bluuebunny/crossref_metadata_2025 huggingface dataset:
Allosteric control of internal electron transfer in cytochrome
cd
1
nitrite reductase
Authors: Farver Ole , Kroneck Peter M. H. , Zumft Walter G. , Pecht Israel
Published: June 2003

Cytochrome
cd
1
nitrite reductase is a bifunctional multiheme enzyme catalyzing the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of dioxygen to water. Kinetics and thermodynamics of the internal electron transfer process in the
Pseudomonas stutzeri
enzyme have been studied and found to be dominated by pronounced interactions between the
c
and the
d
1
hemes. The interactions are expressed both in dramatic changes in the internal electron-transfer rates between these sites and in marked cooperativity in their electron affinity. The results constitute a prime example of intraprotein control of the electron-transfer rates by allosteric interactions.
Comparative genomics ofPhyscomitrella patensgametophytic transcriptome andArabidopsis thaliana: Implication for land plant evolution
Authors: Nishiyama Tomoaki , Fujita Tomomichi , Shin-I Tadasu , Seki Motoaki , Nishide Hiroyo , Uchiyama Ikuo , Kamiya Asako , Carninci Piero , Hayashizaki Yoshihide , Shinozaki Kazuo , Kohara Yuji , Hasebe Mitsuyasu
Published: June 2003

The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants have been inferred to be haploid-dominant, suggesting that genes used in the diploid body of flowering plants were recruited from the genes used in the haploid body of the ancestors during the evolution of land plants. To assess this evolutionary hypothesis, we constructed an EST library of the mossPhyscomitrella patens, and compared the moss transcriptome to the genome ofArabidopsis thaliana. We constructed full-length enriched cDNA libraries from auxin-treated, cytokinin-treated, and untreated gametophytes ofP. patens, and sequenced both ends of >40,000 clones. These data, together with the mRNA sequences in the public databases, were assembled into 15,883 putative transcripts. Sequence comparisons ofA. thalianaandP. patensshowed that at least 66% of theA. thalianagenes had homologues inP. patens. Comparison of theP. patensputative transcripts with all known proteins, revealed 9,907 putative transcripts with high levels of similarity to vascular plant genes, and 850 putative transcripts with high levels of similarity to other organisms. The haploid transcriptome ofP. patensappears to be quite similar to theA. thalianagenome, supporting the evolutionary hypothesis. Our study also revealed that a number of genes are moss specific and were lost in the flowering plant lineage.
Discovery of a fusion kinase in EOL-1 cells and idiopathic hypereosinophilic syndrome
Authors: Griffin John H. , Leung Joey , Bruner Rebecca J. , Caligiuri Michael A. , Briesewitz Roger
Published: June 2003

Idiopathic hypereosinophilic syndrome (HES) is a myeloproliferative disease of unknown etiology. Recently, it has been reported that imatinib mesylate (Gleevec), an inhibitor of Bcr-Abl kinase useful in the treatment of chronic myeloid leukemia, is also effective in treating HES; however, the molecular target of imatinib in HES is unknown. This report identifies a genetic rearrangement in the eosinophilic cell line EOL-1 that results in the expression of a fusion protein comprising an N-terminal region encoded by a gene of unknown function with the GenBank accession number NM_030917 and a C-terminal region derived from the intracellular domain of the platelet-derived growth factor receptor α (PDGFRα). The fusion gene was also detected in blood cells from two patients with HES. We propose naming NM_030917
Rhe
for
R
earranged in
h
yper
e
osinophilia.
Rhe-PDGFR
α fusions result from an apparent interstitial deletion that links
Rhe
to exon 12 of
PDGFR
α on chromosome 4q12. The fusion kinase Rhe-PDGFRα is constitutively phosphorylated and supports IL-3-independent growth when expressed in BaF3 cells. Proliferation and viability of EOL-1 and BaF3 cells expressing
Rhe-PDGFR
α are ablated by the PDGFRα inhibitors imatinib, vatalanib, and THRX-165724.
Additive effects of simulated climate changes, elevated CO
2
, and nitrogen deposition on grassland diversity
Authors: Zavaleta Erika S. , Shaw M. Rebecca , Chiariello Nona R. , Mooney Harold A. , Field Christopher B.
Published: June 2003

Biodiversity responses to ongoing climate and atmospheric changes will affect both ecosystem processes and the delivery of ecosystem goods and services. Combined effects of co-occurring global changes on diversity, however, are poorly understood. We examined plant diversity responses in a California annual grassland to manipulations of four global environmental changes, singly and in combination: elevated CO
2
, warming, precipitation, and nitrogen deposition. After 3 years, elevated CO
2
and nitrogen deposition each reduced plant diversity, whereas elevated precipitation increased it and warming had no significant effect. Diversity responses to both single and combined global change treatments were driven overwhelmingly by gains and losses of forb species, which make up most of the native plant diversity in California grasslands. Diversity responses across treatments also showed no consistent relationship to net primary production responses, illustrating that the diversity effects of these environmental changes could not be explained simply by changes in productivity. In two- to four-way combinations, simulated global changes did not interact in any of their effects on diversity. Our results show that climate and atmospheric changes can rapidly alter biological diversity, with combined effects that, at least in some settings, are simple, additive combinations of single-factor effects.
Connectivity optimization and the positioning of cortical areas
Authors: Klyachko Vitaly A. , Stevens Charles F.
Published: June 2003

