bluuebunny/crossref_metadata_2025 huggingface dataset:
A study of twentieth‐century extreme rainfall events in the United Kingdom with implications for forecasting
Authors: Hand William H. , Fox Neil I. , Collier Christopher G.
Published: March 2004

Rainfall events in the United Kingdom during the twentieth century have been surveyed and those identified as extreme by the Flood Studies Report (1975) standards have been examined for common features. Events of duration up to 60 hours were considered in order to investigate those that could cause flash floods. More than half of the 50 events identified were short‐period convective storms. The rainfall events were classified by meteorological situation, location and season, allowing the identification of conditions under which extreme rainfall occurred.

Suitable conditions for extreme rainfall were split into three categories: orographic, frontal and convective. The frontal and convective classes were then divided into two sub‐classes according to whether significant embedded instability was present in the frontal cases and the nature of the convection in the convective cases. The study revealed a lot of commonality between the cases. For example, all of the orographic events occurred in winter in moist west to southwest airflows, and 80% of the frontal cases involved a slow‐moving depression to the south or east and also a slow moving frontal system. A conceptual airflow diagram has been developed for some of the frontal cases. The key result, however, was the discovery that each category of meteorological situation occupied a unique space in a rainfall amount versus duration diagram for each extreme event. This offers exciting opportunities for applying the results of this study and a framework for studying future events. Copyright © 2004 Royal Meteorological Society.
Neural networks in satellite rainfall estimation
Authors: Tapiador F. J. , Kidd C. , Hsu K.‐L. , Marzano F.
Published: March 2004

Neural networks (NNs) have been successfully used in the environmental sciences over the last two decades. However, only a few review papers have been published, most of which cover image processing, classification, prediction and geophysical retrieval in general, while neglecting rainfall estimation issues. This paper reviews, without aiming to be exhaustive, NN approaches to satellite rainfall estimation (SRE) by providing an overview of some of the methodologies proposed. A basic introduction to NNs is provided and the advantages of using NNs in SRE are explained, illustrating how NNs can be used to complement more computational‐expensive methods to generate quick and accurate results in near real time. The role of the NNs in statistical‐empirical algorithms is also reviewed. The last section aims to generate some discussion through comparing the empirical and deterministic algorithmic approaches and contrasting some of the apparent drawbacks of using NNs with a statistically based view of the satellite geophysical parameter estimation. Copyright © 2004 Royal Meteorological Society.
Self-Reported Suicidal Behavior in Juvenile Offenders in Custody: Prevalence and Associated Factors
Authors: Morgan Jenny , Hawton Keith
Published: March 2004

Summary: Suicide rates in prisons in England and Wales are high, including those in juvenile detention centers. Previous deliberate self-harm (DSH) is the strongest predictor of suicide in the general population. There is limited information on how many juvenile offenders (15 to 18 year-olds) have a history of DSH at the time of entering custody, or on factors associated with previous DSH. We aimed to determine the prevalence of previous DSH and suicidal ideation in a population of juvenile offenders in custody and to identify factors associated with DSH and suicidal ideation. Seven out of 45 subjects (15.6%) reported an act of DSH in the past. Twelve (26.6%) reported past suicidal ideation. Peer relationship difficulties and sexual abuse were significantly associated with DSH (p < 0.05). Other factors showed a trend toward being more common among those with DSH, but the premature ending of the project by the juvenile detention center prevented full investigation of the extent of DSH and associated factors. Nevertheless, the results indicated a much higher rate of DSH in this population than in young males in the community. A larger joint project with juvenile detention centers is required to confirm the extent of previous DSH at the time young offenders are admitted, and the associated risk factors, in order to assist prevention and intervention strategies.
Periokuläre Dermatitis
Authors: Dirschka Thomas , Tronnier Hagen
Published: March 2004

Hintergrund: Bei der perioralen Dermatitis können Hautveränderungen paradoxerweise den Perioralbereich gänzlich aussparen und bisweilen isoliert unter anderem im periokulären Bereich (periokuläre Dermatitis) beobachtet werden.

Patienten/Methoden: Die Karteien von 23 Patienten mit ausschließlich periokulärer Dermatitis wurden hinsichtlich folgender Parameter untersucht: klinischer Befund, Atopieanamnese, topische Behandlungen im Gesichtsbereich, Prick‐ und Epikutanteste, CAP‐SX1, Vortherapien, Abheilzeiten, Rezidive. 23 alters‐ und geschlechtsgleiche Personen, die nie unter einer periokulären Dermatitis litten, wurden als Kontrollpersonen zufällig ausgewählt (Fall‐Kontroll‐Studie).

Ergebnisse: Es traten vornehmlich Mikropapeln im lateralen Augenwinkel‐ und Unterlidbereich auf. Die Untersuchungsgruppen unterschieden sich signifikant (p < 0,05) hinsichtlich der Anamnese atopischer Erkrankungen und reaktiver Prickteste. 22 Patienten verwendeten regelmäßig Gesichts‐ oder Augenpflegeprodukte. Diese unterschieden sich nicht signifikant hinsichtlich Anzahl und Art der Produkte vom Kontrollkollektiv. 6 Patienten waren mit topischen Kortikoiden vorbehandelt. Die Abheilzeit betrug 2 – 8 Wochen (Median: 4 Wochen).

