcium scoring and CT angiography of the coronary arteries with conventional subsecond multi‐slice spiral CT. It turned out that for heart ratesthe partial scan approach 180°MCD yields unsatisfactory results as compared to 180°MCI. Our theoretical considerations show that a freely selectable scanner rotation time chosen as a function of the patient's heart rate, would further improve the relative temporal resolution and thus further reduce motion artifacts. In our case an additional 0.6 s mode besides the available 0.5 s mode would be very helpful. Moreover, if technically feasible, lower rotation times such as 0.3 s or even less would result in improved image quality. The use of multi‐slice techniques for cardiac CT together with the newz‐interpolation methods improves the quality of heart imaging significantly. The high temporal resolution of 180°MCI is adequate for spatial and temporal tracking of anatomic structures of the heart (4D reconstruction).
Monte Carlo and experimental investigations of multileaf collimated electron beams for modulated electron radiation therapy
Authors: Lee Michael C. , Jiang Steve B. , Ma C.‐M.
Published: July 2002

Modulated electron radiation therapy (MERT) has been proposed as a means of delivering conformal dose to shallow tumors while sparing distal structures and surrounding tissues. Conventional systems for electron beam collimation are labor and time intensive in their construction and are therefore inadequate for use in the sequential delivery of multiple complex fields required by MERT. This study investigates two proposed methods of electron beam collimation: the use of existing photon multileaf collimators (MLC) in a helium atmosphere to reduce in‐air electron scatter, and a MLC specifically designed for electron beam collimation. Monte Carlo simulations of a Varian Clinac 2100C were performed using the EGS4/BEAM system and dose calculations performed with the MCDOSE code. Dose penumbras from fields collimated by photon MLCs both with air and with helium at 6, 12, and 20 MeV at a range of SSDs from 70 to 90 cm were examined. Significant improvements were observed for the helium based system. Simulations were also performed on an electron specific MLC located at the level of the last scraper of a 25×25 cm2applicator. A number of leaf materials, thicknesses, end shapes, and widths were simulated to determine optimal construction parameters. The results demonstrated that tungsten leaves 15 mm thick and 5 mm wide with unfocused ends would provide sufficient collimation for MERT fields. A prototype electron MLC was constructed and comparisons between film measurements and simulation demonstrate the validity of the Monte Carlo model. Further simulations of dose penumbras demonstrate that such an electron MLC would provide improvements over the helium filled photon MLC at all energies, and improvements in the 90–10 penumbra of 12% to 45% at 20 MeV and 6 MeV, respectively. These improvements were also seen in isodose curves when a complex field shape was simulated. It is thus concluded that an MLC specific for electron beam collimation is required for MERT.
Patterns of periodic infrared light emission from the human body: A new diagnostic tool
Authors: Tributsch H. , Huenemoerder M.
Published: July 2002

The human body emits infrared light with the periodicity of the heartbeat. The infrared thermal emission occurs in characteristic patterns which, after the heartbeat, migrate over the body. The images are obtained by using the electrocardiographic signal as a trigger to produce a thermal image which is subtracted from another one taken a well defined time later, before the next heart impulse. When these difference images are frequently repeated and averaged a heart pulse induced heat turnover is determined which has no relation to conventional heat images of the human body. Preliminary studies suggest that basically the heat turnover is seen in tissues where oxygen consumption leads to the turnover of chemical energy. When further developed, the proposed technique may provide a novel noninterfering and economically well affordable diagnostic tool for the examination of the external surface of the human body.
A systematic Monte Carlo study of secondary electron fluence perturbation in clinical proton beams (70–250 MeV) for cylindrical and spherical ion chambers
Authors: Verhaegen Frank , Palmans Hugo
Published: July 2002

Current dosimetry protocols for clinical protons do not take into account any secondary electron fluence perturbation in ion chambers. In this work, we performed a systematic study of secondary electron fluence perturbation factors for spherical and cylindrical ion chambers in proton beams (70–250 MeV). The electron fluence perturbation factor,was calculated using Monte Carlo transport of protons and secondary electrons. The influence of proton energy, cavity wall material (graphite, water, A150, PMMA, polystyrene), cavity radius, cavity wall thickness and positioning depth in water is studied. The influence of inelastic nuclear proton interactions is briefly discussed. It was found thatdepends on wall material; the largest values forwere obtained for ion chambers with A150 wallsthe smallest values for graphite walls. The perturbation factor was found to be largely independent of proton energy. A slight decrease ofwith cavity radius was obtained, especially for low energy protons. The wall thickness was found to have no effect onin the range studied (0.025–0.1 cm). The depth of the cavity in a water phantom was also found to have an insignificant effect onBased on the results in the paper for spherical and cylindrical ion chambers, a method to calculatefor a thimble ion chamber is presented. The results presented in this paper for cylindrical and spherical ion chambers are in contradiction to the calculated electron fluence perturbation factors for planar ion chambers in the paper by Casnati et al.