bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitivity to Sunburn Is Associated with Susceptibility to Ultraviolet Radiation–Induced Suppression of Cutaneous Cell–Mediated Immunity
Authors: Kelly Deirdre A. , Young Antony R. , McGregor Jane M. , Seed Paul T. , Potten Christopher S. , Walker Susan L.
Published: July 2002

Skin cancer incidence is highest in white-skinned people. Within this group, skin types I/II (sun sensitive/tan poorly) are at greater risk than skin types III/IV (sun tolerant/tan well). Studies in mice demonstrate that ultraviolet radiation (UVR)-induced suppression of cell-mediated immune function plays an important role in the development of skin cancer and induces a susceptibility to infectious disease. A similar role is suspected in humans, but we lack quantitative human data to make risk assessments of ambient solar exposure on human health. This study demonstrates that ambient levels of solar UVR, typically experienced within 1 h of exposure to noonday summer sunlight, can suppress contact hypersensitivity (CHS) responses in healthy white-skinned humans in vivo (n = 93). There was a linear relationship between increase in erythema and suppression of CHS (P < 0.001), and a moderate sunburn (two minimal erythema doses [2 MED]) was sufficient to suppress CHS in all volunteers by 93%. However, a single suberythemal exposure of either 0.25 or 0.5 MED suppressed CHS responses by 50 and 80%, respectively, in skin types I/II, whereas 1 MED only suppressed CHS by 40% in skin types III/IV. The two- to threefold greater sensitivity of skin types I/II for a given level of sunburn may play a role in their greater sensitivity to skin cancer.
The Neutrophil-Activating Protein (Hp-Nap) ofHelicobacter pyloriIs a Protective Antigen and a Major Virulence Factor
Authors: Satin Barbara , Del Giudice Giuseppe , Della Bianca Vittorina , Dusi Stefano , Laudanna Carlo , Tonello Fiorella , Kelleher Dermot , Rappuoli Rino , Montecucco Cesare , Rossi Filippo
Published: July 2002

Helicobacter pylori infection induces the appearance of inflammatory infiltrates, consisting mainly of neutrophils and monocytes, in the human gastric mucosa. A bacterial protein with neutrophil activating activity (HP-NAP) has been previously identified, but its role in infection and immune response is still largely unknown. Here, we show that vaccination of mice with HP-NAP induces protection against H. pylori challenge, and that the majority of infected patients produce antibodies specific for HP-NAP, suggesting an important role of this factor in immunity. We also show that HP-NAP is chemotactic for human leukocytes and that it activates their NADPH oxidase to produce reactive oxygen intermediates, as demonstrated by the translocation of its cytosolic subunits to the plasma membrane, and by the lack of activity on chronic granulomatous disease leukocytes. This stimulating effect is strongly potentiated by tumor necrosis factor α and interferon γ and is mediated by a rapid increase of the cytosolic calcium concentration. The activation of leukocytes induced by HP-NAP is completely inhibited by pertussis toxin, wortmannin, and PP1. On the basis of these results, we conclude that HP-NAP is a virulence factor important for the H. pylori pathogenic effects at the site of infection and a candidate antigen for vaccine development.
HIV-Specific Cd8+ T Cells Produce Antiviral Cytokines but Are Impaired in Cytolytic Function
Authors: Appay Victor , Nixon Douglas F. , Donahoe Sean M. , Gillespie Geraldine M.A. , Dong Tao , King Abigail , Ogg Graham S. , Spiegel Hans M.L. , Conlon Christopher , Spina Celsa A. , Havlir Diane V. , Richman Douglas D. , Waters Anele , Easterbrook Philippa , McMichael Andrew J. , Rowland-Jones Sarah L.
Published: July 2002

The use of peptide–human histocompatibility leukocyte antigen (HLA) class I tetrameric complexes to identify antigen-specific CD8+ T cells has provided a major development in our understanding of their role in controlling viral infections. However, questions remain about the exact function of these cells, particularly in HIV infection. Virus-specific cytotoxic T lymphocytes exert much of their activity by secreting soluble factors such as cytokines and chemokines. We describe here a method that combines the use of tetramers and intracellular staining to examine the functional heterogeneity of antigen-specific CD8+ T cells ex vivo. After stimulation by specific peptide antigen, secretion of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, macrophage inflammatory protein (MIP)-1β, and perforin is analyzed by FACS® within the tetramer-positive population in peripheral blood. Using this method, we have assessed the functional phenotype of HIV-specific CD8+ T cells compared with cytomegalovirus (CMV)-specific CD8+ T cells in HIV chronic infection. We show that the majority of circulating CD8+ T cells specific for CMV and HIV antigens are functionally active with regards to the secretion of antiviral cytokines in response to antigen, although a subset of tetramer-staining cells was identified that secretes IFN-γ and MIP-1β but not TNF-α. However, a striking finding is that HIV-specific CD8+ T cells express significantly lower levels of perforin than CMV-specific CD8+ T cells. This lack of perforin is linked with persistent CD27 expression on HIV-specific cells, suggesting impaired maturation, and specific lysis ex vivo is lower for HIV-specific compared with CMV-specific cells from the same donor. Thus, HIV-specific CD8+ T cells are impaired in cytolytic activity.
Interferon γ Contributes to Initiation of Uterine Vascular Modification, Decidual Integrity, and Uterine Natural Killer Cell Maturation during Normal Murine Pregnancy
Authors: Ashkar Ali A. , Di Santo James P. , Croy B. Anne
Published: July 2002

