bluuebunny/crossref_metadata_2025 huggingface dataset:
Dopamine-induced Exocytosis of Na,K-ATPase Is Dependent on Activation of Protein Kinase C-ε and -δ
Authors: Ridge Karen M. , Dada Laura , Lecuona Emilia , Bertorello Alejandro M. , Katz Adrian I. , Mochly-Rosen Daria , Sznajder Jacob I.
Published: July 2002

The purpose of this study was to define mechanisms by which dopamine (DA) regulates the Na,K-ATPase in alveolar epithelial type 2 (AT2) cells. The Na,K-ATPase activity increased by twofold in cells incubated with either 1 μM DA or a dopaminergic D1agonist, fenoldopam, but not with the dopaminergic D2agonist quinpirole. The increase in activity paralleled an increase in Na,K-ATPase α1 and β1 protein abundance in the basolateral membrane (BLM) of AT2 cells. This increase in protein abundance was mediated by the exocytosis of Na,K-pumps from late endosomal compartments into the BLM. Down-regulation of diacylglycerol-sensitive types of protein kinase C (PKC) by pretreatment with phorbol 12-myristate 13-acetate or inhibition with bisindolylmaleimide prevented the DA-mediated increase in Na,K-ATPase activity and exocytosis of Na,K-pumps to the BLM. Preincubation of AT2 cells with either 2-[1-(3-dimethylaminopropyl)-5-methoxyindol-3-yl]-3-(1H-indol-3-yl)maleimide (Gö6983), a selective inhibitor of PKC-δ, or isozyme-specific inhibitor peptides for PKC-δ or PKC-ε inhibited the DA-mediated increase in Na,K-ATPase. PKC-δ and PKC-ε, but not PKC-α or -β, translocated from the cytosol to the membrane fraction after exposure to DA. PKC-δ– and PKC-ε–specific peptide agonists increased Na,K-ATPase protein abundance in the BLM. Accordingly, dopamine increased Na,K-ATPase activity in alveolar epithelial cells through the exocytosis of Na,K-pumps from late endosomes into the basolateral membrane in a mechanism-dependent activation of the novel protein kinase C isozymes PKC-δ and PKC-ε.
DictyosteliumLvsB Mutants Model the Lysosomal Defects Associated with Chediak-Higashi Syndrome
Authors: Harris Edward , Wang Ning , Wu Wei-l , Weatherford Alisha , De Lozanne Arturo , Cardelli James
Published: July 2002

Chediak-Higashi syndrome is a genetic disorder caused by mutations in a gene encoding a protein named LYST in humans (“lysosomal trafficking regulator”) or Beige in mice. A prominent feature of this disease is the accumulation of enlarged lysosome-related granules in a variety of cells. The genome of Dictyostelium discoideumcontains six genes encoding proteins that are related to LYST/Beige in amino acid sequence, and disruption of one of these genes,lvsA (large volumesphere), results in profound defects in cytokinesis. To better understand the function of this family of proteins in membrane trafficking, we have analyzed mutants disrupted in lvsA, lvsB, lvsC, lvsD, lvsE, and lvsF. Of all these, onlylvsA and lvsB mutants displayed interesting phenotypes in our assays. lvsA-null cells exhibited defects in phagocytosis and contained abnormal looking contractile vacuole membranes. Loss of LvsB, theDictyostelium protein most similar to LYST/Beige, resulted in the formation of enlarged vesicles that by multiple criteria appeared to be acidic lysosomes. The rates of endocytosis, phagocytosis, and fluid phase exocytosis were normal inlvsB-null cells. Also, the rates of processing and the efficiency of targeting of lysosomal α-mannosidase were normal, although lvsB mutants inefficiently retained α-mannosidase, as well as two other lysosomal cysteine proteinases. Finally, results of pulse-chase experiments indicated that an increase in fusion rates accounted for the enlarged lysosomes inlvsB-null cells, suggesting that LvsB acts as a negative regulator of fusion. Our results support the notion that LvsB/LYST/Beige function in a similar manner to regulate lysosome biogenesis.
Cox18p Is Required for Export of the Mitochondrially EncodedSaccharomyces cerevisiaeCox2p C-Tail and Interacts with Pnt1p and Mss2p in the Inner Membrane
Authors: Saracco Scott A. , Fox Thomas D.
Published: July 2002

The amino- and carboxy-terminal domains of mitochondrially encoded cytochrome c oxidase subunit II (Cox2p) are translocated out of the matrix to the intermembrane space. We have carried out a genetic screen to identify components required to export the biosynthetic enzyme Arg8p, tethered to the Cox2p C terminus by a translational gene fusion inserted into mtDNA. We obtained multiple alleles of COX18, PNT1, and MSS2, as well as mutations in CBP1 and PET309. Focusing on Cox18p, we found that its activity is required to export the C-tail of Cox2p bearing a short C-terminal epitope tag. This is not a consequence of reduced membrane potential due to loss of cytochrome oxidase activity because Cox2p C-tail export was not blocked in mitochondria lacking Cox4p. Cox18p is not required to export the Cox2p N-tail, indicating that these two domains of Cox2p are translocated by genetically distinct mechanisms. Cox18p is a mitochondrial integral inner membrane protein. The inner membrane proteins Mss2p and Pnt1p both coimmunoprecipitate with Cox18p, suggesting that they work together in translocation of Cox2p domains, an inference supported by functional interactions among the three genes.
Gene selection for sample classification based on gene
expression data: study of sensitivity to choice of parameters of the
GA/KNN method
Authors: Li Leping , Weinberg Clarice R. , Darden Thomas A. , Pedersen Lee G.
Published: July 2002

Motivation: We recently introduced a multivariate approach that selects a subset of predictive genes jointly for sample classification based on expression data. We tested the algorithm on colon and leukemia data sets. As an extension to our earlier work, we systematically examine the sensitivity, reproducibility and stability of gene selection/sample classification to the choice of parameters of the algorithm.

