bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Activation by the DNA-Binding Domain of the AraC Family Protein RhaS in the Absence of Its Effector-Binding Domain
Authors: Wickstrum Jason R. , Skredenske Jeff M. , Kolin Ana , Jin Ding J. , Fang Jianwen , Egan Susan M. 
Published: May 2007

ABSTRACT

The
Escherichia coli
l
-rhamnose-responsive transcription activators RhaS and RhaR both consist of two domains, a C-terminal DNA-binding domain and an N-terminal dimerization domain. Both function as dimers and only activate transcription in the presence of
l
-rhamnose. Here, we examined the ability of the DNA-binding domains of RhaS (RhaS-CTD) and RhaR (RhaR-CTD) to bind to DNA and activate transcription. RhaS-CTD and RhaR-CTD were both shown by DNase I footprinting to be capable of binding specifically to the appropriate DNA sites. In vivo as well as in vitro transcription assays showed that RhaS-CTD could activate transcription to high levels, whereas RhaR-CTD was capable of only very low levels of transcription activation. As expected, RhaS-CTD did not require the presence of
l
-rhamnose to activate transcription. The upstream half-site at
rhaBAD
and the downstream half-site at
rhaT
were found to be the strongest of the known RhaS half-sites, and a new putative RhaS half-site with comparable strength to known sites was identified. Given that cyclic AMP receptor protein (CRP), the second activator required for full
rhaBAD
expression, cannot activate
rhaBAD
expression in a Δ
rhaS
strain, it was of interest to test whether CRP could activate transcription in combination with RhaS-CTD. We found that RhaS-CTD allowed significant activation by CRP, both in vivo and in vitro, although full-length RhaS allowed somewhat greater CRP activation. We conclude that RhaS-CTD contains all of the determinants necessary for transcription activation by RhaS.
Multicellular Development in
Myxococcus xanthus
Is Stimulated by Predator-Prey Interactions
Authors: Berleman James E. , Kirby John R. 
Published: May 2007

ABSTRACT

Myxococcus xanthus
is a predatory bacterium that exhibits complex social behavior. The most pronounced behavior is the aggregation of cells into raised fruiting body structures in which cells differentiate into stress-resistant spores. In the laboratory, monocultures of
M. xanthus
at a very high density will reproducibly induce hundreds of randomly localized fruiting bodies when exposed to low nutrient availability and a solid surface. In this report, we analyze how
M. xanthus
fruiting body development proceeds in a coculture with suitable prey. Our analysis indicates that when prey bacteria are provided as a nutrient source, fruiting body aggregation is more organized, such that fruiting bodies form specifically after a step-down or loss of prey availability, whereas a step-up in prey availability inhibits fruiting body formation. This localization of aggregates occurs independently of the basal nutrient levels tested, indicating that starvation is not required for this process. Analysis of early developmental signaling
relA
and
asgD
mutants indicates that they are capable of forming fruiting body aggregates in the presence of prey, demonstrating that the stringent response and A-signal production are surprisingly not required for the initiation of fruiting behavior. However, these strains are still defective in differentiating to spores. We conclude that fruiting body formation does not occur exclusively in response to starvation and propose an alternative model in which multicellular development is driven by the interactions between
M. xanthus
cells and their cognate prey.
Dysembryoplastic neuroepithelial tumours: clinical, proliferative and apoptotic features
Authors: Duggal N , Taylor R , Zou G Y , Hammond R R 
Published: May 2007

Aims:Dysembryoplastic neuroepithelial tumours (DNTs) have been considered benign lesions characterised by a chronic, indolent clinical course. Previous studies have suggested that increased proliferation rates may be balanced by corresponding rates of apoptosis. The objective of this study was to determine whether a correlation exists between histological features and indices of proliferation/apoptosis.Methods:Fourteen consecutive surgical specimens meeting the histological criteria for DNT were retrospectively reviewed for evidence of aggressive histological features, including anaplasia, mitotic activity, and Ki67 labelling. Immunohistochemistry was performed semiquantitatively to evaluate and compare proliferation (Ki76) and apoptosis (TUNEL). The clinical course of the patients was also reviewed.Results:Atypical histological features were demonstrated in the glial component of select complex DNTs. TUNEL indices, however, had negligible correlation with proliferative indices. A balance between cell proliferation and apoptosis was not evident particularly in those cases displaying aggressive histological features.Conclusions:While there is no clearly defined clinical or pathological pattern to indicate aggressive growth of DNTs, elevated proliferative indices coupled with atypical histological features in complex DNTs should be taken into consideration in determining the aggressiveness of surgical extirpation and follow-up until experience with these uncommon tumours is greater.
Scots pine ectomycorrhizal fungal inoculum potential and dynamics in podzol-specific humus, eluvial and illuvial horizons one and four growth seasons after forest clear-cut logging
Authors: Heinonsalo Jussi , Sen Robin 
Published: May 2007

