bluuebunny/crossref_metadata_2025 huggingface dataset:
Flavodoxin hydroquinone reduces
Azotobacter vinelandii
Fe protein to the all-ferrous redox state with a S = 0 spin state
Authors: Lowery Thomas J. , Wilson Phillip E. , Zhang Bo , Bunker Jared , Harrison Roger G. , Nyborg Andrew C. , Thiriot David , Watt Gerald D.
Published: November 2006

Azotobacter vinelandii
flavodoxin hydroquinone (FldHQ) is a physiological reductant to nitrogenase supporting catalysis that is twice as energy efficient (ATP/2e
–
= 2) as dithionite (ATP/2e
–
= 4). This catalytic efficiency results from reduction of Fe protein from
A. vinelandii
(Av2) to the all-ferrous oxidation state ([Fe
4
S
4
]
0
), in contrast to dithionite, which only reduces Av2 to the [Fe
4
S
4
]
1+
state. Like FldHQ, Ti(III) citrate yields ATP/2e
–
= 2, and Ti(III)-reduced [Fe
4
S
4
]
0
Av2 has a S = 4 spin state and characteristic Mossbauer spectrum, a parallel mode g = 16.4 EPR signal, and a shoulder at 520 nm in its UV-vis spectrum, each of which distinguish the S = 4 [Fe
4
S
4
]
0
Av2 from other states. In this study, we demonstrate that FldHQ makes [Fe
4
S
4
]
0
Av2, which is sufficiently characterized to demonstrate unique physical properties that distinguish it from the previously characterized Ti(III)-reduced [Fe
4
S
4
]
0
Av2. In particular, Evans NMR magnetic susceptibility and EPR measurements indicate that FldHQ-reduced [Fe
4
S
4
]
0
Av2 has an S = 0 spin state (like [Fe
4
S
4
]
2+
Av2). There is no
g
= 16.4 EPR signal and no shoulder at 520 nm in its absorbance spectrum, which resembles that of [Fe
4
S
4
]
1+
Av2. That the physiological reductant to Av2 is capable of forming [Fe
4
S
4
]
0
Av2 has important implications for
in vivo
nitrogenase activity.
Biogenesis of actin-like bacterial cytoskeletal filaments destined for positioning prokaryotic magnetic organelles
Authors: Pradel Nathalie , Santini Claire-Lise , Bernadac Alain , Fukumori Yoshihiro , Wu Long-Fei
Published: November 2006

Magnetosomes comprise a magnetic nanocrystal surrounded by a lipid bilayer membrane. These unique prokaryotic organelles align inside magnetotactic bacterial cells and serve as an intracellular compass allowing the bacteria to navigate along the geomagnetic field in aquatic environments. Cryoelectron tomography of
Magnetospirillum
strains has revealed that the magnetosome chain is surrounded by a network of filaments that may be composed of MamK given that the filaments are absent in the
mamK
mutant cells. The process of the MamK filament assembly is unknown. Here we prove the authenticity of the MamK filaments and show that MamK exhibits linear distribution inside
Magnetospirillum
sp. cells even in the area without magnetosomes. The
mamK
gene alone is sufficient to direct the synthesis of straight filaments in
Escherichia coli
, and one extremity of the MamK filaments is located at the cellular pole. By using dual fluorescent labeling of MamK, we found that MamK nucleates at multiple sites and assembles into mosaic filaments. Time-lapse experiments reveal that the assembly of the MamK filaments is a highly dynamic and kinetically asymmetrical process. MamK bundles might initiate the formation of a new filament or associate to one preexistent filament. Our results demonstrate the mechanism of biogenesis of prokaryotic cytoskeletal filaments that are structurally and functionally distinct from the known MreB and ParM filaments. In addition to positioning magnetosomes, other hypothetical functions of the MamK filaments in magnetotaxis might include anchoring magnetosomes and being involved in magnetic reception.
A pivotal role for endogenous TGF-β-activated kinase-1 in the LKB1/AMP-activated protein kinase energy-sensor pathway
Authors: Xie Min , Zhang Dou , Dyck Jason R. B. , Li Yi , Zhang Hui , Morishima Masae , Mann Douglas L. , Taffet George E. , Baldini Antonio , Khoury Dirar S. , Schneider Michael D.
Published: November 2006