By examining many alternative arrangements of cortical areas, we have found that the arrangement actually present in the brain minimizes the volume of the axons required for interconnecting the areas. Our observations support the notion that the organization of cortical areas has evolved to optimize interareal connections.
A low molecular weight mimic of the Toll/IL-1 receptor/resistance domain inhibits IL-1 receptor-mediated responses
Authors: Bartfai Tamas , Behrens M. Margarita , Gaidarova Svetlana , Pemberton Janell , Shivanyuk Alexander , Rebek Julius
Published: June 2003

Toll-like receptors (TLRs) and the type I IL-1 receptor (IL-1RI) are key components of the innate immune system activated by microbial infections and inflammation. The signaling cascade from agonist-occupied TLRs and IL-1Rs involves recruitment of the small cytosolic adapter protein MyD88 that binds to IL-1RI via homotypic interactions mediated by Toll/IL-1R/resistance (TIR) domains. Dominant negative forms and null mutations of MyD88 have recently been shown to preclude bacterial product or IL-1-mediated activation of NF-κB pathways, demonstrating that MyD88 is an essential component of the Toll receptor signaling. Here, we report the synthesis and pharmacological effects of a low molecular weight MyD88 mimic, hydrocinnamoyl-
l
-valyl pyrrolidine (compound 4a), modeled on a tripeptide sequence of the BB-loop [(F/Y)-(V/L/I)-(P/G)] of the TIR domain. Results are presented showing that compound 4a interferes with the interactions between mouse MyD88 and IL-1RI at the TIR domains. Compound 4a inhibited IL-1β-induced phosphorylation of the mitogen-activated protein kinase p38 in EL4 thymoma cells and in freshly isolated murine lymphocytes in a concentration-dependent manner.
In vivo
, compound 4a produced a significant attenuation of the IL-1β-induced fever response (200 mg/kg, i.p.). Inhibition of the TIR domain-mediated MyD88/IL1-RI interaction by a low molecular weight, cell-penetrating TIR domain mimic suggests an intracellular site for antiinflammatory drug action.
Membrane-binding and activation mechanism of PTEN
Authors: Das Sudipto , Dixon Jack E. , Cho Wonhwa
Published: June 2003

PTEN is a tumor suppressor that reverses the action of phosphoinositide 3-kinase by catalyzing the removal of the 3′ phosphate of phosphoinositides. Despite the critical role of PTEN in cell signaling and regulation, the mechanisms of its membrane recruitment and activation is still poorly understood. PTEN is composed of an N-terminal phosphatase domain, a C2 domain, and a C-terminal tail region that contains the PSD-95/Dlg/ZO-1 homology (PDZ) domain-binding sequence and multiple phosphorylation sites. Our
in vitro
surface plasmon resonance measurements using immobilized vesicles showed that both the phosphatase domain and the C2 domain, but not the C-terminal tail, are involved in electrostatic membrane binding of PTEN. Furthermore, the phosphorylation-mimicking mutation on the C-terminal tail of PTEN caused an ≈80-fold reduction in its membrane affinity, mainly by slowing the membrane-association step. Subcellular localization studies of PTEN transfected into HEK293T and HeLa cells indicated that targeting of PTEN to the plasma membrane is coupled with rapid degradation and that the phosphatase domain and the C2 domain are both necessary and sufficient for its membrane recruitment. Results also indicated that the phosphorylation regulates the targeting of PTEN to the plasma membrane not by blocking the PDZ domain-binding site but by interfering with electrostatic membrane binding of PTEN. On the basis of these results, we propose a membrane-binding and activation mechanism for PTEN, in which the phosphorylation/dephosphorylation of the C-terminal region serves as an electrostatic switch that controls the membrane translocation of the protein.
Direct activation of the apoptosis machinery as a mechanism to target cancer cells
Authors: Nguyen Jack T. , Wells James A.
Published: June 2003

Apoptosis plays a pivotal role in the cytotoxic activity of most chemotherapeutic drugs, and defects in this pathway provide a basis for drug resistance in many cancers. Thus the ability to restore apoptosis by using small molecules could have important therapeutic implications. Using a cell-free assay to simultaneously target multiple components of the apoptosis pathway, we identified a class of compounds that activate caspases in a cytochrome
c
-dependent manner and induce apoptosis in whole cells. By reconstituting the apoptosis pathway with purified proteins, we determined that these compounds promote the protein–protein association of Apaf-1 into the functional apoptosome. These compounds exert cytostatic and cytotoxic effects on a variety of cancer cell lines while having little or no activity against the normal cell lines tested. These findings suggest that direct activation of the basic apoptosis machinery may be a viable mechanism to selectively target cancer.
Impairment of reward-related learning by cholinergic cell ablation in the striatum
Authors: Kitabatake Yasuji , Hikida Takatoshi , Watanabe Dai , Pastan Ira , Nakanishi Shigetada
Published: June 2003

