bluuebunny/crossref_metadata_2025 huggingface dataset:
Production of a polyketide natural product in nonpolyketide-producing prokaryotic and eukaryotic hosts
Authors: Kealey James T. , Liu Lu , Santi Daniel V. , Betlach Mary C. , Barr Philip J.
Published: July 2002

The polyketides are a diverse group of natural products with great significance as human and veterinary pharmaceuticals. A significant barrier to the production of novel genetically engineered polyketides has been the lack of available heterologous expression systems for functional polyketide synthases (PKSs). Herein, we report the expression of an intact functional PKS in
Escherichia coli
and
Saccharomyces cerevisiae
. The fungal gene encoding 6-methylsalicylic acid synthase from
Penicillium patulum
was expressed in
E. coli
and
S. cerevisiae
and the polyketide 6-methylsalicylic acid (6-MSA) was produced. In both bacterial and yeast hosts, polyketide production required coexpression of 6-methylsalicylic acid synthase and a heterologous phosphopantetheinyl transferase that was required to convert the expressed apo-PKS to its holo form. Production of 6-MSA in
E. coli
was both temperature- and glycerol-dependent and levels of production were lower than those of
P. patulum
, the native host. In yeast, however, 6-MSA levels greater than 2-fold higher than the native host were observed. The heterologous expression systems described will facilitate the manipulation of PKS genes and consequent production of novel engineered polyketides and polyketide libraries.
The complementary aggregation sites of fibrin investigated through examination of polymers of fibrinogen with fragment E
Authors: Veklich Yuri , Ang Esther K. , Lorand Laszlo , Weisel John W.
Published: July 2002

Fibrin polymerizes through the interaction of sites exposed by the thrombin-mediated cleavage of fibrinopeptides in the central E region of the protein and complementary sites near the ends of the molecules, open in the D regions of both fibrinogen and fibrin. A preparation of fragment E, containing the central domain and part of the coiled-coil regions of fibrin, was used in mixtures with fibrinogen in this electron microscopy study to investigate the formation of fibrillar structures. At short times, linearly ordered oligomers of fibrinogen were observed with an additional mass of E fragments at the end-to-end junctions. At later times, long flexible polymers made up of 30 or more fibrinogen and fragment E units, with a tendency for lateral aggregation and tangle formation, were seen. These single-stranded assemblies could be readily dissociated in dilute acetic acid into their fibrinogen and fragment E components. However, if the aggregates were treated with factor XIIIa so that all γ chains became ligated by N
ɛ
(γ-glutamyl)lysine linkages, the polymers could no longer be taken apart. Because the only γ chains in the preparation are present in the fibrinogen molecules interacting end-to-end, the findings show that the factor XIIIa-induced cross-linking of γ chains in the clotting of fibrinogen or fibrin must occur between molecules that are longitudinal (or end-to-end) rather than transverse (or half-staggered).
β-Phaseolin gene activation is a two-step process: PvALF- facilitated chromatin modification followed by abscisic acid-mediated gene activation
Authors: Li Guofu , Bishop Kenneth J. , Chandrasekharan Mahesh B. , Hall Timothy C.
Published: July 2002

We have shown previously that a rotationally and translationally positioned nucleosome is responsible for the absence of transcriptional expression from the phaseolin (
phas
) gene promoter in leaf tissue and that the repressive chromatin structure is disrupted on transcriptional activation during embryogenesis. To investigate how the chromatin structure is modified, we ectopically expressed PvALF, a putative seed-specific
phas
activator, in leaf tissue of a tobacco line transgenic for a chimeric
phas/uidA
construct. DNase I footprinting
in vivo
revealed that the ectopic expression of PvALF resulted in remodeling of the chromatin architecture over the TATA region of the
phas
promoter but did not lead to transcriptional activation in the absence of abscisic acid (ABA). Treatment of the transgenic tobacco leaves with ABA in the absence of PvALF neither alleviated the repressive chromatin architecture nor activated transcription. However, in the presence of PvALF, high levels of β-glucuronidase expression were obtained on exposure of leaves to ABA. These results reveal that expression from the
phas
promoter involves at least two discrete steps: chromatin potentiation by PvALF followed by ABA-mediated transcriptional activation.
Stimulation of homologous recombination in plants by expression of the bacterial resolvase RuvC
Authors: Shalev Gil , Sitrit Yaron , Avivi-Ragolski Naomi , Lichtenstein Conrad , Levy Avraham A.
Published: July 2002

Targeted gene disruption exploits homologous recombination (HR) as a powerful reverse genetic tool, for example, in bacteria, yeast, and transgenic knockout mice, but it has not been applied to plants, owing to the low frequency of HR and the lack of recombinogenic mutants. To increase the frequency of HR in plants, we constructed transgenic tobacco lines carrying the
Escherichia coli
RuvC
gene fused to a plant viral nuclear localization signal. We show that
RuvC
,
encoding an endonuclease that binds to and resolves recombination intermediates (Holliday junctions) is properly transcribed in these lines and stimulates HR. We observed a 12-fold stimulation of somatic crossover between genomic sequences, a 11-fold stimulation of intrachromosomal recombination, and a 56-fold increase for the frequency of extrachromosomal recombination between plasmids cotransformed into young leaves via particle bombardment. This stimulating effect may be transferred to any plant species to obtain recombinogenic plants and thus constitutes an important step toward gene targeting.
Gene silencing via protein-mediated subcellular localization of DNA
Authors: Kim Sook-Kyung , Wang James C.
Published: July 2002