Schlußfolgerungen: Die periokuläre Dermatitis ist eine Variante der perioralen Dermatitis, wobei gleichartige pathogenetische Faktoren beobachtet werden. Die Elimination von topischen Kortikoiden und die allmähliche Reduktion von Pflegepräparaten führen regelmäßig zur Abheilung.
A Spherical Metric for the Field-Oriented Analysis of Complex Urban Open Spaces
Authors: Teller Jacques
Published: March 2004

The author deals with the analysis of urban open spaces, once conceived as part and parcel of our urban heritage. He introduces a mathematical modelling technique that is capable of mapping the variation of the sky visible from points distributed throughout space. The resulting maps overcome the limits of orthographic (plan, section, and elevation) and perspective methods of analysis by considering the dynamic qualities of the Gibsonian ‘visual world’ that takes account not only of bifocal vision but also of the relatively free movement of the head and shoulders, that is, vision as part of the human ecology. The maps show how a person might experience those volumes of a void that define a space, not from a fixed point but from moving about inside the entire urban open space.
Algorithms for Visibility Computation on Terrains: A Survey
Authors: Floriani Leila , Magillo Paola
Published: March 2004

Several environment applications require the computation of visibility information on a terrain. Examples are optimal placement of observation points, line-of-sight communication, and computation of hidden as well as scenic paths. Visibility computations on a terrain may involve either one or many viewpoints, and range from visibility queries (for example, testing whether a given query point is visible), to the computation of structures that encode the visible portions of the surface. In this paper, the authors consider a number of visibility problems on terrains and present an overview of algorithms to tackle such problems on triangulated irregular networks and regular square grids.
Fringe Belts and the Recycling of Urban Land: An Academic Concept and Planning Practice
Authors: Whitehand J W R , Morton N J
Published: March 2004

It has been well established by urban morphologists that fringe-belt development is an integral part of the historico-geographical development of cities, but such development has attracted little attention from planners. Despite the physical distinctiveness of Birmingham's Edwardian fringe belt, decisionmaking about its development is largely site-by-site. Its survival as a concentric zone with a high incidence of green space partly reflects the fact that the character and occupation of the individual sites of which it is composed have become deeply rooted in the mental maps of those able to influence change. Awareness of the fringe belt as an entity is rare: few landowners, developers, or planners see individual sites as integrated parts of the historical and ecological development of the city as a whole. Initially, pressure to redevelop fringe-belt plots has come largely from landowners. The proposed changes are often at variance with the predilections of local planners. Planners have a sectional perception, strongly related to the land use of cities. For developers, an interest in sites other than the one to which their planning application relates is almost entirely limited to the effects that adjacent sites might have on the viability of their proposal. The integrative quality of the fringe-belt concept is an important aspect of its potential as a citywide planning construct.
Investigating the Syntax Line: Configurational Properties and Cognitive Correlates
Authors: Haq Saif
Published: March 2004

Space syntax research has had significant success over the years and has served to illustrate the importance of configurational measures, especially those that take into account all the spaces in a system. Here, assumptions of axial lines as elementary spatial units have been overwhelming. Although based on a theoretical construct of visibility, this postulation has rarely been extended to perception or cognition and this has given rise to questions about geometric and metric considerations. The research presented here was carried out in three large urban hospitals. In them, 128 volunteers performed ‘open searches’, where they attempted to become familiar with the hospital; ‘directed searches’, where they sought specific locations; and various cognitive mapping tasks such as pointing to locations that were not within sight and sketching the main corridors and routes of the hospital. The hospitals themselves were analyzed through conventional syntax measures of axial lines and a segmented version of those lines. Correlational and regression analyses revealed that, although use of space was best predicted by local measures (connectivity), distribution of people was better explained through integration-3. Performance comparisons between the environmental measures given by ‘whole’ and ‘segmented’ lines suggested that, at least in complex architectural settings, original syntax definitions of axial lines as uninterrupted visibility lines have more predictive power and better cognitive presence than ‘segmented’ lines. The results also support previous findings of intelligibility as a factor in predicting space use by extending it to the cognitive realm. Additionally, it has brought out the reverse role of intelligibility-3. It was also found that mean depth of an entry effects the way a building is explored; therefore, knowledge of this spatial property may provide a fair indication of the relative importance which each space will have on wayfinding.
Modelling Natural Surveillance
Authors: Desyllas Jake , Connoly Philip , Hebbert Frank
Published: March 2004

Many commentators have suggested that the ‘natural surveillance’ of public spaces can have important social consequences such as preventing or deterring crime. In this paper we introduce a model of natural surveillance in public space which uses visibility graph analysis. The model is applied to two study areas with very different urban morphologies: a traditional street network and a modern university campus. Levels of surveillance in the traditional street network are found to be much higher than in the university campus. It is suggested that the model can be used to test for the importance of natural surveillance as a risk-reduction factor in crime prevention through environmental design.
Complete loss of the tumor suppressor MAD2 causes premature cyclin B degradation and mitotic failure in human somatic cells
Authors: Michel Loren , Diaz-Rodriguez Elena , Narayan Gopeshwar , Hernando Eva , Murty Vundavalli V. V. S. , Benezra Robert
Published: March 2004

