bluuebunny/crossref_metadata_2025_split huggingface dataset:
Split-Ubiquitin Two-Hybrid Assay To Analyze Protein-Protein Interactions at the Endosome: Application to
Saccharomyces cerevisiae
Bro1 Interacting with ESCRT Complexes, the Doa4 Ubiquitin Hydrolase, and the Rsp5 Ubiquitin Ligase
Authors: Nikko Elina , André Bruno 
Published: May 2007

ABSTRACT

Targeting of membrane proteins into the lysosomal/vacuolar lumen for degradation requires their prior sorting into multivesicular bodies (MVB). The MVB sorting pathway depends on ESCRT-0, -I, -II, and -III protein complexes functioning on the endosomal membrane and on additional factors, such as Bro1/Alix and the ubiquitin ligase Rsp5/Nedd4. We used the split-ubiquitin two-hybrid assay to analyze the interaction partners of yeast Bro1 at its natural cellular location. We show that Bro1 interacts with ESCRT-I and -III components, including Vps23, the
Saccharomyces cerevisiae
homologue of human Tsg101. These interactions do not require the C-terminal proline-rich domain (PRD) of Bro1. Rather, this PRD interacts with the Doa4 deubiquitinating enzyme to recruit it to the endosome. This interaction is disrupted by a single amino acid substitution in the conserved ELC box motif in Doa4. The PRD of Bro1 also mediates an association with Rsp5, and this interaction appears to be conserved, as Alix, the human homologue of Bro1, coimmunoprecipitates with Nedd4 in yeast lysates. We further show that the Bro1 PRD domain is essential to MVB sorting of only cargo proteins whose sorting to the vacuolar lumen is dependent on their own ubiquitination and Doa4. The Bro1 region preceding the PRD, however, is required for MVB sorting of proteins irrespective of whether their targeting to the vacuole is dependent on their ubiquitination and Doa4. Our data indicate that Bro1 interacts with several ESCRT components and contributes via its PRD to associating ubiquitinating and deubiquitinating enzymes with the MVB sorting machinery.
FtsZ Directs a Second Mode of Peptidoglycan Synthesis inEscherichia coli
Authors: Varma Archana , de Pedro Miguel A. , Young Kevin D. 
Published: May 2007

ABSTRACTCertain penicillin binding protein mutants ofEscherichia coligrow with spirillum-like morphologies when the FtsZ protein is inhibited, suggesting that FtsZ might govern aspects of cell wall growth other than those strictly associated with septation. While investigating the mechanism of spiral cell formation, we discovered conditions for visualizing this second function of FtsZ. Normally, inhibiting the cytoskeleton protein MreB forcesE. colicells to grow as smoothly enlarging spheres from which the poles disappear, yielding coccoid or lemon-shaped forms. However, when FtsZ and MreB were inhibited simultaneously in a strain lacking PBP 5 and PBP 7, the resulting cells ballooned outward but retained conspicuous rod-shaped extensions at sites representing the original poles. This visual phenotype was paralleled by the biochemistry of sacculus growth. Muropeptides are usually inserted homogeneously into the lateral cell walls, but when FtsZ polymerization was inhibited, the incorporation of new material occurred mainly in the central regions of cells and was significantly lower in those portions of side walls abutting a pole. Thus, reduced precursor incorporation into side walls near the poles explained why these regions retained their rod-like morphology while the rest of the cell grew spherically. Also, inhibiting FtsZ increased the amount of pentapeptides in sacculi by about one-third. Finally, the MreB protein directed the helical or diagonal incorporation of new peptidoglycan into the wall, but the location of that incorporation depended on whether FtsZ was active. In sum, the results indicate that in addition to nucleating cell septation inE. coli, FtsZ can direct the insertion of new peptidoglycan into portions of the lateral wall.
An office-place stepping device to promote workplace physical activity
Authors: McAlpine David A , Manohar Chinmay U , McCrady Shelly K , Hensrud Donald , Levine James A 
Published: May 2007