We previously reported that overexpression of SopB, an
Escherichia coli
F plasmid-encoded partition protein, led to silencing of genes linked to, but well-separated from, a cluster of SopB-binding sites termed
sopC
. We show here that in this SopB-mediated repression of
sopC
-linked genes, all but the N-terminal 82 amino acids of SopB can be replaced by the DNA-binding domain of a sequence-specific DNA-binding protein, provided that the
sopC
locus is also replaced by the recognition sequence of the DNA-binding domain. These results, together with our previous finding that the N-terminal fragment of SopB is responsible for its polar localization in cells, suggest a mechanism of gene silencing: patches of closely packed DNA-binding domains are formed if a sequence-specific DNA-binding protein is localized to specific cellular sites; such a patch can capture a DNA carrying the recognition site of the DNA-binding domain and sequestrate genes adjacent to the recognition site through nonspecific binding of DNA. The generalization of this model to gene silencing in eukaryotes is discussed.
Lack of infection in HIV-exposed individuals is associated with a strong CD8+cell noncytotoxic anti-HIV response
Authors: Stranford Sharon A. , Skurnick Joan , Louria Donald , Osmond Dennis , Chang Sheng-Yung , Sninsky John , Ferrari Guido , Weinhold Kent , Lindquist Craig , Levy Jay A.
Published: July 2002

Individuals repeatedly exposed to HIV, but who remain uninfected, form a population enriched for persons likely to have either natural or acquired resistance to the virus. We have studied four such exposed uninfected cohorts, representing 60 individuals, for evidence of protective immunity. This population included participants exposed to HIV through anal or vaginal receptive intercourse on multiple occasions over many years. We observed CD8+-cell noncytotoxic inhibition of HIV replication in acutely infected CD4+cells in the vast majority of individuals most recently exposed to the virus (within 1 year). The levels of this CD8+-cell response were sufficient to inhibit thein vitroinfection of the exposed subjects’ peripheral blood mononuclear cells. We found no evidence of a significant role for CCR5 Δ32 mutation in this population, nor did CD4+cell susceptibility to infection or HIV-specific cytotoxic T-lymphocytes correlate with resistance to infection in the individuals tested. Therefore, the observed strong noncytotoxic CD8+-cell anti-HIV responses may be an antiviral immune activity contributing to the apparent protection from infection in these exposed uninfected individuals.
Unexpected crucial role of residue 225 in serine proteases
Authors: Guinto Enriqueta R. , Caccia Sonia , Rose Thierry , Fütterer Klaus , Waksman Gabriel , Di Cera Enrico
Published: July 2002

Residue 225 in serine proteases of the chymotrypsin family is Pro or Tyr in more than 95% of nearly 300 available sequences. Proteases with Y225 (like some blood coagulation and complement factors) are almost exclusively found in vertebrates, whereas proteases with P225 (like degradative enzymes) are present from bacteria to human. Saturation mutagenesis of Y225 in thrombin shows that residue 225 affects ligand recognition up to 60,000-fold. With the exception of Tyr and Phe, all residues are associated with comparable or greatly reduced catalytic activity relative to Pro. The crystal structures of three mutants that differ widely in catalytic activity (Y225F, Y225P, and Y225I) show that although residue 225 makes no contact with substrate, it drastically influences the shape of the water channel around the primary specificity site. The activity profiles obtained for thrombin also suggest that the conversion of Pro to Tyr or Phe documented in the vertebrates occurred through Ser and was driven by a significant gain (up to 50-fold) in catalytic activity. In fact, Ser and Phe are documented in 4% of serine proteases, which together with Pro and Tyr account for almost the entire distribution of residues at position 225. The unexpected crucial role of residue 225 in serine proteases explains the evolutionary selection of residues at this position and shows that the structural determinants of protease activity and specificity are more complex than currently believed. These findings have broad implications in the rational design of enzymes with enhanced catalytic properties.
Distinctive genetic signatures in the Libyan Jews
Authors: Rosenberg Noah A. , Woolf Eilon , Pritchard Jonathan K. , Schaap Tamar , Gefel Dov , Shpirer Isaac , Lavi Uri , Bonné-Tamir Batsheva , Hillel Jossi , Feldman Marcus W.
Published: July 2002

Unlinked autosomal microsatellites in six Jewish and two non-Jewish populations were genotyped, and the relationships among these populations were explored. Based on considerations of clustering, pairwise population differentiation, and genetic distance, we found that the Libyan Jewish group retains genetic signatures distinguishable from those of the other populations, in agreement with some historical records on the relative isolation of this community. Our methods also identified evidence of some similarity between Ethiopian and Yemenite Jews, reflecting possible migration in the Red Sea region. We suggest that high-resolution statistical methods that use individual multilocus genotypes may make it practical to distinguish related populations of extremely recent common ancestry.
Sleep modifies retinal ganglion cell responses in the normal rat
Authors: Galambos Robert , Szabó-Salfay Orsolya , Szatmári Erzsébet , Szilágyi Nóra , Juhász Gábor
Published: July 2002

