bluuebunny/crossref_metadata_2025 huggingface dataset:
Abnormal development of secondary lymphoid tissues in lymphotoxin β-deficient mice
Authors: Alimzhanov Marat B. , Kuprash Dmitry V. , Kosco-Vilbois Marie H. , Luz Arne , Turetskaya Regina L. , Tarakhovsky Alexander , Rajewsky Klaus , Nedospasov Sergei A. , Pfeffer Klaus
Published: July 2002

The tumor necrosis factor (TNF) family cytokines lymphotoxin (LT) α and LTβ form heterotrimers that are expressed on the surface of activated lymphocytes and natural killer cells; LTα homotrimers can be secreted as well. Mice with a disrupted LTα gene lack lymph nodes (LN), Peyer’s patches (PP), and follicular dendritic cell (FDC) networks and reveal profound defects of the splenic architecture. However, it is unclear which of these abnormalities is the result of the absence in LTα homotrimers or LTαβ heterotrimers. To distinguish between these two possibilities, a mouse strain deficient in LTβ was created employing Cre/loxP-mediated gene targeting. Mice deficient in LTβ reveal severe defects in organogenesis of the lymphoid system similar to those of LTα−/−mice, except that mesenteric and cervical LN are present in most LTβ-deficient mice. Both LTβ- and LTα-deficient mice show significant lymphocytosis in the circulation and peritoneal cavity and lymphocytic infiltrations in lungs and liver. After immunization, PNA-positive B cell clusters were detected in the splenic white pulp of LTβ-deficient mice, but FDC networks were severely underdeveloped. Collectively, these results indicate that LTα can signal independently from LTβ in the formation of PNA-positive foci in the spleen, and especially in the development of mesenteric and cervical LN.
Interleaved concatenated codes: New perspectives on approaching the Shannon limit
Authors: Viterbi A. J. , Viterbi A. M. , Sindhushayana N. T.
Published: July 2002

The last few years have witnessed a significant decrease in the gap between the Shannon channel capacity limit and what is practically achievable. Progress has resulted from novel extensions of previously known coding techniques involving interleaved concatenated codes. A considerable body of simulation results is now available, supported by an important but limited theoretical basis. This paper presents a computational technique which further ties simulation results to the known theory and reveals a considerable reduction in the complexity required to approach the Shannon limit.
Paul–Straubel–Kingdon trap for true zero-point confinement of an individual ion and reservoir
Authors: Dehmelt Hans , Yu Nan
Published: July 2002

A modification of the Paul–Straubel trap previously described by us may profitably be operated in a Paul–Straubel–Kingdon (PSK) mode during the initial loading of an individual ion into the trap. Thereby the coating of the trap ring electrode by the atomic beam directed upon it in earlier experiments is eliminated, as is the ionization of an already trapped ion. Coating created serious problems as it spot-wise changed the work function of the ring electrode, which caused large, uncontrolled dc fields in the trap center that prevented zero-point confinement. Operating the Paul–Straubel trap with a small negative bias on the ring electrode wire is all that is required to realize the PSK mode. In this mode the tiny ring trap in the center of the long, straight wire section is surrounded by a second trapping well shaped like a long, thin-walled cylindrical shell and extending to the end-caps. There, ions may be conveniently created in this well without danger of coating the ring with barium. In addition, the long second well is useful as a multi-ion reservoir.
Gravity and the orientation of cell division
Authors: Helmstetter Charles E.
Published: July 2002

A novel culture system for mammalian cells was used to investigate division orientations in populations of Chinese hamster ovary cells and the influence of gravity on the positioning of division axes. The cells were tethered to adhesive sites, smaller in diameter than a newborn cell, distributed over a nonadhesive substrate positioned vertically. The cells grew and divided while attached to the sites, and the angles and directions of elongation during anaphase, projected in the vertical plane, were found to be random with respect to gravity. However, consecutive divisions of individual cells were generally along the same axis or at 90° to the previous division, with equal probability. Thus, successive divisions were restricted to orthogonal planes, but the choice of plane appeared to be random, unlike the ordered sequence of cleavage orientations seen during early embryo development.
Ribonucleotide reductase in the archaeon
Pyrococcus furiosus
: A critical enzyme in the evolution of DNA genomes?
Authors: Riera Joan , Robb Frank T. , Weiss Robert , Fontecave Marc
Published: July 2002

Ribonucleotide reductase (RNR), the enzyme responsible for deoxyribonucleotide synthesis, has been isolated from
Pyrococcus furiosus
, a deeply branching hyperthermophilic, strictly anaerobic archaeon. Its gene has been cloned, sequenced, and shown to harbor two insertions encoding inteins. The purified enzyme absolutely requires adenosylcobalamin for activity, a trait that defines it as a member of class II (adenosylcobalamin-dependent) prokaryotic RNRs. On the other hand, the archaeal RNR has significant amino acid sequence homology with class I (aerobic non-heme iron-dependent) and class III (anaerobic iron–sulfur-dependent) RNRs present in eukaryotes and bacteria, respectively. It is proposed that this enzyme may be the closest possible relative of the original RNR, which allowed the key “RNA world” to “DNA world” transition, and that the different classes of present-day RNRs are the products of divergent evolution.
Diverse tumorigenesis associated with aberrant development in mice overexpressing hepatocyte growth factor/scatter factor
Authors: Takayama Hisashi , LaRochelle William J. , Sharp Richard , Otsuka Toshiyuki , Kriebel Paul , Anver Miriam , Aaronson Stuart A. , Merlino Glenn
Published: July 2002