The dominant lymphocytes in human and murine implantation sites are transient, pregnancy-associated uterine natural killer (uNK) cells. These cells are a major source of interferon (IFN)-γ. Implantation sites in mice lacking uNK cells (alymphoid recombinase activating gene [RAG]-2−/− common cytokine receptor chain γ [γc]−/−) or IFN-γ signaling (IFN-γ−/− or IFN-γRα−/−) fail to initiate normal pregnancy-induced modification of decidual arteries and display hypocellularity or necrosis of decidua. To investigate the functions of uNK cell–derived IFN-γ during pregnancy, RAG-2−/−γc−/− females were engrafted with bone marrow from IFN-γ−/− mice, IFN-γ signal-disrupted mice (IFN-γRα−/− or signal transducer and activator of transcription [Stat]-1−/−), or from mice able to establish normal uNK cells (severe combined immunodeficient [SCID] or C57BL/6). Mated recipients were analyzed at midgestation. All grafts established uNK cells. Grafts from IFN-γ−/− mice did not reverse host vascular or decidual pathology. Grafts from all other donors promoted modification of decidual arteries and decidual cellularity. Grafts from IFN-γRα−/− or Stat-1−/− mice overproduced uNK cells, all of which were immature. Grafts from IFN-γ−/−, SCID, or C57BL/6 mice produced normal, mature uNK cells. Administration of murine recombinant IFN-γ to pregnant RAG-2−/−γc−/− mice initiated decidual vessel modification and promoted decidual cellularity in the absence of uNK cells. These in vivo findings strongly suggest that uNK cell–derived IFN-γ modifies the expression of genes in the uterine vasculature and stroma, which initiates vessel instability and facilitates pregnancy-induced remodeling of decidual arteries.
Cd1b-Mediated T Cell Recognition of a Glycolipid Antigen Generated from Mycobacterial Lipid and Host Carbohydrate during Infection
Authors: Moody D. Branch , Guy Mark R. , Grant Ethan , Cheng Tan-Yun , Brenner Michael B. , Besra Gurdyal S. , Porcelli Steven A.
Published: July 2002

T cells recognize microbial glycolipids presented by CD1 proteins, but there is no information regarding the generation of natural glycolipid antigens within infected tissues. Therefore, we determined the molecular basis of CD1b-restricted T cell recognition of mycobacterial glycosylated mycolates, including those produced during tissue infection in vivo. Transfection of the T cell receptor (TCR) α and β chains from a glucose monomycolate (GMM)-specific T cell line reconstituted GMM recognition in TCR-deficient T lymphoblastoma cells. This TCR-mediated response was highly specific for natural mycobacterial glucose-6-O-(2R, 3R) monomycolate, including the precise structure of the glucose moiety, the stereochemistry of the mycolate lipid, and the linkage between the carbohydrate and the lipid. Mycobacterial production of antigenic GMM absolutely required a nonmycobacterial source of glucose that could be supplied by adding glucose to media at concentrations found in mammalian tissues or by infecting tissue in vivo. These results indicate that mycobacteria synthesized antigenic GMM by coupling mycobacterial mycolates to host-derived glucose. Specific T cell recognition of an epitope formed by interaction of host and pathogen biosynthetic pathways provides a mechanism for immune response to those pathogenic mycobacteria that have productively infected tissues, as distinguished from ubiquitous, but innocuous, environmental mycobacteria.
Induction of Interleukin 10–Producing, Nonproliferating Cd4+ T Cells with Regulatory Properties by Repetitive Stimulation with Allogeneic Immature Human Dendritic Cells
Authors: Jonuleit Helmut , Schmitt Edgar , Schuler Gerold , Knop Jürgen , Enk Alexander H.
Published: July 2002

The functional properties of dendritic cells (DCs) are strictly dependent on their maturational state. To analyze the influence of the maturational state of DCs on priming and differentiation of T cells, immature CD83− and mature CD83+ human DCs were used for stimulation of naive, allogeneic CD4+ T cells. Repetitive stimulation with mature DCs resulted in a strong expansion of alloreactive T cells and the exclusive development of T helper type 1 (Th1) cells. In contrast, after repetitive stimulation with immature DCs the alloreactive T cells showed an irreversibly inhibited proliferation that could not be restored by restimulation with mature DCs or peripheral blood mononuclear cells, or by the addition of interleukin (IL)-2. Only stimulation of T cells with mature DCs resulted in an upregulation of CD154, CD69, and CD70, whereas T cells activated with immature DCs showed an early upregulation of the negative regulator cytotoxic T lymphocyte–associated molecule 4 (CTLA-4). These T cells lost their ability to produce interferon γ, IL-2, or IL-4 after several stimulations with immature DCs and differentiated into nonproliferating, IL-10–producing T cells. Furthermore, in coculture experiments these T cells inhibited the antigen-driven proliferation of Th1 cells in a contact- and dose-dependent, but antigen-nonspecific manner. These data show that immature and mature DCs induce different types of T cell responses: inflammatory Th1 cells are induced by mature DCs, and IL-10–producing T cell regulatory 1–like cells by immature DCs.
Major Histocompatibility Complex Class I–Recognizing Receptors Are Disease Risk Genes in Rheumatoid Arthritis
Authors: Yen Jeng-Hsien , Moore Brenda E. , Nakajima Takako , Scholl Dirk , Schaid Daniel J. , Weyand Cornelia M. , Goronzy Jörg J.
Published: July 2002