MAD2 inhibits the anaphase-promoting complex when chromosomes are unattached to the mitotic spindle. It acts as a tumor suppressor gene because MAD2+/–cells enter anaphase early and display chromosome instability, leading to the formation of lung tumors in mice. Complete MAD2 inactivation has not been identified in human tumors, although partial defects are prevalent. By employing RNA interference in human somatic cells, we found that severe reduction of MAD2 protein levels results in mitotic failure and extensive cell death arising from defective spindle formation, incomplete chromosome condensation, and premature mitotic exit leading to multinucleation. Cyclin B is degraded prematurely in the MAD2 short interfering RNA-treated cells but not in MAD2+/– cells, suggesting an explanation for the spindle failure and mitotic catastrophe in the MAD2 knockdown cells. Thus, anaphase-promoting complex substrates exhibit distinct sensitivities in the presence of different MAD2 doses, which in turn determine MAD2's role as either a tumor suppressor or an essential gene.
Germ-line expression of an oncogenic
erbB2
allele confers resistance to
erbB2
-induced mammary tumorigenesis
Authors: Andrechek Eran R. , Hardy William R. , Laing Michael A. , Muller William J.
Published: March 2004

We have previously shown that mammary epithelial specific expression of the activated
erbB2
allele under the control of the endogenous promoter in mice resulted in the formation of mammary adenocarcinomas. To assess whether mammary tumorigenesis in this model is influenced by the developmental window of expression, we generated mice that expressed the activated
erbB2
allele in the germ line. Although we were able to derive viable transgenic mice that were heterozygous for the activated
erbB2
allele, mice homozygous for the activated
erbB2
allele died at 12.5 days of embryogenesis. These two separate lines of mice expressed activated
erbB2
at equal levels in the mammary gland. Surprisingly, unlike the tumor-prone mice expressing activated ErbB2 in the mammary epithelium, mice with the germ-line
erbB2
allele failed to develop tumors. Gene expression analysis of the preneoplastic mammary glands revealed that there were a number of luminal epithelial markers expressed at higher levels in the tumor-prone mice. These data suggest either an expansion of a susceptible population in the tumor-prone mice or the loss of this population in the tumor-resistant mice. Taken together, these observations suggest that the temporal pattern of expression of activated ErbB2 is a critical determinant in mammary tumorigenesis. These results strongly suggest that there are feedback mechanisms present that can compensate for the expression of a potent oncogene.
Partially redundant functions of SRC-1 and TIF2 in postnatal survival and male reproduction
Authors: Mark Manuel , Yoshida-Komiya Hiromi , Gehin Martine , Liao Lan , Tsai Ming-Jer , O'Malley Bert W. , Chambon Pierre , Xu Jianming
Published: March 2004

Both SRC-1 and TIF2 are members of the p160 steroid receptor coactivator family. Genetic analyses have shown that inactivation of
TIF2
, but not
SRC-1
, reduces postnatal survival, growth, and male reproductive function. Here, we demonstrate that, through analyses of
SRC-1
/
TIF2
compound mutant mice, SRC-1 can partially compensate for the effects of a loss of TIF2 on mouse survival and growth, whereas SRC-1 and TIF2 are dispensable for primary organogenesis. The highly variable onset of defects observed in
TIF2
–/–
testes due to the absence of TIF2 in Sertoli cells, including abnormal spermiogenesis, age-dependent degeneration of seminiferous epithelium, and disorder of cholesterol homeostasis, is uniformly accelerated upon inactivation of
SRC-1
alleles in the
TIF2
null genetic background, thus demonstrating that TIF2 and SRC-1 can perform redundant functions in Sertoli cells. Massive desquamation of immature germ cells together with an increase in germ cell apoptosis and a decrease in germ cell proliferation may be responsible for the early onset of the severe seminiferous epithelial degeneration observed in
SRC-1
+/–
/
TIF2
–/–
testes. Interestingly, the overall abnormal features displayed by the
SRC-1
+/–
/
TIF2
–/–
and
SRC-1
–/–
/
TIF2
–/–
mutant testes, including spermatid maturation defects, increase in Sertoli cell lipid stores, loss of immature germ cells, and formation of giant multinucleated spermatids, are commonly detected in testes of elderly men, suggesting that deficiencies in molecular pathways involving TIF2 and SRC-1 in Sertoli cells could participate in testicular senescence.
HetR homodimer is a DNA-binding protein required for heterocyst differentiation, and the DNA-binding activity is inhibited by PatS
Authors: Huang Xu , Dong Yuqing , Zhao Jindong
Published: March 2004

HetR plays a key role in regulation of heterocyst differentiation. When the Cys-48 residue of the HetR from
Anabaena
sp. PCC 7120 was replaced with an Ala residue, the mutant HetR (HetR
C48A
) could not dimerize, indicating that HetR forms a homodimer through a disulfide bond. The
Anabaena
strain C48, containing the
hetRc48a
gene, could not produce HetR homodimer and failed to form heterocyst. We show that HetR is a DNA-binding protein and that its homodimerization is required for the DNA binding. HetR binds the promoter regions of
hetR
,
hepA
, and
patS
, suggesting a direct control of the expression of these genes by HetR. We present evidence that shows that the up-regulation of
patS
and
hetR
depends on DNA binding by HetR dimer. The pentapeptide RGSGR, which is present at the C terminus of PatS and blocks heterocyst formation, inhibits the DNA binding of HetR and prevents
hetR
up-regulation.
Self-enforcing climate-change treaties
Authors: Dutta Prajit K. , Radner Roy
Published: March 2004

