bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies to reduce oxidative stress in cardiovascular disease
Authors: HAMILTON Carlene A. , MILLER William H. , AL-BENNA Sammy , Julia BROSNAN M. , DRUMMOND Russell D. , McBRIDE Martin W. , DOMINICZAK Anna F.
Published: February 2004

A multitude of studies in experimental animals, together with clinical data, provide evidence that increased production of ROS (reactive oxygen species) are involved in the development and progression of cardiovascular disease. As ROS appear to have a critical role in atherosclerosis, there has been considerable interest in identifying the enzyme systems involved and in developing strategies to reduce oxidative stress. Prospective clinical trials with vitamins and hormone replacement therapy have not fulfilled earlier promises, although there is still interest in other dietary supplements. Superoxide dismutase mimetics, thiols, xanthine oxidase and NAD(P)H oxidase inhibitors are currently receiving much interest, while animal studies using gene therapy show promise, but are still at an early stage. Of the drugs in common clinical use, there is evidence that ACE (angiotensin-converting enzyme) inhibitors and AT1(angiotensin II type 1) receptor blockers have beneficial effects on oxidative stress above their antihypertensive properties, whereas statins, in addition to improving lipid profiles, may also lower oxidative stress.
S-nitrosylation of endothelial nitric oxide synthase is associated with monomerization and decreased enzyme activity
Authors: Ravi Kandasam , Brennan Lisa A. , Levic Snezana , Ross Patrick A. , Black Stephen M.
Published: February 2004

Endothelial nitric oxide synthase (eNOS) is active only as a homodimer. Recent data has demonstrated that exogenous NO can act as an inhibitor of eNOS activity both in intact animals and vascular endothelial cells. However, the exact mechanism by which NO exerts its inhibitory action is unclear. Our initial experiments in bovine aortic endothelial cells indicated that exogenous NO decreased NOS activity with an associated decrease in eNOS dimer levels. We then undertook a series of studies to investigate the mechanism of dimer disruption. Exposure of purified human eNOS protein to NO donors or calcium-mediated activation of the enzyme resulted in a shift in eNOS from a predominantly dimeric to a predominantly monomeric enzyme. Further studies indicated that endogenous NOS activity or NO exposure caused S-nitrosylation of eNOS and that the presence of the thioredoxin and thioredoxin reductase system could significantly protect eNOS dimer levels and prevent the resultant monomerization and loss of activity. Further, exogenous NO treatment caused zinc tetrathiolate cluster destruction at the dimer interface. To further determine whether S-nitrosylation within this region could explain the effect of NO on eNOS, we purified a C99A eNOS mutant enzyme lacking the tetrathiolate cluster and analyzed its oligomeric state. This enzyme was predominantly monomeric, implicating a role for the tetrathiolate cluster in dimer maintenance and stability. Therefore, this study links the inhibitory action of NO with the destruction of zinc tetrathiolate cluster at the dimeric interface through S-nitrosylation of the cysteine residues.
Long-range histone acetylation of the
Ifng
gene is an essential feature of T cell differentiation
Authors: Zhou Weisong , Chang Shaojing , Aune Thomas M.
Published: February 2004

Histone acetylation of promoters precedes activation of many genes. In addition, long-range histone acetylation patterns can be established over many kilobases of the chromatin of linked families of genes that are under common transcriptional control. It is not known whether establishment of long-range histone acetylation patterns is limited to gene families or is a common feature of many genes. The
Ifng
gene is not known to be a member of a gene family but exhibits complex strain-, cell lineage-, and stimulus-dependent regulation. For example, stimulation of naive T cells through their antigen receptor does not initiate
Ifng
gene transcription. However, stimulation of naive T cells through their antigen and IL-12 receptors initiates differentiation programs that yield effector cells with 100-fold greater rates of transcription of the
Ifng
gene after stimulation through the antigen receptor. Here, we demonstrate that these differentiation programs establish long-range histone hyperacetylation patterns that extend at least 50 kb in both upstream and downstream directions of the
Ifng
gene. Establishment of these histone acetylation patterns and
Ifng
gene expression is relatively IL-12-independent in T cells from autoimmuneprone nonobese diabetic mice. These results indicate that gene expression programs that mediate T cell differentiation are regulated by long-range histone acetylation patterns and that defective control of these patterns may contribute to development of autoimmunity.
Reactivation of developmental programs: The cAMP-response element-binding protein pathway is involved in hydra head regeneration
Authors: Kaloulis Kostas , Chera Simona , Hassel Monika , Gauchat Dominique , Galliot Brigitte
Published: February 2004

Hydra regenerate throughout their life. We previously described early modulations in cAMP-response element-binding protein (CREB) DNA-binding activity during regeneration. We now show that the Ser-67 residue located in the P-box is a target for post-translational regulation. The antihydra CREB antiserum detected CREB-positive nuclei distributed in endoderm and ectoderm, whereas the phosphoSer133-CREB antibody detected phospho-CREB-positive nuclei exclusively in endodermal cells. During early regeneration, we observed a dramatic increase in the number of phospho-CREB-positive nuclei in head-regenerating tips, exceeding 80% of the endodermal cells. We identified among CREB-binding kinases the p80 kinase, which showed an enhanced activity and a hyperphosphorylated status during head but not foot regeneration. According to biochemical and immunological evidence, this p80 kinase belongs to the Ribosomal protein S6 kinase family. Exposure to the U0126 mitogen-activated protein kinase kinase inhibitor inhibited head but not foot regeneration, abolished CREB phosphorylation and activation of the early gene
HyBra1
in head-regenerating tips. These data support a role for the mitogen-activated protein kinase/ribosomal protein S6 kinase/CREB pathway in hydra head organizer activity.
From conversion to aggregation: Protofibril formation of the prion protein
Authors: DeMarco Mari L. , Daggett Valerie
Published: February 2004

