bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of core antigen epitopes of hepatitis B virus
Authors: Belnap D. M. , Watts N. R. , Conway J. F. , Cheng N. , Stahl S. J. , Wingfield P. T. , Steven A. C.
Published: September 2003

Core antigen (cAg), the viral capsid, is one of the three major clinical antigens of hepatitis B virus. cAg has been described as presenting either one or two conformational epitopes involving the “immunodominant loop.” We have investigated cAg antigenicity by cryo-electron microscopy at ≈11-Å resolution of capsids labeled with monoclonal Fabs, combined with molecular modeling, and describe here two conformational epitopes. Both Fabs bind to the dimeric external spikes, and each epitope has contributions from the loops on both subunits, explaining their discontinuous nature: however, their binding aspects and epitopes differ markedly. To date, four cAg epitopes have been characterized: all are distinct. Although only two regions of the capsid surface are accessible to antibodies, local clustering of the limited number of exposed peptide loops generates a potentially extensive set of discontinuous epitopes. This diversity has not been evident from competition experiments because of steric interference effects. These observations suggest an explanation for the distinction between cAg and e-antigen (an unassembled form of capsid protein) and an approach to immunodiagnosis, exploiting the diversity of cAg epitopes.
Dynamic inhibition of excitatory synaptic transmission by astrocyte-derived ATP in hippocampal cultures
Authors: Koizumi Schuichi , Fujishita Kayoko , Tsuda Makoto , Shigemoto-Mogami Yukari , Inoue Kazuhide
Published: September 2003

Originally ascribed passive roles in the CNS, astrocytes are now known to have an active role in the regulation of synaptic transmission. Neuronal activity can evoke Ca2+transients in astrocytes, and Ca2+transients in astrocytes can evoke changes in neuronal activity. The excitatory neurotransmitter glutamate has been shown to mediate such bidirectional communication between astrocytes and neurons. We demonstrate here that ATP, a primary mediator of intercellular Ca2+signaling among astrocytes, also mediates intercellular signaling between astrocytes and neurons in hippocampal cultures. Mechanical stimulation of astrocytes evoked Ca2+waves mediated by the release of ATP and the activation of P2 receptors. Mechanically evoked Ca2+waves led to decreased excitatory glutamatergic synaptic transmission in an ATP-dependent manner. Exogenous application of ATP does not affect postsynaptic glutamatergic responses but decreased presynaptic exocytotic events. Finally, we show that astrocytes exhibit spontaneous Ca2+waves mediated by extracellular ATP and that inhibition of these Ca2+responses enhanced excitatory glutamatergic transmission. We therefore conclude that ATP released from astrocytes exerts tonic and activity-dependent down-regulation of synaptic transmission via presynaptic mechanisms.
A dually active anthrax vaccine that confers protection against both bacilli and toxins
Authors: Rhie Gi-Eun , Roehrl Michael H. , Mourez Michael , Collier R. John , Mekalanos John J. , Wang Julia Y.
Published: September 2003

Systemic anthrax is caused by unimpeded bacillar replication and toxin secretion. We developed a dually active anthrax vaccine (DAAV) that confers simultaneous protection against both bacilli and toxins. DAAV was constructed by conjugating capsular poly-γ-
d
-glutamic acid (PGA) to protective antigen (PA), converting the weakly immunogenic PGA to a potent immunogen, and synergistically enhancing the humoral response to PA. PGA-specific antibodies bound to encapsulated bacilli and promoted the killing of bacilli by complement. PA-specific antibodies neutralized toxin activity and protected immunized mice against lethal challenge with anthrax toxin. Thus, DAAV combines both antibacterial and antitoxic components in a single vaccine against anthrax. DAAV introduces a vaccine design that may be widely applicable against infectious diseases and provides additional tools in medicine and biodefense.
CD4+CD25+T cells responding to serologically defined autoantigens suppress antitumor immune responses
Authors: Nishikawa Hiroyoshi , Kato Takuma , Tanida Koji , Hiasa Atsunori , Tawara Isao , Ikeda Hiroaki , Ikarashi Yoshinori , Wakasugi Hiro , Kronenberg Mitchell , Nakayama Toshinori , Taniguchi Masaru , Kuribayashi Kagemasa , Old Lloyd J. , Shiku Hiroshi
Published: September 2003

A variety of tumor-derived antigens have been defined by IgG antibodies in tumor bearers' sera with serological identification of antigens by recombinant expression cloning (SEREX), a serological expression cloning method. The majority of these antigens show no structural abnormality and seem to be wild-type autoantigens. Coimmunization with DNA encoding these autoantigens and tumor-specific cytotoxic T lymphocytes epitopes heightened CD8+T cell responses and increased resistance to tumor challenge in a CD4+T cell-dependent manner. In contrast, immunization with these SEREX-defined autoantigens alone leads to heightened susceptibility to tumor challenge. This suppressive effect of immunization is mediated by CD4+CD25+T cells. In mice immunized with one of the SEREX-defined autoantigens, Dna J-like 2, the number of α-GalCer/CD1d tetramer+CD3+T cells [representing natural killer T (NKT) cells] was reduced in the pulmonary compartment, whereas no evident change in the number of other T cell subsets was observed. Experiments with Jα281–/–mice lacking most NKT cells indicate that NKT cells are primarily responsible for metastasis suppression and that their activity is inhibited by immunization with Dna J-like 2. We propose that SEREX identifies a pool of autoantigens that maintains and regulates immunological homeostasis via CD4+CD25+regulatory T cells.
Wnt4 overexpression disrupts normal testicular vasculature and inhibits testosterone synthesis by repressing steroidogenic factor 1/β-catenin synergy
Authors: Jordan Brian K. , Shen Jennifer H.-C. , Olaso Robert , Ingraham Holly A. , Vilain Eric
Published: September 2003