Methods: Our approach combines a Genetic Algorithm (GA) and the k-Nearest Neighbor (KNN) method to identify genes that can jointly discriminate between different classes of samples (e.g. normal versus tumor). The GA/KNN method is a stochastic supervised pattern recognition method. The genes identified are subsequently used to classify independent test set samples.

Results: The GA/KNN method is capable of selecting a subset of predictive genes from a large noisy data set for sample classification. It is a multivariate approach that can capture the correlated structure in the data. We find that for a given data set gene selection is highly repeatable in independent runs using the GA/KNN method. In general, however, gene selection may be less robust than classification.

Availability: The method is available at http://dir.niehs.nih.gov/microarray/datamining

Contact: LI3@niehs.nih.gov

* To whom correspondence should be addressed.
An information-based sequence distance and its application to
whole mitochondrial genome phylogeny
Authors: Li Ming , Badger Jonathan H. , Chen Xin , Kwong Sam , Kearney Paul , Zhang Haoyong
Published: July 2002

Motivation: Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance.

Results: We establish the mathematical foundations of our distance and illustrate its use by constructing a phylogeny of the Eutherian orders using complete unaligned mitochondrial genomes. This phylogeny is consistent with the commonly accepted one for the Eutherians. A second, larger mammalian dataset is also analyzed, yielding a phylogeny generally consistent with the commonly accepted one for the mammals.

Availability: The program to estimate our sequence distance, is available at http://www.cs.cityu.edu.hk/~cssamk/gencomp/GenCompress1.htm. The distance matrices used to generate our phylogenies are available at http://www.math.uwaterloo.ca/~mli/distance.html

Contact: mli@wh.math.uwaterloo.ca

* To whom correspondence should be addressed.
VALUING REDUCED RISKS TO CHILDREN: THE CASE OF BICYCLE SAFETY HELMETS
Authors: Jenkins Robin R. , Owens Nicole , Wiggins Lanelle Bembenek
Published: July 2002

The protection of children's health has recently become a mandated priority for federal policy makers. To assess many of the regulations that affect children's health, policy makers need estimates of the monetary value of reducing mortality risks to children. Although the economics literature has provided many estimates of the value of statistical life (VSL) for adult populations, it has provided none for school age children. This article studies the market for bicycle safety helmets and estimates for the first time a separate but comparable VSL for children and adults. We derive three estimates of VSL for each of three age categories (5 to 9, 10 to 14, and 20 to 59) that range from $1.1 to $4.0 million. In all cases, estimates for adults are highest, followed by estimates for the youngest children.
Electron cryo‐microscopy and image reconstruction of adeno‐associated virus type 2 empty capsids
Authors: Kronenberg Stephanie , Kleinschmidt Jürgen A , Böttcher Bettina
Published: July 2002

Adeno‐associated virus type 2 empty capsids are composed of three proteins, VP1, VP2 and VP3, which have relative molecular masses of 87, 72 and 62 kDa, respectively, and differ in their N‐terminal amino acid sequences. They have a likely molar ratio of 1:1:8 and occupy symmetrical equivalent positions in an icosahedrally arranged protein shell. We have investigated empty capsids of adeno‐associated virus type 2 by electron cryo‐microscopy and icosahedral image reconstruction. The three‐dimensional map at 1.05 nm resolution showed sets of three elongated spikes surrounding the three‐fold symmetry axes and narrow empty channels at the five‐fold axes. The inside of the capsid superimposed with the previously determined structure of the canine parvovirus (Q. Xie and M.S. Chapman, 1996, J. Mol. Biol., 264, 497–520), whereas the outer surface showed clear discrepancies. Globular structures at the inner surface of the capsid at the two‐fold symmetry axes were identified as possible positions for the N‐terminal extensions of VP1 and VP2.
H2O2‐induced block of glycolysis as an active ADP‐ribosylation reaction protecting cells from apoptosis
Authors: Colussi C. , Albertini M.C. , Coppola S. , Rovidati S. , Galli F. , Ghibelli L.
Published: July 2002

