bluuebunny/crossref_metadata_2025 huggingface dataset:
TCL1 oncogene expression in AIDS-related lymphomas and lymphoid tissues
Authors: Teitell Michael , Damore Michael A. , Sulur Girija G. , Turner Devin E. , Stern Marc-Henri , Said Jonathan W. , Denny Christopher T. , Wall Randolph
Published: July 2002

AIDS-related non-Hodgkin’s lymphoma (AIDS NHL) comprises a diverse and heterogeneous group of high-grade B cell tumors. Certain classes of AIDS NHL are associated with alterations in oncogenes or tumor-suppressor genes or infections by oncogenic herpesviruses. However, the clinically significant class of AIDS NHL designated immunoblastic lymphoma plasmacytoid (AIDS IBLP) lacks any consistent genetic alterations. We identified the
TCL1
oncogene from a set of AIDS IBLP-associated cDNA fragments generated by subtractive hybridization with non-AIDS IBLP. Aberrant
TCL1
expression has been implicated in T cell leukemia/lymphoma development, and its expression also has been seen in many established B cell tumor lines. However,
TCL1
expression has not been reported in AIDS NHL. We find that
TCL1
is expressed in the majority of AIDS IBLP tumors examined. TCL1 protein expression is restricted to tumor cells in AIDS IBLP tissue samples analyzed with immunohistochemical staining. Hyperplastic lymph node and tonsil also exhibit strong TCL1 protein expression in mantle zone B cells and in rare interfollicular zone cells, whereas follicle-center B cells (centroblasts and centrocytes) show weaker expression. These results establish
TCL1
as the most prevalent of all of the surveyed oncogenes associated with AIDS IBLP. They also indicate that abundant TCL1 expression in quiescent mantle zone B cells is down-regulated in activated germinal center follicular B cells in parallel to the known expression pattern of BCL-2. High-level expression in nonproliferating B cells suggests that TCL1 may function in protecting naïve preactivated B cells from apoptosis.
Native language, gender, and functional organization of the auditory cortex
Authors: Salmelin R. , Schnitzler A. , Parkkonen L. , Biermann K. , Helenius P. , Kiviniemi K. , Kuukka K. , Schmitz F. , Freund H.-J.
Published: July 2002

Whole-head magnetoencephalography was employed in 40 normal subjects to investigate whether the basic functional organization of the auditory cortex varies with linguistic environment. Robust activations of the bilateral supratemporal auditory cortices to 1-kHz pure tones, maximum at about 100 ms after stimulus onset, were studied in Finnish and German female and male subject groups with monolingual background. Activations elicited by the tones were mutually indistinguishable in German and Finnish women. In contrast, German men showed significantly stronger auditory responses to pure tones in the left, language-dominant hemisphere than Finnish men. We discuss the possibility that the prominent left-hemisphere activation in German males reflects higher frequency resolution required for distinguishing between German than Finnish vowels and that the clear effect of native language in male but not in female auditory cortex derives from more pronounced functional lateralization in men. The present data suggest that the influence of native language can extend to auditory cortical processing of pure-tone stimuli with no linguistic content and that this effect is conspicuous in the male brain.
Cloning of gp-340, a putative opsonin receptor for lung surfactant protein D
Authors: Holmskov Uffe , Mollenhauer Jan , Madsen Jens , Vitved Lars , Grønlund Jørn , Tornøe Ida , Kliem Anette , Reid Kenneth B. M. , Poustka Annemarie , Skjødt Karsten
Published: July 2002

Surfactant protein D (SP-D) is an oligomeric C type lectin that promotes phagocytosis by binding to microbial surface carbohydrates. A 340-kDa glycoprotein (gp-340) has been shown to bind SP-D in the presence of calcium but does so independently of carbohydrate recognition. This protein exists both in a soluble form and in association with the membranes of alveolar macrophages. The primary structure of gp-340 has been established by molecular cloning, which yielded a 7,686-bp cDNA sequence encoding a polypeptide chain of 2,413 amino acids. The domain organization features 13 scavenger receptor cysteine-rich (SRCR) domains, each separated by an SRCR-interspersed domain, except for SRCRs 4 and 5, which are contiguous. The 13 SRCR domains are followed by two C1r/C1s Uegf Bmp1 domains separated by a 14th SRCR domain and a zona pellucida domain. gp-340 seems to be an alternative spliced form ofDMBT1. Reverse transcription–PCR analysis showed that the main sites of synthesis of gp-340 are lung, trachea, salivary gland, small intestine, and stomach. Immunohistochemistry revealed strong staining for gp-340 in alveolar and other tissue macrophages. Immunostaining of the macrophage membrane was either uniform or focal in a way that suggested capping, whereas other macrophages showed strong intracellular staining within the phagosome/phagolysosome compartments. In some macrophages, SP-D and gp-340 were located in the same cellular compartment. Immunoreactive gp-340 was also found in epithelial cells of the small intestine and in the ducts of salivary glands. The distribution of gp-340 in macrophages is compatible with a role as an opsonin receptor for SP-D.
A β-1,3-
N
-acetylglucosaminyltransferase with poly-
N
-acetyllactosamine synthase activity is structurally related to β-1,3-galactosyltransferases
Authors: Zhou Dapeng , Dinter André , Gallego Ricardo Gutiérrez , Kamerling Johannis P. , Vliegenthart Johannes F. G. , Berger Eric G. , Hennet Thierry
Published: July 2002