The aims of this microcosm-based study were to characterize Scots pine ectomycorrhizal (EcM) inoculum potential in humus (O) and underlying eluvial (E) and illuvial (B) mineral podzol soil horizons and to compare the inoculum potential 1 and 4 years following clear-cut logging. The specific horizons were collected from a Scots pine control uncut stand, the adjacent interface zone (3–10 m from the forest edge), and the adjoining clear-cut area. The highest Simpson's reciprocal diversity indices (SRDI) of ectomycorrhizal morphotypes and polymerase chain reaction – internal transcribed spacer – restriction fragment length polymorphism (PCR-(ITS)-RFLP) taxa were detected in the humus and E horizon. The B horizon supported the lowest SRDI, but the community consisted of mycorrhizas representing active rhizomorph-forming species. Identified RFLP taxa, confirmed via ITS sequence analysis, highlighted horizon specificity for some genera and species. With respect to clear-cutting impacts, the most dominant ectomycorrhizal morphotypes detected and diversity indices were the same irrespective of the sampling time, which strongly indicates that inoculum potential is maintained up to four growth seasons after the clearcut. No forest treatment dependent differences in Scots pine seedling biomass were detected, but, compared with humus, significantly reduced biomass was recorded in deeper mineral soil horizons. The data are discussed in relation with recent vertical profile studies and forest silvicultural practices.
Pollination and seed production in western white pine
Authors: Owens John N. , Fernando Danilo D. 
Published: May 2007

The reproductive biology of western white pine ( Pinus monticola Dougl. ex D. Don) at the Saanich seed orchard (SSO; a coastal seedling seed orchard) and the Kalamalka seed orchard (KSO; an interior clonal seed orchard) is described. Seed-cone development and morphology determine seed potential and affect filled seed production. Seed potential was high, commonly over 200 seeds per cone and filled seeds per cone averaged 50–60 at both orchards in 1999 from open pollinations combined with operational supplemental mass pollinations (OP-SMP). Filled seeds per cone at SSO in 2004 averaged 115 with open pollinations and OP-SMP. About 30% of ovules aborted before pollination. Another 25% aborted probably because of self-incompatibility at fertilization. Seed efficiency (SEF) was only 5% at KSO with open pollination but increased to 30% with OP-SMP. SEF was the same at SSO with or without OP-SMP. Reproductive success was very low at KSO without OP-SMP but increased to about 10%, similar to that of SSO, with OP-SMP. The optimal time for control pollinations was at cone stages 4 and 5 and optimal amount of pollen per pollination bag was 0.3–0.4 mL. Western white pine is a very good seed producer and can be easily managed in seed orchards to give very high seed production per cone and per tree.
Comparison of thinning and prescribed fire restoration treatments to Sierran mixed-conifer historic conditions
Authors: North Malcolm , Innes Jim , Zald Harold 
Published: May 2007

Thinning and prescribed fire are widely used to restore fire-suppressed forests, yet there are few studies of their effectiveness in Sierran mixed-conifer forest. We compared stand conditions in replicated plots before and after a combination of thinning and burning treatments against a reconstruction of the same forest in 1865. The historical forest had 67 stems/ha (trees ≥5 cm DBH), equal percentages of shade-tolerant and -intolerant tree species, stems randomly distributed at the stand scale, and a flat diameter distribution across size classes. The pretreatment forest averaged 469 stems/ha, which comprised 84% shade-tolerant and 14% shade-intolerant species, were highly clustered, and had a reverse-J-shaped diameter distribution. Thinning treatments failed to approximate historical composition, spatial pattern, or diameter distribution. Treatments left too many small trees, removed too many intermediate-sized trees (50–75 cm DBH), and retained a reverse-J-shaped diameter distribution. Current old growth comprises fewer large trees than historical conditions, suggesting that treatments should retain more intermediate-sized trees to provide for future large-tree recruitment. Understory thinning with prescribed fire significantly reduced stem density and produced a spatial pattern closest to historical conditions. Mixed-conifer restoration needs thinning prescriptions that vary by species and flexible rather than rigid upper diameter limits to retain some trees in all size classes.
Spring-flowering herbaceous plant species of the deciduous forests of eastern Canada and 20th century climate warming
Authors: Houle Gilles 
Published: May 2007