ABSTRACT H2O2 treatment on U937 cells leads to the block of glycolytic flux and the inactivation of glyceraldehyde‐3‐phosphate‐dehydrogenase by a posttranslational modification (possibly ADP‐ribosylation). Glycolysis spontaneously reactivates after 2 h of recovery from oxidative stress; thereafter cells begin to undergo apoptosis. The specific ADP‐ribosylation inhibitor 3‐aminobenzamide inhibits the stress‐induced inactivation of glyceraldehyde‐3‐phosphate‐dehydrogenase and the block of glycolysis; concomitantly, it anticipates and increases apoptosis. Exogenous block of glycolysis (i.e., by culture in glucose‐free medium or with glucose analogs or after NAD depletion), turns the transient block into a stable one: this results in protection from apoptosis, even when downstream cell metabolism is kept active by the addition of pyruvate. All this evidence indicates that the stress‐induced block of glycolysis is not the result of a passive oxidative damage, but rather an active cell reaction programmed via ADP‐ribosylation for cell self‐defense.—Colussi, C., Albertini, M. C., Coppola, S., Rovidati, S., Galli, F., Ghibelli, L. H2O2‐induced block of glycolysis as an active ADP‐ribosylation reaction protecting cells from apoptosis. FASEB J. 14, 2266‐2276 (2000)
C‐peptide inhibits leukocyte‐endothelium interaction in the microcirculation during acute endothelial dysfunction
Authors: Scalia Rosario , Coyle Kathleen M. , Levine Brian J. , Booth Gregory , Lefer Allan M.
Published: July 2002

C‐peptide is a cleavage product that comes from processing proinsulin to insulin that induces nitric oxide (NO) ‐mediated vasodilation. NO modulates leukocyte‐endothelium interaction. We hypothesized that C‐peptide might inhibit leukocyte‐endothelium interaction via increased release of endothelial NO. Using intravital microscopy of the rat mesentery, we measured leukocyte‐ endothelium interactions after administration of C‐peptide to the rat. Superfusion of the rat mesentery with either thrombin or L‐NAME consistently and significantly increased the number of rolling, adhering, and transmigrated leukocytes. C‐peptide significantly attenuated either thrombin‐ or L‐NAME‐induced leukocyte‐endothelium interactions in rat mesenteric venules. A control scrambled sequence of C‐peptide characterized by the same amino acid composition in a randomized sequence failed to inhibit leukocyte‐endothelium interactions. These effects of C‐peptide were associated with decreased surface expression of the cell adhesion molecules P‐selectin and ICAM‐1 on the microvascular endothelium. Endothelial nitric oxide synthase (eNOS) mRNA levels were increased in rats injected with C‐peptide. This enhanced eNOS expression was associated with a marked increase in basal NO release from the aorta of C‐peptide‐treated rats. We conclude that C‐peptide is a potent inhibitor of leukocyte‐endothelium interaction and that this effect is specifically related to inhibition of endothelial cell adhesion molecules via maintenance of NO release from the vascular endothelium.—Scalia, R., Coyle, K. M., Levine, B. J., Booth, G., Lefer, A. M. C‐peptide inhibits leukocyte‐endothelium interaction in the microcirculation during acute endothelial dysfunction. FASEB J. 14, 2357‐2364 (2000)
Vegetation–atmosphere interactions and their role in global warming during the latest Cretaceous
Authors: Upchurch Garland R. , Otto-Bliesner Bette L. , Scotese Christopher
Published: July 2002

Forest vegetation has the ability to warm Recent climate by its effects on albedo and atmospheric water vapour, but the role of vegetation in warming climates of the geologic past is poorly understood. This study evaluates the role of forest vegetation in maintaining warm climates of the Late Cretaceous by (1) reconstructing global palaeovegetation for the latest Cretaceous (Maastrichtian); (2) modelling latest Cretaceous climate under unvegetated conditions and different distributions of palaeovegetation; and (3) comparing model output with a global database of palaeoclimatic indicators. Simulation of Maastrichtian climate with the land surface coded as bare soil produces high–latitude temperatures that are too cold to explain the documented palaeogeographic distribution of forest and woodland vegetation. In contrast, simulations that include forest vegetation at high latitudes show significantly warmer temperatures that are sufficient to explain the widespread geographic distribution of high–latitude deciduous forests. These warmer temperatures result from decreased albedo and feedbacks between the land surface and adjacent oceans. Prescribing a realistic distribution of palaeovegetation in model simulations produces the best agreement between simulated climate and the geologic record of palaeoclimatic indicators. Positive feedbacks between high–latitude forests, the atmosphere, and ocean contributed significantly to high–latitude warming during the latest Cretaceous, and imply that high–latitude forest vegetation was an important source of polar warmth during other warm periods of geologic history.
The developing dorsal ganglion of the salp Thalia democratica, and the nature of the ancestral chordate brain
Authors: Lacalli T. C. , Holland L. Z.
Published: July 2002

The development of the dorsal ganglion of the salp,Thalia democratica, is described from electron microscope reconstructions up to the stage of central neuropile formation. The central nervous system (CNS) rudiment is initially tubular with an open central canal. Early developmental events include: (i) the formation of a thick dorsal mantle of neuroblasts from which paired dorsal paraxial neuropiles arise; (ii) the differentiation of clusters of primary motor neurons along the ventral margin of the mantle; and (iii) the development from the latter of a series of peripheral nerves. The dorsal paraxial neuropiles ultimately connect to the large central neuropile, which develops later. Direct contact between neuroblasts and muscle appears to be involved in the development of some anterior nerves. The caudal nerves responsible for innervating more distant targets in the posterior part of the body develop without such contacts, which suggests that a different patterning mechanism may be employed in this part of the neuromuscular system.

