bluuebunny/crossref_metadata_2025 huggingface dataset:
Electronic Spectra of Carbonyl Sulfide Sulfur Isotopologues
Authors: Colussi Agustín J. , Leung Fok-Yan , Hoffmann Michael R.
Published: July 2004

Environmental Context.Sulfate aerosols have been linked with ozone-depleting reactions, and their influence on cirrus cloud formation may affect climate. One source of sulfate aerosols is sulfur-containing gases such as carbonyl sulfide, which can rise up to the statosphere and become transformed into sulfate under the prevailing sunlight, but the importance and details of the phenomena involved are poorly understood. With a view to providing the fundamental information required to analyze the atmospheric processing of carbonyl sulfide, this paper reports the sulfur isotope effects on its ultraviolet absorption spectrum.

Abstract.Carbonyl sulfide (OCS), a relatively inert tropospheric species that photolyzes into CO + S upon reaching the stratosphere, is deemed a significant contributor to background sulfate aerosol. A recent analysis of atmospheric infrared transmittance data has revealed that OC34S is preferentially depleted above ~10 km. We now report that the OC34S absorption band between 200 ≤ λ [nm] ≤ 260 at 298 K is broader and more intense than its OC32S counterpart. This finding is consistent with the faster photolysis of OC34S, and with a time-dependent formulation of electronic spectra. Since OCS photolysis in the lower stratosphere occurs in a spectral range in which its absorption cross-section is unaffected by temperature, we are able to estimate a 34S-enrichment factor <34ϵ> ~ (67 ± 7)‰ for this process that is commensurate with the value previously inferred from OC34S/OC32S ratio versus altitude profiles.
Sustainability and Environmental Impact of Renewable Energy Resources (Eds R. E. Hester and R. M. Harrison)
Authors: Manwell James
Published: July 2004

Edited by R. E. Hester and R. M. HarrisonRoyal Society of Chemistry,Cambridge 2003, 140 pp.ISBN 0-85404-290-3Softcover, £45
Target of rapamycin-mediated amino acid signaling in mosquito anautogeny
Authors: Hansen Immo A. , Attardo Geoffrey M. , Park Jong-Hwa , Peng Quan , Raikhel Alexander S.
Published: July 2004

Mosquitoes generate an enormous burden on human health worldwide. Disease-transmitting species use a reproductive strategy, termed anautogeny, that requires a blood meal to initiate egg maturation. Whereas this strategy is important for driving disease transmission, the molecular mechanisms underlying this phenomenon are still poorly understood. The production of yolk protein precursors (YPPs), a central event in egg maturation, is called vitellogenesis. YPPs are synthesized in the fat body, the insect analogue of the vertebrate liver. Mosquito vitellogenesis is regulated by the steroid hormone 20 hydroxyecdysone (20E). However, 20E alone is not capable of activating vitellogenesisin vivo. Here, we report that amino acid signaling through the nutrient-sensitive target of rapamycin (TOR) pathway is essential for the activation of YPP gene expression. An increase in extracellular amino acid levels, similar to the increase observed after a blood meal, is critical for 20E stimulation of YPP gene expression. Treatment with the TOR kinase inhibitor rapamycin significantly inhibits YPP expression. We used RNA interference to knockdown the expression of two key proteins of the TOR signaling pathway, TOR, and tuberous sclerosis complex 2. Knockdown of TOR inhibited amino acid stimulation while knockdown of tuberous sclerosis complex 2, a negative regulator of TOR signaling, resulted in enhanced YPP expression. Thus, amino acid-based TOR signaling regulates the activation of egg development after a blood meal, an adaptation to the unique life style of mosquitoes.
Induction of phase 2 genes by sulforaphane protects retinal pigment epithelial cells against photooxidative damage
Authors: Gao Xiangqun , Talalay Paul
Published: July 2004

The retinal pigment epithelial cell (RPE cell) layer protects the photoreceptors of the retina against oxidative stress. The decline of this capacity is believed to be a major factor in the impairment of vision in age-related macular degeneration. Exposure of human adult RPE cells to UV light at predominantly 320–400 nm (UVA light) in the presence of
all
-
trans
-retinaldehyde results in photooxidative cytotoxicity. Significant protection of RPE cells was obtained by prior treatment with phase 2 gene inducers, such as the isothiocyanate sulforaphane or a bis-2-hydroxybenzylideneacetone Michael reaction acceptor. The degree of protection was correlated with the potencies of these inducers in elevating cytoprotective glutathione levels and activities of NAD(P)H:quinone oxidoreductase. In embryonic fibroblasts derived from mice in which the genes for the transcription factor Nrf2, the repressor Keap1, or both Nrf2 and Keap1 were disrupted, the magnitude of resistance to photooxidative damage paralleled the basal levels of glutathione and NAD(P)H:quinone oxidoreductase in each cell type. Demonstration of protection of RPE cells against photooxidative damage by induction of phase 2 proteins may shed light on the role of oxidative injury in ocular disease. Moreover, the finding that dietary inducers provide indirect antioxidant protection suggests novel strategies for preventing chronic degenerative diseases, such as age-related macular degeneration.
PrPCAssociation with Lipid Rafts in the Early Secretory Pathway Stabilizes Its Cellular Conformation
Authors: Sarnataro Daniela , Campana Vincenza , Paladino Simona , Stornaiuolo Mariano , Nitsch Lucio , Zurzolo Chiara
Published: July 2004