Rheumatoid arthritis (RA) is a heterogeneous syndrome of which a subset of patients develops vascular inflammation. The genetic determinants that confer risk for rheumatoid vasculitis are not known, but patients with vascular complications are known to have an expansion of CD4+CD28null T cells, a cell population potentially involved in endothelial damage. CD4+CD28null T cell clones isolated from RA patients with vasculitis were found to express killer cell immunoglobulin–like receptors (KIRs) with the stimulatory KIR2DS2 often present in the absence of opposing inhibitory receptors with related specificities. To test the hypothesis that the KIR2DS2 gene is involved in the development of vasculitis, association studies were performed. The KIR2DS2 gene was significantly enriched among patients with rheumatoid vasculitis compared with normal individuals (odds ratio 5.56, P = 0.001) and patients with RA but no vasculitis (odds ratio 7.96, P = 0.001). Also, the distribution of human histocompatibility leukocyte antigen (HLA)-C, the putative ligand for KIRs, was significantly different in patients with rheumatoid vasculitis in comparison with the control populations. These data suggest that HLA class I–recognizing receptors and HLA class I genes are genetic risk determinants that modulate the pattern of RA expression. Specifically, KIR2DS2 in conjunction with the appropriate HLA-C ligand may have a role in vascular damage by regulating CD4+CD28null T cells.
Mapping Precursor Movement through the Postnatal Thymus Reveals Specific Microenvironments Supporting Defined Stages of Early Lymphoid Development
Authors: Lind Evan F. , Prockop Susan E. , Porritt Helen E. , Petrie Howard T.
Published: July 2002

Cellular differentiation is a complex process involving integrated signals for lineage specification, proliferation, endowment of functional capacity, and survival or cell death. During embryogenesis, spatially discrete environments regulating these processes are established during the growth of tissue mass, a process that also results in temporal separation of developmental events. In tissues that undergo steady-state postnatal differentiation, another means for inducing spatial and temporal separation of developmental cues must be established. Here we show that in the postnatal thymus, this is achieved by inducing blood-borne precursors to enter the organ in a narrow region of the perimedullary cortex, followed by outward migration across the cortex before accumulation in the subcapsular zone. Notably, blood precursors do not transmigrate the cortex in an undifferentiated state, but rather undergo progressive developmental changes during this process, such that defined precursor stages appear in distinct cortical regions. Identification of these cortical regions, together with existing knowledge regarding the genetic potential of the corresponding lymphoid precursors, sets operational boundaries for stromal environments that are likely to induce these differentiative events. We conclude that active cell migration between morphologically similar but functionally distinct stromal regions is an integral component regulating differentiation and homeostasis in the steady-state thymus.
Cell Contact–Dependent Immunosuppression by Cd4+Cd25+Regulatory T Cells Is Mediated by Cell Surface–Bound Transforming Growth Factor β
Authors: Nakamura Kazuhiko , Kitani Atsushi , Strober Warren
Published: July 2002

CD4+CD25+ T cells have been identified as a population of immunoregulatory T cells, which mediate suppression of CD4+CD25− T cells by cell–cell contact and not secretion of suppressor cytokines. In this study, we demonstrated that CD4+CD25+ T cells do produce high levels of transforming growth factor (TGF)-β1 and interleukin (IL)-10 compared with CD4+CD25− T cells when stimulated by plate-bound anti-CD3 and soluble anti-CD28 and/or IL-2, and secretion of TGF-β1 (but not other cytokines), is further enhanced by costimulation via cytotoxic T lymphocyte–associated antigen (CTLA)-4. As in prior studies, we found that CD4+CD25+ T cells suppress proliferation of CD4+CD25− T cells; however, we observed here that such suppression is abolished by the presence of anti–TGF-β. In addition, we found that CD4+CD25+ T cells suppress B cell immunoglobulin production and that anti–TGF-β again abolishes such suppression. Finally, we found that stimulated CD4+CD25+ T cells but not CD4+CD25− T cells express high and persistent levels of TGF-β1 on the cell surface. This, plus the fact that we could find no evidence that a soluble factor mediates suppression, strongly suggests that CD4+CD25+ T cells exert immunosuppression by a cell–cell interaction involving cell surface TGF-β1.
Granulocyte Macrophage Colony-Stimulating Factor
Authors: McQualter Jonathan L. , Darwiche Rima , Ewing Christine , Onuki Manabu , Kay Thomas W. , Hamilton John A. , Reid Hugh H. , Bernard Claude C.A.
Published: July 2002

Experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis, can be induced by immunization with a number of myelin antigens. In particular, myelin oligodendrocyte glycoprotein, a central nervous system (CNS)-specific antigen expressed on the myelin surface, is able to induce a paralytic MS-like disease with extensive CNS inflammation and demyelination in several strains of animals. Although not well understood, the egress of immune cells into the CNS in EAE is governed by a complex interplay between pro and antiinflammatory cytokines and chemokines. The hematopoietic growth factor, granulocyte macrophage colony-stimulating factor (GM-CSF), is considered to play a central role in maintaining chronic inflammation. The present study was designed to investigate the previously unexplored role of GM-CSF in autoimmune-mediated demyelination. GM-CSF−/− mice are resistant to EAE, display decreased antigen-specific proliferation of splenocytes, and fail to sustain immune cell infiltrates in the CNS, thus revealing key activities for GM-CSF in the development of inflammatory demyelinating lesions and control of migration and/or proliferation of leukocytes within the CNS. These results hold implications for the pathogenesis of inflammatory and demyelinating diseases and may provide the basis for more effective therapies for inflammatory diseases, and more specifically for multiple sclerosis.
Distinct Functional Lineages of Human Vα24 Natural Killer T Cells
Authors: Lee Peter T. , Benlagha Kamel , Teyton Luc , Bendelac Albert
Published: July 2002