The results are compared with patterns of brain organization in other chordates. Because the salp CNS is symmetrical and generally less reduced than that of ascidian larvae, it is more easily compared with the CNS of amphioxus and vertebrates. The dorsal paraxial centres in the salp resemble the dorsolateral tectal centres in amphioxus in both position and organization; the central neuropile in salps likewise resembles the translumenal system in amphioxus. The neurons themselves are similar in that many of their neurites appear to be derived from the apical surface instead of the basal surface of the cell. Such neurons, with extensively developed apical neurites, may represent a new cell type that evolved in the earliest chordates in conjunction with the formation of translumenal or intralumenal integrative centres. In comparing the salp ganglion with vertebrates, we suggest that the main core of the ganglion is most like the mes–etencephalic region of the vertebrate brain, i.e. the zone occupied by the midbrain, isthmus, and anterior hindbrain. Counterparts of more anterior regions (forebrain) and posterior ones (segmented hindbrain) appear to be absent in salps, but are found in other tunicates, suggesting that evolution has acted quite differently on the main subdivisions of the CNS in different types of tunicates.
The radular apparatus of cephalopods
Authors: Messenger J. B. , Young J. Z.
Published: July 2002

This paper describes the ontogeny, breakdown and absorption of the radular teeth of cephalopods and, for the first time, considers the function of the ‘bolsters’ or radular support muscles.

The radular ribbon, which bears many regularly arranged transverse rows of teeth one behind the other, lies in a radular canal that emerges from the radular sac. Here the radular teeth are formed by a set of elongate cells with microvilli, the odontoblasts. These are organized into two layers, the outer producing the radular membrane and the bases of the teeth, the inner producing the cusps. The odontoblasts also secrete the hyaline shield and the teeth on the lateral buccal palps, when these are present. At the front end of the radular ribbon the teeth become worn in feeding and are replaced from behind by new ones formed continuously in the radular sac, so that the whole ribbon moves forward during ontogeny. Removal of the old teeth is achieved by cells in the radular organs; these cells, which are formed from modified odontoblasts (‘odontoclasts’), dissolve the teeth and membranes and absorb them. There is a subradular organ in all cephalopods. InOctopus vulgaris, which bores into mollusc shells and crustacean carapaces, it is especially well–developed and there is also a supraradular organ.

A characteristic feature of the cephalopod radular apparatus is the pair of large radular support muscles or ‘bolsters’. Their function seems never to have been investigated, but experiments reported here show that when they elongate, the radular teeth become erect at the bending plane and splayed, presumably enhancing their ability to rake food particles into the pharynx. The bolsters ofOctopusfunction as muscular hydrostats: because their volume is fixed, contraction of their powerful transverse muscles causes them to elongate. In decapods and in nautiloids each bolster contains a ‘support rod’ of semi–fluid material, as well as massive transverse musculature. This rod may elongate to erect the radular teeth. At the extreme front end of the bolsters inOctopusthere are many nerve fibres that may constitute a receptor organ signalling the movements of the radula against hard material. Such nerves are absent from decapods and from octopods that do not bore holes.

The buccal mass ofNautilusis massive, with heavily calcified tips to the beaks and a wide radular ribbon, with 13 rather than nine elements in each row. Nevertheless all the usual coleoid features are present in the radular apparatus and the teeth are formed and broken down in the same way. However,Nautilushas a unique structure, the radular appendage. This comprises a papillate mass extending over the palate in the mid–line and forming paired lateral masses that are in part secretory. The organ is attached to the front of the radula by muscles and connective tissue. Its function is unknown.
The transmission dynamics of gonorrhoea: modelling the reported behaviour of infected patients from Newark, New Jersey
Authors: Garnett Geoff. P. , Mertz Kristen J. , Finelli Lyn , Levine William C. , St Louis Michael E.
Published: July 2002

A survey of the sexual behaviour of gonorrhoea patients in Newark was undertaken to evaluate parameters within a model of gonorrhoea transmission. Modelling work aimed to explain observed epidemiological patterns and to explore the potential impact of interventions. Reported behaviours, along with values derived from the literature, were used within a standard deterministic model of gonorrhoea transmission, where the population was stratified according to sex and rates of sex–partner change. The behaviours reported, particularly among women, are insufficient by themselves to explain the continued existence of gonorrhoea within the population. The majority of symptomatic patients seek treatment within a few days, and report that they do not have unprotected sex while symptomatic. The proportion of patients with low numbers of sex partners suggests that sexual mixing between people categorized according to sexual behaviour is near random. To explain the persistence of gonorrhoea, there must be some patients who, when infected, do not seek care in public clinics. In addition, gonorrhoea incidence in the model is sensitive to change, such that very small reductions in risk behaviour could lead to its elimination. This does not accord with the observed failure of many interventions to eliminate infection, suggesting that the modelled infection is too sensitive to change. The model, which has been influential in gonorrhoea epidemiology, is not consistent with the observed epidemiology of gonorrhoea in populations. Alternative models need to explore the observed stability of gonorrhoea before robust modelling conclusions can be drawn on how best to control infection. However, the current results do highlight the potential importance of asymptomatic infections and infections in those who are diseased and do not attend public health services. Screening and contact–tracing to identify asymptomatic infections in both men and women will be more effective in reaching those who maintain the infection within the community rather than simply treating symptomatic cases.
Reading of concentration gradients by axonal growth cones
Authors: Lö schinger Jürgen , Weth Franco , Bonhoeffer Friedrich
Published: July 2002