Recordings were obtained from the visual system of rats as they cycled normally between waking (W), slow-wave sleep (SWS), and rapid eye movement (REM) sleep. Responses to flashes delivered by a light-emitting diode attached permanently to the skull were recorded through electrodes implanted on the cornea, in the chiasm, and on the cortex. The chiasm response reveals the temporal order in which the activated ganglion cell population exits the eyeball; as reported, this triphasic event is invariably short in latency (5–10 ms) and around 300 ms in duration, called the histogram. Here we describe the differences in the histograms recorded during W, SWS, and REM. SWS histograms are always larger than W histograms, and an REM histogram can resemble either. In other words, the optic nerve response to a given stimulus is labile; its configuration depends on whether the rat is asleep or awake. We link this physiological information with the anatomical fact that the brain dorsal raphe region, which is known to have a sleep regulatory role, sends fibers to the rat retina and receives fibers from it. At the cortical electrode, the visual cortical response amplitudes also vary, being largest during SWS. This well known phenomenon often is explained by changes taking place at the thalamic level. However, in the rat, the labile cortical response covaries with the labile optic nerve response, which suggests the cortical response enhancement during SWS is determined more by what happens in the retina than by what happens in the thalamus.
‘Privileging the Visible’: A critique of the National Learning Targets
Authors: Gorard Stephen , Selwyn Neil , Rees Gareth
Published: July 2002

Abstract This article takes as its background the shift over time in Britain towards models of target setting in education which are based almost entirely on measurable outputs. The original ‘headline’ targets proposed by the National Council for Educational Technology were of a very different nature, as are those of many other developed nations. The article outlines some alternative models involving targets for both inputs and processes, and the use of targets which are exhortative rather than directly measurable. It is suggested that the main reason these more ‘qualitative’ targets have disappeared from British policy‐making is that they are not considered to be directly measurable. This is contrasted, at least in some accounts, with the more visible output indicators. However, the substantive purpose of this article is show how weak the claim is that we can ever adequately measure even these privileged targets. The article therefore argues that if a policy of target setting is to be pursued, and given other findings from the authors' study in Wales this is far from clear, then more sophisticated models than those in current vogue may be required. The expense involved in setting up such an extension to our already heavily audited society may be unjustified—for it is surely better to spend money on improving lifelong learning even if we cannot measure that improvement definitively, than to have an accurate metric revealing a picture of stagnation or worse.
A New Research Programme on Information and Communication Technologies. The E-Society: Understanding the Restructuring of Practices and Institutions in the Digital Age
Authors: The Economic and Social Research Council
Published: July 2002

This is an advance notice of a new research programme, supported by Britain's Economic and Social Research Council (ESRC), investigating the restructuring of practices and institutions in the digital age. The call for applications is planned for November 2001; first projects are expected to commence in October 2002. The ESRC is currently preparing the recruitment of a Programme Director.Further information on the process will be published in due course and will be available on the ESRC's website at: http:/ /www.esrc.ac.uk/E-Society.htm. Below is the text of the proposal on the basis of which the ESRC decided to fund a research programme in this area. This proposal was developed through a consultancy led by Professor William H. Dutton. Please note that there might be changes to the programme outline once the Programme Director is appointed. Contact: Angelika Hamilton, angelika.hamilton@esrc.ac.uk, with any comments or recommendations.
Modifying Residents' Professional Attitudes about Substance Abuse Treatment and Training
Authors: Karam‐Hage Maher , Nerenberg Lucila , Brower Kirk J.
Published: July 2002

Some physicians have negative attitudes and beliefs towards patients with addiction. Moreover, few residents are inclined towards a subspecialty fellowship in addiction psychiatry. We aimed to determine if a one‐day educational conference could facilitate attitudinal change among 52 general psychiatry residents. Significant changes (p < 0.05) in attitudes were reported following the conference, including enhanced beliefs that physicians can motivate their addicted patients to seek treatment and increased physician interest in pursuing advanced addiction training. A one‐day educational intervention may be effective in improving professional attitudes toward addiction treatment by reinforcing previously acquired medical education. The duration of these changes remains to be determined.
Creb-Binding Protein (Cbp/P300) and RNA Polymerase II Colocalize in Transcriptionally Active Domains in the Nucleus
Authors: von Mikecz Anna , Zhang Suisheng , Montminy Marc , Tan Eng M. , Hemmerich Peter
Published: July 2002