The pathological conversion of cellular prion protein (PrPC) into the scrapie prion protein (PrPSc) isoform appears to have a central role in the pathogenesis of transmissible spongiform encephalopathies. However, the identity of the intracellular compartment where this conversion occurs is unknown. Several lines of evidence indicate that detergent-resistant membrane domains (DRMs or rafts) could be involved in this process. We have characterized the association of PrPCto rafts during its biosynthesis. We found that PrPCassociates with rafts already as an immature precursor in the endoplasmic reticulum. Interestingly, compared with the mature protein, the immature diglycosylated form has a different susceptibility to cholesterol depletion vs. sphingolipid depletion, suggesting that the two forms associate with different lipid domains. We also found that cholesterol depletion, which affects raft-association of the immature protein, slows down protein maturation and leads to protein misfolding. On the contrary, sphingolipid depletion does not have any effect on the kinetics of protein maturation or on the conformation of the protein. These data indicate that the early association of PrPCwith cholesterol-enriched rafts facilitates its correct folding and reinforce the hypothesis that cholesterol and sphingolipids have different roles in PrP metabolism.
A Conserved Stress-activated Protein Kinase Regulates a Core Stress Response in the Human PathogenCandida albicans
Authors: Smith Deborah A. , Nicholls Susan , Morgan Brian A. , Brown Alistair J.P. , Quinn Janet
Published: July 2004

Previous work has implicated the Hog1 stress-activated protein kinase (SAPK) in osmotic and oxidative stress responses in the human pathogen Candida albicans. In this study, we have characterized the role of Hog1 in mediating these and other stress responses in C. albicans. We provide evidence that a SAPK-dependent core stress response exists in this pathogen. The Hog1 SAPK is phosphorylated and it accumulates in the nucleus in response to diverse stress conditions. In addition, we have identified Hog1-regulated genes that are induced in response to stress conditions that activate Hog1. These analyses reveal both activator and repressor functions for the Hog1 SAPK. Our results also demonstrate that stress cross-protection, a classical hallmark of the core stress response, occurs in C. albicans between stresses that activate the Hog1 SAPK. Importantly, we find that the core stress response in C. albicans has adapted to the environmental niche of this human pathogen. This niche specificity is reflected by the specific environmental conditions that drive the Hog1-regulated core stress response in C. albicans and by differences in the molecular circuitry that control this response.
Bmx Tyrosine Kinase Transgene Induces Skin Hyperplasia, Inflammatory Angiogenesis, and Accelerated Wound Healing
Authors: Paavonen Karri , Ekman Niklas , Wirzenius Maria , Rajantie Iiro , Poutanen Matti , Alitalo Kari
Published: July 2004

The Bmx gene, a member of the Tec family of nonreceptor protein tyrosine kinases, is expressed in arterial endothelium and in certain hematopoietic and epithelial cells. Previous in vitro studies have implicated Bmx signaling in cell migration and survival and suggested that it contributes to the progression of prostate carcinomas. However, the function of Bmx in normal tissues in vivo is unknown. We show here that Bmx expression is induced in skin keratinocytes during wound healing. To analyze the role of Bmx in epidermal keratinocytes in vivo, we generated transgenic mice overexpressing Bmx in the skin. We show that Bmx overexpression accelerates keratinocyte proliferation and wound reepithelialization. Bmx expression also induces chronic inflammation and angiogenesis in the skin, and gene expression profiling suggests that this occurs via cytokine-mediated recruitment of inflammatory cells. Our studies provide the first data on Bmx function in vivo and form the basis of evaluation of its role in epithelial neoplasia.
Ligand-dependent and -independent Transforming Growth Factor-β Receptor Recycling Regulated by Clathrin-mediated Endocytosis and Rab11
Authors: Mitchell Hugh , Choudhury Amit , Pagano Richard E. , Leof Edward B.
Published: July 2004

Proteins in the transforming growth factor-β (TGF-β) family recognize transmembrane serine/threonine kinases known as type I and type II receptors. Binding of TGF-β to receptors results in receptor down-regulation and signaling. Whereas previous work has focused on activities controlling TGF-β signaling, more recent studies have begun to address the trafficking properties of TGF-β receptors. In this report, it is shown that receptors undergo recycling both in the presence and absence of ligand activation, with the rates of internalization and recycling being unaffected by ligand binding. Recycling occurs as receptors are most likely internalized through clathrin-coated pits, and then returned to the plasma membrane via a rab11-dependent, rab4-independent mechanism. Together, the results suggest a mechanism wherein activated TGF-β receptors are directed to a distinct endocytic pathway for down-regulation and clathrin-dependent degradation after one or more rounds of recycling.
The Phosphorylation of Vinculin on Tyrosine Residues 100 and 1065, Mediated by Src Kinases, Affects Cell Spreading
Authors: Zhang Zhiyong , Izaguirre Gonzalo , Lin Siang-Yo , Lee Hwa Young , Schaefer Erik , Haimovich Beatrice
Published: July 2004