The ability to diagnose and treat prion diseases is limited by our current understanding of the conversion process of the protein from healthy to harmful isoform. Whereas the monomeric, benign species is well characterized, the misfolded conformations responsible for infectivity and neurodegeneration remain elusive. There is mounting evidence that fibrillization intermediates, or protofibrils, but not mature fibrils or plaques, are the pathogenic species in amyloid diseases. Here, we use molecular dynamics to simulate the conversion of the prion protein. Molecular dynamics simulation produces a scrapie prion protein-like conformation enriched in β-structure that is in good agreement with available experimental data. The converted conformation was then used to model a protofibril by means of the docking of hydrophobic patches of the template structure to form hydrogen-bonded sheets spanning adjacent subunits. The resulting protofibril model provides a non-branching aggregate with a 3
1
axis of symmetry that is in good agreement with a wide variety of experimental data; importantly, it was derived from realistic simulation of the conversion process.
Functional bacteriorhodopsin is efficiently solubilized and delivered to membranes by the chaperonin GroEL
Authors: Deaton John , Sun Jingchuan , Holzenburg Andreas , Struck Douglas K. , Berry Joel , Young Ry
Published: February 2004

Soluble complexes between the tetradecameric chaperonin GroEL and integral membrane proteins can be efficiently formed by detergent dialysis. For example, GroEL
14
was found to bind a limit of two molecules of bacteriorhodopsin (BR). The GroEL-solubilized BR molecules were rapidly ejected from the chaperonin complexes on the addition of ATP or adenosine 5′-[β,γ-imido]triphosphate but not AMP, indicating that conformational changes induced by nucleotide binding eliminate a binding site for the hydrophobic transmembrane domains. BR retains its native conformation in the GroEL complexes, as judged by the spectral characteristics of the bound retinal. Moreover, the chaperonin-solubilized BR could be transferred efficiently to liposomes and used to effect a light-driven proton gradient, indicating that both native conformation and vectorial insertion were accomplished. These results suggest new approaches to the study of purified integral membrane proteins in their natural membrane environment and raise the prospect that GroEL may have a role in the integration of proteins into the cytoplasmic membrane
in vivo
.
Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics
Authors: Pan Yan , Kislinger Thomas , Gramolini Anthony O. , Zvaritch Elena , Kranias Evangelia G. , MacLennan David H. , Emili Andrew
Published: February 2004

Phospholamban (PLN) is a critical regulator of cardiac contractility through its binding to and regulation of the activity of the sarco(endo)plasmic reticulum Ca
2+
ATPase. To uncover biochemical adaptations associated with extremes of cardiac muscle contractility, we used high-throughput gel-free tandem MS to monitor differences in the relative abundance of membrane proteins in standard microsomal fractions isolated from the hearts of PLN-null mice (PLN-KO) with high contractility and from transgenic mice overexpressing a superinhibitory PLN mutant in a PLN-null background (I40A-KO) with diminished contractility. Significant differential expression was detected for a subset of the 782 proteins identified, including known membrane-associated biomarkers, components of signaling pathways, and previously uninvestigated proteins. Proteins involved in fat and carbohydrate metabolism and proteins linked to G protein-signaling pathways activating protein kinase C were enriched in I40A-KO cardiac muscle, whereas proteins linked to enhanced contractile function were enriched in PLN-KO mutant hearts. These data demonstrate that Ca
2+
dysregulation, leading to elevated or depressed cardiac contractility, induces compensatory biochemical responses.
Crystal structure of a benzo[
a
]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase
Authors: Ling Hong , Sayer Jane M. , Plosky Brian S. , Yagi Haruhiko , Boudsocq François , Woodgate Roger , Jerina Donald M. , Yang Wei
Published: February 2004

The first occupation-associated cancers to be recognized were the sooty warts (cancers of the scrotum) suffered by chimney sweeps in 18th century England. In the 19th century, high incidences of skin cancers were noted among fuel industry workers. By the early 20th century, malignant skin tumors were produced in laboratory animals by repeatedly painting them with coal tar. The culprit in coal tar that induces cancer was finally isolated in 1933 and determined to be benzo[
a
]pyrene (BP), a polycyclic aromatic hydrocarbon. A residue of fuel and tobacco combustion and frequently ingested by humans, BP is metabolized in mammals to benzo[
a
]pyrene diol epoxide (BPDE), which forms covalent DNA adducts and induces tumor growth. In the 70 yr since its isolation, BP has been the most studied carcinogen. Yet, there has been no crystal structure of a BPDE DNA adduct. We report here the crystal structure of a BPDE–adenine adduct base-paired with thymine at a template–primer junction and complexed with the lesion-bypass DNA polymerase Dpo4 and an incoming nucleotide. Two conformations of the BPDE, one intercalated between base pairs and another solvent-exposed in the major groove, are observed. The latter conformation, which can be stabilized by organic solvents that reduce the dielectric constant, seems more favorable for DNA replication by Dpo4. These structures also suggest a mechanism by which mutations are generated during replication of DNA containing BPDE adducts.
An anti-CD45RO immunotoxin kills HIV-latently infected cells from individuals on HAART with little effect on CD8 memory
Authors: Saavedra-Lozano J. , Cao Y. , Callison J. , Sarode R. , Sodora D. , Edgar J. , Hatfield J. , Picker L. , Peterson D. , Ramilo O. , Vitetta E. S.
Published: February 2004