The striatum in the basal ganglia-thalamocortical circuitry is a key neural substrate that is implicated in motor balance and procedural learning. The projection neurons in the striatum are dynamically modulated by nigrostriatal dopaminergic input and intrastriatal cholinergic input. The role of intrastriatal acetylcholine (ACh) in learning behaviors, however, remains to be fully clarified. In this investigation, we examine the involvement of intrastriatal ACh in different categories of learning by selectively ablating the striatal cholinergic neurons with use of immunotoxin-mediated cell targeting. We show that selective ablation of cholinergic neurons in the striatum impairs procedural learning in the tone-cued T-maze memory task. Spatial delayed alternation in the T-maze learning test is also impaired by cholinergic cell elimination. In contrast, the deficit in striatal ACh transmission has no effect on motor learning in the rota-rod test or spatial learning in the Morris water-maze test or on contextual- and tone-cued conditioning fear responses. We also report that cholinergic cell elimination adaptively up-regulates nicotinic ACh receptors not only within the striatum but also in the cerebral cortex and substantia nigra. The present investigation indicates that cholinergic modulation in the local striatal circuit plays a pivotal role in regulation of neural circuitry involving reward-related procedural learning and working memory.
The complete genome sequence ofMycobacterium bovis
Authors: Garnier Thierry , Eiglmeier Karin , Camus Jean-Christophe , Medina Nadine , Mansoor Huma , Pryor Melinda , Duthoy Stephanie , Grondin Sophie , Lacroix Celine , Monsempe Christel , Simon Sylvie , Harris Barbara , Atkin Rebecca , Doggett Jon , Mayes Rebecca , Keating Lisa , Wheeler Paul R. , Parkhill Julian , Barrell Bart G. , Cole Stewart T. , Gordon Stephen V. , Hewinson R. Glyn
Published: June 2003

Mycobacterium bovisis the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown.M. boviswas also the progenitor for theM. bovisbacillus Calmette–Guérin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence ofM. bovisAF2122/97 and its comparison with the genomes ofMycobacterium tuberculosisandMycobacterium leprae. Strikingly, the genome sequence ofM. bovisis >99.95% identical to that ofM. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison withM. lepraereveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host–bacillus interactions or immune evasion. Furthermore, there are no genes unique toM. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology ofM. bovis.
Evidence for neurogenesis in the adult mammalian substantia nigra
Authors: Zhao Ming , Momma Stefan , Delfani Kioumars , Carlén Marie , Cassidy Robert M. , Johansson Clas B. , Brismar Hjalmar , Shupliakov Oleg , Frisén Jonas , Janson Ann Marie
Published: June 2003

New neurons are generated from stem cells in a few regions of the adult mammalian brain. Here we provide evidence for the generation of dopaminergic projection neurons of the type that are lost in Parkinson's disease from stem cells in the adult rodent brain and show that the rate of neurogenesis is increased after a lesion. The number of new neurons generated under physiological conditions in substantia nigra pars compacta was found to be several orders of magnitude smaller than in the granular cell layer of the dentate gyrus of the hippocampus. However, if the rate of neuronal turnover is constant, the entire population of dopaminergic neurons in substantia nigra could be replaced during the lifespan of a mouse. These data indicate that neurogenesis in the adult brain is more widespread than previously thought and may have implications for our understanding of the pathogenesis and treatment of neurodegenerative disorders such as Parkinson's disease.
Masquerading as self? Endoparasitic Strepsiptera (Insecta) enclose themselves in host-derived epidermal bag
Authors: Kathirithamby Jeyaraney , Ross Larry D. , Johnston J. Spencer
Published: June 2003

We report here the case of a metazoan parasite, a strepsipteran, that manipulates host epidermal tissue and wraps itself within it; which probably camouflages the endoparasite and is recognized as ``self'' by the host. This mechanism is one of immune avoidance among parasitoid insects. The host-derived epidermal ``bag'' might have enabled Strepsiptera to radiate to disparate hosts compared with the relatively few taxa (596 species) described so far. They have been recorded as parasitizing 34 families belonging to seven orders of Insecta. We also report a mechanism of insect ecdysis between the first- and second-instar larva, while enclosed in the bag.
Expression profiles of acute lymphoblastic and myeloblastic leukemias with ALL-1 rearrangements
Authors: Rozovskaia T. , Ravid-Amir O. , Tillib S. , Getz G. , Feinstein E. , Agrawal H. , Nagler A. , Rappaport E. F. , Issaeva I. , Matsuo Y. , Kees U. R. , Lapidot T. , Lo Coco F. , Foa R. , Mazo A. , Nakamura T. , Croce C. M. , Cimino G. , Domany E. , Canaani E.
Published: June 2003