Genetic studies in mice suggest that Wnt4 signaling antagonizes expression of male hormones and effectively blocks male development in the female embryo. We recently identified an XY intersex patient carrying a chromosomal duplication of the
WNT4
locus and proposed that this patient's feminization arises from an increased dosage of WNT4. To test this hypothesis, a transgenic mouse was generated with a large genomic P1 containing the human
WNT4
. Although a complete male to female intersex phenotype was not observed in
WNT4
transgenic male mice, a dramatic reduction in steroidogenic acute regulatory protein was detected consistent with the marked reduction in serum and testicular androgen levels. Furthermore, a mild reduction of germ cells and a disorganized vascular system were observed in testes of
WNT4
transgenic males. Consistent with these
in vivo
data, Wnt4 repressed steroidogenesis in adrenocortical and Leydig cell lines, as evidenced by reduced progesterone secretion and 3β-hydroxysteroid dehydrogenase activity.
In vitro
studies showed that Wnt4 antagonizes the functional synergy observed between the major effector of the Wnt signaling pathway, β-catenin and steroidogenic factor 1, and chromatin immunoprecipitation showed that Wnt4 attenuates recruitment of β-catenin to the steroidogenic acute regulatory protein promoter. Our findings suggest a model in which Wnt4 acts as an anti-male factor by disrupting recruitment of β-catenin at or near steroidogenic factor 1 binding sites present in multiple steroidogenic genes.
Phagocytosis by neutrophils induces an amino acid deprivation response in
Saccharomyces cerevisiae
and
Candida albicans
Authors: Rubin-Bejerano Ifat , Fraser Iain , Grisafi Paula , Fink Gerald R.
Published: September 2003

The transcriptional profiles of yeast cells that have been phagocytosed by either human neutrophils or monocytes were compared by using whole genome arrays. After phagocytosis by neutrophils, both
Saccharomyces cerevisiae
and
Candida albicans
respond by inducing genes of the methionine and arginine pathways. Neither of these pathways is induced upon phagocytosis by monocytes. Both fungi show a similar induction of these pathways when transferred from amino acid-rich medium to amino acid-deficient medium. These data suggest that the internal phagosome of the neutrophil is an amino acid-deficient environment.
Transcription factor JunD, deprived of menin, switches from growth suppressor to growth promoter
Authors: Agarwal Sunita K. , Novotny Elizabeth A. , Crabtree Judy S. , Weitzman Jonathan B. , Yaniv Moshe , Burns A. Lee , Chandrasekharappa Settara C. , Collins Francis S. , Spiegel Allen M. , Marx Stephen J.
Published: September 2003

Different components of the AP1 transcription factor complex appear to have distinct effects on cell proliferation and transformation. In contrast to other AP1 components, JunD has been shown to inhibit cell proliferation. Also, in prior studies, JunD alone bound menin, product of the
MEN1
tumor suppressor gene, and JunD's transcriptional activity was inhibited by menin, suggesting that JunD might achieve all or most of its unique properties through binding to menin. Analyses of JunD and menin effects on proliferation, morphology, and cyclin D1 in stable cell lines unmasked an unexpected growth promoting activity of JunD. Whereas stable overexpression of wild-type (wt) mouse JunD in
JunD
–
/
–
immortalized fibroblasts inhibited their proliferation and reverted their transformed-like phenotype, overexpression of a missense mouse JunD mutant (mJunD
G42E
) with disabled binding to menin showed opposite or growth promoting effects. Similarly, stable overexpression of wt mouse JunD in wt immortalized fibroblasts inhibited growth. In contrast, its overexpression in
Men1
–
/
–
immortalized fibroblasts enhanced their already transformed-like characteristics. To conclude, JunD changed from growth suppressor to growth promoter when its binding to menin was prevented by a JunD mutant unable to bind menin or by
Men1
-null genetic background.
El Niño drives timing of breeding but not population growth in the song sparrow (Melospiza melodia)
Authors: Wilson Scott , Arcese Peter
Published: September 2003

Increasing evidence suggests that climate change affects the timing of breeding in birds, but there is less evidence to show how such changes affect the population dynamics of birds overall. Over the past 43 years, song sparrows (Melospiza melodia) on Mandarte Island, British Columbia, Canada have not shown an advance in breeding date in response to global warming. However, this population did show considerable annual variation in timing of breeding correlated with the El Niño Southern Oscillation. Birds bred earlier in warmer El Niño years and later in colder La Niña years. Early breeding strongly increased reproductive output. However, annual variation in timing of breeding had little effect on population growth, perhaps because the population is strongly regulated by the rate of recruitment by juveniles. The juvenile recruitment rate declined with increasing population density but showed little response to climate. These findings suggest that populations will vary in response to climate change depending on how climate affects the demographic parameters that contribute most to population growth.
Differential substrate-induced signaling through the TonB-dependent transporter BtuB
Authors: Cadieux Nathalie , Phan Phu G. , Cafiso David S. , Kadner Robert J.
Published: September 2003