CD4
+
CD45RO
+
T cells are the major latent viral reservoir in HIV-infected individuals and hence a major obstacle in curing the disease. An anti-CD45RO immunotoxin (IT) can decrease the number of both productively and latently infected CD4
+
T cells obtained from HIV-infected individuals with detectable viremia. In this study, we determined whether this IT could also kill latently infected replication-competent CD4
+
T cells obtained from infected individuals without detectable plasma viremia. Our results demonstrate that
ex vivo
treatment with the anti-CD45RO IT significantly reduced the frequency of these cells. In contrast, the IT had only a modest effect on the cytomegalalovirus-specific memory responses of CD8
+
T cells. These results suggest that purging latent cells from infected individuals on highly active antiretroviral therapy with the anti-CD45RO IT might reduce the HIV latent reservoir without seriously compromising CD8
+
T cell memory responses.
RACK1 binds to inositol 1,4,5-trisphosphate receptors and mediates Ca2+release
Authors: Patterson Randen L. , van Rossum Damian B. , Barrow Roxanne K. , Snyder Solomon H.
Published: February 2004

RACK1 is not a G protein but closely resembles the heterotrimeric Gβ-subunit. RACK1 serves as a scaffold, linking protein kinase C to its substrates. We demonstrate that RACK1 physiologically binds inositol 1,4,5-trisphosphate receptors and regulates Ca2+release by enhancing inositol 1,4,5-trisphosphate receptor binding affinity for inositol 1,4,5-trisphosphate. Overexpression of RACK1 or depletion of RACK1 by interference RNA markedly augments or diminishes Ca2+release, respectively, without affecting Ca2+entry. These findings establish RACK1 as a physiologic mediator of agonist-induced Ca2+release.
Topographic specificity of functional connections from hippocampal CA3 to CA1
Authors: Brivanlou Iman H. , Dantzker Jami L. M. , Stevens Charles F. , Callaway Edward M.
Published: February 2004

The hippocampus is a cortical region thought to play an important role in learning and memory. Most of our knowledge about the detailed organization of hippocampal circuitry responsible for these functions is derived from anatomical studies. These studies present an incomplete picture, however, because the functional character and importance of connections are often not revealed by anatomy. Here, we used a physiological method (photostimulation with caged glutamate) to probe the fine pattern of functional connectivity between the CA3 and CA1 subfields in the mouse hippocampal slice preparation. We recorded intracellularly from CA1 and CA3 pyramidal neurons while scanning with photostimulation across the entire CA3 subfield with high spatial resolution. Our results show that, at a given septotemporal level, nearby CA1 neurons receive synaptic inputs from neighboring CA3 neurons. Thus, the CA3 to CA1 mapping preserves neighbor relations.
Zinc-α2-glycoprotein, a lipid mobilizing factor, is expressed in adipocytes and is up-regulated in mice with cancer cachexia
Authors: Bing Chen , Bao Yi , Jenkins John , Sanders Paul , Manieri Monia , Cinti Saverio , Tisdale Michael J. , Trayhurn Paul
Published: February 2004

Zinc-α2-glycoprotein (ZAG), a 43-kDa protein, is overexpressed in certain human malignant tumors and acts as a lipid-mobilizing factor to stimulate lipolysis in adipocytes leading to cachexia in mice implanted with ZAG-producing tumors. Because white adipose tissue (WAT) is an endocrine organ secreting a wide range of protein factors, including those involved in lipid metabolism, we have investigated whether ZAG is produced locally by adipocytes. ZAG mRNA was detected by RT-PCR in the mouse WAT depots examined (epididymal, perirenal, s.c., and mammary gland) and in interscapular brown fat. In WAT,ZAGgene expression was evident in mature adipocytes and in stromal-vascular cells. Using a ZAG Ab, ZAG protein was located in WAT by Western blotting and immunohistochemistry. Mice bearing the MAC16-tumor displayed substantial losses of body weight and fat mass, which was accompanied by major increases in ZAG mRNA and protein levels in WAT and brown fat. ZAG mRNA was detected in 3T3-L1 cells, before and after the induction of differentiation, with the level increasing progressively after differentiation with a peak at days 8–10. Both dexamethasone and a β3agonist, BRL 37344, increased ZAG mRNA levels in 3T3-L1 adipocytes.ZAGgene expression and protein were also detected in human adipose tissue (visceral and s.c.). It is suggested that ZAG is a new adipose tissue protein factor, which may be involved in the modulation of lipolysis in adipocytes. Overexpression in WAT of tumor-bearing mice suggests a local role for adipocyte-derived ZAG in the substantial reduction of adiposity of cancer cachexia.
Mapping a locus for susceptibility to HIV-1-associated nephropathy to mouse chromosome 3
Authors: Gharavi Ali G. , Ahmad Tariq , Wong Robert D. , Hooshyar Roozbeh , Vaughn Janene , Oller Sarah , Frankel Rachelle Z. , Bruggeman Leslie A. , D'Agati Vivette D. , Klotman Paul E. , Lifton Richard P.
Published: February 2004