Vinculin is a conserved actin binding protein localized in focal adhesions and cell-cell junctions. Here, we report that vinculin is tyrosine phosphorylated in platelets spread on fibrinogen and that the phosphorylation is Src kinases dependent. The phosphorylation of vinculin on tyrosine was reconstituted in vanadate treated COS-7 cells coexpressing c-Src. The tyrosine phosphorylation sites in vinculin were mapped to residues 100 and 1065. A phosphorylation-specific antibody directed against tyrosine residue 1065 reacted with phosphorylated platelet vinculin but failed to react with vinculin from unstimulated platelet lysates. Tyrosine residue 1065 located in the vinculin tail domain was phosphorylated by c-Src in vitro. When phosphorylated, the vinculin tail exhibited significantly less binding to the vinculin head domain than the unphosphorylated tail. In contrast, the phosphorylation did not affect the binding of vinculin to actin in vitro. A double vinculin mutant protein Y100F/Y1065F localized to focal adhesion plaques. Wild-type vinculin and single tyrosine phosphorylation mutant proteins Y100F and Y1065F were significantly more effective at rescuing the spreading defect of vinculin null cells than the double mutant Y100F/Y1065F. The phosphorylation of vinculin by Src kinases may be one mechanism by which these kinases regulate actin filament assembly and cell spreading.
Regional and time-resolved mutation patterns of the human genome
Authors: Arndt Peter F. , Hwa Terence
Published: July 2004

Motivation: Substantial regional variations of substitutional processes have recently been reported from human/mouse comparisons. However, several features including the C + G dependence and the CpG-based transition effect remain obscure.

Results: Utilizing the vast amount of transposable elements in the human genome, we performed detailed analysis of the substitutional and insertion/deletion patterns along the human lineage in a regional and time-resolved fashion. We observed a drastic increase in the CpG-based transition frequency at about the time of the mammalian radiation. We also observed clear regional biases of substitution patterns, most notably a bias to enrich the C+G content toward the telomeres.

Availability: The programs used are available upon request from the authors.
Using convex hulls to extract interaction interfaces from known structures
Authors: Dafas Panos , Bolser Dan , Gomoluch Jacek , Park Jong , Schroeder Michael
Published: July 2004

Motivation: Protein interactions provide an important context for the understanding of function. Experimental approaches have been complemented with computational ones, such as PSIMAP, which computes domain–domain interactions for all multi-domain and multi-chain proteins in the Protein Data Bank (PDB). PSIMAP has been used to determine that superfamilies occurring in many species have many interaction partners, to show examples of convergent evolution through shared interaction partners and to uncover complexes in the interaction map.

To determine an interaction, the original PSIMAP algorithm checks all residue pairs of any domain pair defined by classification systems such as SCOP. The computation takes several days for the PDB. The computation of PSIMAP has two shortcomings: first, the original PSIMAP algorithm considers only interactions of residue pairs rather than atom pairs losing information for detailed analysis of contact patterns. At the atomic level the original algorithm would take months. Second, with the superlinear growth of PDB, PSIMAP is not sustainable.

Results: We address these two shortcomings by developing a family of new algorithms for the computation of domain–domain interactions based on the idea of bounding shapes, which are used to prune the search space. The best of the algorithms improves on the old PSIMAP algorithm by a factor of 60 on the PDB. Additionally, the algorithms allow a distributed computation, which we carry out on a farm of 80 Linux PCs. Overall, the new algorithms reduce the computation at atomic level from months to 20 min. The combination of pruning and distribution makes the new algorithm scalable and sustainable even with the superlinear growth in PDB.
Threshold extraction in metabolite concentration data
Authors: Flöter A. , Nicolas J. , Schaub T. , Selbig J.
Published: July 2004

Motivation: Continued development of analytical techniques based on gas chromatography and mass spectrometry now facilitates the generation of larger sets of metabolite concentration data. An important step towards the understanding of metabolite dynamics is the recognition of stable states where metabolite concentrations exhibit a simple behaviour. Such states can be characterized through the identification of significant thresholds in the concentrations. But general techniques for finding discretization thresholds in continuous data prove to be practically insufficient for detecting states due to the weak conditional dependences in concentration data.

Results: We introduce a method of recognizing states in the framework of decision tree induction. It is based upon a global analysis of decision forests where stability and quality are evaluated. It leads to the detection of thresholds that are both comprehensible and robust. Applied to metabolite concentration data, this method has led to the discovery of hidden states in the corresponding variables. Some of these reflect known properties of the biological experiments, and others point to putative new states.

Availability: An implementation of this approach can be obtained from the authors upon request.
Conserved RNA secondary structures in viral genomes: a survey
Authors: Hofacker I.L. , Stadler P.F. , Stocsits R.R.
Published: July 2004

Summary: The genomes of RNA viruses often carry conserved RNA structures that perform vital functions during the life cycle of the virus. Such structures can be detected using a combination of structure prediction and co-variation analysis. Here we present results from pilot studies on a variety of viral families performed during bioinformatics computer lab courses in past years.
Gene expression analysis on biochemical networks using the Potts spin model
Authors: König Rainer , Eils Roland
Published: July 2004

Motivation: Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly complete image of the metabolic architecture. For less complex organisms, such as Escherichia coli, the biochemical network has been described in much detail. Here, we investigate the clustering of such networks by applying gene expression data that define edge lengths in the network.