The spatial organization of transcription- associated proteins is an important control mechanism of eukaryotic gene expression. Here we analyzed the nuclear distribution of the transcriptional coactivators CREB-binding protein (CBP)/p300 in situ by confocal laser scanning microscopy, and in vivo complex formation by coimmunoprecipitation. A subpopulation of CBP and p300 is targeted to active sites of transcription and partially colocalizes with hyper- and hypophosphorylated RNA polymerase II (pol II) in discrete regions of variable size throughout the nucleus. However, the coactivators were found in tight association with hypophosphorylated, but not hyperphosphorylated pol II. Transcriptional inhibition induced a relocation of CBP/p300 and pol II into speckles. Moreover, double and triple immunofluorescence analyses revealed the presence of CBP, p300, and pol II in a subset of promyelocytic leukemia (PML) bodies. Our results provide evidence for a dynamic spacial link between coactivators of transcription and the basal transcription machinery in discrete nuclear domains dependent upon the transcriptional activity of the cell. The identification of pol II in CBP/PML-containing nuclear bodies supports the idea that transcription takes place at PML bodies.
Pex11p Plays a Primary Role in Medium-Chain Fatty Acid Oxidation, a Process That Affects Peroxisome Number and Size in Saccharomyces cerevisiae
Authors: van Roermund Carlo W.T. , Tabak Henk F. , van den Berg Marlene , Wanders Ronald J.A. , Hettema Ewald H.
Published: July 2002

The Saccharomyces cerevisiae peroxisomal membrane protein Pex11p has previously been implicated in peroxisome proliferation based on morphological observations of PEX11 mutant cells. Pex11p-deficient cells fail to increase peroxisome number in response to growth on fatty acids and instead accumulate a few giant peroxisomes. We report that mutants deficient in genes required for medium-chain fatty acid (MCFA) β-oxidation display the same phenotype as Pex11p-deficient cells. Upon closer inspection, we found that Pex11p is required for MCFA β-oxidation. Disruption of the PEX11 gene results in impaired formation of MCFA-CoA esters as measured in intact cells, whereas their formation is normal in cell lysates. The sole S. cerevisiae MCFA-CoA synthetase (Faa2p) remains properly localized to the inner leaflet of the peroxisomal membrane in PEX11 mutant cells. Therefore, the in vivo latency of MCFA activation observed in Pex11p-deficient cells suggests that Pex11p provides Faa2p with substrate. When PEX11 mutant cells are shifted from glucose to oleate-containing medium, we observed an immediate deficiency in β-oxidation of MCFAs whereas giant peroxisomes and a failure to increase peroxisome abundance only became apparent much later. Our observations suggest that the MCFA oxidation pathway regulates the level of a signaling molecule that modulates the number of peroxisomal structures in a cell.
G protein–coupled receptor/arrestin3 modulation of the endocytic machinery
Authors: Santini Francesca , Gaidarov Ibragim , Keen James H.
Published: July 2002

Nonvisual arrestins (arr) modulate G protein–coupled receptor (GPCR) desensitization and internalization and bind to both clathrin (CL) and AP-2 components of the endocytic coated pit (CP). This raises the possibility that endocytosis of some GPCRs may be a consequence of arr-induced de novo CP formation. To directly test this hypothesis, we examined the behavior of green fluorescent protein (GFP)-arr3 in live cells expressing β2-adrenergic receptors and fluorescent CL. After agonist stimulation, the diffuse GFP-arr3 signal rapidly became punctate and colocalized virtually completely with preexisting CP spots, demonstrating that activated complexes accumulate in previously formed CPs rather than nucleating new CP formation. After arr3 recruitment, CP appeared larger: electron microscopy analysis revealed an increase in both CP number and in the occurrence of clustered CPs. Mutant arr3 proteins with impaired binding to CL or AP-2 displayed reduced recruitment to CPs, but were still capable of inducing CP clustering. In contrast, though constitutively present in CPs, the COOH-terminal moiety of arr3, which contains CP binding sites but lacks receptor binding, did not induce CP clustering. Together, these results indicate that recruitment of functional arr3–GPCR complexes to CP is necessary to induce clustering. Latrunculin B or 16°C blocked CP rearrangements without affecting arr3 recruitment to CP. These results and earlier studies suggest that discrete CP zones exist on cell surfaces, each capable of supporting adjacent CPs, and that the cortical actin membrane skeleton is intimately involved with both the maintenance of existing CPs and the generation of new structures.
Molecular Analysis of Potential Hinge Residues in the Inactivation Gate of Brain Type IIA Na+ Channels
Authors: Kellenberger Stephan , West James W. , Catterall William A. , Scheuer Todd
Published: July 2002

During inactivation of Na+ channels, the intracellular loop connecting domains III and IV is thought to fold into the channel protein and occlude the pore through interaction of the hydrophobic motif isoleucine-phenylalanine-methionine (IFM) with a receptor site. We have searched for amino acid residues flanking the IFM motif which may contribute to formation of molecular hinges that allow this motion of the inactivation gate. Site-directed mutagenesis of proline and glycine residues, which often are components of molecular hinges in proteins, revealed that G1484, G1485, P1512, P1514, and P1516 are required for normal fast inactivation. Mutations of these residues slow the time course of macroscopic inactivation. Single channel analysis of mutations G1484A, G1485A, and P1512A showed that the slowing of macroscopic inactivation is produced by increases in open duration and latency to first opening. These mutant channels also show a higher probability of entering a slow gating mode in which their inactivation is further impaired. The effects on gating transitions in the pathway to open Na+ channels indicate conformational coupling of activation to transitions in the inactivation gate. The results are consistent with the hypothesis that these glycine and proline residues contribute to hinge regions which allow movement of the inactivation gate during the inactivation process of Na+ channels.
Triangular canonical forms for lattice rules of prime-power order
Authors: Lyness J. , Joe S.
Published: July 2002