HIV-1-associated nephropathy (HIVAN) is a major complication of HIV-1 infection with distinct pathologic features. Introduction of the HIV-1 genome into mice results in a renal disease with all of the histologic and clinical hallmarks of HIVAN on the FVB/N genetic background (TgFVB). We assessed the influence of genetic background on the development or progression of HIVAN by making F
1
hybrids of TgFVB with five other inbred strains (CBA, DBA/2, CAST/Ei, C3H/He, BALB/c) and determining phenotypes relevant to renal failure among transgenic offspring (histology, blood urea nitrogen, proteinuria, serum albumin, and serum cholesterol). We found striking variation in phenotypes among F
1
s, ranging from severe renal disease to no renal disease whatsoever (
P
< 0.001 for ANOVA across all groups). To map genes responsible for this variation, we produced a backcross of TgFVB/CAST F
1
× TgFVB. By genome-wide analysis of linkage in 185 heterozygous transgenic backcross mice, we identified a locus on chromosome 3A1–3,
HIVAN1
, that showed highly significant linkage to renal disease [logarithm of odds (lod) score 4.9 at D3Mit203, accounting for 15% of the variance in renal disease]. Other loci on chromosomes 11, 14, and 16 were suggestive of linkage to renal disease, and a locus on chromosome 9 influenced serum cholesterol but not nephropathy. Interestingly,
HIVAN1
is syntenic to human chromosome 3q25–27, an interval showing suggestive evidence of linkage to various nephropathies. These findings demonstrate a strong genetic influence on HIVAN and demonstrate a major renal disease susceptibility locus on mouse chromosome 3A1–3.
Binding of F-spondin to amyloid-β precursor protein: A candidate amyloid-β precursor protein ligand that modulates amyloid-β precursor protein cleavage
Authors: Ho Angela , Südhof Thomas C.
Published: February 2004

Amyloid-β precursor protein (APP), a type I membrane protein, is physiologically processed by α- or β-secretases that cleave APP N-terminal to the transmembrane region. Extracellular α-/β-cleavage of APP generates a large secreted N-terminal fragment, and a smaller cellular C-terminal fragment. Subsequent γ-secretase cleavage in the transmembrane region of the C-terminal fragment induces secretion of small extracellular peptides, including Aβ
40
and Aβ
42
, which are instrumental in the pathogenesis of Alzheimer's disease, and intracellular release of a cytoplasmic tail fragment. Although APP resembles a cell-surface receptor, no functionally active extracellular ligand for APP that might regulate its proteolytic processing has been described. We now show that F-spondin, a secreted signaling molecule implicated in neuronal development and repair, binds to the conserved central extracellular domain of APP and inhibits β-secretase cleavage of APP. Our data indicate that F-spondin may be an endogenous regulator of APP cleavage, and suggest that the extracellular domains of APP are potential drug targets for interfering with β-secretase cleavage.
The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator
Authors: Yang Fajun , DeBeaumont Rosalie , Zhou Sharleen , Näär Anders M.
Published: February 2004

The human activator-recruited cofactor (ARC), a family of large transcriptional coactivator complexes related to the yeast Mediator, was recently identified based on functional association with the activation domains of multiple cellular and viral transcriptional activators, including the herpes simplex viral activator VP16, sterol regulatory element binding protein, and NF-κB. Here we describe the biochemical purification and cloning of the 92-kDa ARC/Mediator subunit, ARC92, that is specifically targeted by the activation domain of the VP16 transactivator. Affinity chromatography using the VP16 activation domain followed by peptide microsequencing led to the identification of ARC92 as a specific cellular interaction partner of the VP16 activation domain. ARC92 associates with the VP16 activation domain
in vitro
and
in vivo
, and the VP16 binding domain of ARC92 is a strong competitive inhibitor of Gal4-VP16
in vivo
. Moreover, small interfering RNA-mediated knockdown of ARC92 in human cells results in selective inhibition of Gal4-VP16 gene activation. Taken together, our results suggest that ARC92 is a direct and specific target of the VP16 transactivator that serves in the context of the ARC/Mediator coactivator as an important transducer of transcription activating signals from the VP16 activation domain to the RNA polymerase II transcriptional machinery.
Carbon monoxide mediates vasoactive intestinal polypeptide-associated nonadrenergic/noncholinergic neurotransmission
Authors: Watkins Crystal C. , Boehning Darren , Kaplin Adam I. , Rao Mahil , Ferris Christopher D. , Snyder Solomon H.
Published: February 2004