Hepatocyte growth factor/scatter factor (HGF/SF) is a mesenchymally derived, multifunctional paracrine regulator possessing mitogenic, motogenic, and morphogenetic activities in cultured epithelial cells containing its tyrosine kinase receptor, Met. c-
met
has been implicated in oncogenesis through correlation of expression with malignant phenotype in specific cell lines and tumors. Paradoxically, however, HGF/SF can also inhibit the growth of some tumor cells. To elucidate the oncogenic role of HGF/SF
in vivo
, transgenic mice were created such that HGF/SF was inappropriately targeted to a variety of tissues. HGF/SF transgenic mice developed a remarkably broad array of histologically distinct tumors of both mesenchymal and epithelial origin. Many neoplasms arose from tissues exhibiting abnormal development, including the mammary gland, skeletal muscle, and melanocytes, suggesting a functional link between mechanisms regulating morphogenesis and those promoting tumorigenesis. Most neoplasms, especially melanomas, demonstrated overexpression of both the HGF/SF transgene and endogenous c-
met
, and had enhanced Met kinase activity, strongly suggesting that autocrine signaling broadly promotes tumorigenesis. Thus, subversion of normal mesenchymal–epithelial paracrine regulation through the forced misdirection of HGF/SF expression induces aberrant morphogenesis and subsequent malignant transformation of cells of diverse origin.
Failure to express the P-selectin gene or P-selectin blockade confers early pulmonary protection after lung ischemia or transplantation
Authors: Naka Yoshifumi , Toda Koichi , Kayano Koichi , Oz Mehmet C. , Pinsky David J.
Published: July 2002

Endothelial P-selectin expression contributes to the first wave of neutrophil (polymorphonuclear leukocyte; PMN) influx in several inflammatory conditions. Although remote tissue ischemia, such as a crush injury to the hindlimb, may result in P-selectin-mediated pulmonary leukosequestration, it is not known whether the lungs exhibit a similar response after hypothermic preservation or when subjected to a direct ischemic insult. To determine if P-selectin may mediate early primary graft failure, left lungs harvested from male Lewis rats were preserved for 6 hr at 4°C and transplanted orthotopically into isogeneic recipients. Recipients immunodepleted of PMNs before transplantation demonstrated improved graft function; pulmonary vascular resistance was reduced ≈6-fold, arterial oxygenation was increased ≈3-fold, and recipient survival was increased ≈4-fold (P< 0.05, 0.05, and 0.005, respectively). Administration of a blocking anti-P-selectin IgG 10 min before reperfusion diminished graft PMN infiltration and resulted in improved graft function and recipient survival compared with controls. To establish the role of P-selectin in normothermic pulmonary ischemia, mice were subjected to temporary left pulmonary artery ligation. After functional removal of the nonischemic right lung, mice deletionally mutant for the P-selectin gene (P-selectin −/−) exhibited reduced PMN infiltration (≈2-fold), improved arterial oxygenation (≈2-fold), and improved survival (≈3-fold) compared with P-selectin +/+ control mice (P< 0.05, 0.01, and 0.05, respectively). These studies isolate and identify the central role of a single gene product (P-selectin) in early PMN recruitment and tissue injury after frank pulmonary ischemia and in the setting of lung transplantation after hypothermic preservation.
Rhodopsin kinase: Expression in baculovirus-infected insect cells, and characterization of post-translational modifications
Authors: Cha Kiweon , Bruel Christophe , Inglese James , Khorana H. Gobind
Published: July 2002

Structure–function studies of rhodopsin kinase (RK; EC
2.7.1.125
) require a variety of mutants. Therefore, there is need for a suitable system for the expression of RK mutant genes. Here we report on a study of expression of the RK gene in baculovirus-infected Sf21 cells and characterization of the enzyme produced as purified to near homogeneity. Particular attention has been paid to the post-translational modifications, autophosphorylation and isoprenylation, found in the native bovine RK. The protein produced has been purified using, successively, heparin-Sepharose, Mono Q, and Mono S FPLC (fast protein liquid chromatography) and was obtained in amounts of about 2 mg from 1 liter of cell culture. The enzyme from the last step of purification was obtained in two main fractions that differ in the level of phosphorylation. The protein peak eluted first carries two phosphate groups per protein, whereas the second protein peak is monophosphorylated. Further, while both peaks are isoprenylated, the isoprenyl groups consist of mixtures of C
5
, C
10
, C
15
, and C
20
isoprenyl moieties. From these results, we conclude that the above expression system is suitable for some but not all aspects of structure–function studies.
Euler characteristics and elliptic curves
Authors: Coates John , Howson Susan
Published: July 2002

Let
E
be a modular elliptic curve over ℚ, without
complex multiplication; let
p
be a prime number where
E
has good ordinary reduction; and let
F
∞
be the field obtained by adjoining to ℚ
all
p
-power division points on
E
. Write
G
∞
for the Galois group of
F
∞
over ℚ. Assume that the complex
L
-series of
E
over ℚ does not vanish at
s
= 1. If
p
⩾ 5, we make a precise conjecture about the value
of the
G
∞
-Euler characteristic of the Selmer
group of
E
over
F
∞
. If one makes
a standard conjecture about the behavior of this Selmer group as a
module over the Iwasawa algebra, we are able to prove our conjecture.
The crucial local calculations in the proof depend on recent joint work
of the first author with R. Greenberg.
Governing step of metastasis visualized
in vitro
Authors: Chishima Takashi , Yang Meng , Miyagi Yohei , Li Lingna , Tan Yuying , Baranov Eugene , Shimada Hiroshi , Moossa A. Rahim , Penman Sheldon , Hoffman Robert M.
Published: July 2002