The BtuB transporter mediates high-affinity binding and TonB-dependent active transport of vitamin B12 [cyanocobalamin (CNCbl)] across the outer membrane of
Escherichia coli
. A characteristic feature of TonB-dependent transporters is the Ton box, a conserved sequence near the N terminus and exposed to the periplasm. Crosslinking to TonB and site-directed spin labeling indicated that the Ton box of BtuB undergoes a substantial conformational transition in response to CNCbl binding, but only slight movement was seen in crystal structures. An
in vivo
method of detecting substrate-induced changes in the Ton box environment measured reaction of a biotin maleimide derivative with cysteine substitutions through the N-terminal region of BtuB between positions 1 and 31. The degree of maleimide labeling of different residues correlated with their accessibility in the crystal structure. Labeling of many positions was increased strongly when CNCbl was present, consistent with the undocking of this region proposed from spin-labeling analyses. The receptor-binding domain of colicin E3, which binds to BtuB competitively with CNCbl, resulted in decreased labeling. Both substrate-induced transitions occur in and beyond the Ton box and were affected by transport-uncoupling substitutions. Thus, two transport substrates that bind competitively to the extracellular face of BtuB stabilize opposite transitions of the Ton box.
Brain imaging in awake infants by near-infrared optical topography
Authors: Taga Gentaro , Asakawa Kayo , Maki Atsushi , Konishi Yukuo , Koizumi Hideaki
Published: September 2003

Studies of young infants are critical to understand perceptual, motor, and cognitive processing in humans. However, brain mechanisms involved are poorly understood, because the use of brain-imaging methods such as functional magnetic resonance imaging in awake infants is difficult. In the present study we show functional brain imaging of awake infants viewing visual stimuli by means of multichannel near-infrared spectroscopy, a technique that permits a measurement of cerebral hemoglobin oxygenation in response to brain activation through the intact skull without subject constraint. We found that event-related increases in oxyhemoglobin were evident in localized areas of the occipital cortex of infants aged 2–4 months in response to a brief presentation of a checkerboard pattern reversal while they maintained fixation to attention-grabbing stimuli. The dynamic change in cerebral blood oxygenation was qualitatively similar to that observed in the adult brain. This result introduces near-infrared optical topography as a method for investigating the functional development of the brain in early infancy.
CD8
+
T cell-mediated CXC chemokine receptor 4-simian/human immunodeficiency virus suppression in dually infected rhesus macaques
Authors: Harouse Janet M. , Buckner Clarisa , Gettie Agegnehu , Fuller Ross , Bohm Rudolf , Blanchard James , Cheng-Mayer Cecilia
Published: September 2003

We coinfected rhesus macaques with CXC chemokine receptor 4- and CC chemokine receptor 5-specific simian/human immunodeficiency viruses (SHIVs) to elucidate the basis for the early dominance of R5-tropic strains seen in HIV-infected humans. We found no intrinsic barrier to the transmission and dissemination of high-dose X4-SHIV in the dually infected macaques. In animals that maintained a viral set point, the R5 virus predominated. The time of appearance of R5 dominance coincided with the development of virus-specific immunity (3–6 weeks postinfection), suggestive of differential immune control of the two viruses. Indeed, after depletion of CD8
+
T cells in the coinfected animals, X4 virus emerged, supporting the concept that differential CD8
+
T cell-mediated immune control of X4- and R5-SHIV replication is responsible for the selective outgrowth of R5 viruses. These findings provide critical insights into a key question related to HIV pathogenesis and have important implications for the development and testing of antiviral vaccines and therapeutics.
Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of
Arabidopsis
responding to pathogen infection
Authors: Katagiri Fumiaki , Glazebrook Jane
Published: September 2003

A major task in computational analysis of mRNA expression profiles is definition of relationships among profiles on the basis of similarities among them. This is generally achieved by pattern recognition in the distribution of data points representing each profile in a high-dimensional space. Some drawbacks of commonly used pattern recognition algorithms stem from their use of a globally linear space and/or limited degrees of freedom. A pattern recognition method called Local Context Finder (LCF) is described here. LCF uses nonlinear dimensionality reduction for pattern recognition. Then it builds a network of profiles based on the nonlinear dimensionality reduction results. LCF was used to analyze mRNA expression profiles of the plant host
Arabidopsis
interacting with the bacterial pathogen
Pseudomonas syringae
. In one case, LCF revealed two dimensions essential to explain the effects of the
NahG
transgene and the
ndr1
mutation on resistant and susceptible responses. In another case, plant mutants deficient in responses to pathogen infection were classified on the basis of LCF analysis of their profiles. The classification by LCF was consistent with the results of biological characterization of the mutants. Thus, LCF is a powerful method for extracting information from expression profile data.
Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates
Authors: Akhunov Eduard D. , Akhunova Alina R. , Linkiewicz Anna M. , Dubcovsky Jorge , Hummel David , Lazo Gerry , Chao Shiaoman , Anderson Olin D. , David Jacques , Qi Lili , Echalier Benjamin , Gill Bikram S. , Miftahudin  , Gustafson J. Perry , La Rota Mauricio , Sorrells Mark E. , Zhang Deshui , Nguyen Henry T. , Kalavacharla Venugopal , Hossain Khwaja , Kianian Shahryar F. , Peng Junhua , Lapitan Nora L. V. , Wennerlind Emily J. , Nduati Vivienne , Anderson James A. , Sidhu Deepak , Gill Kulvinder S. , McGuire Patrick E. , Qualset Calvin O. , Dvorak Jan
Published: September 2003