The ALL-1 gene is directly involved in 5–10% of acute lymphoblastic leukemias (ALLs) and acute myeloid leukemias (AMLs) by fusion to other genes or through internal rearrangements. DNA microarrays were used to determine expression profiles of ALLs and AMLs with ALL-1 rearrangements. These profiles distinguish those tumors from other ALLs and AMLs. The expression patterns of ALL-1-associated tumors, in particular ALLs, involve oncogenes, tumor suppressors, antiapoptotic genes, drug-resistance genes, etc., and correlate with the aggressive nature of the tumors. The genes whose expression differentiates between ALLs with and without ALL-1 rearrangement were further divided into several groups, enabling separation of ALL-1-associated ALLs into two subclasses. One of the groups included 43 genes that exhibited expression profiles closely linked to ALLs with ALL-1 rearrangements. Further, there were evident differences between the expression profiles of AMLs in which ALL-1 had undergone fusion to other genes and AMLs with partial duplication of ALL-1. The extensive analysis described here pinpointed genes that might have a direct role in pathogenesis.
A pattern analysis of the second Rehnquist U.S. Supreme Court
Authors: Sirovich Lawrence
Published: June 2003

The second Rehnquist Court has remained unchanged in composition for 8 yr, resulting in a large temporally stable database. This paper reports on a mathematically objective analysis of this ensemble of rulings aimed at extracting key patterns and latent information. Although the rulings of a nine-justice Court require representation in nine dimensions, smaller spaces describe the Court's actions; e.g., a 2D subspace describes the margins of all decisions, and use of Shannon information shows that the Court acts as if composed of 4.68 ideal justices. Comparison is also made with the 1959–1961 and 1967–1969 Warren Courts. Both Warren Courts have remarkable parallels with the Rehnquist Court. In each instance, we present an optimal mapping of the justices between the Courts, which underscores the similarity in the workings of seemingly dissimilar courts.
piggyBac
-based insertional mutagenesis in the presence of stably integrated
P
elements in
Drosophila
Authors: Häcker Udo , Nystedt Sverker , Barmchi Mojgan Padash , Horn Carsten , Wimmer Ernst A.
Published: June 2003

P
element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for
Drosophila
adult viability. Mutation of all genes in the fly genome, however, poses a problem, because
P
elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of
P
element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are
P
element-based and can therefore not be combined with the use of
P
elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-
P
element transposons. An enhanced yellow fluorescent protein-marked
piggyBac
-based mutator element was mobilized by a
piggyBac
specific transposase source expressed from a
Hermes
-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798
piggyBac
insertions on
FRT
bearing third chromosomes of which 9% have sustained a putatively
piggyBac
-related lethal hit. The
FRTs
present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no
P
element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the
Drosophila
genome. The system is
Drosophila
nonspecific and potentially applicable in a broad spectrum of nonmodel organisms.
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence
Authors: Anzai Tatsuya , Shiina Takashi , Kimura Natsuki , Yanagiya Kazuyo , Kohara Sakae , Shigenari Atsuko , Yamagata Tetsushi , Kulski Jerzy K. , Naruse Taeko K. , Fujimori Yoshifumi , Fukuzumi Yasuhito , Yamazaki Masaaki , Tashiro Hiroyuki , Iwamoto Chie , Umehara Yumi , Imanishi Tadashi , Meyer Alice , Ikeo Kazuho , Gojobori Takashi , Bahram Seiamak , Inoko Hidetoshi
Published: June 2003

Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their closest relative, the chimpanzee, is largely unknown. This report describes a large-scale single-contig comparison between human and chimpanzee genomes via the sequence analysis of almost one-half of the immunologically critical MHC. This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region. This is functionally exemplified by a large deletion of 95 kb between the virtual locations of human
MICA
and
MICB
genes, which results in a single hybrid chimpanzee
MIC
gene, in a segment of the MHC genetically linked to species-specific handling of several viral infections (HIV/SIV, hepatitis B and C) as well as susceptibility to various autoimmune diseases. Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.
Relationship of herpes simplex virus genome configuration to productive and persistent infections
Authors: Jackson Sara A. , DeLuca Neal A.
Published: June 2003

Infection of susceptible cells by herpes simplex virus (HSV) can lead to productive infection or to latency, where the genomes persist in the nuclei of peripheral neurons in a quiescent state. Using the HSV strain d109, which does not express any viral genes and thus establishes a quiescent state in most cells, we observed that a fraction of genomes circularized upon infection. The expression of infected cell protein (ICP) 0, which is known to be involved in reactivation from latency and the promotion of productive infection, inhibited the formation of circular genomes. Circular genomes were not observed upon infection of fully permissive cells by wild-type virus, in either the presence or absence of viral DNA replication. However, productive infection in the absence of ICP0 resulted in the accumulation of a subpopulation of circular genomes. The proportion of circular genomes formed during infection with an ICP0 mutant was greater at low multiplicity of infection, a condition in which ICP0 mutants replicate poorly. In the complete absence of viral gene expression, it was found that only circular genomes persisted in cells. These results suggest that circularization of the HSV genome may not occur early in the productive phase of wild-type HSV infection, but rather during establishment of a quiescent state or latency, providing a possible strategy for long-term persistence. Additionally, the circularization and possible fate of HSV genomes are regulated by an activity of ICP0.
Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus
Authors: Deslandes Laurent , Olivier Jocelyne , Peeters Nemo , Feng Dong Xin , Khounlotham Manirath , Boucher Christian , Somssich Imre , Genin Stéphane , Marco Yves
Published: June 2003