In the absence of world government, an effective treaty to control the emissions of greenhouse gases should be self-enforcing. A self-enforcing treaty has the property that, if a country expects other countries to abide by the treaty, it will be in the self-interest of that country to abide by the treaty too. (A difficulty with the Kyoto Protocol is that it does not appear to lay the groundwork for a self-enforcing treaty). A self-enforcing treaty can be modeled as a Nash equilibrium of a suitably defined dynamic game among a large number of sovereign countries of diverse sizes and economic capabilities. We study such a game and characterize its equilibria (typically there are many) and the global-Pareto-optimal solutions. We identify one of the equilibria, which we call “business as usual,” with the current situation. The multiplicity of equilibria provides an opportunity to move from the inefficient business-as-usual equilibrium to one or more equilibria that are Pareto-superior. Using a calibrated model with 184 countries, we give numerical illustrations of business-as-usual and global-Pareto-optimal trajectories and estimate the potential welfare gains from a self-enforcing treaty.
Temperature dependence of metabolic rates for microbial growth, maintenance, and survival
Authors: Price P. Buford , Sowers Todd
Published: March 2004

Our work was motivated by discoveries of prokaryotic communities that survive with little nutrient in ice and permafrost, with implications for past or present microbial life in Martian permafrost and Europan ice. We compared the temperature dependence of metabolic rates of microbial communities in permafrost, ice, snow, clouds, oceans, lakes, marine and freshwater sediments, and subsurface aquifer sediments. Metabolic rates per cell fall into three groupings: (i) a rate, μg(T), for growth, measured in the laboratory atin situtemperatures with minimal disturbance of the medium; (ii) a rate, μm(T), sufficient for maintenance of functions but for a nutrient level too low for growth; and (iii) a rate, μs(T), for survival of communities imprisoned in deep glacial ice, subsurface sediment, or ocean sediment, in which they can repair macromolecular damage but are probably largely dormant. The three groups have metabolic rates consistent with a single activation energy of ≈110 kJ and that scale as μg(T):μm(T):μs(T) ≈ 106:103:1. There is no evidence of a minimum temperature for metabolism. The rate at -40°C in ice corresponds to ≈10 turnovers of cellular carbon per billion years. Microbes in ice and permafrost have metabolic rates similar to those in water, soil, and sediment at the same temperature. This finding supports the view that, far below the freezing point, liquid water inside ice and permafrost is available for metabolism. The rate μs(T) for repairing molecular damage by means of DNA-repair enzymes and protein-repair enzymes such as methyltransferase is found to be comparable to the rate of spontaneous molecular damage.
Orexin peptides prevent cataplexy and improve wakefulness in an orexin neuron-ablated model of narcolepsy in mice
Authors: Mieda Michihiro , Willie Jon T. , Hara Junko , Sinton Christopher M. , Sakurai Takeshi , Yanagisawa Masashi
Published: March 2004

Narcolepsy-cataplexy is a neurological disorder associated with the inability to maintain wakefulness and abnormal intrusions of rapid eye movement sleep-related phenomena into wakefulness such as cataplexy. The vast majority of narcoleptic-cataplectic individuals have low or undetectable levels of orexin (hypocretin) neuropeptides in the cerebrospinal fluid, likely due to specific loss of the hypothalamic orexin-producing neurons. Currently available treatments for narcolepsy are only palliative, symptom-oriented pharmacotherapies. Here, we demonstrate rescue of the narcolepsy-cataplexy phenotype of orexin neuron-ablated mice by genetic and pharmacological means. Ectopic expression of a
prepro-orexin
transgene in the brain completely prevented cataplectic arrests and other abnormalities of rapid eye movement sleep in the absence of endogenous orexin neurons. Central administration of orexin-A acutely suppressed cataplectic behavioral arrests and increased wakefulness for 3 h. These results indicate that orexin neuron-ablated mice retain the ability to respond to orexin neuropeptides and that a temporally regulated and spatially targeted secretion of orexins is not necessary to prevent narcoleptic symptoms. Orexin receptor agonists would be of potential value for treating human narcolepsy.
Models of granulocyte DNA structure are highly predictive of myelodysplastic syndrome
Authors: Malins Donald C. , Anderson Katie M. , Polissar Nayak L. , Ostrander Gary K. , Knobbe Edward T. , Green Virginia M. , Gilman Naomi K. , Spivak Jerry L.
Published: March 2004

We have used statistical models based on Fourier transform-infrared spectra to differentiate between the DNA structure of normal granulocytes and those obtained from patients with myelodysplastic syndrome (MDS). The substantial degree of discrimination achieved between the two DNA groups is attributed to differences in the nucleotide base and backbone structures. These structural differences allowed for the development of a discriminant analysis model that predicted, with high sensitivity and specificity, which DNA came from normal granulocytes vs. granulocytes from MDS patients. The findings are a promising basis for developing a blood test to diagnose and predict the occurrence of MDS, for which there is currently a paucity of molecular markers.
Melanoma cells transfected to express CD83 induce antitumor immunity that can be increased by also engaging CD137
Authors: Yang Shilin , Yang Yi , Raycraft John , Zhang Hongtao , Kanan Sandra , Guo Yajun , Ronai Ze'ev , Hellstrom Ingegerd , Hellstrom Karl Erik
Published: March 2004