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.
Genetic regulation of telomere-telomere fusions in the yeast
Saccharomyces cerevisae
Authors: Mieczkowski Piotr A. , Mieczkowska Joanna O. , Dominska Margaret , Petes Thomas D.
Published: September 2003

Yeast strains with mutations in both
TEL1
and
MEC1
have short telomeres and elevated rates of chromosome deletions. By using a PCR assay, we demonstrate that
mec1 tel1
strains also have telomere–telomere fusions (T-TFs). T-TFs require Lig4p (a ligase required for nonhomologous end-joining DNA repair). The highest rates of T-TFs are found in strains with combination of mutations that affect telomere length and DNA damage checkpoints (
mec1 tel1
,
mec3 tel1
,
mre11 mec1
, and
ddc1 tel1
strains). Examining many mutant genotypes, we find good agreement between the level of T-TFs and the rate of chromosomal deletions. In addition, if telomeres are elongated in a
mec1 tel1
strain, we eliminate T-TFs and reduce the deletion rate. The correlation between the level of T-TFs and the rate of deletions argues that many of these deletions reflect a cycle of T-TF formation (resulting in dicentric chromosomes), followed by chromosome breakage.
Developmental defects and p53 hyperacetylation in Sir2 homolog (SIRT1)-deficient mice
Authors: Cheng Hwei-Ling , Mostoslavsky Raul , Saito Shin'ichi , Manis John P. , Gu Yansong , Patel Parin , Bronson Roderick , Appella Ettore , Alt Frederick W. , Chua Katrin F.
Published: September 2003

SIRT1 is a mammalian homolog of the
Saccharomyces cerevisiae
chromatin silencing factor Sir2. Dominant-negative and overexpression studies have implicated a role for SIRT1 in deacetylating the p53 tumor suppressor protein to dampen apoptotic and cellular senescence pathways. To elucidate SIRT1 function in normal cells, we used gene-targeted mutation to generate mice that express either a mutant SIRT1 protein that lacks part of the catalytic domain or has no detectable SIRT1 protein at all. Both types of SIRT1 mutant mice and cells had essentially the same phenotypes. SIRT1 mutant mice were small, and exhibited notable developmental defects of the retina and heart, and only infrequently survived postnatally. Moreover, SIRT1-deficient cells exhibited p53 hyperacetylation after DNA damage and increased ionizing radiation-induced thymocyte apoptosis. In SIRT1-deficient embryonic fibroblasts, however, p53 hyperacetylation after DNA damage was not accompanied by increased p21 protein induction or DNA damage sensitivity. Together, our observations provide direct evidence that endogenous SIRT1 protein regulates p53 acetylation and p53-dependent apoptosis, and show that the function of this enzyme is required for specific developmental processes.
GABA-enhanced collective behavior in neuronal axons underlies persistent gamma-frequency oscillations
Authors: Traub R. D. , Cunningham M. O. , Gloveli T. , LeBeau F. E. N. , Bibbig A. , Buhl E. H. , Whittington M. A.
Published: September 2003

Gamma (30–80 Hz) oscillations occur in mammalian electroencephalogram in a manner that indicates cognitive relevance.
In vitro
models of gamma oscillations demonstrate two forms of oscillation: one occurring transiently and driven by discrete afferent input and the second occurring persistently in response to activation of excitatory metabotropic receptors. The mechanism underlying persistent gamma oscillations has been suggested to involve gap-junctional communication between axons of principal neurons, but the precise relationship between this neuronal activity and the gamma oscillation has remained elusive. Here we demonstrate that gamma oscillations coexist with high-frequency oscillations (>90 Hz). High-frequency oscillations can be generated in the axonal plexus even when it is physically isolated from pyramidal cell bodies. They were enhanced in networks by nonsomatic γ-aminobutyric acid type A (GABA
A
) receptor activation, were modulated by perisomatic GABA
A
receptor-mediated synaptic input to principal cells, and provided the phasic input to interneurons required to generate persistent gamma-frequency oscillations. The data suggest that high-frequency oscillations occurred as a consequence of random activity within the axonal plexus. Interneurons provide a mechanism by which this random activity is both amplified and organized into a coherent network rhythm.
The ATRX syndrome protein forms a chromatin-remodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies
Authors: Xue Yutong , Gibbons Richard , Yan Zhijiang , Yang Dafeng , McDowell Tarra L. , Sechi Salvatore , Qin Jun , Zhou Sharleen , Higgs Doug , Wang Weidong
Published: September 2003