Wiring up the nervous system occurs as a self–organizing process during animal development. It has long been proposed that directional growth of axons towards their targets is achieved by gradients of guiding molecules and the conceptual framework of gradient guidance was introduced more than a decade ago. Novel experimental results now allow the formulation of models incorporating more mechanistic detail. We first summarize some crucialin vitroandin vivoresults concerning the development of the chick retinotectal projection. We then review two recent theoretical models based on these findings (the models of Nakamoto and colleagues, and of Honda). Neither model considers the latest observation that putative guidance ligands, in addition to their tectal expression, are expressed in a similar pattern on the retina and that a disturbance of this expression affects topography. These findings suggest that retinal axons might grow into the tectum until they have reached a ligand concentration matching that of their site of origin. We call this the imprint–matching concept of retinotectal guidance. As a framework for pinpointing logical difficulties of the mechanistic description of the guidance process and to stimulate further experiments we finally suggest two extended versions of Honda's model implementing imprint matching, which we call ‘the variable set–point’ and ‘the gradient–sensitive adaptation’ model. Strengths and weaknesses of both mechanisms are discussed.
Acoustic communication and the evolution of hearing in fishes
Authors: Ladich Friedrich
Published: July 2002

Fishes have evolved a diversity of sound–generating organs and acoustic signals of various temporal and spectral content. Additionally, representatives of many teleost families such as otophysines, anabantoids, mormyrids and holocentrids possess accessory structures that enhance hearing abilities by acoustically coupling air–filled cavities to the inner ear. Contrary to the accessory hearing structures such as Weberian ossicles in otophysines and suprabranchial chambers in anabantoids, sonic organs do not occur in all members of these taxa. Comparison of audiograms among nine representatives of seven otophysan families from four orders revealed major differences in auditory sensitivity, especially at higher frequencies (> 1kHz) where thresholds differed by up to 50 dB. These differences showed no apparent correspondence to the ability to produce sounds (vocal versus non–vocal species) or to the spectral content of species–specific sounds. In anabantoids, the lowest auditory thresholds were found in the blue gourami
Trichogaster trichopterus
, a species not thought to be vocal. Dominant frequencies of sounds corresponded with optimal hearing bandwidth in two out of three vocalizing species. Based on these results, it is concluded that the selective pressures involved in the evolution of accessory hearing structures and in the design of vocal signals were other than those serving to optimize acoustic communication.
Are diverse signalling pathways integrated in the regulation of
Arabidopsis
antioxidant defence gene expression in response to excess excitation energy?
Authors: Mullineaux Philip , Ball Louise , Escobar Carolina , Karpinska Barbara , Creissen Gary , Karpinski Stanislaw
Published: July 2002

When low–light–grown
Arabidopsis
rosettes are partially exposed to excess light (EL), the unexposed leaves become acclimated to excess excitation energy (EEE) and consequent photo–oxidative stress. This phenomenon, termed systemic acquired acclimation (SAA), is associated with redox changes in the proximity of photosystem II, changes in foliar H
2
O
2
content and induction of antioxidant defences. The induction of extra–plastidial antioxidant systems is important in the protection of the chloroplast under EL conditions. A larger range of transcripts encoding different antioxidant defence enzymes may be induced in the systemically acclimated leaves and these include those encoded by the glutathione peroxidase (
GPX2
) and glutathione–S–transferase (
GST
) genes, which are also highly induced in the hypersensitive response and associated systemic acquired resistance (SAR) in incompatible plantpathogen interactions. Furthermore, the expression of the SAR–inducible pathogenesis–related protein gene,
PR2
, is enhanced in SAA leaves. Wounded leaf tissue also shows enhanced systemic induction of a cytosolic ascorbate peroxidase gene (
APX2
) under EL conditions. These and other considerations, suggest H
2
O
2
and other reactive oxygen species (ROS) could be the common factor in signalling pathways for diverse environmental stresses. These effects may be mediated by changes in the level and redox state of the cellular glutathione pool. Mutants with constitutive expression of a normally EL–inducible
APX2
gene have much reduced levels of foliar glutathione.