Interactions between CD83 and its ligand(s) can up-regulate immune responses. M2-CD83 cells, derived by transfecting the M2 clone of mouse melanoma K1735 cells to express mouse CD83, were rejected by syngeneic mice, unless they were injected with a CD83Ig fusion protein. Rejection was mediated by CD4+and CD8+T cells plus natural killer cells, whereas rejection of M2-1D8 cells, which express anti-CD137 single-chain variable region fragments (scFv), occurs in the absence of CD8+T cells. Furthermore, the tumor specificity of the immunity induced by the two cell lines differed. Immunization with live or mitomycin C-treated M2-CD83 cells prevented outgrowth of transplanted M2-WT cells and had therapeutic efficacy against established M2-WT tumors. A highly metastatic clone of K1735 cells, SW1-C, and its subline SW1-P2, which expresses an activating transcription factor 2-driven peptide, were then studied because they have particularly low immunogenicity. Neither SW1-C nor SW1-P2 cells became rejectable after expression of CD83 or anti-CD137 scFv. However, outgrowth of cells from either line was delayed in mice immunized against M2-CD83 or M2-1D8 cells, and immunization with a mixture of mitomycin C-treated cells from M2-CD83 plus M2-1D8 prevented tumor formation by SW1-P2 cells in five of five and by SW1-C cells in three of five mice. We conclude that M2 cells expressing CD83 can induce a tumor-destructive immune response also against SW1 cells and that this response can be made more effective by combining them with M2 cells expressing anti-CD137 scFv. A similar approach may be therapeutically beneficial against certain human cancers.
Salmonella typhiencodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway
Authors: Haghjoo Erik , Galán Jorge E.
Published: March 2004

Many bacterial pathogens encode the cytolethal distending toxin (CDT), which causes host cells to arrest during their cell cycle by inflicting DNA damage. CDT is composed of three proteins, CdtA, CdtB, and CdtC. CdtB is the enzymatically active or A subunit, which possesses DNase I-like activity, whereas CdtA and CdtC function as heteromeric B subunits that mediate the delivery of CdtB into host cells. We show here thatSalmonella entericaserovar Typhi encodes CDT activity, which depends on the function of a CdtB homologous protein. Remarkably,S. entericaserovar Typhi does not encode apparent homologs of CdtA or CdtC. Instead, we found that toxicity, as well ascdtBexpression, requires bacterial internalization into host cells. We propose a pathway of toxin delivery in which bacterial internalization relieves the requirement for the functional equivalent of the B subunit of the CDT toxin.
QSulf1, a heparan sulfate 6-
O
-endosulfatase, inhibits fibroblast growth factor signaling in mesoderm induction and angiogenesis
Authors: Wang Shouwen , Ai Xingbin , Freeman Stephen D. , Pownall Mary E. , Lu Qun , Kessler Daniel S. , Emerson Charles P.
Published: March 2004

The signaling activities of multiple developmental ligands require sulfated heparan sulfate (HS) proteoglycans as coreceptors. QSulf1 and its mammalian orthologs are cell surface HS 6-
O
-endosulfatases that are expressed in embryonic mesodermal and neural progenitors and promote Wnt signal transduction. In this study, we have investigated the function of QSulf1 in fibroblast growth factor (FGF) signaling, which requires 6-O-sulfated HS for FGF receptor (FGFR) dimerization and tyrosine kinase activation. Here, we report that QSulf1 inhibits FGF2- and FGF4-induced mesoderm formation in the
Xenopus
embryo and FGF-dependent angiogenesis in the chicken embryo through 6-O-desulfation of cell surface HS. QSulf1 regulates FGF signaling through inhibition of HS-mediated FGFR1 activation by interfering with FGF–HS–FGFR1 ternary complex formation. Furthermore, QSulf1 can produce enzymatically modified soluble heparin that acts as a potent inhibitor of FGF2-induced angiogenesis in the chicken embryo. QSulf1, therefore, has dual regulatory functions as a negative regulator of FGF signaling and a positive regulator of Wnt signaling. Therefore, QSulf1 provides another reagent to produce enzymatically modified heparin compounds,
in vivo
and
in vitro
, to modulate cellular signaling in stem cell-based therapies to promote tissue regeneration and in cancer therapies to control cell growth and block angiogenesis.
Brain-specific deletion of neuropathy target esterase/
swisscheese
results in neurodegeneration
Authors: Akassoglou Katerina , Malester Brian , Xu Jixiang , Tessarollo Lino , Rosenbluth Jack , Chao Moses V.
Published: March 2004

Neuropathy target esterase (NTE) is a neuronal membrane protein originally identified for its property to be modified by organo-phosphates (OPs), which in humans cause neuropathy characterized by axonal degeneration.
Drosophila
mutants for the homolog gene of
NTE, swisscheese
(
sws
), indicated a possible involvement of
sws
in the regulation of axon-glial cell interaction during glial wrapping. However, the role of NTE/
sws
in mammalian brain pathophysiology remains unknown. To investigate NTE function
in vivo
, we used the cre/loxP site-specific recombination strategy to generate mice with a specific deletion of NTE in neuronal tissues. Here we show that loss of NTE leads to prominent neuronal pathology in the hippocampus and thalamus and also defects in the cerebellum. Absence of NTE resulted in disruption of the endoplasmic reticulum, vacuolation of nerve cell bodies, and abnormal reticular aggregates. Thus, these results identify a physiological role for NTE in the nervous system and indicate that a loss-of-function mechanism may contribute to neurodegenerative diseases characterized by vacuolation and neuronal loss.
Highly attenuated smallpox vaccine protects mice with and without immune deficiencies against pathogenic vaccinia virus challenge
Authors: Wyatt Linda S. , Earl Patricia L. , Eller Leigh Anne , Moss Bernard
Published: March 2004