Objective:It was proposed that an office-place stepping device is associated with significant and substantial increases in energy expenditure compared to sitting energy expenditure. The objective was to assess the effect of using an office-place stepping device on the energy expenditure of lean and obese office workers.Methods:The office-place stepping device is an inexpensive, near-silent, low-impact device that can be housed under a standard desk and plugged into an office PC for self-monitoring. Energy expenditure was measured in lean and obese subjects using the stepping device and during rest, sitting and walking. 19 subjects (27±9 years, 85±23 kg): 9 lean (BMI<25 kg/m2) and 10 obese (BMI>29 kg/m2) attended the experimental office facility. Energy expenditure was measured at rest, while seated in an office chair, standing, walking on a treadmill and while using the office-place stepping device.Results:The office-place stepping device was associated with an increase in energy expenditure above sitting in an office chair by 289±102 kcal/hour (p<0.001). The increase in energy expenditure was greater for obese (335±99 kcal/hour) than for lean subjects (235±80 kcal/hour; p = 0.03). The increments in energy expenditure were similar to exercise-style walking.Conclusion:The office-place stepping device could be an approach for office workers to increase their energy expenditure. If the stepping device was used to replace sitting by 2 hours per day and if other components of energy balance were constant, weight loss of 20 kg/year could occur.
BNIP3 expression in endometrial cancer relates to active hypoxia inducible factor 1α pathway and prognosis
Authors: Giatromanolaki A , Koukourakis M I , Gatter K C , Harris A L , Sivridis E 
Published: May 2007

Aims:BNIP3 is a pro-apoptotic mitochondrial protein induced under hypoxic stress, with the BNIP3 gene being under direct regulation of the hypoxia-inducible HIF-1α transcription factor. Induction of BNIP3 leads to caspase-independent necrosis-like cell death and an aggressive tumour phenotype. The role of BNIP3 in endometrial cancer was examined.Methods:The immunohistochemical patterns of BNIP3 expression in 72 early endometrial adenocarcinomas of the endometrioid cell type were studied. Correlation of BNIP3 with the hypoxia-inducible factor HIF-1α pathway and with prognosis was also examined.Results:BNIP3 was strongly and extensively expressed in the cytoplasm of cancer cells in 23/72 (31.9%) cases. This high BNIP3 reactivity was not related to histological grade, depth of myometrial invasion or steroid hormone receptor expression. There was, however, a significant association of BNIP3 reactivity with HIF-1α (p = 0.04), VEGF (p = 0.04) and, particularly, LDH-5 expression (p = 0.0001). Furthermore, high BNIP3 was associated with poor survival in both univariate (p = 0.05) and multivariate (p = 0.03) models.Conclusion:BNIP3 seems to be an important hypoxia-regulated molecule involved in endometrial cancer pathology. Given that high BNIP3 reactivity, being linked with poor post-operative outcome, has been linked with a favourable response to cytotoxic therapy (as previously indicated in experimental studies), high BNIP3 expression may be an indicator for adjuvant chemoradiotherapy in stage I endometrial carcinomas.
Low-grade abdominopelvic sarcoma with myofibroblastic features (low-grade myofibroblastic sarcoma): clinicopathological, immunohistochemical, molecular genetic and ultrastructural study of two cases with literature review
Authors: Agaimy A , Wünsch P H , Schroeder J , Gaumann A , Dietmaier W , Hartmann A , Hofstaedter F , Mentzel T 
Published: May 2007

Aims:Low-grade myofibroblastic sarcoma (LGMS) represents a rare soft tissue neoplasm with a predilection for the head and neck. Intra-abdominal LGMS are rare with only four unequivocal examples reported so far. Two further cases in females in their 60s and 70s are analysed here.Methods:Immunohistochemical stains were applied on fresh-cut sections using the avidin–biotin complex method and the following antibodies: vimentin, α-SMA, desmin, h-caldesmon, S-100, CD117, CD34, fibronectin, HMB45, Pan-keratin, Ki-67, β-catenin, MDM2, PDGFRα, PDGFRβ and ALK-1. Genomic DNA was isolated from microdissected formalin-fixed paraffin-embedded tumour tissue and examined forKITandPDGFRAmutations by PCR and direct sequencing ofKITandPDGFRA.Ultrastructural studies were also performed.Results:The tumours arose in the mesentery and the pelvic peritoneum. Both revealed features intermediate between conventional fibrosarcoma and leiomyosarcoma with fascicles of spindled, stellated or plump cells possessing fusiform indented vesicular nuclei and pale eosinophilic cytoplasm. Mitotic activity ranged from 1 to 15 per 10 HPFs. The tumour cells strongly expressed vimentin, variably α-smooth muscle actin and fibronectin, but were negative for CD117, S-100, desmin, h-caldesmon, β-catenin, ALK-1, MDM2, PDGFRα and PDGFRβ. One tumour showed a weak expression of CD34. Molecular analysis revealed a wild-typeKIT, exons 9, 11 and 13, andPDGFRA, exons 12 and 18. The patients developed multiple peritoneal recurrences at 5, 13 and 25 months, and 10, 19, 25 and 32 months, and were alive at 25 and 32 months, respectively. Distant metastases were not detected.Conclusion:Abdominopelvic LGMS follows a more aggressive clinical course characterised by a higher propensity for local recurrence, contrasting their more superficially located counterparts. LGMS may mimic a variety of benign and low-grade malignant neoplasms and might be under-recognised.
Damage to Abies koreana seeds by soil-borne fungi on Mount Halla, Korea
Authors: Cho HyeKyoung , Miyamoto Toshizumi , Takahashi Kunihide , Hong SungGak , Kim JongJin 
Published: May 2007