Human and mouse cDNAs encoding a new β-1,3-
N
-acetylglucosaminyltransferase (β3GnT) have been isolated from fetal and newborn brain libraries. The human and mouse cDNAs included ORFs coding for predicted type II transmembrane polypeptides of 329 and 325 aa, respectively. The human and mouse β3GnT homologues shared 90% similarity. The β3GnT gene was widely expressed in human and mouse tissues, although differences in the transcript levels were visible, thus indicating possible tissue-specific regulation mechanisms. The β3GnT enzyme showed a marked preference for Gal(β1–4)Glc(NAc)-based acceptors, whereas no activity was detected on type 1 Gal(β1–3)GlcNAc and O-glycan
core 1
Gal(β1–3)GalNAc acceptors. The new β3GnT enzyme was capable of both initiating and elongating poly-
N
-acetyllactosamine chains, which demonstrated its identity with the poly-
N
-acetyllactosamine synthase enzyme (E.C. 2.4.1.149), showed no similarity with the
i antigen
β3GnT enzyme described recently, and, strikingly, included several amino acid motifs in its protein that have been recently identified in β-1,3-galactosyltransferase enzymes. The comparison between the new UDP–GlcNAc:βGal β3GnT and the three UDP–Gal:βGlcNAc β-1,3-galactosyltransferases-I, -II, and -III reveals glycosyltransferases that share conserved sequence motifs though exhibiting inverted donor and acceptor specificities. This suggests that the conserved amino acid motifs likely represent residues required for the catalysis of the glycosidic (β1–3) linkage.
Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins
Authors: Hirt Robert P. , Logsdon John M. , Healy Bryan , Dorey Michael W. , Doolittle W. Ford , Embley T. Martin
Published: July 2002

We have determined complete gene sequences encoding the largest subunit of the RNA polymerase II (RBP1) from two Microsporidia,
Vairimorpha necatrix
and
Nosema locustae
. Phylogenetic analyses of these and other RPB1 sequences strongly support the notion that Microsporidia are not early-diverging eukaryotes but instead are specifically related to Fungi. Our reexamination of elongation factors EF-1α and EF-2 sequence data that had previously been taken as support for an early (Archezoan) divergence of these amitochondriate protists show such support to be weak and likely caused by artifacts in phylogenetic analyses. These EF data sets are, in fact, not inconsistent with a Microsporidia + Fungi relationship. In addition, we show that none of these proteins strongly support a deep divergence of Parabasalia and Metamonada, the other amitochondriate protist groups currently thought to compose early branches. Thus, the phylogenetic placement among eukaryotes for these protist taxa is in need of further critical examination.
Running enhances neurogenesis, learning, and long-term potentiation in mice
Authors: van Praag Henriette , Christie Brian R. , Sejnowski Terrence J. , Gage Fred H.
Published: July 2002

Running increases neurogenesis in the dentate gyrus of the hippocampus, a brain structure that is important for memory function. Consequently, spatial learning and long-term potentiation (LTP) were tested in groups of mice housed either with a running wheel (runners) or under standard conditions (controls). Mice were injected with bromodeoxyuridine to label dividing cells and trained in the Morris water maze. LTP was studied in the dentate gyrus and area CA1 in hippocampal slices from these mice. Running improved water maze performance, increased bromodeoxyuridine-positive cell numbers, and selectively enhanced dentate gyrus LTP. Our results indicate that physical activity can regulate hippocampal neurogenesis, synaptic plasticity, and learning.
Production of cyclic peptides and proteins
in vivo
Authors: Scott Charles P. , Abel-Santos Ernesto , Wall Mark , Wahnon Daphne C. , Benkovic Stephen J.
Published: July 2002

Combinatorial libraries of synthetic and natural products are an important source of molecular information for the interrogation of biological targets. Methods for the intracellular production of libraries of small, stable molecules would be a valuable addition to existing library technologies by combining the discovery potential inherent in small molecules with the large library sizes that can be realized by intracellular methods. We have explored the use of split inteins (
in
ternal pro
teins
) for the intracellular catalysis of peptide backbone cyclization as a method for generating proteins and small peptides that are stabilized against cellular catabolism. The DnaE split intein from
Synechocystis
sp. PCC6803 was used to cyclize the
Escherichia coli
enzyme dihydrofolate reductase and to produce the cyclic, eight-amino acid tyrosinase inhibitor pseudostellarin F in bacteria. Cyclic dihydrofolate reductase displayed improved
in vitro
thermostability, and pseudostellarin F production was readily apparent
in vivo
through its inhibition of melanin production catalyzed by recombinant
Streptomyces antibioticus
tyrosinase. The ability to generate and screen for backbone cyclic products
in vivo
is an important milestone toward the goal of generating intracellular cyclic peptide and protein libraries.
Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network
Authors: Goloubinoff Pierre , Mogk Axel , Zvi Anat Peres Ben , Tomoyasu Toshifumi , Bukau Bernd
Published: July 2002