CD1d-restricted autoreactive natural killer (NK)T cells have been reported to regulate a range of disease conditions, including type I diabetes and immune rejection of cancer, through the secretion of either T helper (Th)2 or Th1 cytokines. However, mechanisms underlying Th2 versus Th1 cytokine secretion by these cells are not well understood. Since most healthy subjects express <1 NKT cell per 1,000 peripheral blood lymphocytes (PBLs), we devised a new method based on the combined used of T cell receptor (TCR)-specific reagents α-galactosylceramide (αGalCer) loaded CD1d-tetramers and anti-Vα24 monoclonal antibody, to specifically identify and characterize these rare cells in fresh PBLs. We report here that CD4+ and CD4−CD8− (double negative [DN]) NKT cell subsets represent functionally distinct lineages with marked differences in their profile of cytokine secretion and pattern of expression of chemokine receptors, integrins, and NK receptors. CD4+ NKT cells were the exclusive producers of interleukin (IL)-4 and IL-13 upon primary stimulation, whereas DN NKT cells had a strict Th1 profile and prominently expressed several NK lineage receptors. These findings may explain how NKT cells could promote Th2 responses in some conditions and Th1 in others, and should be taken into consideration for intervention in relevant diseases.
Culture and Consumption: A Theoretical Account of the Structure and Movement of the Cultural Meaning of Consumer Goods
Authors: McCracken Grant
Published: July 2002

Cultural meaning in a consumer society moves ceaselessly from one location to another. In the usual trajectory, cultural meaning moves first from the culturally constituted world to consumer goods and then from these goods to the individual consumer. Several instruments are responsible for this movement: advertising, the fashion system, and four consumption rituals. This article analyzes the movement of cultural meaning theoretically, showing both where cultural meaning is resident in the contemporary North American consumer system and the means by which this meaning is transferred from one location in this system to another.
A new matrix inverse
Authors: Krattenthaler C.
Published: July 2002

We compute the inverse of a specific infinite-dimensional matrix, thus unifying a number of previous matrix inversions. Our inversion theorem is applied to derive a number of summation formulas of hypergeometric type.
Higher-dimensional Ahlfors-Beurling type inequalities in Clifford analysis
Authors: Martin Mircea
Published: July 2002

A generalization to higher dimensions of a classical inequality due to Ahlfors and Buerling is proved. As a consequence, an extension of Alexander’s quantitative version of Hartogs-Rosenthal Theorem is derived. Both results are stated and proved within the framework of Clifford analysis.
The residues of the resolvent on Damek-Ricci spaces
Authors: Miatello R. , Will C.
Published: July 2002

We determine the poles and residues of the resolvent kernel of the Laplacian on a Damek-Ricci space

S
.

S.

We show that all poles are simple and the residues define convolution operators of finite rank. This generalizes a result of Guillopé-Zworski for the real hyperbolic

n
n

-space. If

S
S

corresponds to a symmetric space of negative curvature

G

/

K

G/K

, the image of each residue is a

g

c

{\frak g}_c

-module with a specific highest weight. We compute the dimension by the Weyl dimension formula.
The diagonal subring and the Cohen-Macaulay property of a multigraded ring
Authors: Hyry Eero
Published: July 2002

Let

T
T

be a multigraded ring defined over a local ring

(
A
,

m

)

(A,\mathfrak {m})

. This paper deals with the question how the Cohen-Macaulay property of

T
T

is related to that of its diagonal subring

T
Δ

T^\Delta

. In the bigraded case we are able to give necessary and sufficient conditions for the Cohen-Macaulayness of

T
T

. If

I
1

,
…
,

I
r

⊂
A

I_1,\dotsc ,I_r\subset A

are ideals of positive height, we can then compare the Cohen-Macaulay property of the multi-Rees algebra

R
A

(

I
1

,
…
,

I
r

)

R_A(I_1,\dotsc ,I_r)

with the Cohen-Macaulay property of the usual Rees algebra

R
A

(

I
1

⋯

I
r

)

R_A(I_1\cdots I_r)

. We also obtain a bound for the joint reduction numbers of two

m

\mathfrak {m}

-primary ideals in the case the corresponding multi-Rees algebra is Cohen-Macaulay.
An efficient spectral method for ordinary differential equations with rational function coefficients
Authors: Coutsias Evangelos , Hagstrom Thomas , Torres David
Published: July 2002

We present some relations that allow the efficient approximate inversion of linear differential operators with rational function coefficients. We employ expansions in terms of a large class of orthogonal polynomial families, including all the classical orthogonal polynomials. These families obey a simple 3-term recurrence relation for differentiation, which implies that on an appropriately restricted domain the differentiation operator has a unique banded inverse. The inverse is an integration operator for the family, and it is simply the tridiagonal coefficient matrix for the recurrence. Since in these families convolution operators (i.e., matrix representations of multiplication by a function) are banded for polynomials, we are able to obtain a banded representation for linear differential operators with rational coefficients. This leads to a method of solution of initial or boundary value problems that, besides having an operation count that scales linearly with the order of truncation