Abies koreana Wilson is an endemic tree species that is facing critical population declines in Korea. To identify factors affecting the natural regeneration of A. koreana, we examined the role of seed pathogens in the overwintering survival of seeds in natural seedbeds on Mount Halla, Korea. In September 2003, seeds of A. koreana were placed on seedbeds in the following three types of sites: Sasa dominated, shaded by rocks, or forest floor; seeds were then recovered from beneath the snow cover in April 2004 and were analyzed for the occurrence of harmful microfungi. Racodium therryanum Thuem. was the fungus most often isolated from retrieved seeds and was also the most detrimental of the eight fungal species tested in a pathogenicity trial. In vitro, R. therryanum caused a total loss of germination ability in A. koreana seeds at 0 °C after 100 days. The infection rate of R. therryanum was negatively correlated with the seed germination rate. The infection rate of R. therryanum was highest on the forest floor and increased with the duration of snow cover. The occurrence of R. therryanum was temporally restricted to the period of snow cover and spatially to the thick A0 soil layer on the forest floor. This study suggests that R. therryanum may be a significant factor inhibiting the natural regeneration of A. koreana at the seed stage.
Spatial effects of retention trees on mycorrhizas and biomass of Douglas-fir seedlings
Authors: Cline E. , Vinyard B. , Edmonds R. 
Published: May 2007

Retention forestry places seedlings in proximity to residual trees, exposing seedlings to additional sources of ectomycorrhizal fungus (EMF) inoculum. To investigate this, Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) seedlings were planted near (2–6 m) and far (16–30 m) from 44- to 72-year-old residual Douglas-fir trees in western Washington, USA. From 1998 through 2000, seedling shoot and root biomass was assessed and EMF taxa were identified using morphology and sequence analysis of internal transcribed spacer and large subunit ribosomal RNA genes. Seedlings near residual trees had significantly greater ectomycorrhiza (ECM) abundance (percent active ECM root tips), less necrotic root tips, and higher root to shoot biomass ratios. Seedlings near trees had a richness index of 4.1 EMF taxa per seedling and 42 total taxa compared with 3.5 taxa per seedling and 33 total taxa for seedlings far from trees. Proximity to residual trees may increase seedling ECM abundance and diversity.
Effects of local changes in active layer and soil climate on seasonal foliar nitrogen concentrations of three boreal forest shrubs
Authors: Rohrs-Richey Jennifer K. , Mulder Christa P.H. 
Published: May 2007

Caribou Poker Creeks Research Watershed is a boreal forest watershed in Interior Alaska that is susceptible to regional warming and permafrost thaw. We measured seasonal foliar N concentrations of the black spruce understory shrubs, Vaccinium uliginosum L., Vaccinium vitis-idaea L., and Ledum palustre L. on north- and south-facing sides of the watershed. We predicted that the shrubs would respond to small-scale changes in active layer and soil climate, and we expected similar responses according to growth strategy (evergreen or deciduous). Overall, foliar N in shrubs was higher on warmer, drier soils with deep active layers: +7.9% N in V. uliginosum, +11.1% N in V. vitis-idaea, and +9.4% N in L. palustre. Each shrub had species-specific foliar N patterns that could not be categorized by growth strategy and were not well explained by soil climate or active layer. Leaf mineral nutrition is influenced by multiple processes, and foliar N was best explained by the combination of environmental variables operating at the study site. For Caribou Poker Creeks Research Watershed, we can expect increased N status of the black spruce understory along with continued climate warming, but changes cannot be predicted based on growth strategy.
Phytolith evidence for the absence of a prehistoric grass understory in a Jeffrey pine – mixed conifer forest in the Sierra San Pedro Mártir, Mexico
Authors: Evett Rand R. , Franco-Vizcaino Ernesto , Stephens Scott L. 
Published: May 2007