Results: The Potts spin model is used as a nearest neighbour based clustering algorithm to discover fragmentation of the network in mutants or in biological samples when treated with drugs. As an example, we tested our method with gene expression data from E.coli treated with tryptophan excess, starvation and trpyptophan repressor mutants. We observed fragmentation of the tryptophan biosynthesis pathway, which corresponds well to the commonly known regulatory response of the cells.
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition
Authors: Swat Maciej , Kel Alexander , Herzel Hanspeter
Published: July 2004

Motivation: Mathematical models of the cell cycle can contribute to an understanding of its basic mechanisms. Modern simulation tools make the analysis of key components and their interactions very effective. This paper focuses on the role of small modules and feedbacks in the gene–protein network governing the G1/S transition in mammalian cells. Mutations in this network may lead to uncontrolled cell proliferation. Bifurcation analysis helps to identify the key components of this extremely complex interaction network.

Results: We identify various positive and negative feedback loops in the network controlling the G1/S transition. It is shown that the positive feedback regulation of E2F1 and a double activator–inhibitor module can lead to bistability. Extensions of the core module preserve the essential features such as bistability. The complete model exhibits a transcritical bifurcation in addition to bistability. We relate these bifurcations to the cell cycle checkpoint and the G1/S phase transition point. Thus, core modules can explain major features of the complex G1/S network and have a robust decision taking function.
Thermodynamic and structural characterization of 2′-nitrogen-modified RNA duplexes
Authors: Pham John W. , Radhakrishnan Ishwar , Sontheimer Erik J.
Published: July 2004

2′-aminonucleosides are commonly used as sites of post-synthetic chemical modification within nucleic acids. As part of a larger cross-linking strategy, we appended alkyl groups onto the N2′ position of 2′-amino-modified RNAs via 2′-ureido and 2′-amido linkages. We have characterized the thermodynamics of 2′-amino, 2′-alkylamido and 2′-alkylureido-modified RNA duplexes and show that 2′-ureido-modified RNAs are significantly more stable than analogous 2′-amido-modified RNAs. Using NMR spectroscopy and NMR-based molecular modeling of 2′-modified RNA duplexes, we examined the effects that 2′-nitrogen modifications have on RNA helices. Our data suggest that the 2′-ureido group forms a specific intra-nucleoside interaction that cannot occur within 2′-amido-modified helices. These results indicate that 2′-ureido modifications are superior to analogous 2′-amido ones for applications that require stable base pairing.
Causes and Treatment of Burns From Grease
Authors: Fiebiger Barbara , Whitmire Faye , Law Edward , Still Joseph M.
Published: July 2004

A large number of burns are sustained every year as the result of kitchen grease. A review of a 13-month period at the Joseph M. Still Burn Center in Augusta, Georgia, revealed 60 cases (9.4% of acute burn admissions). Forty-five (75%) of these patients were adults and 25% were children. There were 23 females and 37 males. Forty-two percent of the adults and 33% of the children had some percentage of third-degree injury. The average total body surface area burn in adults was 5.9% and in children 6.3%. There were no deaths in this series. Burns usually occurred as the result of scalds with grease while cooking. Spilling grease on children in the kitchen was a frequent problem. Burns due to ignition of grease was also a cause of injury. Most of the injuries were potentially preventable, and therefore the importance of burn appropriate safety programs is stressed.
Analysis of Burn Injuries in Frontal Automobile Crashes
Authors: Jernigan M. Virginia , Rath Amber L. , Duma Stefan M.
Published: July 2004

The purpose of this study was to investigate burn injuries resulting from frontal automobile crashes and to determine the effects of frontal airbags on the incidence of burn injuries. The study included 25,464 individual cases from the National Automotive Sampling System database files for the years 1993 to 2000. Occupants were at a significantly higher risk to sustain a burn injury when exposed to an airbag deployment (1.54%) compared with those who received a burn injury when not exposed to an airbag deployment (0.02%; P = 0.02). In contrast to previous publications, this study found that 1.53% of front seat occupants exposed to an airbag deployment sustained an airbag-induced burn injury. The vast majority of airbag-induced burn injuries were minor (98.7%); however, in cases with no airbag deployment, the burns were often much more serious, including fatal burns (29.6%). Occupant weight, height, sex, seatbelt use, and seat position were all found not to be significant in predicting the risk of airbag induced burn injury, whereas age and crash velocity were found to be significant.
The MTE, a new core promoter element for transcription by RNA polymerase II
Authors: Lim Chin Yan , Santoso Buyung , Boulay Thomas , Dong Emily , Ohler Uwe , Kadonaga James T.
Published: July 2004

The core promoter is the ultimate target of the vast network of regulatory factors that contribute to the initiation of transcription by RNA polymerase II. Here we describe the MTE (motif ten element), a new core promoter element that appears to be conserved fromDrosophilato humans. The MTE promotes transcription by RNA polymerase II when it is located precisely at positions +18 to +27 relative to A+1in the initiator (Inr) element. MTE sequences from +18 to +22 relative to A+1are important for basal transcription, and a region from +18 to +27 is sufficient to confer MTE activity to heterologous core promoters. The MTE requires the Inr, but functions independently of the TATA-box and DPE. Notably, the loss of transcriptional activity upon mutation of a TATA-box or DPE can be compensated by the addition of an MTE. In addition, the MTE exhibits strong synergism with the TATA-box as well as the DPE. These findings indicate that the MTE is a novel downstream core promoter element that is important for transcription by RNA polymerase II.
Regulation of the TSC pathway by LKB1: evidence of a molecular link between tuberous sclerosis complex and Peutz-Jeghers syndrome
Authors: Corradetti Michael N. , Inoki Ken , Bardeesy Nabeel , DePinho Ronald A. , Guan Kun-Liang
Published: July 2004