ATRX syndrome is characterized by X-linked mental retardation associated with α-thalassemia. The gene mutated in this disease,
ATRX
, encodes a plant homeodomain-like finger and a SWI2/SNF2-like ATPase motif, both of which are often found in chromatin-remodeling enzymes, but ATRX has not been characterized biochemically. By immunoprecipitation from HeLa extract, we found that ATRX is in a complex with transcription cofactor Daxx. The following evidence supports that ATRX and Daxx are components of an ATP-dependent chromatin-remodeling complex: (
i
) Daxx and ATRX can be coimmunoisolated by antibodies specific for each protein; (
ii
) a proportion of Daxx cofractionates with ATRX as a complex of 1 MDa by gel-filtration analysis; (
iii
) in extract from cells of a patient with ATRX syndrome, the level of the Daxx–ATRX complex is correspondingly reduced; (
iv
) a proportion of ATRX and Daxx colocalize in promyelocytic leukemia nuclear bodies, with which Daxx had previously been located; and (
v
) the ATRX complex displays ATP-dependent activities that resemble those of other chromatin-remodeling complexes, including triple-helix DNA displacement and alteration of mononucleosome disruption patterns. But unlike the previously described SWI/SNF or NURD complexes, the ATRX complex does not randomize DNA phasing of the mononucleosomes, suggesting that it may remodel chromatin differently. Taken together, the results suggest that ATRX functions in conjunction with Daxx in a novel chromatin-remodeling complex. The defects in ATRX syndrome may result from inappropriate expression of genes controlled by this complex.
Multiple Steps of Phosphorylation of Activated Rhodopsin Can Account for the Reproducibility of Vertebrate Rod Single-photon Responses
Authors: Hamer R.D. , Nicholas S.C. , Tranchina D. , Liebman P.A. , Lamb T.D.
Published: September 2003

Single-photon responses (SPRs) in vertebrate rods are considerably less variable than expected if isomerized rhodopsin (R*) inactivated in a single, memoryless step, and no other variability-reducing mechanisms were available. We present a new stochastic model, the core of which is the successive ratcheting down of R* activity, and a concomitant increase in the probability of quenching of R* by arrestin (Arr), with each phosphorylation of R* (Gibson, S.K., J.H. Parkes, and P.A. Liebman. 2000. Biochemistry. 39:5738–5749.). We evaluated the model by means of Monte-Carlo simulations of dim-flash responses, and compared the response statistics derived from them with those obtained from empirical dim-flash data (Whitlock, G.G., and T.D. Lamb. 1999. Neuron. 23:337–351.). The model accounts for four quantitative measures of SPR reproducibility. It also reproduces qualitative features of rod responses obtained with altered nucleotide levels, and thus contradicts the conclusion that such responses imply that phosphorylation cannot dominate R* inactivation (Rieke, F., and D.A. Baylor. 1998a. Biophys. J. 75:1836–1857; Field, G.D., and F. Rieke. 2002. Neuron. 35:733–747.). Moreover, the model is able to reproduce the salient qualitative features of SPRs obtained from mouse rods that had been genetically modified with specific pathways of R* inactivation or Ca2+ feedback disabled. We present a theoretical analysis showing that the variability of the area under the SPR estimates the variability of integrated R* activity, and can provide a valid gauge of the number of R* inactivation steps. We show that there is a heretofore unappreciated tradeoff between variability of SPR amplitude and SPR duration that depends critically on the kinetics of inactivation of R* relative to the net kinetics of the downstream reactions in the cascade. Because of this dependence, neither the variability of SPR amplitude nor duration provides a reliable estimate of the underlying variability of integrated R* activity, and cannot be used to estimate the minimum number of R* inactivation steps. We conclude that multiple phosphorylation-dependent decrements in R* activity (with Arr-quench) can confer the observed reproducibility of rod SPRs; there is no compelling need to invoke a long series of non-phosphorylation dependent state changes in R* (as in Rieke, F., and D.A. Baylor. 1998a. Biophys. J. 75:1836–1857; Field, G.D., and F. Rieke. 2002. Neuron. 35:733–747.). Our analyses, plus data and modeling of others (Rieke, F., and D.A. Baylor. 1998a. Biophys. J. 75:1836–1857; Field, G.D., and F. Rieke. 2002. Neuron. 35:733–747.), also argue strongly against either feedback (including Ca2+-feedback) or depletion of any molecular species downstream to R* as the dominant cause of SPR reproducibility.
Unitary Ca2+ Current through Mammalian Cardiac and Amphibian Skeletal Muscle Ryanodine Receptor Channels under Near-physiological Ionic Conditions
Authors: Kettlun Claudia , González Adom , Ríos Eduardo , Fill Michael
Published: September 2003