Increases in the emission of greenhouse gases, particularly during the second half of the 20th century, have been associated with climate warming at the global scale. High latitude areas have been reported to be particularly sensitive to such changes, with significant impacts on plant phenology. The objectives of the present study were to (i) estimate changes in the flowering dates of 18 spring-flowering herbaceous plant species typical of the deciduous forests of eastern North America in three areas of eastern Canada (Gatineau–Ottawa, Montréal, and Québec) from 1900 to 2000 and (ii) associate these changes with those of annual and spring local temperatures. My results show a 2–6 days advance in flowering date over 100 years, depending on the region considered (corresponding to a ~2–3 days advance per 1 °C); these values are somewhat lower than those published in other studies, but still support the increasing body of literature on the effects of climate warming on plant phenology. Shifts in flowering phenology were particularly evident for Montréal, a large metropolitan region; this suggests that global climate warming, and its effects on plant phenology, may be exacerbated by local conditions, particularly those associated with large urban areas. Furthermore, species-specific responses to climate warming, as those presented here, might lead to significant changes in community composition and ecosystem functions.
Expression of human glutathione S-transferase P1 mediates the chemosensitivity of osteosarcoma cells
Authors: Huang Gangxiong , Mills Lisa , Worth Laura L. 
Published: May 2007

Abstract
Chemoresistance is a major reason that patients with osteosarcoma fail to achieve a lasting chemotherapy response, and it contributes to disease relapse, progression, and death. Human glutathione S-transferase P1 (GSTP1), a phase II detoxification enzyme, contributes to chemoresistance in many cancers. However, the role of GSTP1 in osteosarcoma chemoresistance is ill defined. We hypothesized that GSTP1 has cytoprotective effects in human osteosarcoma. To assess this possibility, we used GSTP1 cDNA transfection or RNA interference to overexpress or suppress GSTP1 in osteosarcoma cells, and assessed the cytotoxic effect of chemotherapeutic agents on these cells. Our results showed that GSTP1 expression was up-regulated in osteosarcoma cells when they were treated with doxorubicin or cisplatin. GSTP1 overexpression in SAOS-2 osteosarcoma cells caused the cells to be more resistant to doxorubicin and cisplatin. In contrast, GSTP1 suppression in HOS cells caused more apoptosis and extensive DNA damage in response to doxorubicin and cisplatin. The cytotoxicity assay also showed that GSTP1 suppression caused a 2.5-fold increase in cell growth inhibition resulting from doxorubicin and cisplatin treatments [the IC50s are ∼0.16 μmol/L (doxorubicin) and 1.8 μmol/L (cisplatin) for parental HOS versus 0.06 μmol/L (doxorubicin) and 0.75 μmol/L (cisplatin) for GSTP1-silenced HOS]. Moreover, GSTP1 suppression decreased the activation of extracellular signal–regulated kinase 1/2, which is induced by cisplatin and doxorubicin. Taken together, these findings show that GSTP1 contributes to doxorubicin and cisplatin resistance in osteosarcoma, which may be mediated in part by the activation of extracellular signal–regulated kinase 1/2. Targeting of GSTP1 combined with chemotherapy may have synergistic therapeutic effects on osteosarcoma. [Mol Cancer Ther 2007;6(5):1610–9]
Cellular FLICE-inhibitory protein regulates chemotherapy-induced apoptosis in breast cancer cells
Authors: Rogers Katherine M.A. , Thomas Michelle , Galligan Leeona , Wilson Timothy R. , Allen Wendy L. , Sakai Hidekazu , Johnston Patrick G. , Longley Daniel B. 
Published: May 2007