Carbon monoxide (CO) synthesized by heme oxygenase 2 (HO2) and nitric oxide (NO) produced by neuronal NO synthase (nNOS) mediate nonadrenergic/noncholinergic (NANC) intestinal relaxation. In many areas of the gastrointestinal tract, NO and CO function as coneurotransmitters. In the internal anal sphincter (IAS), NANC relaxation is mediated primarily by CO. Vasoactive intestinal polypeptide (VIP) has also been shown to participate in NANC relaxation throughout the intestine, including the IAS. By using a combination of pharmacology and genetic knockout of the biosynthetic enzymes for CO and NO, we show that the physiologic effects of exogenous and endogenous VIP in the IAS are mediated by HO2-synthesized CO.
Loss of NFAT5 results in renal atrophy and lack of tonicity-responsive gene expression
Authors: López-Rodríguez Cristina , Antos Christopher L. , Shelton John M. , Richardson James A. , Lin Fangming , Novobrantseva Tatiana I. , Bronson Roderick T. , Igarashi Peter , Rao Anjana , Olson Eric N.
Published: February 2004

The transcription factor NFAT5/TonEBP, a member of the NFAT/Rel family of transcription factors, has been implicated in diverse cellular responses, including the response to osmotic stress, integrin-dependent cell migration, T cell activation, and the Ras pathway in
Drosophila
. To clarify the
in vivo
role of NFAT5, we generated NFAT5-null mice. Homozygous mutants were genetically underrepresented after embryonic day 14.5. Surviving mice manifested a progressive and profound atrophy of the kidney medulla with impaired activation of several osmoprotective genes, including those encoding aldose reductase, Na
+
/Cl
–
-coupled betaine/γ-aminobutyric acid transporter, and the Na
+
/myo-inositol cotransporter. The
aldose reductase
gene is controlled by a tonicity-responsive enhancer, which was refractory to hypertonic stress in fibroblasts lacking NFAT5, establishing this enhancer as a direct transcriptional target of NFAT5. Our findings demonstrate a central role for NFAT5 as a tonicity-responsive transcription factor required for kidney homeostasis and function.
Correlates of parents’ involvement with their adolescent children in restructured and biological two-parent families: The role of child characteristics
Authors: Flouri Eirini
Published: February 2004

This study used data from both 225 fathers and mothers as well as their secondary school age children to explore the role of child characteristics (sex, age, self-esteem, and emotional and behavioural well-being) in mother’s and father’s involvement in biological and restructured (stepfather) two-parent families after controlling for known confounding factors. Parent involvement was assessed by both the child and the parents. Child-reported father’s involvement was positively related to child-reported child’s self-esteem, and child-reported mother’s involvement was higher for girls. The interaction between family structure and father-reported child’s emotional and behavioural problems was significant in predicting father-reported father’s involvement. Stepfathers reported higher involvement when they viewed their stepchildren as psychologically well adjusted than when they viewed them as having emotional and behavioural problems. As a group, child characteristics were more significant in predicting fathers’ than mothers’ involvement.
The peroxisome
Authors: Titorenko Vladimir I. , Rachubinski Richard A.
Published: February 2004

The peroxisome has long been known for its role in lipid metabolism and hydrogen peroxide detoxification. However, growing evidence supports the view that this organelle can also function both as an intracellular signaling compartment and as an organizing platform that orchestrates certain developmental decisions from inside the cell. This review highlights various strategies that peroxisomes employ to regulate the processes of development, differentiation, and morphogenesis and critically evaluates several molecular mechanisms by which peroxisomes promote these processes.
Requirement for TRAF3 in Signaling by LMP1 But Not CD40 in B Lymphocytes
Authors: Xie Ping , Hostager Bruce S. , Bishop Gail A.
Published: February 2004

CD40, a member of the tumor necrosis factor receptor family, and the Epstein-Barr virus–encoded oncoprotein latent membrane protein 1 (LMP1) share several tumor necrosis factor receptor–associated factor (TRAF) adaptor proteins for signaling. Among these, TRAF3 was the first identified to directly bind both receptors, yet its role remains a mystery. To address this, we generated B cell lines deficient in TRAF3 by homologous recombination. We found that CD40 signals were normal in the absence of TRAF3, with the exception of moderately enhanced c-Jun NH2-terminal kinase (JNK) activation and antibody secretion. In sharp contrast, LMP1 signaling was markedly defective in TRAF3−/− B cells. LMP1-induced activation of JNK and nuclear factor κB, up-regulation of CD23 and CD80, and antibody secretion were substantially affected by TRAF3 deficiency. Reconstitution of TRAF3 expression decreased CD40-induced JNK activation and antibody secretion, and fully restored LMP1 signaling. Although TRAF2 is widely believed to be important for LMP1 function, LMP1 signaling was intact in TRAF2−/− B cells. Our data reveal that CD40 and LMP1 unexpectedly use TRAF3 in different ways, and that TRAF3 is required for LMP1-mediated activation of B cells.
FcγRIIb Balances Efficient Pathogen Clearance and the Cytokine-mediated Consequences of Sepsis
Authors: Clatworthy Menna R. , Smith Kenneth G.C.
Published: February 2004

The immune response to infection must be controlled to ensure it is optimal for defense while avoiding the consequences of excessive inflammation, which include fatal septic shock. Mice deficient in FcγRIIb, an inhibitory immunoglobulin G Fc receptor, have enhanced immune responses. Therefore, we examined whether FcγRIIb controls the response to Streptococcus pneumoniae. Macrophages from FcγRIIb-deficient mice showed increased antibody-dependent phagocytosis of pneumococci in vitro, and consistent with this infected FcγRIIb-deficient mice demonstrated increased bacterial clearance and survival. In contrast, previously immunized FcγRIIb-deficient mice challenged with large inocula showed reduced survival. This correlated with increased production of the sepsis-associated cytokines tumor necrosis factor α and interleukin 6. We propose that FcγRIIb controls the balance between efficient pathogen clearance and the cytokine-mediated consequences of sepsis, with potential therapeutic implications.
The Structuralist Conception of Objects
Authors: Chakravartty Anjan
Published: February 2004