In this paper we develop a theory oftt-cycleD−ZD-Zrepresentations forss-dimensional lattice rules of prime-power order. Of particular interest are canonical forms which, by definition, have aDD-matrix consisting of the nontrivial invariants. Among these is a family oftriangularforms, which, besides being canonical, have the defining property that theirZZ-matrix is a column permuted version of a unit upper triangular matrix. Triangular forms may be obtained constructively using sequences of elementary transformations based on elementary matrix algebra. Our main result is to define a unique canonical form for prime-power rules. Thisultratriangularform is a triangular form, is easy to recognize, and may be derived in a straightforward manner.
Some Lie rings associated with Burnside groups
Authors: Newman M. , Vaughan-Lee Michael
Published: July 2002

We describe some calculations in graded Lie rings which provide a fairly sharp upper bound for the nilpotency class and for the order of the restricted Burnside group on two generators with exponent 7.
Z extensions to the RHMAPPER package.
Authors: Soderlund C , Lau T , Deloukas P
Published: July 2002

MOTIVATION: Extensions have been made to the RHMAPPER-1.1 package. One set of extensions computes the totally linked markers and uses the results as input to the salient RHMAPPER functions. The second set of extensions uses TKperl to provide an interactive interface for ease of querying the database and displaying maps. AVAILABILITY: The extensions can be obtained via ftp.sanger.ac.uk/pub/zmapper. Supplementary information: The User's Manual can be viewed from http:/www.sanger.ac.uk/Users/cari/Z.shtml. CONTACT: cari@sanger.ac.uk
Old Dominions and Industrial Commonwealths: The Political Economy of Coal in Virginia and Pennsylvania, 1810–1875
Authors: Adams Sean Patrick
Published: July 2002

During the late eighteenth and early nineteenth century, Great Britain utilized its extensive coal reserves to emerge as the world's leading industrial power. “If a patch of a few square miles has done so much for central England,” one British writer pondered in 1856, “what may fields containing many hundred square leagues do for the United States?” In the story of American coal, the two most important states on the eve of the nineteenth century were Virginia and Pennsylvania. Virginia was endowed with bituminous coal reserves in both the James River Basin and its western counties, while Pennsylvania enjoyed a virtual monopoly on American anthracite coal as well as a massive bituminous region west of the Allegheny Mountains.
Ted Turner’s Corporate Cross-Dressing and the Shifting Images of American Business Leadership
Authors: Guthey Eric
Published: July 2002

The media celebration of media owner Ted Turner's career and personal biography reflects important shifts in the image of American corporate leadership over the past thirty years.Even aspects of Turner’s life we would normally consider private, such as his sex life and his marriage to Jane Fonda, have taken on this very public function.As a result Turner has served as a transitional figure between two competing visions of corporate identity and responsibility: paternalist managerialism and the “real entity” theory of the firm on the one hand, and on the other, antimanagerial market adventurism and the new economic theory of the firm as a nexus of contracts.The story of how Turner has come to serve this gender-charged iconic function helps clarify how the balance of representational power continues to shift back and forth between these two visions during a period of considerable upheaval in the social, legal, and symbolic construction of the American corporation.
The influence of contact chemical signals on mate recognition in an harpacticoid copepod
Authors: Frey Melissa A. , Lonsdale Darcy J. , Snell Terry W.
Published: July 2002

Among copepods, reproduction is facilitated by a combination of sensory modalities, such as mechano– and chemoreception. The role of chemical communication in copepod mate recognition was assessed using behavioural bioassays that were based on precopulatory behaviours of an estuarine harpacticoid,Coullana canadensis, and the sibling speciesCoullanasp. Intra– and interspecific crosses demonstrated that males recognize genetically distinct conspecific and heterospecific females, indicating that prezygotic isolation remains incomplete. There was no association between the frequency of mate–guarding behaviour and geographic distance between populations ofC. canadensis. However, reduced levels of interspecific mate guarding relative to intraspecific frequencies suggest the existence of a species–specific mate–recognition system. Lectins, which possess strong affinities for specific carbohydrate groups, were used to confirm that glycoproteins on the surface of females function as mate–recognition factors. Information regarding the chemical composition of these molecules was derived from observed effects of lectin binding to females on male mate–guarding behaviour. Mate guarding was inhibited within all tested populations when treated withTriticum vulgaris, a lectin that possesses an affinity for carbohydrates of the N–acetylglucosamine group. Surface glycoproteins responsible for mate recognition in the two species ofCoullanamay be glycosylated with monosaccharides from this group. Differential responses to lectin treatments suggested that composition of the contact chemical cues vary among populations ofC. canadensisand between species. Yet, populations that appeared most similar based on shared lectin responses successfully discriminated against each other in mate–selection experiments. These findings indicate that contact chemical cues probably act in concert with additional factors to promote effective mate recognition and thereby contribute to reproductive success.
The distribution, abundance and seasonality of pelagic marine invertebrate larvae in the maritime Antarctic
Authors: Stanwell-Smith Damon , Peck Lloyd S. , Clarke Andrew , Murray Alistair W. A. , Todd Christopher D.
Published: July 2002