A major activity of molecular chaperones is to prevent aggregation and refold misfolded proteins. However, when allowed to form, protein aggregates are refolded poorly by most chaperones. We show here that the sequential action of twoEscherichia colichaperone systems, ClpB and DnaK-DnaJ-GrpE, can efficiently solubilize excess amounts of protein aggregates and refold them into active proteins. Measurements of aggregate turbidity, Congo red, and 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid binding, and of the disaggregation/refolding kinetics by using a specific ClpB inhibitor, suggest a mechanism where (i) ClpB directly binds protein aggregates, ATP induces structural changes in ClpB, which (ii) increase hydrophobic exposure of the aggregates and (iii) allow DnaK-DnaJ-GrpE to bind and mediate dissociation and refolding of solubilized polypeptides into native proteins. This efficient mechanism, whereby chaperones can catalytically solubilize and refold a wide variety of large and stable protein aggregates, is a major addition to the molecular arsenal of the cell to cope with protein damage induced by stress or pathological states.
Possible ecological risks of transgenic organism release when transgenes affect mating success: Sexual selection and the Trojan gene hypothesis
Authors: Muir William M. , Howard Richard D.
Published: July 2002

Widespread interest in producing transgenic organisms is balanced by concern over ecological hazards, such as species extinction if such organisms were to be released into nature. An ecological risk associated with the introduction of a transgenic organism is that the transgene, though rare, can spread in a natural population. An increase in transgene frequency is often assumed to be unlikely because transgenic organisms typically have some viability disadvantage. Reduced viability is assumed to be common because transgenic individuals are best viewed as macromutants that lack any history of selection that could reduce negative fitness effects. However, these arguments ignore the potential advantageous effects of transgenes on some aspect of fitness such as mating success. Here, we examine the risk to a natural population after release of a few transgenic individuals when the transgene trait simultaneously increases transgenic male mating success and lowers the viability of transgenic offspring. We obtained relevant life history data by using the small cyprinodont fish, Japanese medaka (
Oryzias latipes
) as a model. Our deterministic equations predict that a transgene introduced into a natural population by a small number of transgenic fish will spread as a result of enhanced mating advantage, but the reduced viability of offspring will cause eventual local extinction of both populations. Such risks should be evaluated with each new transgenic animal before release.
Suppression of gene silencing: A general strategy used by diverse DNA and RNA viruses of plants
Authors: Voinnet Olivier , Pinto Yvonne M. , Baulcombe David C.
Published: July 2002

In transgenic and nontransgenic plants, viruses are both initiators and targets of a defense mechanism that is similar to posttranscriptional gene silencing (PTGS). Recently, it was found that potyviruses and cucumoviruses encode pathogenicity determinants that suppress this defense mechanism. Here, we test diverse virus types for the ability to suppress PTGS.Nicotiana benthamianaexhibiting PTGS of a green fluorescent protein transgene were infected with a range of unrelated viruses and various potato virus X vectors producing viral pathogenicity factors. Upon infection, suppression of PTGS was assessedin plantathrough reactivation of green fluorescence and confirmed by molecular analysis. These experiments led to the identification of three suppressors of PTGS and showed that suppression of PTGS is widely used as a counter-defense strategy by DNA and RNA viruses. However, the spatial pattern and degree of suppression varied extensively between viruses. At one extreme, there are viruses that suppress in all tissues of all infected leaves, whereas others are able to suppress only in the veins of new emerging leaves. This variation existed even between closely related members of the potexvirus group. Collectively, these results suggest that virus-encoded suppressors of gene silencing have distinct modes of action, are targeted against distinct components of the host gene-silencing machinery, and that there is dynamic evolution of the host and viral components associated with the gene-silencing mechanism.
The 9-
cis
-epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean
Authors: Qin Xiaoqiong , Zeevaart Jan A. D.
Published: July 2002

Abscisic acid (ABA), a cleavage product of carotenoids, is involved in stress responses in plants. A well known response of plants to water stress is accumulation of ABA, which is caused by
de novo
synthesis. The limiting step of ABA biosynthesis in plants is presumably the cleavage of 9-
cis
-epoxycarotenoids, the first committed step of ABA biosynthesis. This step generates the C
15
intermediate xanthoxin and C
25
-apocarotenoids. A cDNA,
PvNCED1
, was cloned from wilted bean (
Phaseolus vulgaris
L.) leaves. The 2,398-bp full-length
PvNCED1
has an ORF of 615 aa and encodes a 68-kDa protein. The PvNCED1 protein is imported into chloroplasts, where it is associated with the thylakoids. The recombinant protein PvNCED1 catalyzes the cleavage of 9-
cis
-violaxanthin and 9′-
cis
-neoxanthin, so that the enzyme is referred to as 9-
cis
-epoxycarotenoid dioxygenase. When detached bean leaves were water stressed, ABA accumulation was preceded by large increases in
PvNCED1
mRNA and protein levels. Conversely, rehydration of stressed leaves caused a rapid decrease in
PvNCED1
mRNA, protein, and ABA levels. In bean roots, a similar correlation among
PvNCED1
mRNA, protein, and ABA levels was observed. However, the ABA content was much less than in leaves, presumably because of the much smaller carotenoid precursor pool in roots than in leaves. At 7°C,
PvNCED1
mRNA and ABA were slowly induced by water stress, but, at 2°C, neither accumulated. The results provide evidence that drought-induced ABA biosynthesis is regulated by the 9-
cis
-epoxycarotenoid cleavage reaction and that this reaction takes place in the thylakoids, where the carotenoid substrate is located.
Pseudomonas aeruginosa
killing of
Caenorhabditis elegans
used to identify
P. aeruginosa
virulence factors
Authors: Tan Man-Wah , Rahme Laurence G. , Sternberg Jeffrey A. , Tompkins Ronald G. , Ausubel Frederick M.
Published: July 2002

