bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and Extraction Behaviour of Calix[4]arenes Partially Substituted at the Wide Rim by Carbamoylmethylphosphine Oxide (CMPO) Functions
Authors: Arnaud-Neu Françoise , Barboso Silvia , Böhmer Volker , Brisach Frédéric , Delmau Laetitia , Dozol Jean-François , Mogck Oliver , Paulus Erich F. , Saadioui Mohamed , Shivanyuk Alexander
Published: October 2003

Tetraethers of calix[4]arenes fixed in the cone conformation and substituted at their wide rim by one to three CMPO residues and hydrogen atoms or t-butyl moieties in the remaining position(s) were synthesized. Liquid/liquid extraction studies of selected lanthanides and actinides were undertaken with these calix[4]arenes, including also a linear trimer, in order to obtain a better understanding for the extraction properties of the corresponding calix[4]arene substituted by four CMPO functions. The structure of the 1,3-di-CMPO derivative was confirmed by single crystal X-ray analysis.
The microstructure of coconut coir dusts for use as alternatives to peat in soilless growing media
Authors: Fornes F. , Belda R. M. , Abad M. , Noguera P. , Puchades R. , Maquieira A. , Noguera V.
Published: October 2003

The microstructure of the mesocarp pithy tissue and short-length fibres of 2 differently processed coconut coir dusts from Mexico and Sri Lanka was studied using scanning electron microscopy and compared with that of a Sphagnum moss peat. Selected physical properties of these materials were also determined for their use in potting media. The 2 coir dusts did not significantly differ in the microstructural parameters studied, whereas they differed remarkably in their particle size and therefore in their physical properties. Pithy tissue was the major constituent of coir dust. Coarse pithy tissue particles (larger than 1 mm) were highly porous, with an internal porosity of 41.0% by volume. These particles exhibited round-shaped external pores which ranged in diameter from 30 to 80 μm, with an average of 44.3 μm, and which accounted for a relative surface porosity of about 40.9%. By contrast, the cells of Sphagnum peat moss leaves showed oval-shaped pores of 20.1 × 11.5 μm, which accounted for a relative surface porosity of only 12.0%. The internal porosity of peat moss leaves was 51.1% by volume. The retting process (soaking in water) applied to the coconut husks in Sri Lanka partially degraded the pithy tissue and coir fibres. Coir dust from Mexico showed lower water-holding capacity and higher aeration than peat, whereas air–water relationships in coir dust from Sri Lanka were similar to those in peat. Although differences observed in microstructure and porosity characteristics could explain the differential physical properties of the three materials studied, the major reason was the different size distribution of their constituent particles.
"They Know Not What They Do" — on William Rodier and his Mission to Exterminate Rabbits and other Vertebrate Pests
Authors: Noble J. C. , Pfitzner G. H.
Published: November 2003

William Rodier (1859–1936) became well known throughout much of southeastern Australia during the late nineteenth and early twentieth centuries, mainly through the vigour with which he expressed his contentious views on how best to control certain vertebrate pests. Much of his 'plan', particularly in regard to rabbits, was based on his experience as a pastoralist in western New South Wales. In this article, we examine what is known about Rodier's family background, his occupations, preoccupations, and particularly, the effectiveness of his endeavours to convince a largely sceptical public as to the wisdom and practicality of his method for vertebrate pest control. Some of the circulars and flyers printed by Rodier are also reproduced for illustrative purposes. These were designed to demonstrate the effectiveness of the Rodier Method, especially for controlling the rabbit, perceived by him to be the most serious threat then facing landholders in Australia. Rodier's activities are appraised in light of the relationship then existing between community-based science and more orthodox, academically-based science in the late nineteenth and early twentieth century. Finally, this relationship is further explored in an historical context by examining the importance attached to local, informal knowledge in contemporary ecological research where landholder collaboration is now often regarded as an integral component.
Developmental amnesia and its relationship to degree of hippocampal atrophy
Authors: Isaacs E. B. , Vargha-Khadem F. , Watkins K. E. , Lucas A. , Mishkin M. , Gadian D. G.
Published: October 2003

Two groups of adolescents, one born preterm and one with a diagnosis of developmental amnesia, were compared with age-matched normal controls on measures of hippocampal volume and memory function. Relative to control values, the preterm group values showed a mean bilateral reduction in hippocampal volume of 8–9% (ranging to 23%), whereas the developmental amnesic group values showed a reduction of 40% (ranging from 27% to 56%). Despite equivalent IQ and immediate memory scores in the two study groups, there were marked differences between them on a wide variety of verbal and visual delayed memory tasks. Consistent with their diagnosis, the developmental amnesic group was impaired relative to both other groups on nearly all delayed memory measures. The preterm group, by contrast, was significantly impaired relative to the controls on only a few memory measures, i.e., route following and prospective memory. We suggest that early hippocampal pathology leads to the disabling memory impairments associated with developmental amnesia when the volume of this structure is reduced below normal by ≈20–30% on each side. Whether this is a sufficient condition for the disorder or whether abnormality in other brain regions is also necessary remains to be determined.
MADS box genes control vernalization-induced flowering in cereals
Authors: Trevaskis Ben , Bagnall David J. , Ellis Marc H. , Peacock W. James , Dennis Elizabeth S.
Published: October 2003