Modified vaccinia virus Ankara (MVA), developed >30 years ago as a highly attenuated candidate smallpox vaccine, was recloned from a 1974 passage and evaluated for safety and immunogenicity. Replication of MVA is impaired in most mammalian cells, and we found that mice with severe combined immunodeficiency disease remained healthy when inoculated with MVA at 1,000 times the lethal dose of vaccinia virus derived from the licensed Dryvax vaccine seed. In BALB/c mice inoculated intramuscularly with MVA, virus-specific CD8+T cells and antibodies to purified virions and membrane protein components of the intracellular and extracellular infectious forms of vaccinia virus were induced in a dose-dependent manner. After one or two inoculations of MVA, the T cell numbers and antibody titers equaled or exceeded those induced by percutaneous injection of Dryvax. Antibodies induced by MVA and Dryvax were neutralizing and inhibited virus spread in cultured cells. Furthermore, vaccinated mice were protected against lethal intranasal challenge with a pathogenic vaccinia virus. B cell-deficient mice unable to generate antibodies and β2-microglobulin-deficient mice unable to express MHC class I molecules for a CD8+T cell response were also protectively vaccinated by MVA. In contrast, mice with decreased CD4 or MHC class II expression and double-knockout mice deficient in MHC class I- and II-restricted activities were poorly protected or unprotected. This study confirmed the safety of MVA and demonstrated that the overlapping immune responses protected normal and partially immune-deficient animals, an encouraging result for this candidate attenuated smallpox vaccine.
Generation of single and double knockdowns in polarized epithelial cells by retrovirus-mediated RNA interference
Authors: Schuck Sebastian , Manninen Aki , Honsho Masanori , Füllekrug Joachim , Simons Kai
Published: March 2004

RNA interference (RNAi) is a ubiquitous mechanism of eukaryotic gene regulation that can be exploited for specific gene silencing. Retroviruses have been successfully used for stable expression of short hairpin RNAs in mammalian cells, leading to persistent inhibition of gene expression by RNAi. Here, we apply retrovirus-mediated RNAi to epithelial Madin-Darby canine kidney cells, whose properties limit the applicability of other RNAi methods. We demonstrate efficient suppression of a set of 13 target genes by retroviral coexpression of short hairpin RNAs and a selectable marker. We characterize the resulting knockdown cell populations with regard to composition and stability, and examine the usefulness of proposed guidelines for choosing RNAi target sequences. Finally, we show that this system can be used to simultaneously target two genes, giving rise to double knockdowns. Thus, retrovirus-mediated RNAi is a convenient method for gene silencing in Madin-Darby canine kidney cells, and is likely to be applicable to virtually any mammalian cell.
Tyrosol is a quorum-sensing molecule in
Candida albicans
Authors: Chen Hao , Fujita Masaki , Feng Qinghua , Clardy Jon , Fink Gerald R.
Published: March 2004

The human fungal pathogen
Candida albicans
shows a significant lag in growth when diluted into fresh minimal medium. This lag is abolished by the addition of conditioned medium from a high-density culture. The active component of conditioned medium is tyrosol, which is released into the medium continuously during growth. Under conditions permissive for germ-tube formation, tyrosol stimulates the formation of these filamentous protrusions. Because germ-tube formation is inhibited by farnesol, another quorum-sensing molecule, this process must be under complex positive and negative control by environmental conditions. The identification of tyrosol as an autoregulatory molecule has important implications on the dynamics of growth and morphogenesis in
Candida
.
Reprogramming of Virus-specific T Cells into Leukemia-reactive T Cells Using T Cell Receptor Gene Transfer
Authors: Heemskerk Mirjam H.M. , Hoogeboom Manja , Hagedoorn Renate , Kester Michel G.D. , Willemze Roel , Falkenburg J.H. Frederik
Published: March 2004

T cells directed against minor histocompatibility antigens (mHags) might be responsible for eradication of hematological malignancies after allogeneic stem cell transplantation. We investigated whether transfer of T cell receptors (TCRs) directed against mHags, exclusively expressed on hematopoietic cells, could redirect virus-specific T cells toward antileukemic reactivity, without the loss of their original specificity. Generation of T cells with dual specificity may lead to survival of these TCR-transferred T cells for prolonged periods of time in vivo due to transactivation of the endogenous TCR of the tumor-reactive T cells by the latent presence of viral antigens. Furthermore, TCR transfer into restricted T cell populations, which are nonself reactive, will minimize the risk of autoimmunity. We demonstrate that cytomegalovirus (CMV)-specific T cells can be efficiently reprogrammed into leukemia-reactive T cells by transfer of TCRs directed against the mHag HA-2. HA-2-TCR–transferred CMV-specific T cells derived from human histocompatibility leukocyte antigen (HLA)-A2+ or HLA-A2− individuals exerted potent antileukemic as well as CMV reactivity, without signs of anti–HLA-A2 alloreactivity. The dual specificity of these mHag-specific, TCR-redirected virus-specific T cells opens new possibilities for the treatment of hematological malignancies of HLA-A2+ HA-2–expressing patients transplanted with HLA-A2–matched or –mismatched donors.
A Defect in Nucleosome Remodeling Prevents IL-12(p35) Gene Transcription in Neonatal Dendritic Cells
Authors: Goriely Stanislas , Van Lint Carine , Dadkhah Réza , Libin Myriam , De Wit Dominique , Demonté Dominique , Willems Fabienne , Goldman Michel
Published: March 2004