We reported recently that the human opportunistic pathogen
Pseudomonas aeruginosa
strain PA14 kills
Caenorhabditis elegans
and that many
P. aeruginosa
virulence factors (genes) required for maximum virulence in mouse pathogenicity are also required for maximum killing of
C. elegans.
Here we report that among eight
P. aeruginosa
PA14 Tn
phoA
mutants isolated that exhibited reduced killing of
C. elegans
, at least five also exhibited reduced virulence in mice. Three of the Tn
phoA
mutants corresponded to the known virulence-related genes
lasR, gacA
, and
lemA
. Three of the mutants corresponded to known genes (
aefA
from
Escherichia coli, pstP
from
Azotobacter vinelandii
, and
mtrR
from
Neisseria gonorrhoeae
) that had not been shown previously to play a role in pathogenesis, and two of the mutants contained Tn
phoA
inserted into novel sequences. These data indicate that the killing of
C. elegans
by
P. aeruginosa
can be exploited to identify novel
P. aeruginosa
virulence factors important for mammalian pathogenesis.
Nuclear waste forms for actinides
Authors: Ewing Rodney C.
Published: July 2002

The disposition of actinides, most recently
239
Pu
from dismantled nuclear weapons, requires effective containment of
waste generated by the nuclear fuel cycle. Because actinides (e.g.,
239
Pu and
237
Np) are long-lived, they have a
major impact on risk assessments of geologic repositories. Thus,
demonstrable, long-term chemical and mechanical durability are
essential properties of waste forms for the immobilization of
actinides. Mineralogic and geologic studies provide excellent candidate
phases for immobilization and a unique database that cannot be
duplicated by a purely materials science approach. The “mineralogic
approach” is illustrated by a discussion of zircon as a phase for
the immobilization of excess weapons plutonium.
Functional identification and reconstitution of an odorant receptor in single olfactory neurons
Authors: Touhara Kazushige , Sengoku Shintaro , Inaki Koichiro , Tsuboi Akio , Hirono Junzo , Sato Takaaki , Sakano Hitoshi , Haga Tatsuya
Published: July 2002

The olfactory system is remarkable in its capacity to discriminate a wide range of odorants through a series of transduction events initiated in olfactory receptor neurons. Each olfactory neuron is expected to express only a single odorant receptor gene that belongs to the G protein coupled receptor family. The ligand–receptor interaction, however, has not been clearly characterized. This study demonstrates the functional identification of olfactory receptor(s) for specific odorant(s) from single olfactory neurons by a combination of Ca
2+
-imaging and reverse transcription–coupled PCR analysis. First, a candidate odorant receptor was cloned from a single tissue-printed olfactory neuron that displayed odorant-induced Ca
2+
increase. Next, recombinant adenovirus-mediated expression of the isolated receptor gene was established in the olfactory epithelium by using green fluorescent protein as a marker. The infected neurons elicited external Ca
2+
entry when exposed to the odorant that originally was used to identify the receptor gene. Experiments performed to determine ligand specificity revealed that the odorant receptor recognized specific structural motifs within odorant molecules. The odorant receptor-mediated signal transduction appears to be reconstituted by this two-step approach: the receptor screening for given odorant(s) from single neurons and the functional expression of the receptor via recombinant adenovirus. The present approach should enable us to examine not only ligand specificity of an odorant receptor but also receptor specificity and diversity for a particular odorant of interest.
Cloning of the
Arabidopsis RTM1
gene, which controls restriction of long-distance movement of tobacco etch virus
Authors: Chisholm Stephen T. , Mahajan Sunita K. , Whitham Steven A. , Yamamoto Miki L. , Carrington James C.
Published: July 2002

The locus
RTM1
is necessary for restriction of
long-distance movement of tobacco etch virus in
Arabidopsis
thaliana
without causing a hypersensitive response or inducing
systemic acquired resistance. The
RTM1
gene was isolated
by map-based cloning. The deduced gene product is similar to the
α-chain of the
Artocarpus integrifolia
lectin,
jacalin, and to several proteins that contain multiple repeats of a
jacalin-like sequence. These proteins comprise a family with members
containing modular organizations of one or more jacalin repeat units
and are implicated in defense against viruses, fungi, and insects.
Potent and nontoxic antisense oligonucleotides containing locked nucleic acids
Authors: Wahlestedt Claes , Salmi Peter , Good Liam , Kela Johanna , Johnsson Thomas , Hökfelt Tomas , Broberger Christian , Porreca Frank , Lai Josephine , Ren Kunkun , Ossipov Michael , Koshkin Alexei , Jakobsen Nana , Skouv Jan , Oerum Henrik , Jacobsen Mogens Havsteen , Wengel Jesper
Published: July 2002

Insufficient efficacy and/or specificity of antisense oligonucleotides limit their
in vivo
usefulness. We demonstrate here that a high-affinity DNA analog, locked nucleic acid (LNA), confers several desired properties to antisense agents. Unlike DNA, LNA/DNA copolymers were not degraded readily in blood serum and cell extracts. However, like DNA, the LNA/DNA copolymers were capable of activating RNase H, an important antisense mechanism of action. In contrast to phosphorothioate-containing oligonucleotides, isosequential LNA analogs did not cause detectable toxic reactions in rat brain. LNA/DNA copolymers exhibited potent antisense activity on assay systems as disparate as a G-protein-coupled receptor in living rat brain and an
Escherichia coli
reporter gene. LNA-containing oligonucleotides will likely be useful for many antisense applications.
Interference fine structure and sarcomere length dependence of the axial x-ray pattern from active single muscle fibers
Authors: Linari M. , Piazzesi G. , Dobbie I. , Koubassova N. , Reconditi M. , Narayanan T. , Diat O. , Irving M. , Lombardi V.
Published: July 2002