By comparing expression levels of MADS box transcription factor genes between near-isogenic winter and spring lines of bread wheat,
Triticum aestivum
, we have identified
WAP1
as the probable candidate for the
Vrn-1
gene, the major locus controlling the vernalization flowering response in wheat.
WAP1
is strongly expressed in spring wheats and moderately expressed in semispring wheats, but is not expressed in winter wheat plants that have not been exposed to vernalization treatment. Vernalization promotes flowering in winter wheats and strongly induces expression of
WAP1. WAP1
is located on chromosome 5 in wheat and, by synteny with other cereal genomes, is likely to be collocated with
Vrn-1
. These results in hexaploid bread wheat cultivars extend the conclusion made by Yan
et al.
[Yan, L., Loukoianov, A., Tranquilli, G., Helguera, M., Fahima, T. & Dubcovsky, J. (2003)
Proc. Natl. Acad. Sci. USA
100, 6263–6268] in the diploid wheat progenitor
Triticum monococcum
that
WAP1
(
TmAP1
) corresponds to the
Vrn-1
gene. The barley homologue of
WAP1, BM5
, shows a similar pattern of expression to
WAP1
and
TmAP1. BM5
is not expressed in winter barleys that have not been vernalized, but as with
WAP1
, expression of
BM5
is strongly induced by vernalization treatment. In spring barleys, the level of
BM5
expression is determined by interactions between the
Vrn-H1
locus and a second locus for spring habit,
Vrn-H2
. There is now evidence that
AP1
-like genes determine the time of flowering in a range of cereal and grass species.
Contrasting patterns of expression of transcription factors in pancreatic α and β cells
Authors: Wang Jie , Webb Gene , Cao Yun , Steiner Donald F.
Published: October 2003

Pancreatic α and β cells are derived from the same progenitors but play opposing roles in the control of glucose homeostasis. Disturbances in their function are associated with diabetes mellitus. To identify many of the proteins that define their unique pathways of differentiation and functional features, we have analyzed patterns of gene expression in αTC1.6 vs. MIN6 cell lines by using oligonucleotide microarrays. Approximately 9–10% of >11,000 transcripts examined showed significant differences between the two cell types. Of >700 known transcripts enriched in either cell type, transcription factors and their regulators (TFR) was one of the most significantly different categories. Ninety-six members of the basic zipper, basic helix–loop–helix, homeodomain, zinc finger, high mobility group, and other transcription factor families were enriched in α cells; in contrast, homeodomain proteins accounted for 51% of a total of 45 TFRs enriched in β cells. Our analysis thus highlights fundamental differences in expression of TFR subtypes within these functionally distinct islet cell types. Interestingly, the α cells appear to express a large proportion of factors associated with progenitor or stem-type cells, perhaps reflecting their earlier appearance during pancreatic development. The implications of these findings for a better understanding of α and β cell dysfunction in diabetes mellitus are also considered.
Differentiation of human embryonic stem cells on three-dimensional polymer scaffolds
Authors: Levenberg Shulamit , Huang Ngan F. , Lavik Erin , Rogers Arlin B. , Itskovitz-Eldor Joseph , Langer Robert
Published: October 2003

Human embryonic stem (hES) cells hold promise as an unlimited source of cells for transplantation therapies. However, control of their proliferation and differentiation into complex, viable 3D tissues is challenging. Here we examine the use of biodegradable polymer scaffolds for promoting hES cell growth and differentiation and formation of 3D structures. We show that complex structures with features of various committed embryonic tissues can be generated,
in vitro
, by using early differentiating hES cells and further inducing their differentiation in a supportive 3D environment such as poly(lactic-
co
-glycolic acid)/poly(
l
-lactic acid) polymer scaffolds. We found that hES cell differentiation and organization can be influenced by the scaffold and directed by growth factors such as retinoic acid, transforming growth factor β, activin-A, or insulin-like growth factor. These growth factors induced differentiation into 3D structures with characteristics of developing neural tissues, cartilage, or liver, respectively. In addition, formation of a 3D vessel-like network was observed. When transplanted into severe combined immunodeficient mice, the constructs continue to express specific human proteins in defined differentiated structures and appear to recruit and anastamose with the host vasculature. This approach provides a unique culture system for addressing questions in cell and developmental biology, and provides a potential mechanism for creating viable human tissue structures for therapeutic applications.
Adaptive mutation: General mutagenesis is not a programmed response to stress but results from rare coamplification of
dinB
with
lac
Authors: Slechta E. Susan , Bunny Kim L. , Kugelberg Elisabeth , Kofoid Eric , Andersson Dan I. , Roth John R.
Published: October 2003

In a particular genetic system, selection stimulates reversion of a
lac
mutation and causes genome-wide mutagenesis (adaptive mutation). Selection allows rare plated cells with a duplication of the leaky
lac
allele to initiate clones within which further
lac
amplification improves growth rate. Growth and amplification add mutational targets to each clone and thereby increase the likelihood of reversion. We suggest that general mutagenesis occurs only in clones whose
lac
amplification includes the nearby
dinB
+
gene (for error-prone DNA polymerase IV). Thus mutagenesis is not a programmed response to stress but a side effect of amplification in a few clones; it is not central to the effect of selection on reversion.
Glia-independent chains of neuroblasts through the subcortical parenchyma of the adult rabbit brain
Authors: Luzzati F. , Peretto P. , Aimar P. , Ponti G. , Fasolo A. , Bonfanti L.
Published: October 2003