Ryanodine receptor (RyR) channels from mammalian cardiac and amphibian skeletal muscle were incorporated into planar lipid bilayers. Unitary Ca2+ currents in the SR lumen-to-cytosol direction were recorded at 0 mV in the presence of caffeine (to minimize gating fluctuations). Currents measured with 20 mM lumenal Ca2+ as exclusive charge carrier were 4.00 and 4.07 pA, respectively, and not significantly different. Currents recorded at 1–30 mM lumenal Ca2+ concentrations were attenuated by physiological [K+] (150 mM) and [Mg2+] (1 mM), in the same proportion (∼55%) in mammalian and amphibian channels. Two amplitudes, differing by ∼35%, were found in amphibian channel studies, probably corresponding to α and β RyR isoforms. In physiological [Mg2+], [K+], and lumenal [Ca2+] (1 mM), the Ca2+ current was just less than 0.5 pA. Comparison of this value with the Ca2+ flux underlying Ca2+ sparks suggests that sparks in mammalian cardiac and amphibian skeletal muscles are generated by opening of multiple RyR channels. Further, symmetric high concentrations of Mg2+ substantially reduced the current carried by 10 mM Ca2+ (∼40% at 10 mM Mg2+), suggesting that high Mg2+ may make sparks smaller by both inhibiting RyR gating and reducing unitary current.
Does Economic Development Lead to Mangrove Loss? A Cross‐Country Analysis
Authors: Barbier Edward B. , Cox Mark
Published: September 2003

Mangroves line one quarter of the world's tropical coastlines, and approximately 117 countries and territories have mangrove resources within their borders. Although over recent years mangrove deforestation has occurred at a phenomenal rate worldwide, there have been few economic studies of the underlying causes. The article attempts such an analysis and particularly examines the role of economic development, with specific reference to those activities that may result in mangrove deforestation, in determining the area of mangrove left within a country. The article develops a model of economic activity and mangrove conversion. From this model, a relationship is established between remaining mangrove area, economic activity, and other important causative factors. The mangrove area relationship is estimated empirically for a cross‐section of 89 countries. Results show that shrimp aquaculture and agriculture are significantly associated with mangrove loss across all countries, whereas the higher the level of GDP per capita the more mangrove area remains. The number of protected areas, length of coastline and political stability were also important in determining the remaining mangrove area of a country. (JEL O13, Q22, Q23, Q24)
Is the Taylor Rule Really Different from the McCallum Rule?
Authors: Razzak W. A.
Published: September 2003

When base velocity is a stable function of the Federal funds rate (FFR), the money base–nominal GDP targeting rule (McCallum rule) can be reparameterized and presented in terms of FFR as the policy instrument. Comparison of this McCallum modified policy rule with the popular Taylor rule suggests that these two rules and the FFR are actually closely related. Model‐based evaluations of the two rules' stabilization properties indicate that the modified McCallum rule is similar to the Taylor rule. The key to this result is the degree of interest rate smoothing applied to the policy rules. (JELE3,E52,E58)
An essential role of Bmp4 in the atrioventricular septation of the mouse heart
Authors: Jiao Kai , Kulessa Holger , Tompkins Kevin , Zhou Yingna , Batts Lorene , Baldwin H. Scott , Hogan Brigid L.M.
Published: September 2003

Proper septation and valvulogenesis during cardiogenesis depend on interactions between the myocardium and the endocardium. By combining use of a hypomorphicBone morphogenetic protein 4(Bmp4) allele with conditional gene inactivation, we here identify Bmp4 as a signal from the myocardium directly mediating atrioventricular septation. Defects in this process cause one of the most common human congenital heart abnormalities, atrioventricular canal defect (AVCD). The spectrum of defects obtained through alteringBmp4expression in the myocardium recapitulates the range of AVCDs diagnosed in patients, thus providing a useful genetic model with AVCD as the primary defect.
Ku interacts with telomerase RNA to promote telomere addition at native and broken chromosome ends
Authors: Stellwagen Anne E. , Haimberger Zara W. , Veatch Joshua R. , Gottschling Daniel E.
Published: September 2003

Ku is a conserved DNA end-binding protein that plays various roles at different kinds of DNA ends. At telomeres, Ku is part of the structure that protects the chromosome end, whereas at broken DNA ends, Ku promotes DNA repair as part of the nonhomologous end-joining (NHEJ) pathway. Here, we present evidence of a new role for Ku that impacts both telomere-length maintenance and DNA repair in Saccharomyces cerevisiae. We show that Ku binds TLC1, the RNA component of telomerase. We also describe a novel separation-of-function allele of Ku that is specifically defective in TLC1 binding. In this mutant, telomeres are short and the kinetics of telomere addition are slow, but other Ku-dependent activities, such as chromosome end protection and NHEJ, are unaffected. At low frequency, yeast will use telomerase to heal DNA damage by capping the broken chromosome with telomeric DNA sequences. We show that when Ku's ability to bind TLC1 is disrupted, DNA repair via telomere healing is reduced 10- to 100-fold, and the spectrum of sequences that can acquire a telomere changes. Thus, the interaction between Ku and TLC1 RNA enables telomerase to act at both broken and normal chromosome ends.
Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli
Authors: Massé Eric , Escorcia Freddy E. , Gottesman Susan
Published: September 2003