Metastasis is the ultimate life-threatening stage of cancer. The lack of accurate model systems thwarted studies of the metastatic cell’s basic biology. To follow continuously the succeeding stages of metastatic colony growth, we heritably labeled cells from the human lung adenocarcinoma cell line ANIP 973 with green fluorescent protein (GFP) by transfection with GFP cDNA. Labeled cells were then injected intravenously into nude mice, where, by 7 days, they formed brilliantly fluorescing metastatic colonies on mouse lung [Chishima, T., Miyagi, Y., Wang, X., Yang, M., Tan, Y., Shimada, H., Moossa, A. R. & Hoffman, R. M. (1997)
Clin. Exp. Metastasis
15, 547–552]. The seeded lung tissue was then excised and incubated in the three-dimensional sponge-gel-matrix-supported histoculture that maintained the critical features of progressive
in vivo
tumor colonization while allowing continuous access for measurement and manipulation. Tumor progression was continuously visualized by GFP fluorescence in the same individual cultures over a 52-day period, during which the tumors spread throughout the lung. Histoculture tumor colonization was selective for lung cancer cells to grow on lung tissue, because no growth occurred on histocultured mouse liver tissue, which was also observed
in vivo
. The ability to support selective organ colonization in histoculture and visualize tumor progression by GFP fluorescence allows the
in vitro
study of the governing processes of metastasis [Kuo, T.-H., Kubota, T., Watanbe, M., Furukawa, T., Teramoto, T., Ishibiki, K., Kitajima, M., Moossa, A. R., Penman, S. & Hoffman, R. M. (1995)
Proc. Natl. Acad. Sci. USA
92, 12085–12089]. The results presented here provide significant, new opportunities to understand and to develop treatments that prevent and possibly reverse metastasis.
Disruption of syntaxin-mediated protein interactions blocks neurotransmitter secretion
Authors: O’Connor V. , Heuss C. , De Bello W. M. , Dresbach T. , Charlton M. P. , Hunt J. H. , Pellegrini L. L. , Hodel A. , Burger M. M. , Betz H. , Augustine G. J. , Schäfer T.
Published: July 2002

The membrane protein syntaxin participates in several protein–protein interactions that have been implicated in neurotransmitter release. To probe the physiological importance of these interactions, we microinjected into the squid giant presynaptic terminal botulinum toxin C1, which cleaves syntaxin, and the H3 domain of syntaxin, which mediates binding to other proteins. Both reagents inhibited synaptic transmission yet did not affect the number or distribution of synaptic vesicles at the presynaptic active zone. Recombinant H3 domain inhibited the interactions between syntaxin and SNAP-25 that underlie the formation of stable SNARE complexes
in vitro
. These data support the notion that syntaxin-mediated SNARE complexes are necessary for docked synaptic vesicles to fuse.
Genomic and cDNA sequence analysis of the cell matrix adhesion regulator gene
Authors: Durbin H. , Novelli M. R. , Bodmer W. F.
Published: July 2002

The cell matrix adhesion regulator (CMAR) gene has been suggested to be a signal transduction molecule influencing cell adhesion to collagen and, through this, possibly involved in tumor suppression. The originally reported CMAR cDNA was 464 bp long with a tyrosine phosphorylation site at the extreme 3′ end, which mutagenesis studies had shown to be central to the function of this gene. Since the discovery of a 4-bp insertion polymorphism within the originally reported coding region, further sequence information has been obtained. The cDNA has been extended 5′ by ≈2 kb revealing a 559-bp region showing strong homology to the proposed 5′ untranslated sequence of a murine protein kinase receptor family member,
v
ariant
i
n
k
inase (vik). CMAR genomic sequencing has shown the presence of an intron, the intron/exon boundary lying within this region of homology. An RNA transcript for CMAR of ≈2.5 kb has also been identified. The data suggest complex mechanisms for control of expression of two closely associated genes, CMAR and the vik- associated sequence.
Point mutations at the purine nucleoside phosphorylase locus impair thymocyte differentiation in the mouse
Authors: Snyder Floyd F. , Jenuth Jack P. , Mably Ellen R. , Mangat Rupinder K.
Published: July 2002

Three point mutations on theNpballele of the purine nucleoside phosphorylase locus in the mouse have been recovered by male germ cell mutagenesis. The mutants were backcrossed, 12–14 generations, and are designated in increasing order of severity of enzyme deficiency and phenotype: B6-NPE, Met-87 → Lys; B6-NPF, Ala-228 → Thr; and B6-NPG, Trp-16 → Arg. A marked decline in total cell numbers per thymus occurs between 2 and 3 months for the more severe B6-NPF and B6-NPG mutants (35% and 52%, respectively) and by 8 months for the less severe B6-NPE mutation. The thymocyte population is thereafter characterized by a 3- or 8-fold expanded precursor, CD4−CD8−double-negative population and 15% or 55% reduced CD4+CD8+double-positive cells for the B6-NPF and B6-NPG strains, respectively. Spleen lymphocyte Thy-1+cells are reduced by 50% and spleen lymphocyte response to T cell mitogen and interleukin 2 is reduced by 80%. Increases of thymocyte dGTP pools of 5- and 2.5-fold for B6-NPF and B6-NPG mutants, respectively, are observed. The purine nucleoside phosphorylase-deficient mouse exhibits age-dependent progressive perturbations in thymocyte differentiation, reduced numbers of thymocytes, and reduced splenic T cell numbers and response. The progressive T cell deficit is similar to the human disorder.
A surface on the G protein β-subunit involved in interactions with adenylyl cyclases
Authors: Chen Yibang , Weng Gezhi , Li Jinrong , Harry Anya , Pieroni Joseph , Dingus Jane , Hildebrandt John D. , Guarnieri Frank , Weinstein Harel , Iyengar Ravi
Published: July 2002