N
N

, is computationally well conditioned. Among the applications considered is the use of rational maps for the resolution of sharp interior layers.
Anti-Gaussian quadrature formulas
Authors: Laurie Dirk
Published: July 2002

An anti-Gaussian quadrature formula is an

(
n
+
1
)

(n+1)

-point formula of degree

2
n
−
1

2n-1

which integrates polynomials of degree up to

2
n
+
1

2n+1

with an error equal in magnitude but of opposite sign to that of the

n
n

-point Gaussian formula. Its intended application is to estimate the error incurred in Gaussian integration by halving the difference between the results obtained from the two formulas. We show that an anti-Gaussian formula has positive weights, and that its nodes are in the integration interval and are interlaced by those of the corresponding Gaussian formula. Similar results for Gaussian formulas with respect to a positive weight are given, except that for some weight functions, at most two of the nodes may be outside the integration interval. The anti-Gaussian formula has only interior nodes in many cases when the Kronrod extension does not, and is as easy to compute as the

(
n
+
1
)

(n+1)

-point Gaussian formula.
The symmetries of solitons
Authors: Palais Richard
Published: July 2002

In this article we will retrace one of the great mathematical adventures of this century—the discovery of the soliton and the gradual explanation of its remarkable properties in terms of hidden symmetries. We will take an historical approach, starting with a famous numerical experiment carried out by Fermi, Pasta, and Ulam on one of the first electronic computers, and with Zabusky and Kruskal’s insightful explanation of the surprising results of that experiment (and of a follow-up experiment of their own) in terms of a new concept they called “solitons”. Solitons however raised even more questions than they answered. In particular, the evolution equations that govern solitons were found to be Hamiltonian and have infinitely many conserved quantities, pointing to the existence of many non-obvious symmetries. We will cover next the elegant approach to solitons in terms of the Inverse Scattering Transform and Lax Pairs, and finally explain how those ideas led step-by-step to the discovery that Loop Groups, acting by “Dressing Transformations”, give a conceptually satisfying explanation of the secret soliton symmetries.
Geometry of Riemann surfaces based on closed geodesics
Authors: Schaller Paul
Published: July 2002

The paper presents a survey on recent results on the geometry of Riemann surfaces showing that the study of closed geodesics provides a link between different aspects of Riemann surface theory such as hyperbolic geometry, topology, spectral theory, and the theory of arithmetic Fuchsian groups. Of particular interest are the systoles, the shortest closed geodesics of a surface; their study leads to the hyperbolic geometry of numbers with close analogues to classical sphere packing problems.
Activation and Caspase-mediated Inhibition of PARP: A Molecular Switch between Fibroblast Necrosis and Apoptosis in Death Receptor Signaling
Authors: Los Marek , Mozoluk Malgorzata , Ferrari Davide , Stepczynska Anna , Stroh Christopher , Renz Andrea , Herceg Zdenko , Wang Zhao-Qi , Schulze-Osthoff Klaus
Published: July 2002

Death ligands not only induce apoptosis but can also trigger necrosis with distinct biochemical and morphological features. We recently showed that in L929 cells CD95 ligation induces apoptosis, whereas TNF elicits necrosis. Treatment with anti-CD95 resulted in typical apoptosis characterized by caspase activation and DNA fragmentation. These events were barely induced by TNF, although TNF triggered cell death to a similar extent as CD95. Surprisingly, whereas the caspase inhibitor zVAD prevented CD95-mediated apoptosis, it potentiated TNF-induced necrosis. Cotreatment with TNF and zVAD was characterized by ATP depletion and accelerated necrosis. To investigate the mechanisms underlying TNF-induced cell death and its potentiation by zVAD, we examined the role of poly(ADP-ribose)polymerase-1 (PARP-1). TNF but not CD95 mediated PARP activation, whereas a PARP inhibitor suppressed TNF-induced necrosis and the sensitizing effect of zVAD. In addition, fibroblasts expressing a noncleavable PARP-1 mutant were more sensitive to TNF than wild-type cells. Our results indicate that TNF induces PARP activation leading to ATP depletion and subsequent necrosis. In contrast, in CD95-mediated apoptosis caspases cause PARP-1 cleavage and thereby maintain ATP levels. Because ATP is required for apoptosis, we suggest that PARP-1 cleavage functions as a molecular switch between apoptotic and necrotic modes of death receptor-induced cell death.
ASEdb: a database of alanine mutations and their effects on the

free energy of binding in protein interactions
Authors: Thorn Kurt S. , Bogan Andrew A.
Published: July 2002

Summary: The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein–protein, protein–nucleic acid, and protein–small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studying the contribution of single amino acids to the energetics of protein interactions, and can be updated by researchers as new data are generated.

Availability: ASEdb is accessible on the Web at http://www.asedb.org

Contact: thorn@itsa.ucsf.edu

* To whom correspondence should be addressed.
Automated ortholog inference from phylogenetic trees and
calculation of orthology reliability
Authors: Storm Christian E. V. , Sonnhammer Erik L. L.
Published: July 2002

Motivation: Orthologous proteins in different species are likely to have similar biochemical function and biological role. When annotating a newly sequenced genome by sequencehomology, the most precise and reliable functional information can thus be derived from orthologs in other species. A standard method of finding orthologs is to compare the sequence tree with the species tree. However, since the topology of phylogenetic tree is not always reliable one might get incorrect assignments.