RyhB is a small antisense regulatory RNA that is repressed by the Fur repressor and negatively regulates at least six mRNAs encoding Fe-binding or Fe-storage proteins in Escherichia coli. When Fe is limiting, RyhB levels rise, and target mRNAs are rapidly degraded. RyhB is very stable when measured after treatment of cells with the transcription inhibitor rifampicin, but is unstable when overall mRNA transcription continues. We propose that RyhB turnover is coupled to and dependent on pairing with the target mRNAs. Degradation of both mRNA targets and RyhB is dependent on RNase E and is slowed in degradosome mutants. RyhB requires the RNA chaperone Hfq. In the absence of Hfq, RyhB is unstable, even when general transcription is inhibited; degradation is dependent upon RNase E. Hfq and RNase E bind similar sites on the RNA; pairing may allow loss of Hfq and access by RNase E. Two other Hfq-dependent small RNAs, DsrA and OxyS, are also stable when overall transcription is off, and unstable when it is not, suggesting that they, too, are degraded when their target mRNAs are available for pairing. Thus, this large class of regulatory RNAs share an unexpected intrinsic mechanism for shutting off their action.
The budding yeast silencing protein Sir1 is a functional component of centromeric chromatin
Authors: Sharp Judith A. , Krawitz Denise C. , Gardner Kelly A. , Fox Catherine A. , Kaufman Paul D.
Published: September 2003

In fission yeast and multicellular organisms, centromere-proximal regions of chromosomes are heterochromatic, containing proteins that silence gene expression. In contrast, the relationship between heterochromatin proteins and kinetochore function in the budding yeast Saccharomyces cerevisiae remains largely unexplored. Here we report that the yeast heterochromatin protein Sir1 is a component of centromeric chromatin and contributes to mitotic chromosome stability. Sir1 recruitment to centromeres occurred through a novel mechanism independent of its interaction with the origin recognition complex (ORC). Sir1 function at centromeres was distinct from its role in forming heterochromatin, because the Sir2-4 proteins were not associated with centromeric regions. Sir1 bound to Cac1, a subunit of chromatin assembly factor I (CAF-I), and helped to retain Cac1 at centromeric loci. These studies reveal that although budding yeast and mammalian cells use fundamentally different mechanisms of forming heterochromatin, they both use silencing proteins to attract the histone deposition factor CAF-I to centromeric chromatin.
The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment
Authors: Clark Hilary F. , Gurney Austin L. , Abaya Evangeline , Baker Kevin , Baldwin Daryl , Brush Jennifer , Chen Jian , Chow Bernard , Chui Clarissa , Crowley Craig , Currell Bridget , Deuel Bethanne , Dowd Patrick , Eaton Dan , Foster Jessica , Grimaldi Christopher , Gu Qimin , Hass Philip E. , Heldens Sherry , Huang Arthur , Kim Hok Seon , Klimowski Laura , Jin Yisheng , Johnson Stephanie , Lee James , Lewis Lhney , Liao Dongzhou , Mark Melanie , Robbie Edward , Sanchez Celina , Schoenfeld Jill , Seshagiri Somasekar , Simmons Laura , Singh Jennifer , Smith Victoria , Stinson Jeremy , Vagts Alicia , Vandlen Richard , Watanabe Colin , Wieand David , Woods Kathryn , Xie Ming-Hong , Yansura Daniel , Yi Sothy , Yu Guoying , Yuan Jean , Zhang Min , Zhang Zemin , Goddard Audrey , Wood William I. , Godowski Paul
Published: September 2003

A large-scale effort, termed the Secreted Protein Discovery Initiative (SPDI), was undertaken to identify novel secreted and transmembrane proteins. In the first of several approaches, a biological signal sequence trap in yeast cells was utilized to identify cDNA clones encoding putative secreted proteins. A second strategy utilized various algorithms that recognize features such as the hydrophobic properties of signal sequences to identify putative proteins encoded by expressed sequence tags (ESTs) from human cDNA libraries. A third approach surveyed ESTs for protein sequence similarity to a set of known receptors and their ligands with the BLAST algorithm. Finally, both signal-sequence prediction algorithms and BLAST were used to identify single exons of potential genes from within human genomic sequence. The isolation of full-length cDNA clones for each of these candidate genes resulted in the identification of >1000 novel proteins. A total of 256 of these cDNAs are still novel, including variants and novel genes, per the most recent GenBank release version. The success of this large-scale effort was assessed by a bioinformatics analysis of the proteins through predictions of protein domains, subcellular localizations, and possible functional roles. The SPDI collection should facilitate efforts to better understand intercellular communication, may lead to new understandings of human diseases, and provides potential opportunities for the development of therapeutics.
Microfabricated Fountain Pens for High-Density DNA Arrays
Authors: Reese Matthew O. , van Dam R. Michae , Scherer Axel , Quake Stephen R.
Published: September 2003

We used photolithographic microfabrication techniques to create very small stainless steel fountain pens that were installed in place of conventional pens on a microarray spotter. Because of the small feature size produced by the microfabricated pens, we were able to print arrays with up to 25,000 spots/cm2, significantly higher than can be achieved by other deposition methods. This feature density is sufficiently large that a standard microscope slide can contain multiple replicates of every gene in a complex organism such as a mouse or human. We tested carryover during array printing with dye solution, labeled DNA, and hybridized DNA, and we found it to be indistinguishable from background. Hybridization also showed good sequence specificity to printed oligonucleotides. In addition to improved slide capacity, the microfabrication process offers the possibility of low-cost mass-produced pens and the flexibility to include novel pen features that cannot be machined with conventional techniques.
The Signature of Selection Mediated by Expression on Human Genes
Authors: Urrutia Araxi O. , Hurst Laurence D.
Published: September 2003