Receptor activation of heterotrimeric G proteins dissociates Gα from the Gβγ complex, allowing both to regulate effectors. Little is known about the effector-interaction regions of Gβγ. We had used molecular modeling to dock a peptide encoding the region of residues 956–982 of adenylyl cyclase (AC) 2 onto Gβ to identify residues on Gβ that may interact with effectors. Based on predictions from the model, we synthesized peptides encoding sequences of residues 86–105 (Gβ86–105) and 115–135 (Gβ115–135) from Gβ. The Gβ86–105 peptide inhibited Gβγ stimulation of AC2 and blocked Gβγ inhibition of AC1 and by itself inhibited calmodulin-stimulated AC1, thus displaying partial agonist activity. Substitution of Met-101 with Asn in this peptide resulted in the loss of both the inhibitory and partial agonist activities. Most activities of the Gβ115–135 peptide were similar to those of Gβ86–105 but Gβ115–135 was less efficacious in blocking Gβγ inhibition of AC1. Substitution of Tyr-124 with Val in the Gβ115–135 peptide diminished all of its activities. These results identify the region encoded by amino acids 84–143 of Gβ as a surface that is involved in transmitting signals to effectors.
The capital-asset-pricing model and arbitrage pricing theory: A unification
Authors: Khan M. Ali , Sun Yeneng
Published: July 2002

We present a model of a financial market in which naive diversification, based simply on portfolio size and obtained as a consequence of the law of large numbers, is distinguished from efficient diversification, based on mean-variance analysis. This distinction yields a valuation formula involving only the
essential
risk embodied in an asset’s return, where the overall risk can be decomposed into a
systematic
and an
unsystematic
part, as in the arbitrage pricing theory; and the systematic component further decomposed into an
essential
and an
inessential
part, as in the capital-asset-pricing model. The two theories are thus unified, and their individual asset-pricing formulas shown to be equivalent to the pervasive economic principle of no arbitrage. The factors in the model are endogenously chosen by a procedure analogous to the Karhunen–Loéve expansion of continuous time stochastic processes; it has an optimality property justifying the use of a relatively small number of them to describe the underlying correlational structures. Our idealized limit model is based on a continuum of assets indexed by a hyperfinite Loeb measure space, and it is asymptotically implementable in a setting with a large but finite number of assets. Because the difficulties in the formulation of the law of large numbers with a standard continuum of random variables are well known, the model uncovers some basic phenomena not amenable to classical methods, and whose approximate counterparts are not already, or even readily, apparent in the asymptotic setting.
Locomotion and body proportions of the Saint-Césaire 1 Châtelperronian Neandertal
Authors: Trinkaus Erik , Ruff Christopher B. , Churchill Steven E. , Vandermeersch Bernard
Published: July 2002

The initial Upper Paleolithic (Châtelperronian) of western Europe was associated with late European Neandertals, best known through the Saint-Césaire 1 partial skeleton. Biomechanical cross-sectional analysis of the Saint-Césaire 1 femoral diaphysis at the subtrochanteric and midshaft levels, given the plasticity of mammalian diaphyseal cortical bone, provides insights into the habitual levels and patterns of loading on the lower limbs from body mass, proportions, and locomotion. The overall robustnesses of the femoral diaphyses of European Neandertals and early modern humans are similar once contrasts in body proportions are incorporated into the body size scaling. Saint-Césaire 1 matches these samples only if it is provided with Neandertal-like hyperarctic body proportions. And the rounded proximal femoral diaphysis of Saint-Césaire 1 is similar to those of earlier Neandertals, likely also reflecting similar cold-adapted broad pelvic regions. However, although morphologically similar to those of archaic
Homo
, the Saint-Césaire 1 femoral midshaft exhibits the anteroposterior reinforcement characteristic of early modern humans. Consequently, Saint-Césaire 1 appears as a morphological Neandertal with hyperarctic body proportions who nonetheless had shifted locomotor patterns to more closely resemble those of other Upper Paleolithic humans.
Weight functions, double reciprocity laws, and volume formulas for lattice polyhedra
Authors: Chen Beifang
Published: July 2002

We extend the concept of manifold with boundary to weight and boundary weight functions. With the new concept, we obtained the double reciprocity laws for simplicial complexes, cubical complexes, and lattice polyhedra with weight functions. For a polyhedral manifold with boundary, if the weight function has the constant value 1, then the boundary weight function has the constant value 1 on the boundary and 0 elsewhere. In particular, for a lattice polyhedral manifold with boundary, our double reciprocity law with a special parameter reduces to the functional equation of Macdonald; for a lattice polytope especially, the double reciprocity law with a special parameter reduces to the reciprocity law of Ehrhart. Several volume formulas for lattice polyhedra are obtained from the properties of the double reciprocity law. Moreover, the idea of weight and boundary weight leads to a new homology that is not homotopy invariant, but only homeomorphic invariant.
A role for the actin-bundling proteinl-plastin in the regulation of leukocyte integrin function
Authors: Jones Samuel L. , Wang Jun , Turck Christoph W. , Brown Eric J.
Published: July 2002