Tuberous sclerosis complex (TSC) and Peutz-Jeghers syndrome (PJS) are dominantly inherited benign tumor syndromes that share striking histopathological similarities. Here we show that LKB1, the gene mutated in PJS, acts as a tumor suppressor by activating TSC2, the gene mutated in TSC. Like TSC2, LKB1 inhibits the phosphorylation of the key translational regulators S6K and 4EBP1. Furthermore, we show that LKB1 activates TSC2 through the AMP-dependent protein kinase (AMPK), indicating that LKB1 plays a role in cell growth regulation in response to cellular energy levels. Our results suggest that PJS and other benign tumor syndromes could be caused by dysregulation of the TSC2/mTOR pathway.
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27
Authors: Kirmizis Antonis , Bartley Stephanie M. , Kuzmichev Andrei , Margueron Raphael , Reinberg Danny , Green Roland , Farnham Peggy J.
Published: July 2004

Polycomb group (PcG) complexes 2 and 3 are involved in transcriptional silencing. These complexes contain a histone lysine methyltransferase (HKMT) activity that targets different lysine residues on histones H1 or H3 in vitro. However, it is not known if these histones are methylation targets in vivo because the human PRC2/3 complexes have not been studied in the context of a natural promoter because of the lack of known target genes. Here we report the use of RNA expression arrays and CpG-island DNA arrays to identify and characterize human PRC2/3 target genes. Using oligonucleotide arrays, we first identified a cohort of genes whose expression changes upon siRNA-mediated removal of Suz12, a core component of PRC2/3, from colon cancer cells. To determine which of the putative target genes are directly bound by Suz12 and to precisely map the binding of Suz12 to those promoters, we combined a high-resolution chromatin immunoprecipitation (ChIP) analysis with custom oligonucleotide promoter arrays. We next identified additional putative Suz12 target genes by using ChIP coupled to CpG-island microarrays. We showed that HKMT-Ezh2 and Eed, two other components of the PRC2/3 complexes, colocalize to the target promoters with Suz12. Importantly, recruitment of Suz12, Ezh2 and Eed to target promoters coincides with methylation of histone H3 on Lys 27.
Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA
Authors: Duquette Michelle L. , Handa Priya , Vincent Jack A. , Taylor Andrew F. , Maizels Nancy
Published: July 2004

We show that intracellular transcription of G-rich regions produces novel DNA structures, visible by electron microscopy as large (150–500 bp) loops. These G-loops are formed cotranscriptionally, and they contain G4 DNA on one strand and a stable RNA/DNA hybrid on the other. G-loop formation requires a G-rich nontemplate strand and reflects the unusual stability of the rG/dC base pair. G-loops and G4 DNA form efficiently within plasmid genomes transcribed in vitro or inEscherichia coli. These results establish that G4 DNA can form in vivo, a finding with implications for stability and maintenance of all G-rich genomic regions.
Adaptive Radiation from Resource Competition in Digital Organisms
Authors: Chow Stephanie S. , Wilke Claus O. , Ofria Charles , Lenski Richard E. , Adami Christoph
Published: July 2004

Species richness often peaks at intermediate productivity and decreases as resources become more or less abundant. The mechanisms that produce this pattern are not completely known, but several previous studies have suggested environmental heterogeneity as a cause. In experiments with evolving digital organisms and populations of fixed size, maximum species richness emerges at intermediate productivity, even in a spatially homogeneous environment, owing to frequency-dependent selection to exploit an influx of mixed resources. A diverse pool of limiting resources is sufficient to cause adaptive radiation, which is manifest by the origin and maintenance of phenotypically and phylogenetically distinct groups of organisms.
Path Integration in Desert Ants Controls Aggressiveness
Authors: Knaden Markus , Wehner Rüdiger
Published: July 2004

Cataglyphis
ants of the Sahara Desert are extremely aggressive toward members of other colonies if they are close to their nest entrance, but not once they have embarked on their wide foraging journeys. We show that the ants reach the same level of aggressiveness when they are far from their actual nesting site but their path integrator--their main navigational toolkit--tells them that they are close, indicating a role for the animal's path integrator beyond navigation.
Chiral Fiber Gratings
Authors: Kopp Victor I. , Churikov Victor M. , Singer Jonathan , Chao Norman , Neugroschl Daniel , Genack Azriel Z.
Published: July 2004

Chiral gratings with double helix symmetry were produced by twisting glass optical fiber with a noncircular core cross section as it passed through a miniature oven. We observed polarization-selective transmission in chiral fibers with pitches of tens of micrometers. Two modes of optical interaction were differentiated. In chirallong-period gratings, dips in transmission were observed at wavelengths associated with scattering into distinct cladding modes mediated by the chiral grating. In chiral intermediateperiod gratings, a broad scattering band was observed. These gratings can be used to produce sharp or broad polarization-selective filters.
Self-Assembling Protein Microarrays
Authors: Ramachandran Niroshan , Hainsworth Eugenie , Bhullar Bhupinder , Eisenstein Samuel , Rosen Benjamin , Lau Albert Y. , Walter Johannes C. , LaBaer Joshua
Published: July 2004