RRS1-R
confers broad-spectrum resistance to several strains of the causal agent of bacterial wilt,
Ralstonia solanacearum
. Although genetically defined as recessive, this
R
gene encodes a protein whose structure combines the TIR-NBS-LRR domains found in several R proteins and a WRKY motif characteristic of some plant transcriptional factors and behaves as a dominant gene in transgenic susceptible plants. Here we show that PopP2, a
R. solanacearum
type III effector, which belongs to the YopJ/AvrRxv protein family, is the avirulence protein recognized by RRS1-R. Furthermore, an interaction between PopP2 and both RRS1-R and RRS1-S, present in the resistant Nd-1 and susceptible Col-5
Arabidopsis thaliana
ecotypes, respectively, was detected by using the yeast split-ubiquitin two-hybrid system. This interaction, which required the full-length R protein, was not observed between the RRS1 proteins and PopP1, another member of the YopJ/AvrRxv family present in strain GMI1000 and that confers avirulence in
Petunia
. We further demonstrate that both the Avr protein and the RRS1 proteins colocalize in the nucleus and that the nuclear localization of the RRS1 proteins are dependent on the presence of PopP2.
The Notch ligand Delta1 is sequentially cleaved by an ADAM protease and γ-secretase
Authors: Six Emmanuelle , Ndiaye Delphine , Laâbi Yacine , Brou Christel , Gupta-Rossi Neetu , Israël Alain , Logeat Frédérique
Published: June 2003

Notch signaling is involved in numerous cell fate decisions in invertebrates and vertebrates. The Notch receptor is a type I transmembrane (TM) protein that undergoes two proteolytic steps after ligand binding, first by an ADAM (a distintegrin and metalloprotease) in the extracellular region, followed by γ-secretase-mediated cleavage inside the TM domain. We demonstrate here that the murine ligand Delta1 (Dll1) undergoes the same sequence of cleavages, in an apparently signal-independent manner. Identification of the ADAM-mediated shedding site localized 10 aa N-terminal to the TM domain has enabled us to generate a noncleavable mutant. Kuzbanian/ADAM10 is involved in this processing event, but other proteases can probably substitute for it. We then show that Dll1 is part of a high-molecular-weight complex containing presenilin1 and undergoes further cleavage by a γ-secretase-like activity, therefore releasing the intracellular domain that localizes in part to the nucleus. Using the shedding-resistant mutant, we demonstrate that this γ-secretase cleavage depends on prior ectodomain shedding. Therefore Dll1 is a substrate for regulated intramembrane proteolysis, and its intracellular region possibly fulfills a specific function in the nucleus.
Germ-line transgenesis of the Tc1/
mariner
superfamily transposon
Minos
in
Ciona intestinalis
Authors: Sasakura Yasunori , Awazu Satoko , Chiba Shota , Satoh Nori
Published: June 2003

The tadpole larva of the basal chordate
Ciona intestinalis
has the most simplified, basic body-plan of chordates. Because it has a compact genome with a complete draft sequence, a large quantity of EST/cDNA information, and a short generation time,
Ciona
is a suitable model for future genetics. We establish here a transgenic technique in
Ciona
that uses the Tc1/
mariner
superfamily transposon
Minos. Minos
was integrated efficiently into the genome of germ cells and transmitted stably to subsequent generations. In addition, an enhancer-trap line was obtained. This is a demonstration of efficient,
Minos
-mediated transgenesis in marine invertebrates.
Detailed map of a cis-regulatory input function
Authors: Setty Y. , Mayo A. E. , Surette M. G. , Alon U.
Published: June 2003

Most genes are regulated by multiple transcription factors that bind specific sites in DNA regulatory regions. These cis-regulatory regions perform a computation: the rate of transcription is a function of the active concentrations of each of the input transcription factors. Here, we used accurate gene expression measurements from living cell cultures, bearing GFP reporters, to map in detail the input function of the classic
lacZYA
operon of
Escherichia coli
, as a function of about a hundred combinations of its two inducers, cAMP and isopropyl β-
d
-thiogalactoside (IPTG). We found an unexpectedly intricate function with four plateau levels and four thresholds. This result compares well with a mathematical model of the binding of the regulatory proteins cAMP receptor protein (CRP) and LacI to the
lac
regulatory region. The model is also used to demonstrate that with few mutations, the same region could encode much purer AND-like or even OR-like functions. This possibility means that the wild-type region is selected to perform an elaborate computation in setting the transcription rate. The present approach can be generally used to map the input functions of other genes.
Selective impairment of hippocampal neurogenesis by chronic alcoholism: Protective effects of an antioxidant
Authors: Herrera Daniel G. , Yagüe Almudena G. , Johnsen-Soriano Siv , Bosch-Morell Francisco , Collado-Morente Lucía , Muriach Maria , Romero Francisco J. , García-Verdugo J. Manuel
Published: June 2003