A survey of pelagic larvae was undertaken between November 1992 and February 1995 at Signy Island, Antarctica (60° 43′ S, 45° 36′ W). A diver–towed net and hand–held plankton pump were used at five sites of varying depths (6–30 m) and benthic substrata, in a combination of monthly and fortnightly samples. Overall larval ecological diversity was much higher than expected, with 131 morphologically distinct larval forms collected, apparently representing most of the benthic phyla present. The species richness observed is comparable with levels recorded at temperate latitudes, and higher than Arctic data and the implications for Thorson's rule (the inferred cline of reduced pelagic larval diversity towards high latitudes) is discussed. Larval abundances were low (mean 2.6 individuals per m3) which were two to six orders of magnitude lower than peaks in comparable data from temperate and tropical zones. We suggest that the low abundances recorded are a reflection of both slow developmental rates and a high dilution of larvae, reducing synchrony and spreading larvae over larger distances. Three seasonal periods, during which different larval types occur, have been identified. Summer, late summer and winter spawning strategies were discernable, and in some groups larvae occurred throughout the year.
The antigenicity of tobacco mosaic virus
Authors: Regenmortel M. H. V. van
Published: July 2002

The antigenic properties of the tobacco mosaic virus (TMV) have been studied extensively for more than 50 years. Distinct antigenic determinants called neotopes and cryptotopes have been identified at the surface of intact virions and dissociated coat protein subunits, respectively, indicating that the quaternary structure of the virus influences the antigenic properties. A correlation has been found to exist between the location of seven to ten residue–long continuous epitopes in the TMV coat protein and the degree of segmental mobility along the polypeptide chain. Immunoelectron microscopy, using antibodies specific for the bottom surface of the protein subunit, showed that these antibodies reacted with both ends of the stacked disk aggregates of viral protein. This finding indicates that the stacked disks are bipolar and cannot be converted directly into helical viral rods as has been previously assumed. TMV epitopes have been mapped at the surface of coat protein subunits using biosensor technology. The ability of certain monoclonal antibodies to block the co–translational disassembly of virions during the infection process was found to be linked to the precise location of their complementary epitopes and not to their binding affinity. Such blocking antibodies, which act by sterically preventing the interaction between virions and ribosomes may, when expressed in plants, be useful for controlling virus infection.
Mechanisms of molecular evolution
Authors: Ohta Tomoko
Published: July 2002

Both drift and selection are important for nucleotide substitutions in evolution. The nearly neutral theory was developed to clarify the effects of these processes. In this article, the nearly neutral theory is presented with special reference to the nature of weak selection. The mean selection coefficient is negative, and the variance is dependent on the environmental diversity. Some facts relating to the theory are reviewed. As well as nucleotide substitutions, illegitimate recombination events such as duplications, deletions and gene conversions leave indelible marks on molecular evolution. Gene duplication and conversion are sources of the evolution of new gene functions. Positive selection is necessary for the evolution of novel functions. However, many examples of current gene families suggest that both drift and selection are at work on their evolution.
Putting theLeishmaniagenome to work: functional genomics by transposon trapping and expression profiling
Authors: Beverley Stephen M. , Akopyants Natalia S. , Goyard Sophie , Matlib Robin S. , Gordon Jennifer L. , Brownstein Bernard H. , Stormo Gary D. , Bukanova Elena N. , Hott Christian T. , Li Fugen , MacMillan Sandra , Muo James N. , Schwertman Libbey A. , Smeds Matthew R. , Wang Yujia
Published: July 2002

Leishmaniaare important protozoan pathogens of humans in temperate and tropical regions. The study of gene expression during the infectious cycle, in mutants or after environmental or chemical stimuli, is a powerful approach towards understanding parasite virulence and the development of control measures. Like other trypanosomatids,Leishmaniagene expression is mediated by a polycistronic transcriptional process that places increased emphasis on post–transcriptional regulatory mechanisms including RNA processing and protein translation. With the impending completion of theLeishmaniagenome, global approaches surveying mRNA and protein expression are now feasible. Our laboratory has developed theDrosophilatransposonmarineras a tool for trappingLeishmaniagenes and studying their regulation in the form of protein fusions; a classic approach in other microbes that can be termed ‘proteogenomics’. Similarly, we have developed reagents and approaches for the creation of DNA microarrays, which permit the measurement of RNA abundance across the parasite genome. Progress in these areas promises to greatly increase our understanding of global mechanisms of gene regulation at both mRNA and protein levels, and to lead to the identification of many candidate genes involved in virulence.
Solution structure of a K+‐channel blocker from the scorpion Tityus cambridgei
Authors: Wang Iren , Wu Shih‐Hsiung , Chang Hsueh‐Kai , Shieh Ru‐Chi , Yu Hui‐Ming , Chen Chinpan
Published: July 2002