This paper explores the consequences of the two most prominent forms of contemporary structural realism for the notion of objecthood. Epistemic structuralists hold that we can know structural aspects of reality, but nothing about the natures of unobservable relata whose relations define structures. Ontic structuralists hold that we can know structural aspects of reality, and that there is nothing else to know—objects are useful heuristic posits, but are ultimately ontologically dispensable. I argue that structuralism does not succeed in ridding a structuralist ontology of objects.
Functional Analysis and the Autonomy of Psychology
Authors: Feest Uljana
Published: February 2004

This paper examines the notion that psychology is autonomous. It is argued that we need to distinguish between (a) the question of whether psychological explanations are autonomous, and (b) the question of whether the process of psychological discovery is autonomous. The issue is approached by providing a reinterpretation of Robert Cummins's notion of functional analysis (FA). A distinction is drawn between FA as an explanatory strategy and FA as an investigative strategy. It is argued that the identification of functional components of the cognitive system may draw on knowledge about brain structure, without thereby jeopardizing the explanatory autonomy of psychology.
Constant Factors and Hedgeless Hedges: On Heuristics and Biases in Biological Research
Authors: Robert Jason Scott
Published: February 2004

How does a complex organism develop from a relatively simple, homogeneous mass? The usual answer is: through the (context-dependent) execution of species-specific genetic instructions specifying the development of that organism. Commentators are sometimes skeptical of this usual answer, but of course not all commentators, and not always for the same reasons. Here I attempt to lay bare the logical structure of the usual answer through an extended analysis of the heuristics and methodological principles at play in the exploration and explanation of development—and also to show a critical ambiguity that renders the usual answer suspect.
Making Populations: Bounding Genes in Space and in Time
Authors: Gannett Lisa
Published: February 2004

At least below the level of species, biological populations are not mind-independent objects that scientists discover. Rather, biological populations are pragmatically constructed as objects of investigation according to the aims, interests, and values that inform particular research contexts. The relations among organisms that are constitutive of population-level phenomena (e.g., mating propensity, genealogy, and competition) occur as matters of degree and so give rise to statistically defined open-ended biological systems. These systems are rendered discrete units to satisfy practical needs and theoretical preferences associated with specific contexts of investigation. While it may be possible to defend a realist position regarding biological relations among organisms, biological populations are “made” when contextual features determine which kinds and degrees of relations to privilege over others, and so how to bound genes in space and time. Consequently, the objectivity of population-based approaches to species genome diversity cannot rest in the mind-independence of populations themselves.
The Emergence of the Macroworld: A Study of Intertheory Relations in Classical and Quantum Mechanics
Authors: Forster Malcolm R. , Kryukov Alexey
Published: February 2004

Classical mechanics is empirically successful because the probabilistic mean values of quantum mechanical observables follow the classical equations of motion to a good approximation (Messiah 1970, 215). We examine this claim for the one-dimensional motion of a particle in a box, and extend the idea by deriving a special case of the ideal gas law in terms of the mean value of a generalized force used to define “pressure.” The examples illustrate the importance of probabilistic averaging as a method of abstracting away from the messy details of microphenomena, not only in physics, but in other sciences as well.
Field Unification in the Maxwell-Lorentz Theory with Absolute Space
Authors: Rynasiewicz Robert
Published: February 2004

Although Trautman (1966) appears to give a unified-field treatment of electrodynamics in Newtonian spacetime, there are difficulties in cogently interpreting it as such in relation to the facts of electromagnetic and magneto-electric induction. Presented here is a covariant, nonunified field treatment of the Maxwell-Lorentz theory with absolute space. This dispels a worry in Earman (1989) as to whether there are any historically realistic examples in which absolute space plays an indispensable role. It also shows how Trautman's formulation can be rendered coherent, albeit at the cost of deunification, by reinterpreting the Maxwell tensor as a composite object involving, in part, elements from Newtonian spacetime.
The Constructible and the Intelligible in Newton's Philosophy of Geometry
Authors: Domski Mary
Published: February 2004

In the preface to thePrincipia(1687) Newton famously states that “geometry is founded on mechanical practice.” Several commentators have taken this and similar remarks as an indication that Newton was firmly situated in the constructivist tradition of geometry that was prevalent in the seventeenth century. By drawing on a selection of Newton's unpublished texts, I hope to show the faults of such an interpretation. In these texts, Newton not only rejects the constructivism that took its birth in Descartes'sGéométrie(1637); he also presents the science of geometry as being more powerful than hisPrincipiaremarks may lead us to believe.
Motivational Realism: The Natural Classification for Pierre Duhem
Authors: Darling Karen Merikangas
Published: February 2004

This paper addresses a central interpretive problem in understanding Pierre Duhem's philosophy of science. The problem arises because there is textual support for both realist and antirealist readings of his work. I argue that his realist and antirealist claims are different. For Duhem, scientific reasoning leads straight to antirealism. But intuition (reasons of the heart) motivates, without justifying, a kind of realism. I develop this idea to suggest a motivational realist interpretation of Duhem's philosophy.
Experimental Localism and External Validity
Authors: Guala Francesco
Published: February 2004