A major pathogenic mechanism of chronic alcoholism involves oxidative burden to liver and other cell types. We show that adult neurogenesis within the dentate gyrus of the hippocampus is selectively impaired in a rat model of alcoholism, and that it can be completely prevented by the antioxidant ebselen. Rats fed for 6 weeks with a liquid diet containing moderate doses of ethanol had a 66.3% decrease in the number of new neurons and a 227–279% increase in cell death in the dentate gyrus as compared with paired controls. Neurogenesis within the olfactory bulb was not affected by alcohol. Our studies indicate that alcohol abuse, even for a short duration, results in the death of newly formed neurons within the adult brain and that the underlying mechanism is related to oxidative or nitrosative stress. Moreover, these findings suggest that the impaired neurogenesis may be a mechanism mediating cognitive deficits observed in alcoholism.
Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga
Bigelowiella natans
Authors: Archibald John M. , Rogers Matthew B. , Toop Michael , Ishida Ken-ichiro , Keeling Patrick J.
Published: June 2003

Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary endosymbiosis in chlorarachniophytes is that most of the nuclear genes encoding plastid-targeted proteins have moved from the nucleus of the endosymbiont to the host nucleus. We have sequenced and analyzed 83 cDNAs encoding 78 plastid-targeted proteins from the model chlorarachniophyte
Bigelowiella natans
(formerly
Chlorarachnion
sp. CCMP621). Phylogenies inferred from the majority of these genes are consistent with a chlorophyte green algal origin. However, a significant number of genes (≈21%) show signs of having been acquired by lateral gene transfer from numerous other sources: streptophyte algae, red algae (or algae with red algal endosymbionts), as well as bacteria. The chlorarachniophyte plastid proteome may therefore be regarded as a mosaic derived from various organisms in addition to the ancestral chlorophyte plastid. In contrast, the homologous genes from the chlorophyte
Chlamydomonas reinhardtii
do not show any indications of lateral gene transfer. This difference is likely a reflection of the mixotrophic nature of
Bigelowiella
(i.e., it is photosynthetic and phagotrophic), whereas
Chlamydomonas
is strictly autotrophic. These results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage.
Effective behavioral treatment of focal hand dystonia in musicians alters somatosensory cortical organization
Authors: Candia Victor , Wienbruch Christian , Elbert Thomas , Rockstroh Brigitte , Ray William
Published: June 2003

New perspectives in neurorehabilitation suggest that behavioral treatments of movement disorders may modify the functional organization of central somatosensory neural networks. On the basis of the assumption that use-dependent reorganization in these networks contributes to the fundamental abnormalities seen in focal dystonia, we treated 10 affected musicians and measured the concomitant somatosensory changes by using whole-head magnetoencephalography. We found that effective treatment, using the method of sensory motor retuning, leads to alterations in the functional organization of the somatosensory cortex. Specifically, before treatment, somatosensory relationships of the individual fingers differ between the affected and unaffected hands, whereas after treatment, finger representations contralateral to the dystonic side become more similar to the less-affected side. Further, somatosensory finger representations are ordered more according to homuncular principles after treatment. In addition, the observed physiologic changes correlated with behavioral data. These results confirm that plastic changes in parallel with emergent neurological dysfunction may be reversed by context-specific, intensive training-based remediation.
CD40 ligand is a critical effector of Epstein–Barr virus in host cell survival and transformation
Authors: Imadome Ken-Ichi , Shirakata Masaki , Shimizu Norio , Nonoyama Shigeaki , Yamanashi Yuji
Published: June 2003

Epstein–Barr virus (EBV), implicated in numerous human diseases, including lymphoid malignancies, persistently infects peripheral B cells and transforms them into lymphoblastoid cell lines. Here we found that EBV equally infected B cells from patients with X-linked hyper IgM syndrome and those from healthy donors; however, it hardly transformed X-linked hyper IgM syndrome B cells, because of the dysfunctional gene of CD40 ligand (CD40L) of the patients. Unlike CD40, CD40L is not usually expressed on B cells. However, we found that EBV infection of normal B cells induced CD40L expression as a critical effector in host cell transformation and survival. Moreover, chronic active EBV infection of peripheral T cells, implicated in T cell malignancies, was associated with ectopic expression of CD40, and, in Jurkat T cells, EBV infection induced CD40 expression. These results suggest that EBV infection induces CD40L/CD40 signaling in host cells, which appears to play an essential role in its persistent infection and malignancies of lymphocytes.
Mast cells disrupt epithelial barrier function during enteric nematode infection
Authors: McDermott Jacqueline R. , Bartram Ruth E. , Knight Pamela A. , Miller Hugh R. P. , Garrod David R. , Grencis Richard K.
Published: June 2003

We have investigated the influence of mast cells on the barrier function of intestinal epithelium during nematode infection.Trichinella spiralisinfection induces a strong type 2 cytokine-mediated inflammation, resulting in a critical mucosal mastocytosis that is known to mediate expulsion of the parasites from the intestine. The host response to infection is also characterized by an increase in mucosal leakiness. We show here that intestinal epithelial permeability is markedly elevated during infection, with kinetics that mirror the adaptive immune response to primary and secondary infection. Furthermore, we have identified degradation of the tight junction protein, occludin, thereby providing a mechanism for increased paracellular permeability during helminth infection. We further demonstrate by using anti-c-kitantibody and IL-9 transgenic mice that mast cells are directly responsible for increasing epithelial paracellular permeability and that mice deficient in a mast cell-specific protease fail to increase intestinal permeability and fail to expel their parasite burden. These results provide the mechanism whereby mucosal mast cells mediate parasite expulsion from the intestine.
Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1Pseudomonas aeruginosabiofilms
Authors: Wozniak Daniel J. , Wyckoff Timna J. O. , Starkey Melissa , Keyser Rebecca , Azadi Parastoo , O'Toole George A. , Parsek Matthew R.
Published: June 2003