The expression of
APX1
and
APX3
, encoding cytosolic and peroxisome–associated isoforms, respectively, are also under phytochrome–A–mediated control. The expression of these genes is tightly linked to the greening of plastids in etiolated seedlings. These data suggest that part of the developmental processes that bring about the acclimation of leaves to high light includes the configuration of antioxidant defences. Therefore, the linkage between immediate responses of leaves to EL, acclimation of chloroplasts to EEE and the subsequent changes to leaf form and function in high light could be mediated by the activity of foliar antioxidant defences and changes in the concentration of ROS.
c(3)G encodes a Drosophila synaptonemal complex protein
Authors: Page Scott L. , Hawley R. Scott
Published: July 2002

The meiotic mutant c(3)G (crossover suppressor on 3 of Gowen) abolishes both synaptonemal complex (SC) formation and meiotic recombination, whereas mutations in the mei-W68 and mei-P22 genes prevent recombination but allow normal SC to form. These data, as well as a century of cytogenetic studies, support the argument that meiotic recombination between homologous chromosomes in Drosophila females requires synapsis and SC formation. We have cloned the c(3)G gene and shown that it encodes a protein that is structurally similar to SC proteins from yeast and mammals. Immunolocalization of the C(3)G protein, as well as the analysis of a C(3)G-eGFP expression construct, reveals that C(3)G is present in a thread-like pattern along the lengths of chromosomes in meiotic prophase, consistent with a role as an SC protein present on meiotic bivalents. The availability of a marker for SC in Drosophila allowed the investigation of the extent of synapsis in exchange-defective mutants. These studies indicate that SC formation is impaired in certain meiotic mutants and that the synaptic defect correlates with the exchange defects. Moreover, the observation of interference among the residual exchanges in these mutant oocytes implies that complete SC formation is not required for crossover interference in Drosophila.
Myf5 is a direct target of long-range Shh signaling and Gli regulation for muscle specification
Authors: Gustafsson Marcus K. , Pan Hua , Pinney Deborah F. , Liu Yongliang , Lewandowski Anna , Epstein Douglas J. , Emerson Charles P.
Published: July 2002

Sonic hedgehog (Shh) is a secreted signaling molecule for tissue patterning and stem cell specification in vertebrate embryos. Shh mediates both long-range and short-range signaling responses in embryonic tissues through the activation and repression of target genes by its Gli transcription factor effectors. Despite the well-established functions of Shh signaling in development and human disease, developmental target genes of Gli regulation are virtually unknown. In this study, we investigate the role of Shh signaling in the control ofMyf5, a skeletal muscle regulatory gene for specification of muscle stem cells in vertebrate embryos. In previous genetic studies, we showed that Shh is required for Myf5 expression in the specification of dorsal somite, epaxial muscle progenitors. However, these studies did not distinguish whether Myf5 is a direct target of Gli regulation through long-range Shh signaling, or alternatively, whether Myf5 regulation is a secondary response to Shh signaling. To address this question, we have used transgenic analysis with lacZ reporter genes to characterize anMyf5 transcription enhancer that controls the activation ofMyf5 expression in the somite epaxial muscle progenitors in mouse embryos. This Myf5 epaxial somite (ES) enhancer is Shh-dependent, as shown by its complete inactivity in somites of homozygous Shh mutant embryos, and by its reduced activity in heterozygous Shh mutant embryos. Furthermore, Shh and downstream Shh signal transducers specifically induce ES enhancer/luciferase reporters in Shh-responsive 3T3 cells. A Gli-binding site located within the ES enhancer is required for enhancer activation by Shh signaling in transfected 3T3 cells and in epaxial somite progenitors in transgenic embryos. These findings establish that Myf5 is a direct target of long-range Shh signaling through positive regulation by Gli transcription factors, providing evidence that Shh signaling has a direct inductive function in cell lineage specification.
Detecting equilibrium cytochrome c folding intermediates by electrospray ionisation mass spectrometry: Two partially folded forms populate the molten‐globule state
Authors: Grandori Rita
Published: July 2002

Nanoelectrospray ionization mass spectrometry (nano‐ESI‐MS) is applied to the characterization of ferric cytochromec (cytc) conformational states under different solvent conditions. The methanol‐induced molten‐globule state in the pH range 2.6–3.0 is found to be populated by two distinct, partially folded conformers IA and IB. The more compact intermediate IB resembles that induced by glycerol in acid‐unfolded cytc. The less compact one, IA, also can be induced by destabilization of the native structure by trifluoroethanol. IA and IB can be detected, in the absence of additives, around the midpoint of the acid‐induced unfolding transition, providing direct evidence for involvement of equilibrium folding intermediates in cytc conformational transitions at low pH. This study shows that mass spectrometry can contribute to the characterization of molten‐globule states of proteins by detection of distinct, although poorly populated, conformations involved in a dynamic equilibrium.
Effects of turn residues in directing the formation of the β‐sheet and in the stability of the β‐sheet
Authors: Chen Pei‐Yeh , Lin Chih‐Kai , Lee Chung‐Tien , Jan Howard , Chan Sunney I.
Published: July 2002

The designed peptide (denoted 20‐mer, sequence VFITSDPGKTYTEVDPGOKILQ) has been shown to form a three‐strand antiparallel β‐sheet. It is generally believed that the DPro‐Gly segment has the propensity to adopt a type II′ β‐turn, thereby promoting the formation of this β‐sheet. Here, we replaced DPro‐Gly with Asp‐Gly, which should favor a type I′ turn, to examine the influence of different type of turns on the stability of the β‐sheet. Contrary to our expectation, the mutant peptide, denoted P6D, forms a five‐residue type I turn plus a β‐bulge between the first two strands due to a one amino‐acid frameshift in the hydrogen bonding network and side‐chain inversion of the first β‐strand. In contrast, the same kind of substitution at DPro‐14 in the double mutant, denoted P6DP14D, does not yield the same effect. These observations suggest that the SDGK sequence disfavors the type I′ conformation while the VDGO sequence favors a type I′ turn, and that the frameshift in the first strand provides a way for the peptide to accommodate a disfavored turn sequence by protruding a bulge in the formation of the β‐hairpin. Thus, different types of turns can affect the stability of a β‐structure.
Measurement of transit time of a remote after‐loading high dose rate brachytherapy source
Authors: Sahoo Narayan
Published: July 2002