Results: Here we present a novel method that resolves this problem by analyzing a set of bootstrap trees instead of the optimal tree. The frequency of orthology assignments in the bootstrap trees can be interpreted as a support value for the possible orthology of the sequences. Our method is efficient enough to analyze data in the scale of whole genomes. It is implemented in Java and calculates orthology support levels for all pairwise combinations of homologous sequences of two species. The method was tested on simulated datasets and on real data of homologous proteins.

Availability: Downloadable free of charge from ftp://ftp.cgb.ki.se/pub/prog/orthostrapper/or on request from the authors.

Contact: christian.storm@cgb.ki.se
PatternHunter: faster and more sensitive homology search
Authors: Ma Bin , Tromp John , Li Ming
Published: July 2002

Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation.

Results: We present a new homology search algorithm ‘PatternHunter’ that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop.

Availability: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.

Contact: mli@cs.ucsb.edu
Sequence complexity profiles of prokaryotic genomic
sequences: A fast algorithm for calculating linguistic
complexity
Authors: Troyanskaya Olga G. , Arbell Ora , Koren Yair , Landau Gad M. , Bolshoy Alexander
Published: July 2002

Motivation: One of the major features of genomic DNA sequences, distinguishing them from texts in most spoken or artificial languages, is their high repetitiveness. Variation in the repetitiveness of genomic texts reflects the presence and density of different biologically important messages. Thus, deviation from an expected number of repeats in both directions indicates a possible presence of a biological signal. Linguistic complexity corresponds to repetitiveness of a genomic text, and potential regulatory sites may be discovered through construction of typical patterns of complexity distribution.

Results: We developed software for fast calculation of linguistic sequence complexity of DNA sequences. Our program utilizes suffix trees to compute the number of subwords present in genomic sequences, thereby allowing calculation of linguistic complexity in time linear in genome size. The measure of linguistic complexity was applied to the complete genome of Haemophilus influenzae. Maps of complexity along the entire genome were obtained using sliding windows of 40, 100, and 2000 nucleotides. This approach provided an efficient way to detect simple sequence repeats in this genome. In addition, local profiles of complexity distribution around the starts of translation were constructed for 21 complete prokaryotic genomes. We hypothesize that complexity profiles correspond to evolutionary relationships between organisms. We found principal differences in profiles of the GC-rich and other (non-GC-rich) genomes. We also found characteristic differences in profiles of AT genomes, which probably reflect individual species variations in translational regulation.

Availability: The program is available upon request from Alexander Bolshoy or at http://csweb.haifa.ac.il/library/#complex

Contact: bolshoy@research.haifa.ac.il

* To whom correspondence should be addressed.

4 O.T. was a summer student at Haifa University. Her present address is Stanford Medical Informatics, Stanford University, CA 94305, USA.
HNF1α controls renal glucose reabsorption in mouse and man
Authors: Pontoglio Marco , Prié Dominique , Cheret Claire , Doyen Antonia , Leroy Christine , Froguel Philippe , Velho Gilberto , Yaniv Moshe , Friedlander Gérard
Published: July 2002

Recently it has been shown that dominant mutations in the human hepatocyte nuclear factor 1 α (HNF1α) gene, encoding for a homeoprotein that is expressed in liver, kidney, pancreas and intestine, result in maturity onset diabetes of the young type 3 (MODY3). HNF1α‐null mice are diabetic, but at the same time suffer from a renal Fanconi syndrome characterized by urinary glucose loss. Here we show that MODY3 patients are also characterized by a reduced tubular reabsorption of glucose. The renal murine defect is due to reduced expression of the low affinity/high capacity glucose cotransporter (SGLT2). Our results show that HNF1α directly controls SGLT2 gene expression. Together these data indicate that HNF1α plays a key role in glucose homeostasis in mammals.
The Drosophila caspase Dredd is required to resist Gram‐negative bacterial infection
Authors: Leulier François , Rodriguez Antony , Khush Ranjiv S , Abrams John M , Lemaitre Bruno
Published: July 2002

The Drosophila innate immune system discriminates between pathogens and responds by inducing the expression of specific antimicrobial peptide‐encoding genes through distinct signaling cascades. Fungal infection activates NF‐κB‐like transcription factors via the Toll pathway, which also regulates innate immune responses in mammals. The pathways that mediate antibacterial defenses, however, are less defined. We have isolated loss‐of‐function mutations in the caspase encoding gene dredd, which block the expression of all genes that code for peptides with antibacterial activity. These mutations also render flies highly susceptible to infection by Gram‐negative bacteria. Our results demonstrate that Dredd regulates antibacterial peptide gene expression, and we propose that Dredd, Immune Deficiency and the P105‐like rel protein Relish define a pathway that is required to resist Gram‐negative bacterial infections.
Methylation at arginine 17 of histone H3 is linked to gene activation
Authors: Bauer Uta‐Maria , Daujat Sylvain , Nielsen Søren J , Nightingale Karl , Kouzarides Tony
Published: July 2002