In the brains of adult mammals long-distance cell migration of neuronal precursors is known to occur in the rostral migratory stream, involving chains of cells sliding into astrocytic glial tubes. By combining immunocytochemistry for polysialylated neural cell adhesion molecule (PSA-NCAM), neuronal and glial antigens, endogenous and exogenously administered cell-proliferation markers, and light and electron microscopy 3D reconstructions, we show that chains of newly generated neuroblasts exist both inside and outside the subventricular zone of adult rabbits. Two groups of chains were detectable within the mature brain parenchyma: anterior chains, into the anterior forceps of the corpus callosum, and posterior chains, close to the external capsule. Parenchymal chains were not associated with any special glial structures, thus coming widely in contact with the mature nervous tissue, including unmyelinated/myelinated fibers, astrocytes, neurons, and oligodendrocytes. These chains of cells, unlike those in the subventricular zone, do not display cell proliferation, but they contain BrdUrd administered several weeks before. Telencephalic areas, such as the putamen, amygdala, claustrum, and cortex, adjacent to the chains harbor numerous PSA-NCAM-positive cells. The counting of newly generated cells in these areas shows small differences in comparison with others, and a few cells double-labeled for BrdUrd/PSA-NCAM (after 1-month survival) and for BrdUrd/NeuN (after 2 months) were detectable. These results demonstrate the occurrence of glial-independent chains of migrating neuroblasts, which directly contact the mature brain parenchyma of adult mammals. These chains could provide a possible link between the adult germinative layers and a very low-rate/long-term process of cell addition in the telencephalon.
The Nagata automorphism is wild
Authors: Shestakov Ivan P. , Umirbaev Ualbai U.
Published: October 2003

It is proved that the well known Nagata automorphism of the polynomial ring in three variables over a field of characteristic zero is wild, that is, it can not be decomposed into a product of elementary automorphisms.
The Tat/TAR-dependent phosphorylation of RNA polymerase II C-terminal domain stimulates cotranscriptional capping of HIV-1 mRNA
Authors: Zhou Meisheng , Deng Longwen , Kashanchi Fatah , Brady John N. , Shatkin Aaron J. , Kumar Ajit
Published: October 2003

The HIV type 1 (HIV-1) Tat protein stimulates transcription elongation by recruiting P-TEFb (CDK9/cyclin T1) to the transactivation response (TAR) RNA structure. Tat-induced CDK9 kinase has been shown to phosphorylate Ser-5 of RNA polymerase II (RNAP II) C-terminal domain (CTD). Results presented here demonstrate that Tat-induced Ser-5 phosphorylation of CTD by P-TEFb stimulates the guanylyltransferase activity of human capping enzyme and RNA cap formation. Sequential phosphorylation of CTD by Tat-induced P-TEFb enhances the stimulation of human capping enzyme guanylyltransferase activity and RNA cap formation by transcription factor IIH-mediated CTD phosphorylation. Using an immobilized template assay that permits isolation of transcription complexes, we show that Tat/TAR-dependent phosphorylation of RNAP II CTD stimulates cotranscriptional capping of HIV-1 mRNA. Upon transcriptional induction of latently infected cells, accumulation of capped transcripts occurs along with Ser-5-phosphorylated RNAP II in the promoter proximal region of the HIV-1 genome. Therefore, these observations suggest that Tat/TAR-dependent phosphorylation of RNAP II CTD is crucial not only in promoting transcription elongation but also in stimulating nascent viral RNA capping.
Twin concordance and sibling recurrence rates in multiple sclerosis
Authors: Willer C. J. , Dyment D. A. , Risch N. J. , Sadovnick A. D. , Ebers G. C. ,   The Canadian Collaborative Study Group§§
Published: October 2003

Size and ascertainment constraints often limit twin studies to concordance comparisons between identical and fraternal twins. Here we report the final results of a longitudinal, population-based study of twins with multiple sclerosis (MS) in Canada. Bias was demonstrably minimized, and an estimated 75% of all Canadian MS twin pairs were ascertained, giving a sample sufficiently large (n= 370) to permit additional informative comparisons. Twinning was not found to affect prevalence, and twins with MS did not differ from nontwins for DR15 allele frequency nor for MS risk to their siblings. Probandwise concordance rates of 25.3% (SE ± 4.4) for monozygotic (MZ), 5.4% (±2.8) for dizygotic (DZ), and 2.9% (±0.6) for their nontwin siblings were found. MZ twin concordance was in excess of DZ twin concordance. The excess concordance in MZ was derived primarily from like-sexed female pairs with a probandwise concordance rate of 34 of 100 (34 ± 5.7%) compared with 3 of 79 (3.8 ± 2.8%) for female DZ pairs. We did not demonstrate an MZ/DZ difference in males, although the sample size was small. We observed a 2-fold increase in risk to DZ twins over nontwin siblings of twins, but the difference was not significant.
DNA-mediated charge transport for DNA repair
Authors: Boon Elizabeth M. , Livingston Alison L. , Chmiel Nikolas H. , David Sheila S. , Barton Jacqueline K.
Published: October 2003