The bacteriumPseudomonas aeruginosacauses chronic respiratory infections in cystic fibrosis (CF) patients. Such infections are extremely difficult to control because the bacteria exhibit a biofilm-mode of growth, renderingP. aeruginosaresistant to antibiotics and phagocytic cells. During the course of infection,P. aeruginosausually undergoes a phenotypic switch to a mucoid colony, which is characterized by the overproduction of the exopolysaccharide alginate. Alginate overproduction has been implicated in protectingP. aeruginosafrom the harsh environment present in the CF lung, as well as facilitating its persistence as a biofilm by providing an extracellular matrix that promotes adherence. Because of its association with biofilms in CF patients, it has been assumed that alginate is also the primary exopolysaccharide expressed in biofilms of environmental nonmucoidP. aeruginosa. In this study, we examined the chemical nature of the biofilm matrix produced by wild-type and isogenic alginate biosynthetic mutants ofP. aeruginosa. The results clearly indicate that alginate biosynthetic genes are not expressed and that alginate is not required during the formation of nonmucoid biofilms in twoP. aeruginosastrains, PAO1 and PA14, that have traditionally been used to study biofilms. Because nonmucoidP. aeruginosastrains are the predominant environmental phenotype and are also involved in the initial colonization in CF patients, these studies have implications in understanding the early events of the infectious process in the CF airway.
Division site selection in
Escherichia coli
involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles
Authors: Shih Yu-Ling , Le Trung , Rothfield Lawrence
Published: June 2003

The MinCDE proteins of
Escherichia coli
are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the
E. coli
MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in
Bacillus subtilis.
The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in
E. coli
and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.
Differential proteasomal processing of hydrophobic and hydrophilic protein regions: Contribution to cytotoxic T lymphocyte epitope clustering in HIV-1-Nef
Authors: Lucchiari-Hartz Maria , Lindo Viv , Hitziger Niclas , Gaedicke Simone , Saveanu Loredana , van Endert Peter M. , Greer Fiona , Eichmann Klaus , Niedermann Gabriele
Published: June 2003

HIV proteins contain a multitude of naturally processed cytotoxic T lymphocyte (CTL) epitopes that concentrate in clusters. The molecular basis of epitope clustering is of interest for understanding HIV immunogenicity and for vaccine design. We show that the CTL epitope clusters of HIV proteins predominantly coincide with hydrophobic regions, whereas the noncluster regions are predominantly hydrophilic. Analysis of the proteasomal degradation products of full-length HIV-Nef revealed a differential sensitivity of cluster and noncluster regions to proteasomal processing. Compared with the epitope-scarce noncluster regions, cluster regions are digested by proteasomes more intensively and with greater preference for hydrophobic P1 residues, resulting in substantially greater numbers of fragments with the sizes and COOH termini typical of epitopes and their precursors. Indeed, many of these fragments correspond to endogenously processed Nef epitopes and/or their potential precursors. The results suggest that differential proteasomal processing contributes importantly to the clustering of CTL epitopes in hydrophobic regions.
Prostate intraepithelial neoplasia induced by prostate restricted Akt activation: The MPAKT model
Authors: Majumder Pradip K. , Yeh Jen Jen , George Daniel J. , Febbo Phillip G. , Kum Jennifer , Xue Qi , Bikoff Rachel , Ma Hongfeng , Kantoff Philip W. , Golub Todd R. , Loda Massimo , Sellers William R.
Published: June 2003

To determine whether Akt activation was sufficient for the transformation of normal prostate epithelial cells,
m
urine
p
rostate restricted
A
kt
k
inase activity was generated in
t
ransgenic mice (MPAKT mice). Akt expression led to p70
S6K
activation, prostatic intraepithelial neoplasia (PIN), and bladder obstruction. mRNA expression profiles from MPAKT ventral prostate revealed similarities to human cancer and an angiogenic signature that included three angiogenin family members, one of which was found elevated in the plasma of men with prostate cancer. Thus, the MPAKT model may be useful in studying the role of Akt in prostate epithelial cell transformation and in the discovery of molecular markers relevant to human disease.
Mdm20 protein functions with Nat3 protein to acetylate Tpm1 protein and regulate tropomyosin–actin interactions in budding yeast
Authors: Singer Jason M. , Shaw Janet M.
Published: June 2003