The nuclear hormone receptor co‐activator CARM1 has the potential to methylate histone H3 at arginine residues in vitro. The methyltransferase activity of CARM1 is necessary for its co‐activator functions in transient transfection assays. However, the role of this methyltransferase in vivo is unclear, given that methylation of arginines is not easily detectable on histones. We have raised an antibody that specifically recognizes methylated arginine 17 (R17) of histone H3, the major site of methylation by CARM1. Using this antibody we show that methylated R17 exists in vivo. Chromatin immunoprecipitation analysis shows that R17 methylation on histone H3 is dramatically upregulated when the estrogen receptor‐regulated pS2 gene is activated. Coincident with the appearance of methylated R17, CARM1 is found associated with the histones on the pS2 gene. Together these results demonstrate that CARM1 is recruited to an active promoter and that CARM1‐mediated R17 methylation on histone H3 takes place in vivo during this active state.
Visual attention mediated by biased competition in extrastriate visual cortex
Authors: Desimone Robert
Published: July 2002

According to conventional neurobiological accounts of visual attention, attention serves to enhance extrastriate neuronal responses to a stimulus at one spatial location in the visual field. However, recent results from recordings in extrastriate cortex of monkeys suggest that any enhancing effect of attention is best understood in the context of competitive interactions among neurons representing all of the stimuli present in the visual field. These interactions can be biased in favour of behaviourally relevant stimuli as a result of many different processes, both spatial and non–spatial, and both bottom–up and top–down. The resolution of this competition results in the suppression of the neuronal representations of behaviourally irrelevant stimuli in extrastriate cortex. A main source of top–down influence may derive from neuronal systems underlying working memory.
Amphiphysin is necessary for organization of the excitation–contraction coupling machinery of muscles, but not for synaptic vesicle endocytosis inDrosophila
Authors: Razzaq Azam , Robinson Iain M. , McMahon Harvey T. , Skepper Jeremy N. , Su Ya , Zelhof Andrew C. , Jackson Antony P. , Gay Nicholas J. , O'Kane Cahir J.
Published: July 2002

Amphiphysins 1 and 2 are enriched in the mammalian brain and are proposed to recruit dynamin to sites of endocytosis. Shorter amphiphysin 2 splice variants are also found ubiquitously, with an enrichment in skeletal muscle. At theDrosophilalarval neuromuscular junction, amphiphysin is localized postsynaptically andamphiphysinmutants have no major defects in neurotransmission; they are also viable, but flightless. Like mammalian amphiphysin 2 in muscles,Drosophilaamphiphysin does not bind clathrin, but can tubulate lipids and is localized on T-tubules.Amphiphysinmutants have a novel phenotype, a severely disorganized T-tubule/sarcoplasmic reticulum system. We therefore propose that muscle amphiphysin is not involved in clathrin-mediated endocytosis, but in the structural organization of the membrane-bound compartments of the excitation–contraction coupling machinery of muscles.
Inactivation of AtRac1 by abscisic acid is essential for stomatal closure
Authors: Lemichez Emmanuel , Wu Yan , Sanchez Juan-Pablo , Mettouchi Amel , Mathur Jaideep , Chua Nam-Hai
Published: July 2002

Plant water homeostasis is maintained by the phytohormone abscisic acid (ABA), which triggers stomatal pore closure in response to drought stress. We identified the Arabidopsis small guanosine triphosphatase (GTPase) protein AtRac1 as a central component in the ABA-mediated stomatal closure process. ABA treatment induced inactivation of AtRac GTPases and disruption of the guard cell actin cytoskeleton. In contrast, in the ABA-insensitive mutantabi1-1, which is impaired in stomatal closure, neither AtRac inactivation nor actin cytoskeleton disruption was observed on ABA treatment. These observations indicate that AtRac1 inactivation is a limiting step in the ABA-signaling cascade leading to stomatal closure. Consistent with these findings, expression of a dominant-positive mutant of AtRac1 blocked the ABA-mediated effects on actin cytoskeleton and stomatal closure in wild-type plants, whereas expression of a dominant-negative AtRac1 mutant recapitulated the ABA effects in the absence of the hormone. Moreover, the dominant-negative form of AtRac1 could also restore stomatal closure inabi1-1. These results define AtRac1 as a central element for plant adaptation to drought.
Genomic Characterization of Recent Human LINE-1 Insertions: Evidence Supporting Random Insertion
Authors: Ovchinnikov Igor , Troxel Andrea B. , Swergold Gary D.
Published: July 2002

LINE-1 (L1) elements play an important creative role in genomic evolution by distributing both L1 and non-L1 DNA in a process called retrotransposition. A large percentage of the human genome consists of DNA that has been dispersed by the L1 transposition machinery. L1 elements are not randomly distributed in genomic DNA but are concentrated in regions with lower GC content. In an effort to understand the consequences of L1 insertions, we have begun an investigation of their genomic characteristics and the changes that occur to them over time. We compare human L1 insertions that were created either during recent human evolution or during the primate radiation. We report that L1 insertions are an important source for the creation of new microsatellites. We provide evidence that L1 first strand cDNA synthesis can occur from an internal priming event. We note that in contrast to older L1 insertions, recent L1s are distributed randomly in genomic DNA, and the shift in the L1 genomic distribution occurs relatively rapidly. Taken together, our data indicate that strong forces act on newly inserted L1 retrotransposons to alter their structure and distribution.
Sequence‐structure analysis of FAD‐containing proteins
Authors: Dym Orly , Eisenberg David
Published: July 2002