Protein microarrays provide a powerful tool for the study of protein function. However, they are not widely used, in part because of the challenges in producing proteins to spot on the arrays. We generated protein microarrays by printing complementary DNAs onto glass slides and then translating target proteins with mammalian reticulocyte lysate. Epitope tags fused to the proteins allowed them to be immobilized in situ. This obviated the need to purify proteins, avoided protein stability problems during storage, and captured sufficient protein for functional studies. We used the technology to map pairwise interactions among 29 human DNA replication initiation proteins, recapitulate the regulation of Cdt1 binding to select replication proteins, and map its geminin-binding domain.
Small Mid-Pleistocene Hominin Associated with East African Acheulean Technology
Authors: Potts Richard , Behrensmeyer Anna K. , Deino Alan , Ditchfield Peter , Clark Jennifer
Published: July 2004

Hominin fossils from the African mid-Pleistocene are rare despite abundant Acheulean tools in Africa and apparently African-derived hominins in Eurasia between 1.0 and 0.5 million years ago (Ma). Here we describe an African fossil cranium constrained by
40
Ar/
39
Ar analyses, magnetostratigraphy, and sedimentary features to 0.97 to 0.90 Ma, and stratigraphically associated with Acheulean handaxes. Although the cranium represents possibly the smallest adult or near-adult known between 1.7 and 0.5 Ma, it retains features observed in larger
Homo erectus
individuals, yet shows a distinct suite of traits indicative of wide population variation in the hominins of this period.
Dynamic Patterns of Subcellular Protein Localization during Spore Coat Morphogenesis in
Bacillus subtilis
Authors: van Ooij Christiaan , Eichenberger Patrick , Losick Richard
Published: July 2004

Endospores of
Bacillus subtilis
are encased in a thick, proteinaceous shell known as the coat, which is composed of a large number of different proteins. Here we report the identification of three previously uncharacterized coat-associated proteins, YabP, YheD, and YutH, and their patterns of subcellular localization during the process of sporulation, obtained by using fusions of the proteins to the green fluorescent protein (GFP). YabP-GFP was found to form both a shell and a ring around the center of the forespore across the short axis of the sporangium. YheD-GFP, in contrast, formed two rings around the forespore that were offset from its midpoint, before it eventually redistributed to form a shell around the developing spore. Finally, YutH-GFP initially localized to a focus at one end of the forespore, which then underwent transformation into a ring that was located adjacent to the forespore. Next, the ring became a cap at the mother cell pole of the forespore that eventually spread around the entire developing spore. Thus, each protein exhibited its own distinct pattern of subcellular localization during the course of coat morphogenesis. We concluded that spore coat assembly is a dynamic process involving diverse patterns of protein assembly and localization.
Phosphorus Limitation Enhances Biofilm Formation of the Plant Pathogen
Agrobacterium tumefaciens
through the PhoR-PhoB Regulatory System
Authors: Danhorn Thomas , Hentzer Morten , Givskov Michael , Parsek Matthew R. , Fuqua Clay
Published: July 2004

The plant pathogen
Agrobacterium tumefaciens
forms architecturally complex biofilms on inert surfaces. Adherence of
A. tumefaciens
C58 was significantly enhanced under phosphate limitation compared to phosphate-replete conditions, despite slower overall growth under low-phosphate conditions. Replacement of P
i
with
sn
-glycerol-3-phosphate and 2-aminoethylphosphonate yielded similar results. The increase in surface interactions under phosphate limitation was observed in both static culture and continuous-culture flow cells. Statistical analysis of confocal micrographs obtained from the flow cell biofilms revealed that phosphate limitation increased both the overall attached biomass and the surface coverage, whereas the maximum thickness of the biofilm was not affected. Functions encoded on the two large plasmids of
A. tumefaciens
C58, pTiC58 and pAtC58, were not required for the observed phosphate effect. The phosphate concentration at which increased attachment was observed triggered the phosphate limitation response, controlled in many bacteria by the two-component regulatory system PhoR-PhoB. The
A. tumefaciens phoB
and
phoR
orthologues could only be disrupted in the presence of plasmid-borne copies of the genes, suggesting that this regulatory system might be essential. Expression of the
A. tumefaciens phoB
gene from a tightly regulated inducible promoter, however, correlated with the amount of biofilm under both phosphate-limiting and nonlimiting conditions, demonstrating that components of the Pho regulon influence
A. tumefaciens
surface interactions.
Helicobacter pyloriFlgR Is an Enhancer-Independent Activator of σ54-RNA Polymerase Holoenzyme
Authors: Brahmachary Priyanka , Dashti Mona G. , Olson Jonathan W. , Hoover Timothy R.
Published: July 2004