Abstract
Combination treatment regimens that include topoisomerase-II–targeted drugs, such as doxorubicin, are widely used in the treatment of breast cancer. Previously, we showed that IFN-γ and doxorubicin cotreatment synergistically induced apoptosis in MDA435 breast cancer cells in a signal transducer and activator of transcription 1–dependent manner. In this study, we found that this synergy was caspase-8 dependent. In addition, we found that IFN-γ down-regulated the expression of the caspase-8 inhibitor cellular FLICE-inhibitory protein (c-FLIP). Furthermore, IFN-γ down-regulated c-FLIP in a manner that was dependent on the transcription factors signal transducer and activator of transcription 1 and IFN regulatory factor-1. However, IFN-γ had no effect on c-FLIP mRNA levels, indicating that c-FLIP was down-regulated at a posttranscriptional level following IFN-γ treatment. Characterization of the functional significance of c-FLIP modulation by small interfering RNA gene silencing and stable overexpression studies revealed it to be a key regulator of IFN-γ– and doxorubicin-induced apoptosis in MDA435 cells. Analysis of a panel of breast cancer cell lines indicated that c-FLIP was an important general determinant of doxorubicin- and IFN-γ–induced apoptosis in breast cancer cells. Furthermore, c-FLIP gene silencing sensitized MDA435 cells to other chemotherapies, including etoposide, mitoxantrone, and SN-38. These results suggest that c-FLIP plays a pivotal role in modulating drug-induced apoptosis in breast cancer cells. [Mol Cancer Ther 2007;6(5):1544–51]
A bioactive withanolide Tubocapsanolide A inhibits proliferation of human lung cancer cells via repressing Skp2 expression
Authors: Chang Hui-Chiu , Chang Fang-Rong , Wang Yu-Chu , Pan Mei-Ren , Hung Wen-Chun , Wu Yang-Chang 
Published: May 2007

AbstractWithanolides are generally defined as C28 steroidal lactones built on an intact or rearranged ergostane skeleton and have been shown to exhibit antiproliferative activity on various types of cancer cells. In this study, we investigated the effect of a new withanolide Tubocapsanolide A isolated from Tubocapsicum anomalum and addressed its molecular action. Tubocapsanolide A inhibited proliferation of A549, H358, and H226 human lung cancer cells via induction of G1 growth arrest. We found that Tubocapsanolide A treatment led to up-regulation of cyclin E, p21, and p27, whereas other cyclins and cyclin-dependent kinases were not affected in A549 cells. Conversely, Skp2, the F-box protein that is implicated in the mediation of degradation of p21 and p27, was significantly down-regulated. Chromatin immunoprecipitation assay suggested that Tubocapsanolide A suppressed Skp2 expression by inhibiting the binding of Rel A to the nuclear factor-κB site of Skp2 gene promoter. In addition, we showed that inhibition of Skp2 is a critical step for the suppression of cell proliferation by Tubocapsanolide A because ectoexpression of Skp2 effectively reversed Tubocapsanolide A–induced p27 up-regulation and growth inhibition in human lung cancer cells. Collectively, we have identified Skp2 as a molecular target for Tubocapsanolide A and suggest that this withanolide may be useful for the prevention or treatment of cancer cells with Skp2 overexpression. [Mol Cancer Ther 2007;6(5):1572–8]
Structure-dependent activity of glycyrrhetinic acid derivatives as peroxisome proliferator–activated receptor γ agonists in colon cancer cells
Authors: Chintharlapalli Sudhakar , Papineni Sabitha , Jutooru Indira , McAlees Alan , Safe Stephen 
Published: May 2007

Abstract
Glycyrrhizin, a pentacyclic triterpene glycoside, is the major phytochemical in licorice. This compound and its hydrolysis product glycyrrhetinic acid have been associated with the multiple therapeutic properties of licorice extracts. We have investigated the effects of 2-cyano substituted analogues of glycyrrhetinic acid on their cytotoxicities and activity as selective peroxisome proliferator–activated receptor γ (PPARγ) agonists. Methyl 2-cyano-3,11-dioxo-18β-olean-1,12-dien-30-oate (β-CDODA-Me) and methyl 2-cyano-3,11-dioxo-18α-olean-1,12-dien-30-oate (α-CDODA-Me) were more cytotoxic to colon cancer cells than their des-cyano analogues and introduction of the 2-cyano group into the pentacyclic ring system was necessary for the PPARγ agonist activity of α-CDODA-Me and β-CDODA-Me isomers. However, in mammalian two-hybrid assays, both compounds differentially induced interactions of PPARγ with coactivators, suggesting that these isomers, which differ only in the stereochemistry at C18 which affects conformation of the E-ring, are selective receptor modulators. This selectivity in colon cancer cells was shown for the induction of two proapoptotic proteins, namely caveolin-1 and the tumor-suppressor gene Krüppel-like factor-4 (KLF-4). β-CDODA-Me but not α-CDODA-Me induced caveolin-1 in SW480 colon cancer cells, whereas caveolin-1 was induced by both compounds in HT-29 and HCT-15 colon cancer cells. The CDODA-Me isomers induced KLF-4 mRNA levels in HT-29 and SW480 cells but had minimal effects on KLF-4 expression in HCT-15 cells. These induced responses were inhibited by cotreatment with a PPARγ antagonist. This shows for the first time that PPARγ agonists derived from glycyrrhetinic acid induced cell-dependent caveolin-1 and KLF-4 expression through receptor-dependent pathways. [Mol Cancer Ther 2007;6(5):1588–98]
Four-Dimensional Dynamic Radar Mosaic
Authors: Langston Carrie , Zhang Jian , Howard Kenneth 
Published: May 2007