As the efficacy of natural selection is expected to be a function of population size, in humans it is usually presumed that selection is a weak force and hence that gene characteristics are mostly determined by stochastic forces. In contrast, in species with large population sizes, selection is expected to be a much more effective force. Evidence for this has come from examining how genic parameters vary with expression level, which appears to determine many of a gene's features, such as codon bias, amino acid composition, and size. However, not until now has it been possible to examine whether human genes show the signature of selection mediated by expression level. Here, then, to investigate this issue, we gathered expression data for >10,000 human genes from public data sets obtained by different technologies (SAGE and high-density oligonucleotide chip arrays) and compared them with gene parameters. We find that, even after controlling for regional effects, highly expressed genes code for smaller proteins, have less intronic DNA, and higher codon and amino acid biases. We conclude that, contrary to the usual supposition, human genes show signatures consistent with selection mediated by expression level.
Conceptualising community consumption
Authors: Szmigin Isabelle , Maddock Sarah , Carrigan Marylyn
Published: September 2003

Since the late 1990s farmers’ markets have been growing in popularity as an alternative outlet for: healthy, local, organic and non‐organic, produce consistent with the values of green and ethical consumers, local and small producers to sell their goods and a venue where direct contact with the producers is possible and information about the goods may be sought. This paper seeks to explore further the concept of community as a key attribute of such markets. The paper argues that farmers’ markets can provide many of the exchanges consistent with the concept of community and that these are of significant importance to many shoppers but are particularly valued by older consumers.
Fighting an uphill battle: teaching information literacy in Danish institutions of higher education
Authors: Skov Annette , Skærbak Helli
Published: September 2003

The article addresses the development and present state of information literacy activities in Danish institutions of higher education. It outlines the national policy on information literacy, emphasising the crucial role of the Danish Electronic Research Library (DEF). The importance of integrating information literacy sessions into the curriculum is highlighted together with an examination of the barriers that make integration difficult. Strategic alliances and new forms of liaison schemes are presented followed by a description of learning resource centres and Web‐based tutorials and e‐learning activities. The important role of professional groups in setting the agenda for information literacy discussions and knowledge sharing is recognised; and finally, the paper outlines the various educational opportunities open to library school students and academic librarians engaged in teaching information literacy.
The video role model as an enterprise teaching aid
Authors: Robertson Martyn , Collins Amanda
Published: September 2003

This article examines the need to develop a more enterprising approach to learning by adopting an experiential approach. It specifically examines the use of video case studies of entrepreneurial role models within an enterprise module at Leeds Metropolitan University. The exercise enables students to act as a consultant or counsellor and apply models, theories, tools and techniques to gain an understanding of the entrepreneurial process and the entrepreneur. The transcript from one video role model, Vio, a digital data and network company, has been summarised for examination, so that its use by a variety of specialists might be explored. The learning outcomes from using the video case study and the module being undertaken by the students are analysed to determine the changes that have taken place in the areas of awareness of skills, self‐development, confidence and career aspirations.
The controversial role of personality traits in entrepreneurial psychology
Authors: Llewellyn David J. , Wilson Kerry M.
Published: September 2003

The usefulness of personality traits in the explanation and prediction of entrepreneurship is critically evaluated, and both contemporary theory and existing empirical findings are reviewed, emphasizing the need for conceptual clarity and methodological reform. Detailed recommendations for future research are outlined, and this critique is complemented by a detailed case study of a practical research design drawn from an ongoing project. Taken together, these provide a powerful illustration of how abstract principles can be used to inform research practices, and the underlying message emanating from this evolving body of knowledge can be used to enrich teaching materials and educational activities.
Computational models for biological tissues and biomedical implants
Authors: Contro R. , Vena P.
Published: September 2003

This paper aims at showing that the finite element method is the most important numerical tool to analyse bio‐solids or bio‐fluids because of the constitutive complexity and unusual clinical input data and requirements involved. These features are absolutely mandatory and modify the mentality of an expert of FEM when he wants to contribute really to the progress of medical practice in their several forms, from biological basis to the surgical assistance. In this context, a clear view of the hierarchic importance of the phenomena involved is necessary to reply correctly to medical operators and to choose the right level of scale. While a scholarly culture of FEM and relative developments have to appeal the attention of biomedical engineers, at the same time their attention mainly is focused on the problem to solve, which must be validated clinically and experimentally. So while convergence remain a typical goal of the analyst, accuracy must be compared with the medical sensitivity. To do this, some physical conditions, less important in other application fields, as the boundary conditions, must be modelled in order to avoid that any model refinement gives unappreciable precision while tends to disregard what a clinician or a surgeon is able to understand and to use in the context of his professional practice. Setting up correct boundary conditions is an emblematic topic because it concerns a typical approach of computational methods applied to biomedical engineering which must consider two separate scale into analysis or a design approach. When a district of the body is to be analysed, the main goal should be to define correctly the subdomain that the district represents with respect to the whole and then to analyse other subdomains inside, at a level more and more micro, as into a system of Chinese boxes. When a medical device is to be designed a systemic view must be acquired. In this paper, we will start from this underlying feature concerning just FEM applications of a knee design carried out by the research staff of the Laboratory of Biological Structure Mechanics. Then other uses of FEM will be described as analysis fragments through problems studied by the authors and referenced in bibliography.