Helicobacter pyloriFlgR activates transcription with σ54-RNA polymerase holoenzyme (σ54-holoenzyme) from at least five flagellar operons. Activators of σ54-holoenzyme generally bind enhancer sequences located >70 bp upstream of the promoter and contact σ54-holoenzyme bound at the promoter through DNA looping to activate transcription.H. pyloriFlgR lacks the carboxy-terminal DNA-binding domain present in most σ54-dependent activators. As little as 42 bp of DNA upstream of theflaBpromoter and 26 bp of DNA sequence downstream of the transcriptional start site were sufficient for efficient FlgR-mediated expression from aflaB′-′xylEreporter gene inH. pylori, indicating that FlgR does not use an enhancer to activate transcription. Other examples of σ54-dependent activators that lack a DNA-binding domain includeChlamydia trachomatisCtcC and activators from the otherChlamydiaspp. whose genomes have been sequenced. FlgR fromHelicobacter hepaticusandCampylobacter jejuni, which are closely related toH. pylori, appear to have carboxy-terminal DNA-binding domains, suggesting that the loss of the DNA-binding domain fromH. pyloriFlgR occurred after the divergence of these bacterial species. Removal of the amino-terminal regulatory domain of FlgR resulted in a constitutively active form of the protein that activated transcription from σ54-dependent genes inEscherichia coli. The truncated FlgR protein also activated transcription withE. coliσ54-holoenzyme in an in vitro transcription assay.
TheLactobacillus casei ptsHI47T Mutation Causes Overexpression of a LevR-Regulated but RpoN-Independent Operon Encoding a Mannose Class Phosphotransferase System
Authors: Mazé Alain , Boël Grégory , Poncet Sandrine , Mijakovic Ivan , Le Breton Yoann , Benachour Abdellah , Monedero Vicente , Deutscher Josef , Hartke Axel
Published: July 2004

A proteome analysis ofLactobacillus caseimutants that are affected in carbon catabolite repression revealed that a 15-kDa protein was strongly overproduced in aptsHI47T mutant. This protein was identified as EIIA of a mannose class phosphotransferase system (PTS). A 7.1-kb DNA fragment containing the EIIA-encoding open reading frame and five other genes was sequenced. The first gene encodes a protein resembling the RpoN (σ54)-dependentBacillus subtilistranscription activator LevR. The following pentacistronic operon is oriented in the opposite direction and encodes four proteins with strong similarity to the proteins of theB. subtilisLev-PTS and one protein of unknown function. The genes present on the 7.1-kb DNA fragment were therefore calledlevRandlevABCDX. ThelevABCDXoperon was induced by fructose and mannose. No “−12, −24” promoter typical of RpoN-dependent genes precedes theL. casei levoperon, and its expression was therefore RpoN independent but required LevR. Phosphorylation of LevR by P∼His-HPr stimulates its activity, while phosphorylation by P∼EIIBLevinhibits it. Disruption of the EIIBLev-encodinglevBgene therefore led to strong constitutive expression of thelevoperon, which was weaker in a strain carrying aptsImutation preventing phosphorylation by both P∼EIIBLevand P∼His-HPr. Expression of theL. casei levoperon is also subject to P-Ser-HPr-mediated catabolite repression. The observed slow phosphoenolpyruvate- and ATP-dependent phosphorylation of HPrI47T as well as the slow phosphoryl group transfer from the mutant P∼His-HPr to EIIALevare assumed to be responsible for the elevated expression of thelevoperon in theptsHI47T mutant.
Transposition of the Heat-Stable ToxinastAGene into a Gifsy-2-Related Prophage ofSalmonella entericaSerovar Abortusovis
Authors: Bacciu Donatella , Falchi Giovanni , Spazziani Alessandra , Bossi Lionello , Marogna Gavino , Leori Guido Sisinnio , Rubino Salvatore , Uzzau Sergio
Published: July 2004

The horizontal transfer and acquisition of virulence genes via mobile genetic elements have been a major driving force in the evolution ofSalmonellapathogenicity. Serovars ofSalmonella entericacarry variable assortments of phage-encoded virulence genes, suggesting that temperate phages play a pivotal role in this process. Epidemic isolates ofS. entericaserovar Typhimurium are consistently lysogenic for two lambdoid phages, Gifsy-1 and Gifsy-2, carrying known virulence genes. Other serovars ofS. enterica, including serovars Dublin, Gallinarum, Enteritidis, and Hadar, carry distinct prophages with similarity to the Gifsy phages. In this study, we analyzed Gifsy-related loci fromS. entericaserovar Abortusovis, a pathogen associated exclusively with ovine infection. A cryptic prophage, closely related to serovar Typhimurium phage Gifsy-2, was identified. This element, named Gifsy-2AO, was shown to contribute to serovar Abortusovis systemic infection in lambs. Sequence analysis of the prophage b region showed a large deletion which covers genes encoding phage tail fiber proteins and putative virulence factors, including type III secreted effector protein SseI (GtgB, SrfH). This deletion was identified in most of the serovar Abortusovis isolates tested and might be dependent on the replicative transposition of an adjacent insertion sequence, IS1414, previously identified in pathogenicEscherichia colistrains. IS1414encodes heat-stable toxin EAST1 (astA) and showed multiple genomic copies in isolates of serovar Abortusovis. To our knowledge, this is the first evidence of intergeneric transfer of virulence genes via insertion sequence elements inSalmonella. The acquisition of IS1414(EAST1) and its frequent transposition within the chromosome might improve the fitness of serovar Abortusovis within its narrow ecological niche.
First Characterization of an Archaeal GTP-Dependent Phosphoenolpyruvate Carboxykinase from the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
KOD1
Authors: Fukuda Wakao , Fukui Toshiaki , Atomi Haruyuki , Imanaka Tadayuki
Published: July 2004

Phosphoenolpyruvate carboxykinase (PCK), which catalyzes the nucleotide-dependent, reversible decarboxylation of oxaloacetate to yield phosphoenolpyruvate and CO
2
, is one of the important enzymes in the interconversion between C
3
and C
4
metabolites. This study focused on the first characterization of the enzymatic properties and expression profile of an archaeal PCK from the hyperthermophilic archaeon
Thermococcus kodakaraensis
(Pck