Quantification of transit time of a remote after‐loading high dose rate (HDR) brachytherapy source is important both for accurate treatment planning and for quality assurance checks. In this investigation, an HDR‐1000 well ionization chamber and a precision electrometer are used to measure the transit time of the Ir‐192 source of a Nucletron Micro‐Selectron HDR brachytherapy unit. The charge generated both during source dwelling at a selected position in an endobronchial catheter inserted into the chamber and during source travel to this position from another location at a distance of 0.5 to 10 cm from it was measured. A linear regression analysis of the measured charge as a function of dwell time was made. The interdwell position transit time was calculated from the ratio of the charge intercept and the slope of the straight line obtained from the regression analysis. The values of the effective transit time, which is a combination of interdwell position transit time and dwell time error of the after‐loading unit, were found to be 0.03 and 0.45 s for 0.5 and 10 cm separation between two dwell positions, respectively. The average time for 1 cm travel of the source between two dwell positions was found to be 0.022 s, resulting in an average speed of 45.5 cm/s. This simple procedure has the potential to be utilized for routine quality assurance check of the interdwell position transit time of any remote after‐loading HDR brachytherapy source.
Multitapered x‐ray capillary optics for mammography
Authors: Bradford Carla D. , Peppler Walter W. , Ross Richard E.
Published: July 2002

X‐ray mammography is currently the primary tool used for breast cancer detection. However, studies have shown that 5%–15% of breast cancers are not visualized mammographically. The long term goal of this project is to improve the x‐ray mammographic imaging system using capillary optics. A post‐patient capillary optic lens has the potential to increase spatial resolution and eliminate the detection of scattered x rays, thereby improving image contrast and the signal‐to‐noise ratio (SNR). Several individual and two prototype multitapered optics were studied to determine the feasibility of a full‐field multitapered optic. Scatter fraction, contrast, transmission, uniformity, and the modulation transfer function (MTF) were measured for a Mo target tube/computed radiography (CR) imaging system when this prototype was applied. The results were compared with standard grid and airgap techniques. The multitapered optic lens removed 85% of the scattered photons as compared to 66% and 39% for the air gap and grid methods, respectively. This resulted in an improvement of contrast by approximately 80% for the optics, 51% for the air gap, and 30% for grid methods. The single optic lens improved the limiting resolution (5% MTF level) of the CR detector by 78% due to magnification with very little focal spot blurring, while the multitapered prototype improved resolution significantly, but not as much as the single optic. These measurements have shown that it is feasible to create a multitapered optic lens that significantly improves system MTF and virtually eliminates scatter. With continued improvements in fabrication techniques, a full‐field multitapered lens will be feasible.
A CT‐based Monte Carlo simulation tool for dosimetry planning and analysis
Authors: DeMarco J. J. , Solberg T. D. , Smathers J. B.
Published: July 2002

The Los Alamos code MCNP4A (M_onte C_arlo N_‐P_article version 4A) is currently used to simulate a variety of problems ranging from nuclear reactor analysis to boron neutron capture therapy. A graphical user interface has been developed that automatically sets up the MCNP4A geometry and radiation source requirements for a three‐dimensional Monte Carlo simulation using computed tomography data. The major drawback for this dosimetry system is the amount of time to obtain a statistically significant answer. A specialized patch file has been developed that optimizes photon particle transport and dose scoring within the standard MCNP4A lattice geometry. The transport modifications produce a performance increase (number of histories per minute) of approximately 4.7 based upon a 6 MV point source centered within a lattice water phantom and voxels. The dose scoring modifications produce a performance increase of approximately 470 based upon a tally section of greater than lattice elements and a voxel size of Homogeneous and heterogeneous benchmark calculations produce good agreement with measurements using a standard water phantom and a high‐ and low‐density heterogeneity phantom. The dose distribution from a typical mediastinum treatment planning setup is presented for qualitative analysis and comparison versus a conventional treatment planning system.
Independent verification using portal imaging of intensity‐modulated beam delivery by the dynamic MLC technique
Authors: Partridge Michael , Evans Philip M. , Mosleh‐Shirazi Amin , Convery David
Published: July 2002

The use of intensity‐modulated radiation fields in radiotherapy treatment has been shown to have the potential to deliver highly conformal dose distributions. One technique for delivering these intensity‐modulated beams is a computerized dynamic multileaf collimator (MLC). A major current impediment to the development of dynamic MLC therapy is verification of these highly complex treatments. Electronic portal imaging is shown here to be a solution to this verification problem. Experimental results are presented showing that leaf penumbra measured with a portal imager can be used to accurately define the positions of moving leaves. The random error in these leaf positions is compared with mean leaf positions along each leaf bank and specified leaf positions at prescription control points to check mechanical performance. Individual leaves are also checked for systematic motion errors. All leaf positions are found to be well within the manufacturer's specifications at all times. Finally, integral intensity images are presented that can be related to the dose distribution delivered. Portal imaging is shown to have the potential to become a valuable tool for the verification of dynamic MLC irradiation.
Radiochromic film dosimetry: Recommendations of AAPM Radiation Therapy Committee Task Group 55
Authors: Niroomand‐Rad Azam , Blackwell Charles Robert , Coursey Bert M. , Gall Kenneth P. , Galvin James M. , McLaughlin William L. , Meigooni Ali S. , Nath Ravinder , Rodgers James E. , Soares Christopher G.
Published: July 2002