Experimental “localism” stresses the importance of context-specific knowledge, and the limitations of universal theories in science. I illustrate Latour's radical approach to localism and show that it has some unpalatable consequences, in particular the suggestion that problems of external validity (or how to generalize experimental results to nonlaboratory circumstances) cannot be solved. In the last part of the paper I try to sketch a solution to the problem of external validity by extending Mayo's error-probabilistic approach.
Objectivity, Information, and Maxwell's Demon
Authors: Weinstein Steven
Published: February 2004

This paper examines some common measures of complexity, structure, and information, with an eye toward understanding the extent to which complexity or information-content may be regarded as objective properties of individual objects. A form of contextual objectivity is proposed which renders the measures objective, and which largely resolves the puzzle of Maxwell's Demon.
A Loophole in Bell's Theorem? Parameter Dependence in the Hess-Philipp Model
Authors: Myrvold Wayne C.
Published: February 2004

The hidden-variables model constructed by Karl Hess and Walter Philipp is claimed by its authors to exploit a “loophole” in Bell's theorem; according to Hess and Philipp, the parameters employed in their model extend beyond those considered by Bell. Furthermore, they claim that their model satisfies Einstein locality and is free of any “suspicion of spooky action at a distance.” Both of these claims are false; the Hess-Philipp model achieves agreement with the quantum-mechanical predictions, not by circumventing Bell's theorem, but via Parameter Dependence.
On the Metaphysics of Probabilistic Causation: Lessons from Social Epidemiology
Authors: Glymour Bruce
Published: February 2004

I argue that the orthodox account of probabilistic causation, on which probabilistic causes determine the probability of their effects, is inconsistent with certain ontological assumptions implicit in scientific practice. In particular, scientists recognize the possibility that properties of populations can cause the behavior of members of the populations. Such emergent population-level causation is metaphysically impossible on the orthodoxy.
Is Quantum Mechanics Pointless?
Authors: Arntzenius Frank
Published: February 2004

There exist well-known conundrums, such as measure-theoretic paradoxes and problems of contact, which, within the context of classical physics, can be used to argue against the existence of points in space and space-time. I examine whether quantum mechanics provides additional reasons for supposing that there are no points in space and space-time.
A Parser as an Epistemic Artifact: A Material View on Models
Authors: Knuuttila Tarja , Voutilainen Atro
Published: February 2004

The purpose of this paper is to suggest that models in scientific practice can be conceived of asepistemic artifacts.Approaching models this way accommodates many such things that working scientists themselves call models but that the semantic conception of models does not duly recognize as such. That models are epistemic artifacts implies, firstly, that they cannot be understood apart from purposeful human activity; secondly, that they are somehow materialized inhabitants of the intersubjective field of that activity; and thirdly, that they can function also as knowledge objects. We argue that models as epistemic artifacts provide knowledge in many other ways than just via direct representative links. To substantiate our view we use a language-technological artifact, a parser, as an example.
A Mechanistic Model for the Organization of Microtubule Asters by Motor and Non-Motor Proteins in a Mammalian Mitotic Extract
Authors: Chakravarty Arijit , Howard Louisa , Compton Duane A.
Published: February 2004

We used computer simulation to understand the functional relationships between motor (dynein, HSET, and Eg5) and non-motor (NuMA) proteins involved in microtubule aster organization. The simulation accurately predicted microtubule organization under all combinations of motor and non-motor proteins, provided that microtubule cross-links at minus-ends were dynamic, and dynein and HSET were restricted to cross-linking microtubules in parallel orientation only. A mechanistic model was derived from these data in which a combination of two aggregate properties, Net Minus-end–directed Force and microtubule Cross-linking Orientation Bias, determine microtubule organization. This model uses motor and non-motor proteins, accounts for motor antagonism, and predicts that alterations in microtubule Cross-linking Orientation Bias should compensate for imbalances in motor force during microtubule aster formation. We tested this prediction in the mammalian mitotic extract and, consistent with the model, found that increasing the contribution of microtubule cross-linking by NuMA compensated for the loss of Eg5 motor activity. Thus, this model proposes a precise mechanism of action of each noncentrosomal protein during microtubule aster organization and suggests that microtubule organization in spindles involves both motile forces from motors and static forces from non-motor cross-linking proteins.
A Role for Sorting Nexin 2 in Epidermal Growth Factor Receptor Down-regulation: Evidence for Distinct Functions of Sorting Nexin 1 and 2 in Protein Trafficking
Authors: Gullapalli Anuradha , Garrett Tiana A. , Paing May M. , Griffin Courtney T. , Yang Yonghua , Trejo JoAnn
Published: February 2004