A new K+‐channel blocking peptide identified from the scorpion venom of Tityus cambridgei (Tc1) is composed of 23 amino acid residues linked with three disulfide bridges. Tc1 is the shortest known toxin from scorpion venom that recognizes the Shaker B K+ channels and the voltage‐dependent K+ channels in the brain. Synthetic Tc1 was produced using solid‐phase synthesis, and its activity was found to be the same as that of native Tc1. The pairings of three disulfide bridges in the synthetic Tc1 were identified by NMR experiments. The NMR solution structures of Tc1 were determined by simulated annealing and energy‐minimization calculations using the X‐PLOR program. The results showed that Tc1 contains an α‐helix and a 310‐helix at N‐terminal Gly4–Lys10 and a double‐stranded β‐sheet at Gly13–Ile16 and Arg19–Tyr23, with a type I′ β‐turn at Asn17–Gly18. Superposition of each structure with the best structure yielded an average root mean square deviation of 0.26 ± 0.05 Å for the backbone atoms and of 1.40 ± 0.23 Å for heavy atoms in residues 2 to 23. The three‐dimensional structure of Tc1 was compared with two structurally and functionally related scorpion toxins, charybdotoxin (ChTx) and noxiustoxin (NTx). We concluded that the C‐terminal structure is the most important region for the blocking activity of voltage‐gated (Kv‐type) channels for scorpion K+‐channel blockers. We also found that some of the residues in the larger scorpion K+‐channel blockers (31 to 40 amino acids) are not involved in K+‐channel blocking activity.
Fluorescence correlation spectroscopy as a method for assessment of interactions between phage displaying antibodies and soluble antigen
Authors: Lagerkvist Ann Catrin , Földes‐Papp Zeno , Persson Mats A.A. , Rigler Rudolf
Published: July 2002

Phage display is widely used for expression of combinatorial libraries, not least for protein engineering purposes. Precise selection at the single molecule level will provide an improved tool for generating proteins with complex and distinct properties from large molecular libraries. To establish such an improved selection system, we here report the detection of specific interactions between phage with displayed antibody fragments and fluorescently labeled soluble antigen based on Fluorescence Correlation Spectroscopy (FCS). Our novel strategy comprises the use of two separate fluorochromes for detection of the phage–antigen complex, either with labeled antiphage antibody or using a labeled antigen. As a model system, we studied a human monoclonal antibody to the hepatitis‐C virus (HCV) envelope protein E2 and its cognate antigen (rE2 or rE1/E2). We could thus assess the specific interactions and determine the fraction of specific versus background phage (26% specific phage). Aggregation of these particular antigens made it difficult to reliably utilize the full potential of cross‐correlation studies using the two labels simultaneously. However, with true monomeric proteins, this will certainly be possible, offering a great advantage in a safer and highly specific detection system.
Asymmetric zonal shim coils for magnetic resonance applications
Authors: Forbes Larry K. , Crozier Stuart
Published: July 2002

A method is presented for the systematic design of asymmetric zonal shim coils for magnetic resonance applications. Fourier‐series methods are used to represent the magnetic field inside and outside a circular cylinder of length and radius a. The current density on the cylinder is also represented using Fourier series. Any desired field can be specified in advance on the cylinder's radius, over some nonsymmetric portion of the coil's length Periodic extension of the field is used, in a way that guarantees the continuity of the field, and therefore gives good convergence of the Fourier series. All that is required is to calculate the Fourier coefficients associated with the specified desired field, and from these, the current density on the coil and the magnetic field components then follow automatically. The method is illustrated by applying it to three sample zonal coil designs, namely, linear, quadratic, and cubic fields located asymmetrically in the coil. Current densities and corresponding coil winding patterns are shown for these three illustrative cases. Field calculations directly from the coil patterns and spherical harmonic deconvolutions of these fields indicate that the example designs match the theory well. Asymmetric shim coils can be used in conventional symmetric MRI magnets, particularly those architected for “head‐only” studies. One of their major applications is expected to be in the newly developed asymmetric magnet systems.
A fast and efficient method for sequential cone‐beam tomography
Authors: Köhler Th. , Proksa R. , Grass M.
Published: July 2002

Sequential cone‐beam tomography is a method that uses data of two or more parallel circular trajectories of a cone‐beam scanner to reconstruct the object function. We propose a condition for the data acquisition that ensures that all object points between two successive circles are irradiated over an angular span of the x‐ray source position of exactly 360° in total as seen along the rotation axis. A fast and efficient approximative reconstruction method for the proposed acquisition is presented which uses data from exactly 360° for every object point. It is based on the Tent‐FDK method which was recently developed for single circular cone‐beam CT. The measurement geometry does not provide sufficient data for exact reconstruction but it is shown that the proposed reconstruction method provides satisfying image quality for small cone angles.
Calibration and quality assurance for rounded leaf‐end MLC systems
Authors: Graves Maria N. , Thompson Antoinette V. , Martel Mary K. , McShan Daniel L. , Fraass Benedick A.
Published: July 2002