Phytolith analysis was applied to several sites in a Jeffrey pine ( Pinus jeffreyi Grev. & Balf.) – mixed conifer forest in the Sierra San Pedro Mártir, Baja California, Mexico, to explore the hypothesis that the introduction of livestock in the late 18th century led to overgrazing of a prehistoric grass understory, resulting in changes to the prehistoric fire regime observed in the tree-ring fire-scar record. Stable soils in regions with extensive prehistoric grass cover retain a high concentration of total phytoliths and high percentage of grass phytoliths, regardless of historic vegetation changes. Phytoliths extracted from soil samples collected from several sites in the Sierra San Pedro Mártir revealed total phytolith concentrations in forest soils were generally <0.5% by mass, with most <0.1%, whereas grass phytoliths were generally <10% of the total, values consistent with the interpretation of a forest with sparse grass cover in the understory. Phytolith evidence suggests that there was minimal grass available for grazing in prehistoric Sierra San Pedro Mártir forests; overgrazing a grass understory was probably not a major driver of changes in the prehistoric fire regime.
Comparing modern and past fire regimes to assess changes in prehistoric lightning and anthropogenic ignitions in a Jeffrey pine – mixed conifer forest in the Sierra San Pedro Mártir, Mexico
Authors: Evett Rand R. , Franco-Vizcaino Ernesto , Stephens Scott L. 
Published: May 2007

Fire histories of Jeffrey pine ( Pinus jeffreyi Grev. & Balf.) – mixed conifer forests in the Sierra San Pedro Mártir, Baja California, Mexico, recently described through analysis of 300 years of tree-ring fire-scars, indicate there have been four distinct fire-regime periods based on fire frequency and size. We used modern lightning and fire data to assess whether the current lightning regime could have supported the prehistoric fire regime. Although there are several sources of uncertainty, the present lightning regime, concentrated in the summer with little spring activity, may be insufficient to support the high number and spring seasonality of fires recorded during some periods in the past. Changes in the ignition regime recorded during the past 300 years could have been due to anthropogenic and (or) climatic factors; available evidence suggests periods of frequent fire were dominated by anthropogenic ignitions.
BASIC PROPERTIES AND CHAOTIC SYNCHRONIZATION OF COMPLEX LORENZ SYSTEM
Authors: MAHMOUD GAMAL M. , Al-KASHIF M. A. , ALY SHABAN A. 
Published: May 2007

This paper aims at studying the basic properties and chaotic synchronization of complex Lorenz system: [Formula: see text] where α, γ, β are positive (real or complex) parameters, x and y are complex variables, z is a real variable, an overbar denotes complex conjugate variable and dots represent derivatives with respect to time. This system arises in many important applications in physics, for example, in laser physics and rotating fluids dynamics. Numerically we show that this system is a chaotic system and exhibits chaotic attractors. The necessary conditions for system (⋆) to generate chaos are obtained. Analytical and numerical calculations are presented to achieve synchronization. Active control technique is used to synchronize chaotic attractors of equations (⋆).
Shikonin circumvents cancer drug resistance by induction of a necroptotic death
Authors: Han Weidong , Li Ling , Qiu Shuang , Lu Qinghua , Pan Qiangrong , Gu Ying , Luo Jianhong , Hu Xun 
Published: May 2007