Axial x-ray diffraction patterns from single intact fibers of frog skeletal muscle were recorded by using a highly collimated x-ray beam at the European Synchrotron Radiation Facility. During isometric contraction at sarcomere lengths 2.2–3.2 μm, the M3 x-ray reflection, associated with the repeat of myosin heads along the filaments, was resolved into two peaks. The total M3 intensity decreased linearly with increasing sarcomere length and was directly proportional to the degree of overlap between myosin and actin filaments, showing that it comes from myosin heads in the overlap region. The separation between the M3 peaks was smaller at longer sarcomere length and was quantitatively explained by x-ray interference between myosin heads in the two overlap regions of each sarcomere. The relative intensity of the M3 peaks was independent of sarcomere length, showing that the axial periodicities of the nonoverlap and overlap regions of the myosin filament have the same value, 14.57 nm, during active contraction. In resting fibers the periodicity is 14.34 nm, so muscle activation produces a change in myosin filament structure in the nonoverlap as well as the overlap part of the filament. The results establish x-ray interferometry as a new tool for studying the motions of myosin heads during muscle contraction with unprecedented spatial resolution.
Identification and characterization of an enzyme involved in the elongation of n-6 and n-3 polyunsaturated fatty acids
Authors: Parker-Barnes Jennifer M. , Das Tapas , Bobik Emil , Leonard Amanda E. , Thurmond Jennifer M. , Chaung Lu-Te , Huang Yung-Sheng , Mukerji Pradip
Published: July 2002

The enzymes that are involved in the elongation of fatty acids differ in terms of the substrates on which they act. To date, the enzymes specifically involved in the biosynthesis of polyunsaturated fatty acids have not yet been identified. In an attempt to identify a gene(s) encoding an enzyme(s) specific for the elongation of γ-linolenic acid (GLA) (18:3n-6), a cDNA expression library was made from the fungus
Mortierella alpina
. The cDNA library constructed in a yeast expression vector was screened by measuring the expressed elongase activity [conversion of GLA to dihomo-GLA (20:3n-6)] from an individual yeast clone. In this report, we demonstrate the isolation of a cDNA (
GLELO
) whose encoded protein (GLELOp) was involved in the conversion of GLA to dihomo-GLA in an efficient manner (60% conversion). This cDNA contains a 957-nucleotide ORF that encodes a protein of 318 amino acids. Substrate specificity analysis revealed that this fungal enzyme acted also on stearidonic acid (18:4n-3). This report identifies and characterizes an elongase subunit that acts specifically on the two Δ6-desaturation products, 18:3n-6 and 18:4n-3. When this
GLELO
cDNA was coexpressed with
M. alpina
Δ5-desaturase cDNA in yeast, it resulted in the conversion of GLA to arachidonic acid (20:4n-6) as well as the conversion of stearidonic acid to eicosopentaenoic acid (20:5n-3). Thus, this
GLELO
gene may play an critical role in the bio-production of both n-6 and n-3 polyunsaturated fatty acids.
The serine and threonine residues in the Ig-α cytoplasmic tail negatively regulate immunoreceptor tyrosine-based activation motif-mediated signal transduction
Authors: Müller Ralph , Wienands Jürgen , Reth Michael
Published: July 2002

The B cell antigen receptor (BCR) is a multiprotein complex consisting of the membrane-bound Ig molecule and the Ig-α/Ig-β heterodimer. On BCR engagement, Ig-α and Ig-β become phosphorylated not only on tyrosine residues of the immunoreceptor tyrosine-based activation motif but also on serine and threonine residues. We have mutated all serine and threonine residues in the Ig-α tail to alanine and valine, respectively. The mutated Ig-α sequence was expressed either as a single-chain Fv/Ig-α molecule or in the context of the complete BCR. In both cases, the mutated Ig-α showed a stronger tyrosine phosphorylation than the wild-type Ig-α and initiated increased signaling on stimulation. These findings suggest that serine/threonine kinases can negatively regulate signal transduction from the BCR.
A single amino acid substitution (F363I) converts the regiochemistry of the spearmint (−)-limonene hydroxylase from a C6- to a C3-hydroxylase
Authors: Schalk Michel , Croteau Rodney
Published: July 2002

The essential oils of peppermint and spearmint are distinguished by
the position of oxygenation on the constituent
p
-menthane monoterpenes. Peppermint produces
monoterpenes bearing an oxygen at C3, whereas spearmint produces
monoterpenes bearing an oxygen at C6. Branching of the monoterpene
biosynthetic pathways in these species is determined by two distinct
cytochrome P450s that catalyze the regiospecific hydroxylation of
(−)-4
S
-limonene at C3 or C6 exclusively. cDNAs encoding
the limonene-3-hydroxylase from peppermint and the
limonene-6-hydroxylase from spearmint have been isolated, shown to be
70% identical at the amino acid level, and functionally expressed. A
combination of domain swapping and reciprocal site-directed mutagenesis
between these two enzymes demonstrated that the exchange of a single
residue (F363I) in the spearmint limonene-6-hydroxylase led to complete
conversion to the regiospecificity and catalytic efficiency of the
peppermint limonene-3-hydroxylase.
Correlation between plasmid content and infectivity in
Borrelia burgdorferi
Authors: Purser Joye E. , Norris Steven J.
Published: July 2002