MutY, like many DNA base excision repair enzymes, contains a [4Fe4S]2+cluster of undetermined function. Electrochemical studies of MutY bound to a DNA-modified gold electrode demonstrate that the [4Fe4S] cluster of MutY can be accessed in a DNA-mediated redox reaction. Although not detectable without DNA, the redox potential of DNA-bound MutY is ≈275 mV versus NHE, which is characteristic of HiPiP iron proteins. Binding to DNA is thus associated with a change in [4Fe4S]3+/2+potential, activating the cluster toward oxidation. Given that DNA charge transport chemistry is exquisitely sensitive to perturbations in base pair structure, such as mismatches, we propose that this redox process of MutY bound to DNA exploits DNA charge transport and provides a DNA signaling mechanism to scan for mismatches and lesionsin vivo.
Mixotrophs combine resource use to outcompete specialists: Implications for aquatic food webs
Authors: Tittel Jörg , Bissinger Vera , Zippel Barbara , Gaedke Ursula , Bell Elanor , Lorke Andreas , Kamjunke Norbert
Published: October 2003

The majority of organisms can be grouped into those relying solely on photosynthesis (phototrophy) or those relying solely on the assimilation of organic substances (heterotrophy) to meet their requirements for energy and carbon. However, a special life history trait exists in which organisms combine both phototrophy and heterotrophy. Such “mixotrophy” is a widespread phenomenon in aquatic habitats and is observed in many protozoan and metazoan organisms. The strategy requires investment in both photosynthetic and heterotrophic cellular apparatus, and the benefits must outweigh these costs. In accordance with mechanistic resource competition theory, laboratory experiments revealed that pigmented mixotrophs combined light, mineral nutrients, and prey as substitutable resources. Thereby, they reduced prey abundance below the critical food concentration of competing specialist grazers [Rothhaupt, K. O. (1996)
Ecology
77, 716–724]. Here, we demonstrate the important consequences of this strategy for an aquatic community. In the illuminated surface strata of a lake, mixotrophs reduced prey abundance steeply. The data suggest that, as a consequence, grazers from higher trophic levels, consuming both the mixotrophs and their prey, could not persist. Thus, the mixotrophs escaped from competition with and losses to higher grazers. Furthermore, the mixotrophs structured prey abundance along the vertical light gradient, creating low densities near the surface and a pronounced maximum of their algal prey at depth. Such deep algal accumulations are typical features of nutrient-poor aquatic habitats, previously explained by resource availability. We hypothesize instead that the mixotrophic grazing strategy is responsible for deep algal accumulations in many aquatic environments.
Combinatorial discovery of two-photon photoremovable protecting groups
Authors: Pirrung Michael C. , Pieper Wolfgang H. , Kaliappan Krishna P. , Dhananjeyan Mugunthu R.
Published: October 2003

A design principle for a two-photon photochemically removable protecting group based on sequential one-photon processes has been established. The expected performance of such groups in spatially directed photoactivation/photodeprotection has been shown by a kinetic analysis. One particular molecular class fitting into this design, the nitrobenzyl ethers of
o
-hydroxycinnamates, has been presented. An initial demonstration of two-photon deprotection of one such group prompted further optimization with respect to photochemical deprotection rate. This was accomplished by the preparation and screening of a 135-member indexed combinatorial library. Optimum performance for λ >350 nm deprotection in organic solvent was found with 4,5-dialkoxy and α-cyano substitution in the nitrobenzyl group and 4-methoxy substitution in the cinnamate.
Predicting protein functions from redundancies in large-scale protein interaction networks
Authors: Samanta Manoj Pratim , Liang Shoudan
Published: October 2003

Interpreting data from large-scale protein interaction experiments has been a challenging task because of the widespread presence of random false positives. Here, we present a network-based statistical algorithm that overcomes this difficulty and allows us to derive functions of unannotated proteins from large-scale interaction data. Our algorithm uses the insight that if two proteins share significantly larger number of common interaction partners than random, they have close functional associations. Analysis of publicly available data from
Saccharomyces cerevisiae
reveals >2,800 reliable functional associations, 29% of which involve at least one unannotated protein. By further analyzing these associations, we derive tentative functions for 81 unannotated proteins with high certainty. Our method is not overly sensitive to the false positives present in the data. Even after adding 50% randomly generated interactions to the measured data set, we are able to recover almost all (≈89%) of the original associations.
Worker policing without genetic conflicts in a clonal ant
Authors: Hartmann A. , Wantia J. , Torres J. A. , Heinze J.
Published: October 2003

In group-living animals, mutual policing to suppress reproduction is an important mechanism in the resolution of conflict between selfish group members and the group as a whole. In societies of bees, ants, and wasps, policing against the production of males by other workers is expected when egg laying by workers decreases the average inclusive fitness of individual group members. This may result (i) from the relatedness of workers being lower to workerthan to queen-derived males or (ii) from a lowered overall colony efficiency. Whereas good evidence exists for policing behavior caused by genetic conflicts, policing caused by efficiency factors has not been demonstrated. We investigated the regulation of reproduction in the antPlatythyrea punctata, a species in which colonies are clones because workers are capable of producing female offspring by thelytokous parthenogenesis. Reproductive conflicts resulting from differences in genetic relatedness are therefore not expected, but uncontrolled reproduction by all workers could lead to the destruction of sociality. Here we show that worker policing by aggressive attacks against additionally reproducing workers keeps the number of reproducing workers low. Furthermore, through experimental manipulation of the number of brood items per colony, we show that worker policing can enhance group efficiency.
Eradication of pathogenic β-catenin by Skp1/Cullin/F box ubiquitination machinery
Authors: Su Yunyun , Ishikawa Shinji , Kojima Masayuki , Liu Bo
Published: October 2003