Regulation of leukocyte integrin avidity is a crucial aspect of inflammation and immunity. The actin cytoskeleton has an important role in the regulation of integrin function, but the cytoskeletal proteins involved are largely unknown. Because inflammatory stimuli that activate integrin-mediated adhesion in human polymorphonuclear neutrophils (PMN) and monocytes cause phosphorylation of the actin-bundling proteinl-plastin, we tested whetherl-plastin phosphorylation was involved in integrin activation.l-plastin-derived peptides that included the phosphorylation site (Ser-5) rapidly induced leukocyte integrin-mediated adhesion when introduced into the cytosol of freshly isolated primary human PMN and monocytes. Substitution of Ala for Ser-5 abolished the ability of the peptide to induce adhesion. Peptide-induced adhesion was sensitive to pharmacologic inhibition of phosphoinositol 3-kinase and protein kinase C, but adhesion induced by a peptide containing a phosphoserine at position 5 was insensitive to inhibition. These data establish a novel role forl-plastin in the regulation of leukocyte adhesion and suggest that many signaling events implicated in integrin regulation act via induction ofl-plastin phosphorylation.
Geometry of circular vectors and pattern recognition of shape of a boundary
Authors: Rao Calyampudi R.
Published: July 2002

This paper deals with pattern recognition of the shape of the boundary of closed figures on the basis of a circular sequence of measurements taken on the boundary at equal intervals of a suitably chosen argument with an arbitrary starting point. A distance measure between two boundaries is defined in such a way that it has zero value when the associated sequences of measurements coincide by shifting the starting point of one of the sequences. Such a distance measure, which is invariant to the starting point of the sequence of measurements, is used in identification or discrimination by the shape of the boundary of a closed figure. The mean shape of a given set of closed figures is defined, and tests of significance of differences in mean shape between populations are proposed.
Homogeneous immunoconjugates for boron neutron-capture therapy: Design, synthesis, and preliminary characterization
Authors: Guan Lufeng , Wims Letitia A. , Kane Robert R. , Smuckler Mark B. , Morrison Sherie L. , Hawthorne M. Frederick
Published: July 2002

The application of immunoprotein-based targeting strategies to the boron neutron-capture therapy of cancer poses an exceptional challenge, because viable boron neutron-capture therapy by this method will require the efficient delivery of 10
3
boron-10 atoms by each antigen-binding protein. Our recent investigations in this area have been focused on the development of efficient methods for the assembly of homogeneous immunoprotein conjugates containing the requisite boron load. In this regard, engineered immunoproteins fitted with unique, exposed cysteine residues provide attractive vehicles for site-specific modification. Additionally, homogeneous oligomeric boron-rich phosphodiesters (oligophosphates) have been identified as promising conjugation reagents. The coupling of two such boron-rich oligophosphates to sulfhydryls introduced to the C
H
2 domain of a chimeric IgG3 has been demonstrated. The resulting boron-rich immunoconjugates are formed efficiently, are readily purified, and have promising
in vitro
and
in vivo
characteristics. Encouragingly, these studies showed subtle differences in the properties of the conjugates derived from the two oligophosphate molecules studied, providing a basis for the application of rational design to future work. Such subtle details would not have been as readily discernible in heterogeneous conjugates, thus validating the rigorous experimental design employed here.
Mössbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of
Escherichia coli
Authors: Popescu Codrina V. , Bates Donna M. , Beinert Helmut , Münck Eckard , Kiley Patricia J.
Published: July 2002

The global regulator FNR (for fumarate nitrate reduction) controls the transcription of >100 genes whose products facilitate adaptation of
Escherichia coli
to growth under O
2
-limiting conditions. Previous Mössbauer studies have shown that anaerobically purified FNR contains a [4Fe-4S]
2+
cluster that, on exposure to oxygen, is converted into a [2Fe-2S]
2+
cluster, a process that decreases DNA binding by FNR. Using
57
Fe Mössbauer spectroscopy of
E. coli
cells containing overexpressed FNR, we show here that the same cluster conversion also occurs
in vivo
on exposure to O
2
. Furthermore, the data show that a significant amount of the [4Fe-4S]
2+
cluster is regenerated when the cells are shifted back to an anaerobic environment. The present study also demonstrates that
57
Fe Mössbauer spectroscopy can be employed to study the
in vivo
behavior of (overexpressed) proteins. The use of this technique to study other iron-containing cell components is discussed.
The β subunit sliding DNA clamp is responsible for unassisted mutagenic translesion replication by DNA polymerase III holoenzyme
Authors: Tomer Guy , Reuven Nina Bacher , Livneh Zvi
Published: July 2002