Abstract
Defect in apoptotic signaling and up-regulation of drug transporters in cancer cells significantly limits the effectiveness of cancer chemotherapy. We propose that an agent inducing non-apoptotic cell death may overcome cancer drug resistance and showed that shikonin, a naturally occurring naphthoquinone, induced a cell death in MCF-7 and HEK293 distinct from apoptosis and characterized with (a) a morphology of necrotic cell death; (b) loss of plasma membrane integrity; (c) loss of mitochondrial membrane potentials; (d) activation of autophagy as a downstream consequence of cell death, but not a contributing factor; (e) elevation of reactive oxygen species with no critical roles contributing to cell death; and (f) that the cell death was prevented by a small molecule, necrostatin-1, that specifically prevents cells from necroptosis. The characteristics fully comply with those of necroptosis, a basic cell-death pathway recently identified by Degterev et al. with potential relevance to human pathology. Furthermore, we proved that shikonin showed a similar potency toward drug-sensitive cancer cell lines (MCF-7 and HEK293) and their drug-resistant lines overexpressing P-glycoprotein, Bcl-2, or Bcl-xL, which account for most of the clinical cancer drug resistance. To our best knowledge, this is the first report to document the induction of necroptosis by a small molecular compound to circumvent cancer drug resistance. [Mol Cancer Ther 2007;6(5):1641–9]
Enhanced tumor cell kill by combined treatment with a small-molecule antagonist of mouse double minute 2 and adenoviruses encoding p53
Authors: Graat Harm C.A. , Carette Jan E. , Schagen Frederik H.E. , Vassilev Lyubomir T. , Gerritsen Winald R. , Kaspers Gertjan J.L. , Wuisman Paul I.J.M. , van Beusechem Victor W. 
Published: May 2007

Abstract
Strategies to treat cancer by restoring p53 tumor suppressor functions are being actively investigated. These approaches range from expressing an exogenous p53 gene in p53 mutant cancers to antagonizing a p53 inhibitor in p53 wild-type (WT) cancer cells. In addition, exogenous p53 is used to strengthen the anticancer efficacy of oncolytic adenoviruses. Many cancers express high levels of the major negative regulator of p53, mouse double minute 2 (MDM2) protein. Recently, a novel class of highly potent and specific MDM2 antagonists, the Nutlins, was identified. We envisioned that Nutlins could protect both endogenous and exogenous p53 from MDM2-mediated inactivation. We therefore investigated treating human cancer cells with a combination of adenovirus-mediated p53 gene therapy and Nutlin. Combination treatment resulted in broadly effective cell kill of p53 WT and p53-negative cancer cells. Cytotoxicity was associated with profound cell cycle checkpoint activation and apoptosis induction. We also tested Nutlin in combination with oncolytic adenoviruses. Nutlin treatment accelerated viral progeny burst from oncolytic adenovirus-infected cancer cells and caused an estimated 10- to 1,000-fold augmented eradication of p53 WT cancer cells. These findings suggest that Nutlins are promising compounds to be combined with p53 gene therapy and oncolytic virotherapy for cancer. [Mol Cancer Ther 2007;6(5):1552–61]
Rad51 overexpression contributes to chemoresistance in human soft tissue sarcoma cells: a role for p53/activator protein 2 transcriptional regulation
Authors: Hannay Jonathan A.F. , Liu Juehui , Zhu Quan-Sheng , Bolshakov Svetlana V. , Li Lan , Pisters Peter W.T. , Lazar Alexander J.F. , Yu Dihua , Pollock Raphael E. , Lev Dina 
Published: May 2007

Abstract
We investigated whether Rad51 overexpression plays a role in soft tissue sarcoma (STS) chemoresistance as well as the regulatory mechanisms underlying its expression. The studies reported here show that Rad51 protein is overexpressed in a large panel of human STS specimens. Human STS cell lines showed increased Rad51 protein expression, as was also observed in nude rat STS xenografts. STS cells treated with doxorubicin exhibited up-regulation of Rad51 protein while arrested in the S-G2 phase of the cell cycle. Treatment with anti-Rad51 small interfering RNA decreased Rad51 protein expression and increased chemosensitivity to doxorubicin. Because we previously showed that reintroduction of wild-type p53 (wtp53) into STS cells harboring a p53 mutation led to increased doxorubicin chemosensitivity, we hypothesized that p53 participates in regulating Rad51 expression in STS. Reintroduction of wtp53 into STS cell lines resulted in decreased Rad51 protein and mRNA expression. Using luciferase reporter assays, we showed that reconstitution of wtp53 function decreased Rad51 promoter activity. Deletion constructs identified a specific Rad51 promoter region containing a p53-responsive element but no p53 consensus binding site. Electrophoretic mobility shift assays verified activator protein 2 (AP2) binding to this region and increased AP2 binding to the promoter in the presence of wtp53. Mutating this AP2 binding site eliminated the wtp53 repressive effect. Furthermore, AP2 knockdown resulted in increased Rad51 expression. In light of the importance of Rad51 in modulating STS chemoresistance, these findings point to a potential novel strategy for molecular-based treatments that may be of relevance to patients burdened by STS. [Mol Cancer Ther 2007;6(5):1650–60]