Tk

). Pck

Tk

showed 30 to 35% identities to GTP-dependent PCKs from mammals and bacteria but was located in a branch distinct from that of the classical enzymes in the phylogenetic tree, together with other archaeal homologs from
Pyrococcus
and
Sulfolobus
spp. Several catalytically important regions and residues, found in all known PCKs irrespective of their nucleotide specificities, were conserved in Pck

Tk

. However, the predicted GTP-binding region was unique compared to those in other GTP-dependent PCKs. The recombinant Pck

Tk

actually exhibited GTP-dependent activity and was suggested to possess dual cation-binding sites specific for Mn
2+
and Mg
2+
. The enzyme preferred phosphoenolpyruvate formation from oxaloacetate, since the

K
m

value for oxaloacetate was much lower than that for phosphoenolpyruvate. The transcription and activity levels in
T. kodakaraensis
were higher under gluconeogenic conditions than under glycolytic conditions. These results agreed with the role of Pck

Tk

in providing phosphoenolpyruvate from oxaloacetate as the first step of gluconeogenesis in this hyperthermophilic archaeon. Additionally, under gluconeogenic conditions, we observed higher expression levels of Pck

Tk

on pyruvate than on amino acids, implying that it plays an additional role in the recycling of excess phosphoenolpyruvate produced from pyruvate, replacing the function of the anaplerotic phosphoenolpyruvate carboxylase that is missing from this archaeon.
Delineation of Upstream Signaling Events in theSalmonellaPathogenicity Island 2 Transcriptional Activation Pathway
Authors: Kim Charles C. , Falkow Stanley
Published: July 2004

Survival and replication in the intracellular environment are critical components of the ability ofSalmonella entericaserovar Typhimurium to establish systemic infection in the murine host. Intracellular survival is mediated by a number of genetic loci, includingSalmonellapathogenicity island 2 (SPI2). SPI2 is a 40-kb locus encoding a type III secretion system that secretes effector molecules, which permits bacterial survival and replication in the intracellular environment of host cells. A two-component regulatory system,ssrAB, is also encoded in SPI2 and controls expression of the secretion system and effectors. While the environmental signals to which SPI2 responds in vivo are not known, activation of expression is dependent on OmpR and can be stimulated in vitro by chelation of cations or by a shift from rich to acidic minimal medium. In this work, we demonstrated that SPI2 activation is associated with OmpR in the phosphorylated form (OmpR-P). Mutations inenvZandackA-pta, which disrupted two distinct sources of OmpR phosphorylation, indicated that SPI2 activation by chelators or a shift from rich to acidic minimal medium is largely dependent on functional EnvZ. In contrast, the PhoPQ pathway is not required for SPI2 activation in the presence of OmpR-P. As in the case of in vitro stimulation, SPI2 expression in macrophages correlates with the presence of OmpR-P. Additionally, EnvZ, but not acetyl phosphate, is required for maximal expression of SPI2 in the intracellular environment, suggesting that the in vitro SPI2 activation pathway is the same as that used in vivo.
Iron Acquisition and Regulation in
Campylobacter jejuni
Authors: Palyada Kiran , Threadgill Deborah , Stintzi Alain
Published: July 2004

Iron affects the physiology of bacteria in two different ways: as a micronutrient for bacterial growth and as a catalyst for the formation of hydroxyl radicals. In this study, we used DNA microarrays to identify the
C. jejuni
genes that have their transcript abundance affected by iron availability. The transcript levels of 647 genes were affected after the addition of iron to iron-limited
C. jejuni
cells. Several classes of affected genes were revealed within 15 min, including immediate-early response genes as well as those specific to iron acquisition and metabolism. In contrast, only 208 genes were differentially expressed during steady-state experiments comparing iron-rich and iron-limited growth conditions. As expected, genes annotated as being involved in either iron acquisition or oxidative stress defense were downregulated during both time course and steady-state experiments, while genes encoding proteins involved in energy metabolism were upregulated. Because the level of protein glycosylation increased with iron limitation, iron may modulate the level of
C. jejuni
virulence by affecting the degree of protein glycosylation. Since iron homeostasis has been shown to be Fur regulated in
C. jejuni
, an isogenic
fur
mutant was used to define the Fur regulon by transcriptome profiling. A total of 53 genes were Fur regulated, including many genes not previously associated with Fur regulation. A putative Fur binding consensus sequence was identified in the promoter region of most iron-repressed and Fur-regulated genes. Interestingly, a
fur
mutant was found to be significantly affected in its ability to colonize the gastrointestinal tract of chicks, highlighting the importance of iron homeostasis in vivo. Directed mutagenesis of other genes identified by the microarray analyses allowed the characterization of the ferric enterobactin receptor, previously named CfrA. Chick colonization assays indicated that mutants defective in enterobactin-mediated iron acquisition were unable to colonize the gastrointestinal tract. In addition, a mutation in a receptor (Cj0178) for an uncharacterized iron source also resulted in reduced colonization potential. Overall, this work documents the complex response of
C. jejuni
to iron availability, describes the genetic network between the Fur and iron regulons, and provides insight regarding the role of iron in
C. jejuni
colonization in vivo.