The replication of damaged nucleotides that have escaped DNA repair leads to the formation of mutations caused by misincorporation opposite the lesion. In
Escherichia coli
, this process is under tight regulation of the SOS stress response and is carried out by DNA polymerase III in a process that involves also the RecA, UmuD′ and UmuC proteins. We have shown that DNA polymerase III holoenzyme is able to replicate, unassisted, through a synthetic abasic site in a gapped duplex plasmid. Here, we show that DNA polymerase III*, a subassembly of DNA polymerase III holoenzyme lacking the β subunit, is blocked very effectively by the synthetic abasic site in the same DNA substrate. Addition of the β subunit caused a dramatic increase of at least 28-fold in the ability of the polymerase to perform translesion replication, reaching 52% bypass in 5 min. When the ssDNA region in the gapped plasmid was extended from 22 nucleotides to 350 nucleotides, translesion replication still depended on the β subunit, but it was reduced by 80%. DNA sequence analysis of translesion replication products revealed mostly −1 frameshifts. This mutation type is changed to base substitution by the addition of UmuD′, UmuC, and RecA, as demonstrated in a reconstituted SOS translesion replication reaction. These results indicate that the β subunit sliding DNA clamp is the major determinant in the ability of DNA polymerase III holoenzyme to perform unassisted translesion replication and that this unassisted bypass produces primarily frameshifts.
An experimental test for lineage-specific position effects on alcohol dehydrogenase (
Adh
) genes in
Drosophila
Authors: Siegal Mark L. , Hartl Daniel L.
Published: July 2002

Independent transgene insertions differ in expression based on their location in the genome; these position effects are of interest because they reflect the influence of genome organization on gene regulation. Position effects also represent potentially insurmountable obstacles to the rigorous functional comparison of homologous genes from different species because (
i
) quantitative variation in expression of each gene across genomic positions (generalized position effects, or GPEs) may overwhelm differences between the genes of interest, or (
ii
) divergent genes may be differentially sensitive to position effects, reflecting unique interactions between each gene and its genomic milieu (lineage-specific position effects, or LSPEs). We have investigated both types of position-effect variation by applying our method of transgene coplacement, which allows comparisons of transgenes in the same position in the genome of
Drosophila melanogaster
. Here we report an experimental test for LSPE in
Drosophila
. The alcohol dehydrogenase
(Adh)
genes of
D. melanogaster
and
Drosophila affinidisjuncta
differ in both tissue distribution and amounts of ADH activity. Despite this striking regulatory divergence, we found a very high correlation in overall ADH activity between the genes of the two species when placed in the same genomic position as assayed in otherwise
Adh
-null adults and larvae. These results argue against the influence of LSPE for these sequences, although the effects of GPE are significant. Our new findings validate the coplacement approach and show that it greatly magnifies the power to detect differences in expression between transgenes. Transgene coplacement thus dramatically extends the range of functional and evolutionary questions that can be addressed by transgenic technology.
On Calderón’s conjecture for the bilinear Hilbert transform
Authors: Lacey Michael T. , Thiele Christoph M.
Published: July 2002

We show that the bilinear Hilbert transform defined by

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\begin{equation*}\boldsymbol{{\mathit{Hfg}}}(\boldsymbol{{\mathit{x}}})\boldsymbol{{\mathrm{\hspace{.167em}=\hspace{.167em}p.v.}}{\mathit{\hspace{.167em}}}}{\int }\boldsymbol{{\mathit{\hspace{.167em}f}}}(\boldsymbol{{\mathit{x\hspace{.167em}-\hspace{.167em}y}}})\boldsymbol{{\mathit{g}}}(\boldsymbol{{\mathit{x\hspace{.167em}+\hspace{.167em}y}}})\boldsymbol{{\mathit{\hspace{.167em}}}}\frac{\boldsymbol{{\mathit{dy}}}}{\boldsymbol{{\mathit{y}}}}\end{equation*}\end{document}

maps

L
p
× L
q

into

L
r

for 1 <
p,
q ≤ ∞
, 1/
p +
1/
q =
1/
r
, and 2/3 <
r
< ∞.
A paracrine role for the epithelial progesterone receptor in mammary gland development
Authors: Brisken Cathrin , Park Sissela , Vass Tibor , Lydon John P. , O’Malley Bert W. , Weinberg Robert A.
Published: July 2002

Recently generated progesterone receptor (PR)-negative (PR
−/−
) mice provide an excellent model for dissecting the role of progesterone in the development of the mammary gland during puberty and pregnancy. However, the full extent of the mammary gland defect in these mice caused by the absence of the PR cannot be assessed, because PR
−/−
mice do not exhibit estrous cycles and fail to become pregnant. To circumvent this difficulty, we have transplanted PR
−/−
breasts into wild-type mice, and we have demonstrated that the development of the mammary gland in the absence of the PR is arrested at the stage of the simple ductal system found in the young virgin mouse. Mammary transplants lacking the PR in the stromal compartment give rise to normal alveolar growth, whereas transplants containing PR
−/−
epithelium conserve the abnormal phenotype. Chimeric epithelia in which PR
−/−
cells are in close vicinity to PR wild-type cells go through complete alveolar development to which the PR
−/−
cells contribute. Together, these results indicate that progesterone acts by a paracrine mechanism on a subset of mammary epithelial cells to allow for alveolar growth and that expression of the PR is not required in all the cells of the mammary epithelium in order for alveolar development to proceed normally.
Field theory in superfluid
3
He: What are the lessons for particle physics, gravity, and high-temperature superconductivity?
Authors: Volovik G. E.
Published: July 2002