The use of Skp1/Cull 1/F box (SCF) ubiquitin-conjugation machinery as a potential knockout tool offers a means of eradicating disease-causing proteins. Here a chimeric F box protein (CFP) was engineered to achieve selective eradication of pathogenic β-catenin in colorectal cancer. We show that CFP specifically searches for and subsequently links the abnormal β-catenin to the cellular SCF ubiquitination complex. Introduction of the CFP to colorectal cancer cells induced targeted ubiquitination and proteolytic degradation of nuclear and cytoplasmic free β-catenin while preserving its normal cellular adhesion counterpart. Elimination of pathogenic β-catenin suppressed constitutive Wingless/Wnt signaling and inhibited
in vitro
and
in vivo
tumor cell growth. This study demonstrates a practical utility of a SCF-based knockout system as a tool in targeting an abnormal protein that affects growth and transformation.
Energetics of hydrogen bonds in peptides
Authors: Sheu Sheh-Yi , Yang Dah-Yen , Selzle H. L. , Schlag E. W.
Published: October 2003

Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from ≈5–6 kcal/mol for the isolated bond to ≈0.5–1.5 kcal/mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a β-sheet under isolated conditions is 4.76 kcal/mol, and the activation energy is 1.58 kcal/mol for the same β-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.
Proteorhodopsin genes are distributed among divergent marine bacterial taxa
Authors: de la Torre José R. , Christianson Lynne M. , Béjà Oded , Suzuki Marcelino T. , Karl David M. , Heidelberg John , DeLong Edward F.
Published: October 2003

Proteorhodopsin (PR) is a retinal-binding bacterial integral membrane protein that functions as a light-driven proton pump. The gene encoding this photoprotein was originally discovered on a large genome fragment derived from an uncultured marine γ-proteobacterium of the SAR86 group. Subsequently, many variants of the PR gene have been detected in marine plankton, via PCR-based gene surveys. It has not been clear, however, whether these different PR genes are widely distributed among different bacterial groups, or whether they have a restricted taxonomic distribution. We report here comparative analyses of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula. Sequence analysis of an Antarctic genome fragment harboring PR (ANT32C12) revealed moderate conservation in gene order and identity, compared with a previously reported PR-containing genome fragment from a Monterey Bay γ-proteobacterium (EBAC31A08). Outside the limited region of synteny shared between these clones, however, no significant DNA or protein identity was evident. Analysis of a third PR-containing genome fragment (HOT2C01) from the North Pacific subtropical gyre showed even more divergence from the γ-proteobacterial PR-flanking region. Subsequent phylogenetic and comparative genomic analyses revealed that the Central North Pacific PR-containing genome fragment (HOT2C01) originated from a planktonic α-proteobacterium. These data indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both α- and γ-proteobacteria. Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes.
The small RING finger protein Z drives arenavirus budding: Implications for antiviral strategies
Authors: Perez Mar , Craven Rebecca C. , de la Torre Juan C.
Published: October 2003

By using a reverse genetics system that is based on the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV), we have identified the arenavirus small RING finger Z protein as the main driving force of virus budding. Both LCMV and Lassa fever virus (LFV) Z proteins exhibited self-budding activity, and both substituted efficiently for the late domain that is present in the Gag protein of Rous sarcoma virus. LCMV and LFV Z proteins contain proline-rich motifs that are characteristic of late domains. Mutations in the PPPY motif of LCMV Z severely impaired the formation of virus-like particles. LFV Z contains two different proline-rich motifs, PPPY and PTAP, which are separated by eight amino acids. Mutational analysis revealed that both motifs are required for efficient LFV Z-mediated budding. Both LCMV and LFV Z proteins recruited to the plasma membrane Tsg101, which is a component of the class E vacuolar protein sorting machinery that has been implicated in budding of HIV and Ebola virus. Targeting of Tsg101 by RNA interference caused a strong reduction in Z-mediated budding. These results indicate that Z is the arenavirus functional counterpart of the matrix proteins found in other negative strand enveloped RNA viruses. Moreover, members of the vacuolar protein sorting pathway appear to play an important role in arena-virus budding. These findings open possibilities for antiviral strategies to combat LFV and other hemorrhagic fever arenaviruses.
Positional cloning of the major quantitative trait locus underlying lung tumor susceptibility in mice
Authors: Zhang Zhongqiu , Futamura Manabu , Vikis Haris G. , Wang Min , Li Jie , Wang Yian , Guan Kun-Liang , You Ming
Published: October 2003

Pulmonary adenoma susceptibility 1 (Pas1), located on chromosome 6, is the major locus affecting inherited predisposition to lung tumor development in mice. We have fine mapped thePas1locus to a region of ≈0.5 megabases by using congenic strains of mice, constructed by placing thePas1region of chromosome 6 from A/J mice onto the genetic background of C57BL/6J mice. Systematic characterization ofPas1candidates establishes theLas1(lung adenoma susceptibility 1) andKras2(Kirsten rat sarcoma oncogene 2) genes as primary candidates for thePas1locus. Clearly,Kras2affects lung tumor progression only, andLas1is likely to affect lung tumor multiplicity.
Revealing the hidden atom in graphite by low-temperature atomic force microscopy
Authors: Hembacher Stefan , Giessibl Franz J. , Mannhart Jochen , Quate Calvin F.
Published: October 2003