Infectivity-associated plasmids were identified in
Borrelia
burgdorferi
B31 by using PCR to detect each of the plasmids in
a panel of 19 clonal isolates. The clones exhibited high-, low-, and
intermediate-infectivity phenotypes based on their frequency of
isolation from needle-inoculated C3H/HeN mice. Presence or absence of
21 of the 22 plasmids was determined in each of the clones by using PCR
primers specific for regions unique to each plasmid, as identified in
the recently available genome sequence. Southern blot hybridization
results were used to confirm the PCR results in some cases. Plasmid
lp25 exhibited a direct correlation with infectivity in that it was
consistently present in all clones of high or intermediate infectivity
and was absent in all low-infectivity clones. lp28–1, containing the
vmp
-like sequence locus, also correlated with
infectivity; all clones that lacked lp28–1 but contained lp25 had
an intermediate infectivity phenotype, in which infection was
primarily restricted to the joints. Plasmids cp9, cp32–3, lp21,
lp28–2, lp28–4, and lp56 apparently are not required for infection in
this model, because clones lacking these plasmids exhibited a
high-infectivity phenotype. Plasmids cp26, cp32–1,
cp32–2 and/or cp32–7, cp32–4, cp32–6, cp32–8, cp32–9, lp17,
lp28–3, lp36, lp38, and lp54 were consistently present in all
clones examined. On the basis of these results, lp25 and lp28–1 appear
to encode virulence factors important in the pathogenesis of
B. burgdorferi
B31.
A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides
Authors: Yang Zhe , Mochalkin Igor , Doolittle Russell F.
Published: July 2002

A blood clot is a meshwork of fibrin fibers built up by the
systematic assembly of fibrinogen molecules proteolyzed by thrombin.
Here, we describe a model of how the assembly process occurs. Five
kinds of interaction are explicitly defined, including two different
knob–hole interactions, an end-to-end association between γ-chains,
a lateral association between γ-chains, and a hypothetical lateral
interaction between β-chains. The last two of these interactions are
responsible for protofibril association and are predicated on
intermolecular packing arrangements observed in crystal structures of
fibrin double-D fragments cocrystallized with synthetic peptides
corresponding to the knobs exposed by the release of the
fibrinopeptides A and B.
HuR binding to cytoplasmic mRNA is perturbed by heat shock
Authors: Gallouzi Imed-Eddine , Brennan Christopher M. , Stenberg Myrna G. , Swanson Maurice S. , Eversole Ashley , Maizels Nancy , Steitz Joan A.
Published: July 2002

AU-rich elements (AREs) located in the 3′ untranslated region target the mRNAs encoding many protooncoproteins, cytokines, and lymphokines for rapid degradation. HuR, a ubiquitously expressed member of the embryonic lethal abnormal vision (ELAV) family of RNA-binding proteins, binds ARE sequences and selectively stabilizes ARE-containing reporter mRNAs when overexpressed in transiently transfected cells. HuR appears predominantly nucleoplasmic but has been shown to shuttle between the nucleus and cytoplasm via a novel shuttling sequence HNS. We report generation of a mouse monoclonal antibody 3A2 that both immunoblots and immunoprecipitates HuR protein; it recognizes an epitope located in the first of HuR's three RNA recognition motifs. This antibody was used to probe HuR interactions with mRNA before and after heat shock, a condition that has been reported to stabilize ARE-containing mRNAs. At 37°C, approximately one-third of the cytoplasmic HuR appears polysome associated, and
in vivo
UV crosslinking reveals that HuR interactions with poly(A)
+
RNA are predominantly cytoplasmic rather than nuclear. This comprises evidence that HuR directly interacts with mRNA
in vivo
. After heat shock, 12–15% of HuR accumulates in discrete foci in the cytoplasm, but surprisingly the majority of HuR crosslinks instead to nuclear poly(A)
+
RNA, whose levels are dramatically increased in the stressed cells. This behavior of HuR differs from that of another ARE-binding protein, hnRNP D, which has been implicated as an effector of mRNA decay rather than mRNA stabilization and of the general pre-RNA-binding protein hnRNP A1. We interpret these differences to mean that the temporal association of HuR with ARE-containing mRNAs is different from that of these other two proteins.
Lamprey
Dlx
genes and early vertebrate evolution
Authors: Neidert Adam H. , Virupannavar Vikrant , Hooker Gillian W. , Langeland James A.
Published: July 2002

Gnathostome vertebrates have multiple members of the
Dlx
family of transcription factors that are expressed
during the development of several tissues considered to be vertebrate
synapomorphies, including the forebrain, cranial neural crest,
placodes, and pharyngeal arches. The
Dlx
gene family
thus presents an ideal system in which to examine the relationship
between gene duplication and morphological innovation during vertebrate
evolution. Toward this end, we have cloned
Dlx
genes
from the lamprey
Petromyzon marinus
, an agnathan
vertebrate that occupies a critical phylogenetic position between
cephalochordates and gnathostomes. We have identified four
Dlx
genes in
P. marinus
, whose orthology
with gnathostome
Dlx
genes provides a model for how this
gene family evolved in the vertebrate lineage. Differential expression
of these lamprey
Dlx
genes in the forebrain, cranial
neural crest, pharyngeal arches, and sensory placodes of lamprey
embryos provides insight into the developmental evolution of these
structures as well as a model of regulatory evolution after
Dlx
gene duplication events.
Ancient origin of pathogen recognition specificity conferred by the tomato disease resistance gene
Pto
Authors: Riely Brendan K. , Martin Gregory B.
Published: July 2002