The evolutionarily conserved Mdm20 protein (Mdm20p) plays an important role in tropomyosin–F-actin interactions that generate actin filaments and cables in budding yeast. However, Mdm20p is not a structural component of actin filaments or cables, and its exact function in cable stability has remained a mystery. Here, we show that cells lacking Mdm20p fail to N-terminally acetylate Tpm1p, an abundant form of tropomyosin that binds and stabilizes actin filaments and cables. The F-actin-binding activity of unacetylated Tpm1p is reduced severely relative to the acetylated form. These results are complemented by the recent report that Mdm20p copurifies with one of three acetyltransferases in yeast, the NatB complex. We present genetic evidence that Mdm20p functions cooperatively with Nat3p, the catalytic subunit of the NatB acetyltransferase. These combined results strongly suggest that Mdm20p-dependent, N-terminal acetylation of Tpm1p by the NatB complex is required for Tpm1p association with, and stabilization of, actin filaments and cables.
Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle
Authors: Hanotte O. , Ronin Y. , Agaba M. , Nilsson P. , Gelhaus A. , Horstmann R. , Sugimoto Y. , Kemp S. , Gibson J. , Korol A. , Soller M. , Teale A.
Published: June 2003

Trypanosomosis, or sleeping sickness, is a major disease constraint on livestock productivity in sub-Saharan Africa. To identify quantitative trait loci (QTL) controlling resistance to trypanosomosis in cattle, an experimental cross was made between trypanotolerant African N'Dama (Bos taurus) and trypanosusceptible improved Kenya Boran (Bos indicus) cattle. Sixteen phenotypic traits were defined describing anemia, body weight, and parasitemia. One hundred seventy-seven F2animals and their parents and grandparents were genotyped at 477 molecular marker loci covering all 29 cattle autosomes. Total genome coverage was 82%. Putative QTL were mapped to 18 autosomes at a genomewise false discovery rate of <0.20. The results are consistent with a single QTL on 17 chromosomes and two QTL on BTA16. Individual QTL effects ranged from ≈6% to 20% of the phenotypic variance of the trait. Excluding chromosomes with ambiguous or nontrypanotolerance effects, the allele for resistance to trypanosomosis originated from the N'Dama parent at nine QTL and from the Kenya Boran at five QTL, and at four QTL there is evidence of an overdominant mode of inheritance. These results suggest that selection for trypanotolerance within an F2cross between N'Dama and Boran cattle could produce a synthetic breed with higher trypanotolerance levels than currently exist in the parental breeds.
End-sequence profiling: Sequence-based analysis of aberrant genomes
Authors: Volik Stanislav , Zhao Shaying , Chin Koei , Brebner John H. , Herndon David R. , Tao Quanzhou , Kowbel David , Huang Guiqing , Lapuk Anna , Kuo Wen-Lin , Magrane Gregg , de Jong Pieter , Gray Joe W. , Collins Colin
Published: June 2003

Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have been developed for this purpose. We show here that end-sequence profiling (ESP) is particularly well suited to this purpose. ESP is accomplished by constructing a bacterial artificial chromosome (BAC) library from a test genome, measuring BAC end sequences, and mapping end-sequence pairs onto the normal genome sequence. Plots of BAC end-sequences density identify copy number abnormalities at high resolution. BACs spanning structural aberrations have end pairs that map abnormally far apart on the normal genome sequence. These pairs can then be sequenced to determine the involved genes and breakpoint sequences. ESP analysis of the breast cancer cell line MCF-7 demonstrated its utility for analysis of complex genomes. End sequencing of ≈8,000 clones (0.37-fold haploid genome clonal coverage) produced a comprehensive genome copy number map of the MCF-7 genome at better than 300-kb resolution and identified 381 genome breakpoints, a subset of which was verified by fluorescence
in situ
hybridization mapping and sequencing.
Runx3 and Runx1 are required for CD8 T cell development during thymopoiesis
Authors: Woolf Eilon , Xiao Cuiying , Fainaru Ofer , Lotem Joseph , Rosen Dalia , Negreanu Varda , Bernstein Yael , Goldenberg Dalia , Brenner Ori , Berke Gideon , Levanon Ditsa , Groner Yoram
Published: June 2003

The RUNX transcription factors are important regulators of lineage-specific gene expression. RUNX are bifunctional, acting both as activators and repressors of tissue-specific target genes. Recently, we have demonstrated that Runx3 is a neurogenic transcription factor, which regulates development and survival of proprioceptive neurons in dorsal root ganglia. Here we report that Runx3 and Runx1 are highly expressed in thymic medulla and cortex, respectively, and function in development of CD8 T cells during thymopoiesis. Runx3-deficient (Runx3 KO) mice display abnormalities in CD4 expression during lineage decisions and impairment of CD8 T cell maturation in the thymus. A large proportion of Runx3 KO peripheral CD8 T cells also expressed CD4, and in contrast to wild-type, their proliferation ability was largely reduced. In addition, thein vitrocytotoxic activity of alloimmunized peritoneal exudate lymphocytes was significantly lower in Runx3 KO compared with WT mice. In a compound mutant mouse, null for Runx3 and heterozygous for Runx1 (Runx3-/-;Runx1+/-), all peripheral CD8 T cells also expressed CD4, resulting in a complete lack of single-positive CD8+T cells in the spleen. The results provide information on the role of Runx3 and Runx1 in thymopoiesis and suggest that both act as transcriptional repressors ofCD4expression during T cell lineage decisions.