We have analyzed structure‐sequence relationships in 32 families of flavin adenine dinucleotide (FAD)‐binding proteins, to prepare for genomic‐scale analyses of this family. Four different FAD‐family folds were identified, each containing at least two or more protein families. Three of these families, exemplified by glutathione reductase (GR), ferredoxin reductase (FR), and p‐cresol methylhydroxylase (PCMH) were previously defined, and a family represented by pyruvate oxidase (PO) is newly defined. For each of the families, several conserved sequence motifs have been characterized. Several newly recognized sequence motifs are reported here for the PO, GR, and PCMH families. Each FAD fold can be uniquely identified by the presence of distinctive conserved sequence motifs. We also analyzed cofactor properties, some of which are conserved within a family fold while others display variability. Among the conserved properties is cofactor directionality: in some FAD‐structural families, the adenine ring of the FAD points toward the FAD‐binding domain, whereas in others the isoalloxazine ring points toward this domain. In contrast, the FAD conformation and orientation are conserved in some families while in others it displays some variability. Nevertheless, there are clear correlations among the FAD‐family fold, the shape of the pocket, and the FAD conformation. Our general findings are as follows: (a) no single protein ‘pharmacophore’ exists for binding FAD; (b) in every FAD‐binding family, the pyrophosphate moiety binds to the most strongly conserved sequence motif, suggesting that pyrophosphate binding is a significant component of molecular recognition; and (c) sequence motifs can identify proteins that bind phosphate‐containing ligands.
Improved affinity of engineered streptavidin for the Strep‐tag II peptide is due to a fixed open conformation of the lid‐like loop at the binding site
Authors: Korndörfer Ingo P. , Skerra Arne
Published: July 2002

The Strep‐tag II is a nine‐amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants '1' and '2,' which had been engineered for 10‐fold higher affinity towards the Strep‐tag II. Both streptavidin mutants carry mutations at positions 44, 45, and 47, that is, in a flexible loop region close to the binding site. The crystal structures of the two apo‐proteins and their complexes with the Strep‐tag II peptide were refined at resolutions below 2 Å. Both in the presence and absence of the peptide, the lid‐like loop next to the ligand pocket—comprising residues 45 through 52—adopts an 'open' conformation in all four subunits within the asymmetric unit. The same loop was previously described to be disordered in the wild‐type apo‐streptavidin and to close over the pocket upon complexation of the natural ligand biotin. Our findings suggest that stabilization of the 'open' loop conformation in the absence of a ligand abolishes the need for conformational rearrangement prior to the docking of the voluminous peptide. Because no direct contacts between the flexible part of the loop and the peptide ligand were detected, it seems likely that the higher affinity of the two streptavidin mutants for the Strep‐tag II is caused by a predominantly entropic mechanism.
Dosimetry of beta‐ray ophthalmic applicators: Comparison of different measurement methods
Authors: Soares C. G. , Vynckier S. , Järvinen H. , Cross W. G. , Sipilä P. , Flühs D. , Schaeken B. , Mourtada F. A. , Bass G. A. , Williams T. T.
Published: July 2002

An international intercomparison of the dosimetry of three beta particle emitting ophthalmic applicators was performed, which involved measurements with radiochromic film, thermoluminescence dosimeters (TLDs), alanine pellets, plastic scintillators, extrapolation ionization chambers, a small fixed‐volume ionization chambers, a diode detector and a diamond detector. The sources studied were planar applicators of and and a concave applicator of Comparisons were made of absolute dosimetry determined at 1 mm from the source surface in water or water‐equivalent plastic, and relative dosimetry along and perpendicular to the source axes. The results of the intercomparison indicate that the various methods yield consistent absolute dosimetry results at the level of 10%–14% (one standard deviation) depending on the source. For relative dosimetry along the source axis at depths of 5 mm or less, the agreement was 3%–9% (one standard deviation) depending on the source and the depth. Crucial to the proper interpretation of the measurement results is an accurate knowledge of the detector geometry, i.e., sensitive volume and amount of insensitive covering material. From the results of these measurements, functions which describe the relative dose rate along and perpendicular to the source axes are suggested.
Method of identifying dynamic multileaf collimator irradiation that is highly sensitive to a systematic MLC calibration error
Authors: Zygmanski P. , Kung J. H.
Published: July 2002

In intensity modulated radiotherapy (IMRT), radiation is delivered in a multiple of multileaf collimator (MLC) subfields. A subfield with a small leaf‐to‐leaf opening is highly sensitive to a leaf‐ positional error. We introduce a method of identifying and rejecting IMRT plans that are highly sensitive to a systematic MLC gap error (sensitivity to possible random leaf‐positional errors is not addressed here). There are two sources of a systematic MLC gap error: centerline mechanical offset (CMO) and, in the case of a rounded end MLC, radiation field offset (RFO). In IMRT planning system, using an incorrect value of RFO introduces a systematic error ΔRFO that results in all leaf‐to‐leaf gaps that are either too large or too small by (2⋅ΔRFO), whereas assuming that CMO is zero introduces systematic error ΔCMO that results in all gaps that are too large by ΔCMO=CMO. We introduce a concept of the average leaf pair Opening (ALPO) that can be calculated from a dynamic MLC delivery file. We derive an analytic formula for a fractional average fluence error resulting from a systematic gap error of and show that it is inversely proportional to ALPO; explicitly it is equal to in which is generally of the order of 1 mm and This analytic relationship is verified with independent numerical calculations.