We have investigated the origin of the
Pto
disease
resistance (
R
) gene that was previously identified in
the wild tomato species
Lycopersicon pimpinellifolium
and isolated by map-based cloning.
Pto
encodes a
serine-threonine protein kinase that specifically recognizes strains of
Pseudomonas syringae
pv. tomato (
Pst
)
that express the avirulence gene
avrPto.
We examined an
accession of the distantly related wild species
Lycopersicon
hirsutum
var.
glabratum
that exhibits
avrPto-
specific resistance to
Pst
. The
Pst
resistance of
L. hirsutum
was
introgressed into a susceptible
Lycopersicon esculentum
background to create the near-isogenic line 96T133-3. Resistance to
Pst(avrPto)
in 96T133-3 was inherited as a single
dominant locus and cosegregated with a restriction fragment length
polymorphism detected by the
Pto
gene. This observation
suggested that a member of the
Pto
gene family confers
Pst(avrPto)
resistance in this
L.
hirsutum
line. Here we report the cloning and characterization
of four members of the
Pto
family from 96T133-3. One
gene (
LhirPto
) is 97% identical to
Pto
and encodes a catalytically active protein kinase that elicits a
hypersensitive response when coexpressed with
avrPto
in
leaves of
Nicotiana benthamiana
. In common with the Pto
kinase, the LhirPto protein physically interacts with AvrPto and
downstream members of the
Pto
signaling pathway. Our
studies indicate that
R
genes of the protein kinase
class may not evolve rapidly in response to pathogen pressure and
rather that their ability to recognize specific Avr proteins can be
highly conserved.
The Effect of Social Cohesion on Levels of Recorded Crime in Disadvantaged Areas
Authors: Hirschfield A. , Bowers K.J.
Published: July 2002

This paper investigates the hypothesis that the level of crime in disadvantaged areas will be influenced by their levels of social cohesion. This issue is examined using two methods for delineating areas of disadvantage (geodemographic classifications and the British government's official deprivation measure, the Index of Local Conditions) and two independent components of social cohesion, one defines the level of 'social control' in an area and the other identifies 'ethnic heterogeneity'. The results suggest that levels of crime are significantly lower than expected in disadvantaged areas with high levels of social cohesion and vice versa. A complementary analysis of Homewatch schemes revealed that such schemes lead to reduced levels of burglary in affluent areas, but appear to have the opposite effect to that desired in more disadvantaged areas.
Can Land-use Policy Really Affect Travel Behaviour? A Study of the Link between Non-work Travel and Land-use Characteristics
Authors: Boarnet Marlon G. , Sarmiento Sharon
Published: July 2002

Planners are increasingly viewing land-use policy as a way to manage transport demand. Yet the evidence on the link between land use and travel behaviour is inconclusive. This paper uses travel diary data for southern California residents to examine the link between land-use patterns at the neighbourhood level and non-work trip generation for a sample of 769 individuals. The number of non-work automobile trips that an individual makes in a two-day period is modelled as a function of socio-demographic variables and land-use characteristics near the person's place of residence. The land-use variables are statistically insignificant in all but one of the specifications. The results suggest that choices about how to measure the variables and how to specify the regressions can influence the conclusions from these studies in potentially important ways. This underscores the need for continued careful attention to these research issues.
Searching for the Sustainable City: Competing Philosophical Rationales and Processes of 'Ideological Capture' in Adelaide, South Australia
Authors: Haughton Graham
Published: July 2002

The growing debate around sustainable cities has generated a substantial academic and policy literature. It is becoming increasingly clear that there are a number of different approaches being considered. This article develops four models of sustainable urban development from this literature, ranging from light green to deep green in their underlying environmental philosophy. The models are then used as the framework for analysing four different experiments in sustainable urban development in the city of Adelaide, South Australia, which broadly fit into the four models. Overall, the models are useful in highlighting the different underlying rationales of the four approaches, although they also show that in the process of trying to gain political favour there is a fair amount of 'ideological capture' in respect of the rhetorics and the practice of sustainable urban development.
Integrating Women's Reproductive Roles with Productive Activities in Commerce: The Case of Businesswomen in Kampala, Uganda
Authors: Kwagala Betty
Published: July 2002

Uganda has registered significant improvement regarding economic growth and the raising of women's status at the macro level. Commerce is one of the sectors that attracts women of varying social status. The paper is based on an exploratory and cross-sectional study that focused on Kampala businesswomen's experiences in coping with productive and reproductive roles. Quantitative and qualitative methods of data collection were utilised. The survey involved a total of 224 women. Results reveal an increasingly asymmetric gender division of roles, to women's disadvantage, especially as their incomes increase. Women's experiences in integrating reproductive roles and productive activities in commerce, which have a strong bearing on their economic performance, are discussed.
Experience and Well-being: Explorations on Domains of Life and How they Matter
Authors: Ryff Carol D. , Heidrich Susan M.
Published: July 2002