Sorting nexin 1 (SNX1) and SNX2, homologues of the yeast vacuolar protein-sorting (Vps)5p, contain a phospholipid-binding motif termed the phox homology (PX) domain and a carboxyl terminal coiled-coil region. A role for SNX1 in trafficking of cell surface receptors from endosomes to lysosomes has been proposed; however, the function of SNX2 remains unknown. Toward understanding the function of SNX2, we first examined the distribution of endogenous protein in HeLa cells. We show that SNX2 resides primarily in early endosomes, whereas SNX1 is found partially in early endosomes and in tubulovesicular-like structures distributed throughout the cytoplasm. We also demonstrate that SNX1 interacts with the mammalian retromer complex through its amino terminal domain, whereas SNX2 does not. Moreover, activated endogenous epidermal growth factor receptor (EGFR) colocalizes markedly with SNX2-positive endosomes, but minimally with SNX1-containing vesicles. To assess SNX2 function, we examined the effect of a PX domain-mutated SNX2 that is defective in vesicle localization on EGFR trafficking. Mutant SNX2 markedly inhibited agonist-induced EGFR degradation, whereas internalization remained intact. In contrast, SNX1 PX domain mutants failed to effect EGFR degradation, whereas a SNX1 deletion mutant significantly inhibited receptor down-regulation. Interestingly, knockdown of SNX1 and SNX2 expression by RNA interference failed to alter agonist-induced EGFR down-regulation. Together, these findings suggest that both SNX1 and SNX2 are involved in regulating lysosomal sorting of internalized EGFR, but neither protein is essential for this process. These studies are the first to demonstrate a function for SNX2 in protein trafficking.
Isoflurane and Sevoflurane Precondition against Neutrophil-induced Contractile Dysfunction in Isolated Rat Hearts
Authors: Hu Guochang , Salem M. Ramez , Crystal George J.
Published: February 2004

Background

The authors tested the hypothesis that pretreatment with isoflurane or sevoflurane can protect the heart against neutrophil-induced contractile dysfunction.

Methods

Studies were conducted in buffer-perfused and paced isolated rat hearts. Left ventricular developed pressure served as an index of contractility. Pretreatment consisted of administration of 1.0 minimum alveolar concentration isoflurane or sevoflurane for 15 min followed by a 10-min washout and was performed in the absence and presence of the adenosine triphosphate-sensitive potassium channel inhibitor glibenclamide (10 microM). Polymorphonuclear neutrophils and platelet-activating factor were then added to the perfusate for 10 min, followed by 30 min of recovery. Neutrophil retention was assessed from the difference between those administered and collected in coronary effluent and measurements of myeloperoxidase in myocardial samples. Isolated hearts were also used to assess the effect of volatile anesthetic pretreatment on cardiac dysfunction caused by enzymatically generated superoxide. In additional studies, the authors evaluated the effect of volatile anesthetic pretreatment on the adherence of neutrophils to isolated rat aortic segments.

Results

Platelet-activating factor-stimulated neutrophils caused marked and persistent reductions (> 50%) in left ventricular developed pressure. Pretreatment with either isoflurane or sevoflurane abolished these effects, as well as the associated increases in neutrophil retention. Glibenclamide did not alter these actions of the anesthetics. Pretreatment with either volatile anesthetic attenuated the reductions in left ventricular developed pressure caused by exogenous superoxide and abolished the increases in neutrophil adherence in the aortic segments.

Conclusion

Isoflurane and sevoflurane preconditioned the heart against neutrophil-induced contractile dysfunction. This action was associated with an inhibition to neutrophil adherence and likely involved an increased resistance of the myocardium to oxidant-induced injury; the adenosine triphosphate-sensitive potassium channels played no apparent role.
Isoflurane Produces Delayed Preconditioning against Myocardial Ischemia and Reperfusion Injury
Authors: Tanaka Katsuya , Ludwig Lynda M. , Krolikowski John G. , Alcindor Dunbar , Pratt Phillip F. , Kersten Judy R. , Pagel Paul S. , Warltier David C.
Published: February 2004

Background

Whether volatile anesthetics produce a second window of preconditioning is unclear. The authors tested the hypothesis that isoflurane causes delayed preconditioning against infarction and, further, that cyclooxygenase (COX)-2 mediates this beneficial effect.

Methods

Rabbits (n = 43) were randomly assigned to receive 0.9% intravenous saline, the selective COX-2 inhibitor celecoxib (3 mg/kg intraperitoneal) five times over 2 days before coronary artery occlusion and reperfusion, or isoflurane (1.0 minimum alveolar concentration) 24 h before acute experimentation in the absence or presence of celecoxib pretreatment. Two additional groups of rabbits received a single dose of celecoxib either 30 min before or 21.5 h after administration of isoflurane. Rabbits were then instrumented for measurement of hemodynamics and underwent 30 min of coronary occlusion followed by 3 h of reperfusion. Myocardial infarct size was measured using triphenyltetrazolium staining. Western immunoblotting to examine COX-1 and COX-2 protein expression was performed in rabbit hearts that had or had not been exposed to isoflurane.

Results

Isoflurane significantly (P < 0.05) reduced infarct size (22 +/- 3% of the left ventricular area at risk) as compared with control (39 +/- 2%). Celecoxib alone had no effect on infarct size (36 +/- 4%) but abolished isoflurane-induced cardioprotection (36 +/- 4%). A single dose of celecoxib administered 2.5 h before coronary occlusion and reperfusion also abolished the delayed protective effects of isoflurane (36 +/- 4%), but celecoxib given 30 min before exposure to isoflurane had no effect (22 +/- 4%). Isoflurane did not alter COX-1 and COX-2 protein expression.

Conclusions

The results indicate that the volatile anesthetic isoflurane produces a second window of preconditioning against myocardial ischemia and reperfusion injury. Furthermore, COX-2 is an important mediator of isoflurane-induced delayed preconditioning.