To gain insight into the inability of newborns to mount efficient Th1 responses, we analyzed the molecular basis of defective IL-12(p35) expression in human neonatal monocyte-derived dendritic cells (DCs). Determination of IL-12(p35) pre-mRNA levels by real-time RT-PCR revealed that transcriptional activation of the gene in lipopolysaccharide-stimulated neonatal DCs was strongly impaired compared with adult DCs. We next showed that p50/p65 and p65/p65 dimers interact with kB#1 site, a critical cis-acting element of the IL-12(p35) promoter. We found that LPS-induced p65 activation was similar in adult and newborn DCs. Likewise, in vitro binding activity to the Sp1#1 site, previously shown to be critical for IL-12(p35) gene activation, did not differ in adults and newborns. Since the accessibility to this Sp1#1 site was found to depend on nucleosome remodeling, we used a chromatin accessibility assay to compare remodeling of the relevant nucleosome (nuc-2) in adult and neonatal DCs. We observed that nuc-2 remodeling in neonatal DCs was profoundly impaired in response to lipopolysaccharide. Both nuc-2 remodeling and IL-12(p35) gene transcription were restored upon addition of recombinant interferon-γ. We conclude that IL-12(p35) transcriptional repression in neonatal DCs takes place at the chromatin level.
Absence of DNA Polymerase η Reveals Targeting of C Mutations on the Nontranscribed Strand in Immunoglobulin Switch Regions
Authors: Zeng Xianmin , Negrete George A. , Kasmer Cynthia , Yang William W. , Gearhart Patricia J.
Published: March 2004

Activation-induced cytosine deaminase preferentially deaminates C in DNA on the nontranscribed strand in vitro, which theoretically should produce a large increase in mutations of C during hypermutation of immunoglobulin genes. However, a bias for C mutations has not been observed among the mutations in variable genes. Therefore, we examined mutations in the μ and γ switch regions, which can form stable secondary structures, to look for C mutations. To further simplify the pattern, mutations were studied in the absence of DNA polymerase (pol) η, which may produce substitutions of nucleotides downstream of C. DNA from lymphocytes of patients with xeroderma pigmentosum variant (XP-V) disease, whose polymerase η is defective, had the same frequency of switching to all four γ isotypes and hypermutation in μ-γ switch sites (0.5% mutations per basepair) as control subjects. There were fewer mutations of A and T bases in the XP-V clones, similar to variable gene mutations from these patients, which confirms that polymerase η produces substitutions opposite A and T. Most importantly, the absence of polymerase η revealed an increase in C mutations on the nontranscribed strand. This data shows for the first time that C is preferentially mutated in vivo and pol η generates hypermutation in the μ and γ switch regions.
Ryanodine Receptor Regulation by Intramolecular Interaction between Cytoplasmic and Transmembrane Domains
Authors: George Christopher H. , Jundi Hala , Thomas N. Lowri , Scoote Mark , Walters Nicola , Williams Alan J. , Lai F. Anthony
Published: March 2004

Ryanodine receptors (RyR) function as Ca2+channels that regulate Ca2+release from intracellular stores to control a diverse array of cellular processes. The massive cytoplasmic domain of RyR is believed to be responsible for regulating channel function. We investigated interaction between the transmembrane Ca2+-releasing pore and a panel of cytoplasmic domains of the human cardiac RyR in living cells. Expression of eGFP-tagged RyR constructs encoding distinct transmembrane topological models profoundly altered intracellular Ca2+handling and was refractory to modulation by ryanodine, FKBP12.6 and caffeine. The impact of coexpressing dsRed-tagged cytoplasmic domains of RyR2 on intracellular Ca2+phenotype was assessed using confocal microscopy coupled with parallel determination of in situ protein: protein interaction using fluorescence resonance energy transfer (FRET). Dynamic interactions between RyR cytoplasmic and transmembrane domains were mediated by amino acids 3722-4610 (Interacting or “I”-domain) which critically modulated intracellular Ca2+handling and restored RyR sensitivity to caffeine activation. These results provide compelling evidence that specific interaction between cytoplasmic and transmembrane domains is an important mechanism in the intrinsic modulation of RyR Ca2+release channels.
AKAP350 Interaction with cdc42 Interacting Protein 4 at the Golgi Apparatus
Authors: Larocca M. Cecilia , Shanks Ryan A. , Tian Lan , Nelson David L. , Stewart Donn M. , Goldenring James R.
Published: March 2004