Carbon, the backbone material of life on Earth, comes in three modifications: diamond, graphite, and fullerenes. Diamond develops tetrahedral sp3bonds, forming a cubic crystal structure, whereas graphite and fullerenes are characterized by planar sp2bonds. Polycrystalline graphite is the basis for many products of everyday life: pencils, lubricants, batteries, arc lamps, and brushes for electric motors. In crystalline form, highly oriented pyrolytic graphite is used as a diffracting element in monochromators for x-ray and neutron scattering and as a calibration standard for scanning tunneling microscopy (STM). The graphite surface is easily prepared as a clean atomically flat surface by cleavage. This feature is attractive and is used in many laboratories as the surface of choice for “seeing atoms.” Despite the proverbial ease of imaging graphite by STM with atomic resolution, every second atom in the hexagonal surface unit cell remains hidden, and STM images show only a single atom in the unit cell. Here we present measurements with a low-temperature atomic force microscope with pico-Newton force sensitivity that reveal the hidden surface atom.
AIPL1, a protein implicated in Leber's congenital amaurosis, interacts with and aids in processing of farnesylated proteins
Authors: Ramamurthy Visvanathan , Roberts Melanie , van den Akker Focco , Niemi Gregory , Reh T. A. , Hurley James B.
Published: October 2003

The most common form of blindness at birth, Leber's congenital amaurosis (LCA), is inherited in an autosomal recessive fashion. Mutations in six different retina-specific genes, including a recently discovered gene,
AIPL1
, have been linked to LCA in humans. To understand the molecular basis of LCA caused by aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) mutations, and to elucidate the normal function of AIPL1, we performed a yeast two-hybrid screen using AIPL1 as bait. The screen demonstrated that AIPL1 interacts specifically with farnesylated proteins. Mutations in AIPL1 linked to LCA compromise this activity. These findings suggest that the essential function of AIPL1 within photoreceptors requires interactions with farnesylated proteins. Analysis of isoprenylation in cultured human cells shows that AIPL1 enhances the processing of farnesylated proteins. Based on these findings, we propose that AIPL1 interacts with farnesylated proteins and plays an essential role in processing of farnesylated proteins in retina.
An endogenous retroviral long terminal repeat is the dominant promoter for human β1,3-galactosyltransferase 5 in the colon
Authors: Dunn Catherine A. , Medstrand Patrik , Mager Dixie L.
Published: October 2003

LTRs of endogenous retroviruses are known to affect expression of several human genes, typically as a relatively minor alternative promoter. Here, we report that an endogenous retrovirus LTR acts as one of at least two alternative promoters for the human β1,3-galactosyltransferase 5 gene, involved in type 1 Lewis antigen synthesis, and show that the LTR promoter is most active in the gastrointestinal tract and mammary gland. Indeed, the LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression. Using colorectal cancer cell lines and electrophoretic mobility-shift assays, we found that hepatocyte nuclear factor 1 (HNF-1) binds a site within the retroviral promoter and that expression of HNF-1 and interaction with its binding site correlated with promoter activation. We conclude that HNF-1 is at least partially responsible for the tissue-specific activation of the LTR promoter of human β1,3-galactosyltransferase 5. We demonstrate that this tissue-specific transcription factor is implicated in the activation of an LTR gene promoter.
Active sites of thioredoxin reductases: Why selenoproteins?
Authors: Gromer Stephan , Johansson Linda , Bauer Holger , Arscott L. David , Rauch Susanne , Ballou David P. , Williams Charles H. , Schirmer R. Heiner , Arnér Elias S. J.
Published: October 2003

Selenium, an essential trace element for mammals, is incorporated into a selected class of selenoproteins as selenocysteine. All known isoenzymes of mammalian thioredoxin (Trx) reductases (TrxRs) employ selenium in the C-terminal redox center -Gly-Cys-Sec-Gly-COOH for reduction of Trx and other substrates, whereas the corresponding sequence in
Drosophila melanogaster
TrxR is -Ser-Cys-Cys-Ser-COOH. Surprisingly, the catalytic competence of these orthologous enzymes is similar, whereas direct Sec-to-Cys substitution of mammalian TrxR, or other selenoenzymes, yields almost inactive enzyme. TrxRs are therefore ideal for studying the biology of selenocysteine by comparative enzymology. Here we show that the serine residues flanking the C-terminal Cys residues of
Drosophila
TrxRs are responsible for activating the cysteines to match the catalytic efficiency of a selenocysteine-cysteine pair as in mammalian TrxR, obviating the need for selenium. This finding suggests that the occurrence of selenoenzymes, which implies that the organism is selenium-dependent, is not necessarily associated with improved enzyme efficiency. Our data suggest that the selective advantage of selenoenzymes is a broader range of substrates and a broader range of microenvironmental conditions in which enzyme activity is possible.
Cardiomyocyte-restricted knockout of STAT3 results in higher sensitivity to inflammation, cardiac fibrosis, and heart failure with advanced age
Authors: Jacoby Jörg J. , Kalinowski April , Liu Mu-Gen , Zhang Samuel S.-M. , Gao Qian , Chai Gui-Xuan , Ji Lan , Iwamoto Yoshiki , Li En , Schneider Michael , Russell Kerry S. , Fu Xin-Yuan
Published: October 2003