The guiding question was how past life experiences are linked with adults’ assessments of their present and future well-being. Typical events and transitions (normative experiences) were contrasted with atypical stresses (non-normative experiences). A sample of 308 men and women, divided between young, midlife, and older adults, completed past life event inventories and rated themselves on multiple dimensions of well-being (concurrently and prospectively). Hierarchical regression analyses revealed that normative events were significant predictors of multiple aspects of present and future wellness, but there were marked age differences in which domains were key influences: For young adults, life activities were primary; for midlife adults, greatest variance was explained by the family and friends domain; in late life, prior work and educational experiences were strongest predictors of well-being. Non-normative events were significant positive predictors of only personal growth in young adults.
Multigenerational Perspectives on Coping with the Holocaust Experience: An Attachment Perspective for Understanding the Developmental Sequelae of Trauma across Generations
Authors: Bar-On Dan , Eland Jeanette , Kleber Rolf J. , Krell Robert , Moore Yael , Sagi Abraham , Soriano Erin , Suedfeld Peter , van der Velden Peter G. , van IJzendoorn Marinus H.
Published: July 2002

In this paper, we advance a new approach to the intergenerational transmission of Holocaust experiences, by focusing on attachment theory. The approach is used as a framework for interpretation of the results of three studies on Holocaust survivors and their offspring, from different countries (The Netherlands, Canada, and Israel), and based on different conceptual approaches and methods of data collection (quantitative as well as qualitative). The literature is divided with regard to the extent and depth of long-term effects of the Holocaust. Attachment theory allows the integration of the phenomena of attachment, separation, and loss, which appear to be core concepts in the three studies presented here. The notion of insecure-ambivalent attachment sheds some light on the observed preoccupation with issues of attachment and separation in the second generation. Furthermore, the theme of “the conspiracy of silence” is discussed in the context of attachment disorganisation. Attachment theory transcends the traditional boundaries between clinical and nonclinical interpretations, in stressing the continuous and cumulative nature of favourable and unfavourable child-rearing circumstances. In this context, insecure attachment should be regarded as coping with suboptimal child-rearing environments.
Icelandic umlaut in Optimality Theory
Authors: Gibson Courtenay St. John , Ringen Catherine O.
Published: July 2002

This paper presents an analysis of Icelandic umlaut in Optimality Theory. We account for umlaut insal[œ]t-[Y]m‘lettuce’ (dat. pl.) andd[œ:]g-[Y]m‘day’ (dat. pl.), in which /a/ is fronted and rounded when followed by [Y], as well as forms such asj[œ]kli‘glacier’ (dat. sg.) andb[œ]rn‘child’ (ace. pl.) with an umlauted vowel, but no overt trigger. We explain why there isnoumlaut in forms such asdal-n[Y]m‘valley’ (def.),kakt[Y]s‘cactus’ (nom. sg.), ord[a:]g-[Y]r‘day’ (nom. sg.) despite the fact that /a/ occurs in the umlaut environment. We also explain why there is one umlauted vowel insal[œ]t-[Y]m≪ /salat + Ym/, but two umlauted vowels inf[œ]t-n[Y]ð-[Y]m≪ /fat + nað + Ym/ ‘clothing’ (dat. pl.) and why the umlauted vowel is sometimes [Y] and sometimes [œ].
Perspectives on the Scientific Systems of the Post-Soviet States: A Pessimistic View
Authors: Egorov Igor
Published: July 2002

This paper deals with the research and development/science and technology situation in the post-Soviet states. Since the collapse of the Soviet Union, these countries have chosen different ways to transform their S&T systems but all have so far failed to reach positive results in this process. Key features and problems of science in the main post-Soviet states, Russia and Ukraine, are the focus of this analysis. The conclusion is that further decline in S&T in these countries seems inevitable in the near future.
Biological phenotypes associated with individuals at high risk for developing alcohol‐related disorders. Part 2
Authors: Schuckit Marc A.
Published: July 2002

This paper reviews comparisons of populations at higher and lower risk for alcoholism on biological phenotypes. The results of studies must be considered in the context of the research methods used including the need for large, carefully defined samples and longitudinal designs. Comparisons of children of alcoholics and controls have revealed potentially important differences on level of response to alcohol, cognitive attributes and differences in alcohol‐metabolizing and other enzyme systems responsible for various aspects of the body's reaction to alcohol. Many opportunities for future research in this area exist, including large‐scale, longitudinal studies that simultaneously evaluate multiple domains of influence, and searches for candidate genes or other biological material that will simplify procedures and increase the accuracy of measurement.
Adhesive But Not Lateral E-cadherin Complexes Require Calcium and Catenins for Their Formation
Authors: Chitaev Nikolai A. , Troyanovsky Sergey M.
Published: July 2002

We examined intercadherin interactions in epithelial A-431 cells producing endogenous E-cadherin and recombinant forms of E-cadherin tagged either by myc or by flag epitopes. Three distinct E-cadherin complexes were found. The first is a conventional E-cadherin–catenin complex consisting of one E-cadherin molecule linked either to β-catenin/α-catenin or to plakoglobin/α-catenin dimers. The second is a lateral E-cadherin complex incorporating two E-cadherin– catenin conventional complexes combined in parallel fashion via dimerization of the NH2-terminal extracellular domain of E-cadherin. The third complex is likely to contain two E-cadherin–catenin conventional complexes derived from two opposing cells and arranged in an antiparallel fashion. Formation of the antiparallel but not lateral complex strictly depends on extracellular calcium and E-cadherin binding to catenins. Double amino acid substitution Trp156Ala/Val157Gly within the extracellular NH2-terminal E-cadherin domain completely abolished both lateral and antiparallel inter–E-cadherin association. These data support an idea that the antiparallel complex has the adhesion function. Furthermore, they allow us to suggest that antiparallel complexes derive from lateral dimers and this complex process requires catenins and calcium ions.