The A kinase anchoring protein 350 (AKAP350) is a multiply spliced type II protein kinase A anchoring protein that localizes to the centrosomes in most cells and to the Golgi apparatus in epithelial cells. In the present study, we sought to identify AKAP350 interacting proteins that could yield insights into AKAP350 function at the Golgi apparatus. Using yeast two-hybrid and pull-down assays, we found that AKAP350 interacts with a family of structurally related proteins, including FBP17, FBP17b, and cdc42 interacting protein 4 (CIP4). CIP4 interacts with the GTP-bound form of cdc42, with the Wiscott Aldrich Syndrome group of proteins, and with microtubules, and exerts regulatory effects on cytoskeleton and membrane trafficking. CIP4 is phosphorylated by protein kinase A in vitro, and elevation of intracellular cyclic AMP with forskolin stimulates in situ phosphorylation of CIP4. Our results indicate that CIP4 interacts with AKAP350 at the Golgi apparatus and that either disruption of this interaction by expressing the CIP4 binding domain in AKAP350, or reduction of AKAP350 expression by RNA interference leads to changes in Golgi structure. The results suggest that AKAP350 and CIP4 influence the maintenance of normal Golgi apparatus structure.
Organellar Proteomics Reveals Golgi Arginine Dimethylation
Authors: Wu Christine C. , MacCoss Michael J. , Mardones Gonzalo , Finnigan Claire , Mogelsvang Soren , Yates John R. , Howell Kathryn E.
Published: March 2004

The Golgi complex functions to posttranslationally modify newly synthesized proteins and lipids and to sort them to their sites of function. In this study, a stacked Golgi fraction was isolated by classical cell fractionation, and the protein complement (the Golgi proteome) was characterized using multidimensional protein identification technology. Many of the proteins identified are known residents of the Golgi, and 64% of these are predicted transmembrane proteins. Proteins localized to other organelles also were identified, strengthening reports of functional interfacing between the Golgi and the endoplasmic reticulum and cytoskeleton. Importantly, 41 proteins of unknown function were identified. Two were selected for further analysis, and Golgi localization was confirmed. One of these, a putative methyltransferase, was shown to be arginine dimethylated, and upon further proteomic analysis, arginine dimethylation was identified on 18 total proteins in the Golgi proteome. This survey illustrates the utility of proteomics in the discovery of novel organellar functions and resulted in 1) a protein profile of an enriched Golgi fraction; 2) identification of 41 previously uncharacterized proteins, two with confirmed Golgi localization; 3) the identification of arginine dimethylated residues in Golgi proteins; and 4) a confirmation of methyltransferase activity within the Golgi fraction.
A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes
Authors: Aerts Stein , Van Loo Peter , Moreau Yves , De Moor Bart
Published: March 2004

Summary: The implementation of a genetic algorithm is described that provides a fast method of searching for the optimal combination of transcription factor binding sites in a set of regulatory sequences.

Availability: The algorithm can be used transparently as a web service from within the Toucan software. Toucan can be accessed at http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php. A standalone version of the software is available upon request.
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference
Authors: Lawrence Carolyn J. , Zmasek Christian M. , Dawe R. Kelly , Malmberg Russell L.
Published: March 2004

Summary: LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an alignment in a revealing way. LumberJack creates non-random jackknifed alignments by progressively sliding a window of omission along the alignment. A neighbor-joining tree is built from the full alignment and from each jackknifed alignment, and then the likelihood for each topology (given the original full alignment) is calculated. To determine whether any of the topologies generated is significantly more likely than the others, Kishino-Hasegawa, Shimodaira-Hasegawa and ELW tests are implemented.

Availability and Supplementary information:  http://www.plantbio.uga.edu/~russell/software.html
Hypothesis-driven approach to predict transcriptional units from gene expression data
Authors: Steinhauser Dirk , Junker Björn H. , Luedemann Alexander , Selbig Joachim , Kopka Joachim
Published: March 2004

Motivation: A major issue in computational biology is the reconstruction of functional relationships among genes, for example the definition of regulatory or biochemical pathways. One step towards this aim is the elucidation of transcriptional units, which are characterized by co-responding changes in mRNA expression levels. These units of genes will allow the generation of hypotheses about respective functional interrelationships. Thus, the focus of analysis currently moves from well-established functional assignment through comparison of protein and DNA sequences towards analysis of transcriptional co-response. Tools that allow deducing common control of gene expression have the potential to complement and extend routine BLAST comparisons, because gene function may be inferred from common transcriptional control.

Results: We present a co-clustering strategy of genome sequence information and gene expression data, which was applied to identify transcriptional units within diverse compendia of expression profiles. The phenomenon of prokaryotic operons was selected as an ideal test case to generate well-founded hypotheses about transcriptional units. The existence of overlapping and ambiguous operon definitions allowed the investigation of constitutive and conditional expression of transcriptional units in independent gene expression experiments of Escherichia coli. Our approach allowed identification of operons with high accuracy. Furthermore, both constitutive mRNA co-response as well as conditional differences became apparent. Thus, we were able to generate insight into the possible biological relevance of gene co-response. We conclude that the suggested strategy will be amenable in general to the identification of transcriptional units beyond the chosen example of E.coli operons.

Availability: The analyses of E.coli transcript data presented here are available upon request or at http://csbdb.mpimp-golm.mpg.de/
A tool for gene expression based PubMed search through combining data sources
Authors: Korotkiy Maksym , Middelburg Rutger , Dekker Henk , van Harmelen Frank , Lankelma Jan
Published: March 2004

Summary: We present a new tool for the semi-automated querying of PubMed using a batch of tens to thousands of GenBank accession numbers or UniGene cluster ids. By combining information from UniGene and SWISS-PROT, microGENIE obtains information on the biological relevance of expressed genes, as identified by micro-array experiments, with minimal user intervention and time investment.

Availability: microGENIE is freely available from http://www.cs.vu.nl/microgenie

Supplementary information: The web site above supplies examples of input and output files.