There are several classes of homogeneous Fermi systems that are characterized by the topology of the energy spectrum of fermionic quasiparticles: (
i
) gapless systems with a Fermi surface, (
ii
) systems with a gap in their spectrum, (
iii
) gapless systems with topologically stable point nodes (Fermi points), and (
iv
) gapless systems with topologically unstable lines of nodes (Fermi lines). Superfluid
3
He-A and electroweak vacuum belong to the universality class 3. The fermionic quasiparticles (particles) in this class are chiral: they are left-handed or right-handed. The collective bosonic modes of systems of class 3 are the effective gauge and gravitational fields. The great advantage of superfluid
3
He-A is that we can perform experiments by using this condensed matter and thereby simulate many phenomena in high energy physics, including axial anomaly, baryoproduction, and magnetogenesis.
3
He-A textures induce a nontrivial effective metrics of the space, where the free quasiparticles move along geodesics. With
3
He-A one can simulate event horizons, Hawking radiation, rotating vacuum, etc. High-temperature superconductors are believed to belong to class 4. They have gapless fermionic quasiparticles with a “relativistic” spectrum close to gap nodes, which allows application of ideas developed for superfluid
3
He-A.
An agouti mutation lacking the basic domain induces yellow pigmentation but not obesity in transgenic mice
Authors: Miltenberger R. J. , Mynatt R. L. , Bruce B. D. , Wilkison W. O. , Woychik R. P. , Michaud E. J.
Published: July 2002

Chronic antagonism of melanocortin receptors by the paracrine-acting
agouti
gene product induces both yellow fur and a maturity-onset obesity syndrome in mice that ubiquitously express wild-type
agouti
. Functional analysis of
agouti
mutations in transgenic mice indicate that the cysteine-rich C terminus, signal peptide, and glycosylation site are required for agouti activity
in vivo
. In contrast, no biological activity has been ascribed to the conserved basic domain. To examine the functional significance of the agouti basic domain, the entire 29-aa region was deleted from the
agouti
cDNA, and the resulting mutation (
agouti
Δbasic) was expressed in transgenic mice under the control of the β-actin promoter (BAPaΔbasic). Three independent lines of BAPaΔbasic transgenic mice all developed some degree of yellow pigment in the fur, indicating that the agoutiΔbasic protein was functional
in vivo
. However, none of the BAPaΔbasic transgenic mice developed completely yellow fur, obesity, hyperinsulinemia, or hyperglycemia. High levels of
agouti
Δbasic expression in relevant tissues exceeded the level of
agouti
expression in obese
viable yellow
mice, suggesting that suboptimal activity or synthesis of the agoutiΔbasic protein, rather than insufficient RNA synthesis, accounts for the phenotype of the BAPaΔbasic transgenic mice. These findings implicate a functional role for the agouti basic domain
in vivo
, possibly influencing the biogenesis of secreted agouti protein or modulating protein–protein interactions that contribute to effective antagonism of melanocortin receptors.
Ablation of a specific cell population by the replacement of a uniquely expressed gene with a toxin gene
Authors: Arase Kanako , Saijo Kaoru , Watanabe Hiroyuki , Konno Akiyoshi , Arase Hisashi , Saito Takashi
Published: July 2002

The transgenic expression of a toxin gene or a thymidine kinase gene under the control of cell type-specific promoter/enhancer has been shown to be useful for removing a specific cell population in mice. However, this approach requires extensive analysis of the control elements for gene expression in the preparation of the transgenic constructs, and furthermore, the toxin gene might be expressed ectopically because of random integration, resulting in aberrant depletion of unrelated cells. To avoid such difficulties with the transgenic approach, we established a method for the specific depletion of a cell population by replacing a uniquely expressed gene in the population with the diphtheria toxin gene by using homologous recombination. The NKR-P1 gene, a specific cell surface marker of natural killer (NK) cells, was selected as the target gene for depleting NK cells. In chimeric mice reconstituted with embryonic stem cells in which the NKR-P1 gene was replaced by the toxin gene, NKR-P1+cells were almost completely depleted, and NK cell function was abrogated in the embryonic stem cell-derived lymphoid cells. Other cell lineages developed normally. These results show that all NK cells express NKR-P1, that NKR-P1+cells do not influence the development of T and B cells, and further, that this technology of cell targeting is a fast and powerful method of generating mice lacking any chosen cell population.
Follicle cell proteasome activity and acid extract from the egg vitelline coat prompt the onset of self-sterility in
Ciona intestinalis
oocytes
Authors: Marino Rita , De Santis Rosaria , Giuliano Paola , Pinto Maria Rosaria
Published: July 2002

In the hermaphrodite ascidian
Ciona intestinalis
, the egg vitelline coat (VC) controls gamete self–nonself discrimination. Oocytes, after germinal vesicle breakdown, can be fertilized by both self and nonself sperm. However, a barrier to fertilization by self sperm progressively develops in the VC in the 3 hours after germinal vesicle breakdown. During this period, follicle cells attached to the outer surface of the VC release self-sterility factors that bind to the VC. Within the follicle cells, these factors (possibly peptides) are thought to be shuttled to the cell membrane by an hsp70 homolog (
Cihsp70
). In fact, antibodies to hsp70 block the development of self-sterility. Proteasomes are central to the production of antigen peptides. Specific inhibition of proteasome activity with clasto-lactacystin β-lactone (CLβL) prevented the onset of self-sterility, but had no effect once this process had started. CLβL did not block fertilization by nonself sperm. The self-sterility factors were removed from mature oocytes by exposure to acidified media, and their biological activity was transferred to immature oocytes treated with CLβL. The obvious high multiplicity of self–nonself recognition alleles involved in fertilization, and the involvement of an hsp70 and a proteasome in processing self-sterility factors, suggests that this system may be evolutionarily related to the vertebrate immune system.
Noninvasive quantitation of cytosine deaminase transgene expression in human tumor xenografts with
in vivo
magnetic resonance spectroscopy
Authors: Stegman Lauren D. , Rehemtulla Alnawaz , Beattie Bradley , Kievit Els , Lawrence Theodore S. , Blasberg Ronald G. , Tjuvajev Juri G. , Ross Brian D.
Published: July 2002