Abstract
Communities and many industries are affected by severe weather and have a need for real-time accurate Weather Surveillance Radar-1988 Doppler (WSR-88D) data spanning several regions. To fulfill this need the National Severe Storms Laboratory has developed a Four-Dimensional Dynamic Grid (4DDG) to accurately represent discontinuous radar reflectivity data over a continuous 4D domain. The objective is to create a seamless, rapidly updating radar mosaic that is well suited for use by forecasters in addition to advance radar applications such as qualitative precipitation estimates. Several challenges are associated with creating a 3D radar mosaic given the nature of radar data and the spherical coordinates of radar observations. The 4DDG uses spatial and temporal weighting schemes to overcome these challenges, with the intention of applying minimal smoothing to the radar data. Previous multiple radar mosaics functioned in two or three dimensions using a variety of established weighting schemes. The 4DDG has the advantage of temporal weighting to smooth radar observations over time. Using an exponentially decaying weighting scheme, this paper will examine different weather scenarios and show the effects of temporal smoothing using different time scales. Specifically, case examples of the 4DDG approach involving a rapidly evolving convective event and a slowly developing stratiform weather regime are considered.
Spaced-Antenna Interferometry to Measure Crossbeam Wind, Shear, and Turbulence: Theory and Formulation
Authors: Zhang Guifu , Doviak Richard J. 
Published: May 2007

Abstract
The theory of measuring crossbeam wind, shear, and turbulence within the radar’s resolution volume V6 is described. Spaced-antenna weather radar interferometry is formulated for such measurements using phased-array weather radar. The formulation for a spaced-antenna interferometer (SAI) includes shear of the mean wind, allows turbulence to be anisotropic, and allows receiving beams to have elliptical cross sections. Auto- and cross-correlation functions are derived based on wave scattering by randomly distributed particles. Antenna separation, mean wind, shear, and turbulence all contribute to signal decorrelation. Crossbeam wind cannot be separated from shear, and thus crossbeam wind measurements are biased by shear. It is shown that SAI measures an apparent crossbeam wind (i.e., the angular shear of the radial wind component). Whereas the apparent crossbeam wind and turbulence within V6 cannot be separated using monostatic Doppler techniques, angular shear and turbulence can be separated using the SAI.
Advancements in Techniques for Calibration and Characterization of In Situ Optical Particle Measuring Probes, and Applications to the FSSP-100 Probe
Authors: Nagel Dagmar , Maixner Uwe , Strapp Walter , Wasey Mohammed 
Published: May 2007

Abstract
Advancements in techniques for the operational calibration and characterization of instrument performance of the Particle Measuring Systems, Inc. (PMS), forward scattering spectrometer probe (FSSP) and optical array probes (OAPs) are presented, which also can be used for most in situ particle-measuring optical probes on the market. These techniques include the determination of a distortion matrix to correct for instrumental broadening of the measured particle size distribution. A new version of a monodisperse droplet generator is introduced for absolute calibration in the size range between 10 and 100 μm. In addition, a high-speed technique was employed for the determination of airspeed influence on the sample volume and the sizing of particles.
The calibration of a PMS FSSP with real water droplets may be significantly different from the usual calibration with glass beads. High-speed measurements simulate particles at speeds of up to about 250 m s−1. Particle undersizing and the decrease of the sample volume with increasing airspeed are described. The use of the modular tools, built for this work, is discussed for probe alignment, functionality checks, and general characterization and diagnostics both in laboratory and field environments.