Cytokines and inflammation have been implicated in the pathogenesis of heart failure. For example, IL-6 family cytokines and the gp130 receptor play important roles in cardiac myocyte survival and hypertrophy. Signal transducer and activator of transcription 3 (STAT3) is a major signaling protein that is activated through gp130. We have created mice with a cardiomyocyte-restricted deletion of STAT3. As measured by serial echocardiograms, mice with cardiac specific deletion of STAT3 are significantly more susceptible to cardiac injury after doxorubicin treatment than age-matched controls. Intriguingly, STAT3 appears to have a critical role in protection of inflammation-induced heart damage. STAT3-deficient mice treated with lipopolysaccharide demonstrated significantly more apoptosis than their WT counterparts. At the cellular level, cardiomyocytes with STAT3 deleted secrete significantly more tumor necrosis factor α in response to lipopolysaccharide than those with WT STAT3. Furthermore, histologic examination of the cardiomyocyte-restricted STAT3-deficient mice reveals a dramatic increase in cardiac fibrosis in aged mice. Although no overt signs of heart failure are present in young STAT3-deficient mice, they spontaneously develop heart dysfunction with advancing age. These results indicate the crucial functions of STAT3 in cardiomyocyte resistance to inflammation and other acute injury and in pathogenesis of age-related heart failure.
Fitness consequences of a regulatory polymorphism in a seasonal environment
Authors: Suiter Amy M. , Bänziger Otmar , Dean Antony M.
Published: October 2003

Gene regulation is commonly assumed to have evolved in response to environmental variability. Although tightly regulated in
Escherichia coli
strain K12, transcriptional control of arginine biosynthesis is deregulated in strain B. Caused by a single amino acid replacement in the arginine repressor, these contrasting regulatory strategies result in a fitness tradeoff. The K12 repressor is selectively favored in the presence of arginine and disfavored in its absence. In environments that cycle between high and low arginine, short seasons favor the K12 allele, whereas long seasons favor the B allele. Unexpectedly then, deregulated expression is adaptive in some seasonal habitats.
Hepatocyte growth factor/scatter factor mediates angiogenesis through positive VEGF and negative thrombospondin 1 regulation
Authors: Zhang Yu-Wen , Su Yanli , Volpert Olga V. , Woude George F. Vande
Published: October 2003

Hepatocyte growth factor/scatter factor (HGF/SF), acting through the Met receptor, plays an important role in most human solid tumors, and inappropriate expression of this ligand–receptor pair is often associated with poor prognosis. The molecular basis for the malignant potential of the HGF/SF–Met signal in cancer cells has mostly been attributed to its mitogenic and invasive properties. However, HGF/SF also induces angiogenesis, but the signaling mechanism has not been fully explained, nor has this activity been directly associated with HGF/SF–Met-mediated tumorigenesis. It is known that HGF/SF induces
in vitro
expression of vascular endothelial growth factor (VEGF), a key agonist of tumor angiogenesis; by contrast, thrombospondin 1 (TSP-1) is a negative regulator of angiogenesis. Here, we show that, in the very same tumor cells, in addition to inducing VEGF expression, HGF/SF dramatically down-regulates TSP-1 expression. We show that TSP-1 shut-off plays an important, extrinsic role in HGF/SF-mediated tumor development, because ectopic expression of TSP-1 markedly inhibits tumor formation through the suppression of angiogenesis. Interestingly, although VEGF-induced expression is sensitive to inhibitors of several pathways, including mitogen-activated protein kinase, phosphoinositide 3-kinase, and signal transducer and activator of transcription 3, TSP-1 shut-off by HGF/SF is prevented solely by inhibiting mitogen-activated protein kinase activation. These studies identify HGF/SF as a key switch for turning on angiogenesis. They suggest that TSP-1 is a useful antagonist to tumor angiogenesis and that it may have therapeutic value when used in conjunction with inhibitors of VEGF.
Treatment ofHelicobactergastritis with IL-4 requires somatostatin
Authors: Zavros Yana , Rathinavelu Sivaprakash , Kao John Y. , Todisco Andrea , Del Valle John , Weinstock Joel V. , Low Malcolm J. , Merchant Juanita L.
Published: October 2003

Fifty percent of the world's population is infected withHelicobacter pylori; however, treatment has been insufficient to eradicate the organisms due to rising antibiotic resistance.Helicobacterinfection is characterized by induction of a T helper 1 lymphocyte (Th1) immune response, hypergastrinemia, and suppressed tissue somatostatin (SOM) levels. However, the mechanism by which the immune response regulates acid secretion is not known. We show here that treatment with IFN-γ, a Th1 cytokine, was sufficient to induce gastritis, increase gastrin, and decrease SOM levels within 7 days. In contrast, the T helper 2 lymphocyte cytokine IL-4 increased SOM levels and effectively suppressed gastrin expression and secretion. This result demonstrated reciprocal regulation of acid regulatory peptides by immune modulators. IL-4 pretreatment prevented gastritis in infected wild-type but not in SOM null mice. Thus, the ability of IL-4 to oppose a Th1-mediated infection required SOM. Immunofluorescence was used to document the presence of IL-4 receptors on the gastric SOM-secreting cell (D cell). Moreover, IL-4 stimulated SOM release from primary D cell cultures. Treatment of mice chronically infected withHelicobacter felisfor 2 mo with the SOM analogue octreotide resolved the inflammation. Thus, a mechanism by which IL-4 resolves inflammation in the stomach is by stimulating the release of SOM from gastric D cells.
Thrombospondin 1, a mediator of the antiangiogenic effects of low-dose metronomic chemotherapy
Authors: Bocci Guido , Francia Giulio , Man Shan , Lawler Jack , Kerbel Robert S.
Published: October 2003