Analysis of transgene expression
in vivo
currently requires destructive and invasive molecular assays of tissue specimens. Noninvasive methodology for assessing the location, magnitude, and duration of transgene expression
in vivo
will facilitate subject-by-subject correlation of therapeutic outcomes with transgene expression and will be useful in vector development. Cytosine deaminase (CD) is a microbial gene undergoing clinical trials in gene-directed enzyme prodrug gene therapy. We hypothesized that
in vivo
magnetic resonance spectroscopy could be used to measure CD transgene expression in genetically modified tumors by directly observing the CD-catalyzed conversion of the 5-fluorocytosine (5-FC) prodrug to the chemotherapeutic agent 5-fluorouracil (5-FU). The feasibility of this approach is demonstrated in subcutaneous human colorectal carcinoma xenografts in nude mice by using yeast CD (yCD). A three-compartment model was used to analyze the metabolic fluxes of 5-FC and its metabolites. The rate constants for yCD-catalyzed prodrug conversion (
k
1
app
), 5-FU efflux from the observable tumor volume (
k
2
app
), and formation of cytotoxic fluorinated nucleotides from 5-FU (
k
3
app
) were 0.49 ± 0.27 min
−1
, 0.766 ± 0.006 min
−1
, and 0.0023 ± 0.0007 min
−1
, respectively. The best fits of the 5-FU concentration data assumed first-order kinetics, suggesting that yCD was not saturated
in vivo
in the presence of measured intratumoral 5-FC concentrations well above the
in vitro
K
m
. These results demonstrate the feasibility of using magnetic resonance spectroscopy to noninvasively monitor therapeutic transgene expression in tumors. This capability provides an approach for measuring gene expression that will be useful in clinical gene therapy trials.
Self-organized defensive behavior in honeybees
Authors: Millor J. , Pham-Delegue M. , Deneubourg J. L. , Camazine S.
Published: July 2002

We investigated the defensive behavior of honeybees under controlled experimental conditions. During an attack on two identical targets, the spatial distribution of stings varied as a function of the total number of stings, evincing the classic “pitchfork bifurcation” phenomenon of nonlinear dynamics. The experimental results support a model of defensive behavior based on a self-organizing mechanism. The model helps to explain several of the characteristic features of the honeybee defensive response: (i) the ability of the colony to localize and focus its attack, (ii) the strong variability between different hives in the intensity of attack, as well as (iii) the variability observed within the same hive, and (iv) the ability of the colony to amplify small differences between the targets.
Task-related and item-related brain processes of memory retrieval
Authors: Düzel Emrah , Cabeza Roberto , Picton Terence W. , Yonelinas Andrew P. , Scheich Henning , Heinze Hans-Jochen , Tulving Endel
Published: July 2002

In all cognitive tasks, general task-related processes operate
throughout a given task on all items, whereas specific item-related
processes operate differentially on individual items. In typical
functional neuroimaging experiments, these two sets of processes have
usually been confounded. Herein we report a combined positron emission
tomography and event-related potential (ERP) experiment that was
designed to distinguish between neural correlates of task-related and
item-related processes of memory retrieval. Two retrieval tasks,
episodic and semantic, were crossed with episodic (old/new) and
semantic (living/nonliving) properties of individual items to yield
evidence of regional brain activity associated with task-related
processes, item-related processes, and their interaction. The results
showed that episodic retrieval task was associated with increased blood
flow in right prefrontal and posterior cingulate cortex, as well as
with a sustained right-frontopolar-positive ERP, but that the semantic
retrieval task was associated with left frontal and temporal lobe
activity. Retrieval of old items was associated with increased blood
flow in the left medial temporal lobe and with a brief late positive
ERP component. The results provide converging hemodynamic and
electrophysiological evidence for the distinction of task- and
item-related processes, show that they map onto spatially and
temporally distinct patterns of brain activity, and clarify the
hemispheric encoding/retrieval asymmetry (HERA) model of prefrontal
encoding and retrieval asymmetry.
A selective role of calcineurin Aα in synaptic depotentiation in hippocampus
Authors: Zhuo Min , Zhang Wei , Son Hyeon , Mansuy Isabelle , Sobel Raymond A. , Seidman Jonathan , Kandel Eric R.
Published: July 2002

Pharmacological studies have suggested that long-term potentiation (LTP) and long-term depression (LTD) and depotentiation, three forms of synaptic plasticity in the hippocampus, require the activity of the phosphatase calcineurin. At least two different isoforms of calcineurin are found in the central nervous system. To investigate whether all of these forms of synaptic plasticity require the same isoforms of calcineurin, we have examined LTD, depotentiation, and LTP in mice lacking the predominant calcineurin isoform in the central nervous system, Aα−/−mice. Depotentiation was abolished completely whereas neither LTD nor LTP were affected. These studies provide genetic evidence that the Aα isoform of calcineurin is important for the reversal of LTP in the hippocampus and indicate that depotentiation and LTD operate through somewhat different molecular mechanisms.