Multileaf collimator (MLC) systems are available on most commercial linear accelerators, and many of these MLC systems utilize a design with rounded leaf ends and linear motion of the leaves. In this kind of system, the agreement between the digital MLC position readouts and the light field or radiation field edges must be achieved with software, since the leaves do not move in a focused motion like that used for most collimator jaw systems. In this work we address a number of the calibration and quality assurance issues associated with the acceptance, commissioning, and routine clinical use of this type of MLC system. These issues are particularly important for MLCs used for various types of intensity modulated radiation therapy (IMRT) and small, conformal fields. For rounded leaf end MLCs, it is generally not possible to make both the light and radiation field edges agree with the digital readout, so differences between the two kinds of calibrations are illustrated in this work using one vendor's MLC system. It is increasingly critical that the MLC leaf calibration be very consistent with the radiation field edges, so in this work a methodology for performing accurate radiation field size calibration is discussed. A system external to the vendor's MLC control system is used to correct or handle limitations in the MLC control system. When such a system of corrections is utilized, it is found that the MLC radiation field size can be defined with an accuracy of approximately 0.3 mm, much more accurate than most vendor's specifications for MLC accuracy. Quality assurance testing for such a calibration correction system is also demonstrated.
Experiments with electrical resistive networks
Authors: Denardo Bruce , Earwood John , Sazonova Vera
Published: July 2002

Theoretical problems involving equivalent resistances of large or infinite networks of resistors have received substantial attention. We consider two actual networks. In the first, the resistance is measured across one end of a ladder whose number of loops is incremented until the precision of the multimeter is exceeded. In the second, resistances are measured across nodes near the center of a 12 by 12 square grid of resistors. These experiments are useful in the introductory physics laboratory as interesting examples of equivalent resistance, and can be added to a standard Ohm’s law experiment. The square grid apparatus also can be employed for lecture demonstrations. In addition, this apparatus offers approximate experimental confirmation of complicated theoretical calculations for the equivalent resistance between two nonadjacent nodes of an infinite square grid. These experimental results are verified numerically.
Room reverberation effects in hearing aid feedback cancellation
Authors: Kates James M.
Published: July 2002

Room reverberation can affect feedback cancellation in hearing aids, with the strength of the effects depending on the acoustical conditions. These effects were studied using a behind the ear (BTE) hearing aid mounted on a dummy head and coupled to the ear canal via an open fitting. The hearing aid impulse response was measured for the dummy head placed at eight closely spaced locations in a typical office. The feedback cancellation in the hearing aid used a set of filter coefficients that were initialized for one location within the room, and then allowed to adapt to the feedback path measured at the same or to a different location. The maximum stable gain for the hearing aid was then estimated without feedback cancellation, for the initial set of feedback cancellation filter coefficients prior to adaptation, and for the feedback cancellation filter after adaptation. A low-order ARMA model combining a fixed set of poles with an adaptive FIR filter is shown to be effective in representing the feedback path exclusive of reverberation. Increasing the adaptive filter length has only a small benefit in improving the feedback cancellation performance due to the inability of the system to model the room reverberation. The mismatch between the modeled and actual feedback paths limits the headroom increase that can be achieved when using feedback cancellation, and varies with the location within the room.
Coding of concurrent vocal signals by the auditory midbrain: Effects of stimulus level and depth of modulation
Authors: Bodnar Deana A. , Bass Andrew H.
Published: July 2002

The segregation of concurrent vocal signals is an auditory processing task faced by all vocal species. To segregate concurrent signals, the auditory system must encode the spectral and temporal features of the fused waveforms such that at least one signal can be individually detected. In the plainfin midshipman fish (Porichthys notatus), the overlapping mate calls of neighboring males produce acoustic beats with amplitude and phase modulations at the difference frequencies (dF) between spectral components. Prior studies in midshipman have shown that midbrain neurons provide a combinatorial code of the temporal and spectral characteristics of beats via synchronization of spike bursts to dF and changes in spike rate and interspike intervals with changes in spectral composition. In the present study we examine the effects of changes in signal parameters of beats (overall intensity level and depth of modulation) on the spike train outputs of midbrain neurons. The observed changes in spike train parameters further support the hypothesis that midbrain neurons provide a combinatorial code of the spectral and temporal features of concurrent vocal signals.
Blocking property of energy vortices in elastic waveguides
Authors: Glushkov Evgeny , Glushkova Natalya
Published: July 2002

Energy vortices in time-averaged energy flows of time-harmonic fields are considered. The purpose of the paper is to verify the supposition that the energy flux along an elastic waveguide with an obstacle is blocked completely at the stop frequencies by the vortices. It is hoped that this work will draw attention to the analogy between energy and fluid flows which is potentially fruitful for understanding various wave phenomena. The normal-mode diffraction by a surface punch on an elastic layer is taken as an example. For tracing energy streamlines in the near field up to the obstacle, a special efficient semianalytical approach has been developed. To illustrate the stated supposition, plots of transmission coefficients versus frequency and figures of the near-field streamline structures are given.