Recommendations of the American Association of Physicists in Medicine (AAPM) for the radiochromic film dosimetry are presented. These guidelines were prepared by a task group of the AAPM Radiation Therapy Committee and have been reviewed and approved by the AAPM Science Council.
Physical characteristics of a miniature multileaf collimator
Authors: Xia P. , Geis P. , Xing L. , Ma C. , Findley D. , Forster K. , Boyer A.
Published: July 2002

A preliminary study of the physical characteristics of a miniature multileaf collimator (mMLC) used with 4 MV x rays is reported. The mMLC attached to the accessory mount of a class C or D Varian linear accelerator (Varian Oncology Systems, Palo Alto, CA) with a source to aperture distance of 65 cm. The field penumbra using the small leaves was found to be consistent with the anticipated field penumbra using photon jaws at the same source to aperture distance as the mMLC. The percentage depth dose values of square fields were found to be consistent with the fields collimated with the upper and lower jaws. Output factors for the very small fields were found to vary rapidly. Circular fields could be produced with depth dose characteristics similar to those produced using conical tertiary collimators, commonly used for radiosurgery, but with a broader penumbra.
Monte Carlo investigation of electron beam output factors versus size of square cutout
Authors: Zhang G. G. , Rogers D. W. O. , Cygler J. E. , Mackie T. R.
Published: July 2002

A major task in commissioning an electron accelerator is to measure relative output factors versus cutout size (i.e., cutout factors) for various electron beam energies and applicator sizes. We use the BEAM Monte Carlo code [Med Phys. 22, 503–524 (1995)] to stimulate clinical electron beams and to calculate the relative output factors for square cutouts. Calculations are performed for a Siemens MD2 linear accelerator with beam energies, 6, 9, 11, and 13 MeV. The calculated cutout factors for square cutouts in and applicators at SSDs of 100 and 115 cm agree with the measurements made using a silicon diode within about 1% except for the smallest cutouts at where they agree within 0.015. The details of each component of the dose, such as the dose from particles scattered off the jaws and the applicator, the dose from contaminant photons, the dose from direct electrons, etc., are also analyzed. The calculations show that in‐phantom side‐scatter equilibrium is a major factor for the contribution from the direct component which usually dominates the output of a beam. It takes about 6 h of CPU time on a Pentium Pro 200MHz computer to simulate an accelerator and additional 2 h to calculate the relative output factor for each cutout with a statistical uncertainty of 1%.
Improved image quality in digital mammography with image processing
Authors: Baydush Alan H. , Floyd Carey E.
Published: July 2002

Purpose: The effect of image processing, specifically Bayesian image estimation (BIE), on digital mammographic images is studied. BIE is an iterative, nonlinear statistical estimation technique that has previously been used in chest radiography to reduce image scatter content and improve the contrast‐to‐noise ratio (CNR). We adapt this technique to digital mammography and examine its effect. Methods/Materials: Images of the American College of Radiologists (ACR) breast phantom were acquired on a calibrated digital mammography system at a normal mammographic exposure both with and without a grid. An iterative Bayesian estimation algorithm was formulated and used to process the images acquired without a grid. Quantitative scatter fractions were measured and compared for the image acquired with the grid, the image acquired without the grid, and the image acquired without the grid and processed by the Bayesian algorithm. CNR values were also computed for the four visible masses in the ACR phantom before and after processing and compared to a grid. Results: Initial images acquired without an antiscatter grid had scatter fractions of 0.46. Processing this image with BIE reduced the scatter content to under 0.04. In comparison, the image acquired with a grid had scatter of 0.19. BIE processing accounted for CNR improvements from 29% to 219% for the masses seen in the ACR phantom as compared to the unprocessed image. Visibility of the four masses in the phantom was improved. Conclusions: Bayesian image estimation can be used with digital mammography to reduce scatter fractions. This technique is very useful as it can reduce scatter content effectively without introducing any adverse effects, such as grid line aliasing. Bayesian processing can also increase image CNR, which may potentially increase the visualization of subtle masses. Preliminary work shows an improvement in CNR to values greater than that provided by a standard grid.
On the dynamic stabilization of an inverted pendulum
Authors: Butikov Eugene I.
Published: July 2002

A simple qualitative physical explanation is suggested for the phenomenon of dynamic stabilization of the inverted rigid planar pendulum whose pivot is constrained to oscillate with a high frequency in the vertical direction. A quantitative theory based on the suggested approach is developed. A computer program simulating the physical system supports the analytical investigation. The simulation reveals subtle details of the motion and aids the analytical study of the subject in a manner that is mutually reinforcing.