Chemotherapeutic drugs chronically administered to tumor-bearing mice, using a frequent schedule at doses substantially lower than the maximum tolerated dose (MTD) (i.e., metronomic dosing), can cause sustained and potent antiangiogenic effects by targeting the endothelial cells of newly growing tumor blood vessels. These effects appear to occur in the absence of an increase in the severity of side effects caused by destruction of other cell types normally sensitive to MTD chemotherapy, suggesting a marked and selective sensitivity of activated endothelial cells, the basis of which is unknown. Here we report that protracted exposure of endothelial cellsin vitroto low concentrations of several different anticancer agents, including microtubule inhibitors and an alkylating agent, caused marked induction of gene and protein expression of TSP-1, a potent and endothelial-specific inhibitor of angiogenesis. Increases in circulating TSP-1 were also detected in the plasma of human tumor-bearing severe combined immunodeficient mice treated with metronomic low-dose cyclophosphamide. Most importantly, the antiangiogenic and antitumor effects of low-dose continuous cyclophosphamide were lost in TSP-1-null C57BL/6 mice, whereas, in contrast, these effects were retained by using a MTD schedule of the same drug. Taken together, the results implicate TSP-1 as a secondary mediator of the antiangiogenic effects of at least some low-dose metronomic chemotherapy regimens.
Endogenous DNA double-strand breaks: Production, fidelity of repair, and induction of cancer
Authors: Vilenchik Michael M. , Knudson Alfred G.
Published: October 2003

This article extends our previous quantitative analysis of the relationship between the dynamics of the primary structure of DNA and mutagenesis associated with single-strand lesions to an analysis of the production and processing of endogenous double-strand breaks (EDSBs) and to their implications for oncogenesis. We estimate that in normal human cells ≈1% of single-strand lesions are converted to ≈50 EDSBs per cell per cell cycle. This number is similar to that for EDSBs produced by 1.5–2.0 Gy of sparsely ionizing radiation. Although EDSBs are usually repaired with high fidelity, errors in their repair contribute significantly to the rate of cancer in humans. The doubling dose for induced DSBs is similar to doubling doses for mutation and for the induction of carcinomas by ionizing radiation. We conclude that rates of production of EDSBs and of ensuing spontaneous mitotic recombination events can account for a substantial fraction of the earliest oncogenic events in human carcinomas.
Antiviral immune responses in gene-targeted mice expressing the immunoglobulin heavy chain of virus-neutralizing antibodies
Authors: Hangartner Lars , Senn Beatrice M. , Ledermann Birgit , Kalinke Ulrich , Seiler Peter , Bucher Etienne , Zellweger Raphaël M. , Fink Katja , Odermatt Bernhard , Bürki Kurt , Zinkernagel Rolf M. , Hengartner Hans
Published: October 2003

Two gene-targeted immunoglobulin heavy chain transgenic mouse strains, TgH(KL25) and TgH(VI10), expressing neutralizing specificities for lymphocytic choriomeningitis virus and vesicular stomatitis virus, respectively, have been generated. Three days after lymphocytic choriomeningitis virus infection, TgH(KL25) mice showed a thymus-independent neutralizing IgM response followed by thymus-dependent (TD) IgG. In contrast, WT mice mounted only a TD IgG response around day 80. These observations indicated that not only structural properties of the virus but also immunological parameters such as the frequency of B cells were indicative for the induction of thymus-independent versus TD Ig responses. Naïve vesicular stomatitis virusspecific Ig heavy chain transgenic mice displayed greatly elevated natural antibody titers. However, despite these high naïve titers,de novoactivation of naïve CD4+T and B cells was not blocked. Therefore, B cells giving rise to natural antibodies do not participate in virus-induced antibody responses.
Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system
Authors: Stanley Sarah A. , Raghavan Sridharan , Hwang William W. , Cox Jeffery S.
Published: October 2003

Although many bacterial pathogens use specialized secretion systems for virulence, no such systems have been described for
Mycobacterium tuberculosis
, a major pathogen of humans that proliferates in host macrophages. In a screen to identify genes required for virulence of
M. tuberculosis
, we have discovered three components and two substrates of the first Sec-independent secretion pathway described in
M. tuberculosis
, which we designate the Snm pathway. Here we demonstrate that the proteins Snm1, -2, and -4 are required for the secretion of ESAT-6 and CFP-10, small proteins previously identified as major T cell antigens. Snm2, a member of the AAA ATPase family, interacts with substrates and with Snm1, another AAA ATPase. We show that
M. tuberculosis
mutants lacking either the Snm system or these substrates exhibit defects in bacterial growth during the acute phase of a mouse infection and are attenuated for virulence. Strikingly,
snm
mutants fail to replicate in cultured macrophages and to inhibit macrophage inflammatory responses, two well established activities of wild-type
M. tuberculosis
bacilli. Thus, the Snm secretion pathway works to subvert normal macrophage responses and is a major determinant of
M. tuberculosis
virulence.