TGF-β-activated kinase-1 (TAK1), also known as MAPKK kinase-7 (MAP3K7), is a candidate effector of multiple circuits in cardiac biology and disease. Here, we show that inhibition of TAK1 in mice by a cardiac-specific dominant-negative mutation evokes electrophysiological and biochemical properties reminiscent of human Wolff–Parkinson–White syndrome, arising from mutations in AMP-activated protein kinase (AMPK), most notably, accelerated atrioventricular conduction and impaired AMPK activation. To test conclusively the biochemical connection from TAK1 to AMPK suggested by this phenotype, we disrupted TAK1 in mouse embryos and embryonic fibroblasts by Cre-mediated recombination. In TAK1-null embryos, the activating phosphorylation of AMPK at T172 was blocked, accompanied by defective AMPK activity. However, loss of endogenous TAK1 causes midgestation lethality, with defective yolk sac and intraembryonic vasculature. To preclude confounding lethal defects, we acutely ablated floxed TAK1 in culture by viral delivery of Cre. In culture, endogenous TAK1 was activated by oligomycin, the antidiabetic drug metformin, 5-aminoimidazole-4-carboxamide riboside (AICAR), and ischemia, well established triggers of AMPK activity. Loss of TAK1 in culture blocked T172 phosphorylation induced by all three agents, interfered with AMPK activation, impaired phosphorylation of the endogenous AMPK substrate acetyl CoA carboxylase, and also interfered with activation of the AMPK kinase LKB1. Thus, by disrupting the endogenous TAK1 locus, we prove a pivotal role for TAK1 in the LKB1/AMPK signaling axis, an essential governor of cell metabolism.
Dual recognition of herpes simplex viruses by TLR2 and TLR9 in dendritic cells
Authors: Sato Ayuko , Linehan Melissa M. , Iwasaki Akiko
Published: November 2006

Dendritic cells (DCs) express multiple Toll-like receptors (TLR) in distinct cellular locations. Herpes simplex viruses (HSV) have been reported to engage both the surface TLR2 and intracellular TLR9 in conventional DCs. However, the contributions of these TLRs in recognition of HSV and the induction of proinflammatory cytokines in DCs remain unclear. Here, we demonstrate that a rare population of HSV, both in laboratory strains and in primary clinical isolates from humans, has the capacity to activate TLR2. This virus population is recognized through both TLR2 and TLR9 for the induction of IL-6 and IL-12 secretion from bone marrow-derived DCs. Further, we describe a previously uncharacterized pathway of viral recognition in which TLR2 and TLR9 are engaged in sequence within the same DC. Live viral infection results in two additional agonists of TLR2 and TLR9. These results indicate that in cells that express multiple TLRs, pathogens that contain multiple pathogen-associated molecular patterns can be detected in an orchestrated sequence and suggest that the innate immune system in DCs is optimized to linking uptake and degradation of pathogens to microbial recognition.
Telomere-mediated chromosomal truncation in maize
Authors: Yu Weichang , Lamb Jonathan C. , Han Fangpu , Birchler James A.
Published: November 2006

Direct repeats of
Arabidopsis
telomeric sequence were constructed to test telomere-mediated chromosomal truncation in maize. Two constructs with 2.6 kb of telomeric sequence were used to transform maize immature embryos by
Agrobacterium
-mediated transformation. One hundred seventy-six transgenic lines were recovered in which 231 transgene loci were revealed by a FISH analysis. To analyze chromosomal truncations that result in transgenes located near chromosomal termini, Southern hybridization analyses were performed. A pattern of smear in truncated lines was seen as compared with discrete bands for internal integrations, because telomeres in different cells are elongated differently by telomerase. When multiple restriction enzymes were used to map the transgene positions, the size of the smears shifted in accordance with the locations of restriction sites on the construct. This result demonstrated that the transgene was present at the end of the chromosome immediately before the integrated telomere sequence. Direct evidence for chromosomal truncation came from the results of FISH karyotyping, which revealed broken chromosomes with transgene signals at the ends. These results demonstrate that telomere-mediated chromosomal truncation operates in plant species. This technology will be useful for chromosomal engineering in maize as well as other plant species.
Quantitative multispectral biosensing and 1D imaging using quasi-3D plasmonic crystals
Authors: Stewart Matthew E. , Mack Nathan H. , Malyarchuk Viktor , Soares Julio A. N. T. , Lee Tae-Woo , Gray Stephen K. , Nuzzo Ralph G. , Rogers John A.
Published: November 2006

We developed a class of quasi-3D plasmonic crystal that consists of multilayered, regular arrays of subwavelength metal nanostructures. The complex, highly sensitive structure of the optical transmission spectra of these crystals makes them especially well suited for sensing applications. Coupled with quantitative electrodynamics modeling of their optical response, they enable full multiwavelength spectroscopic detection of molecular binding events with sensitivities that correspond to small fractions of a monolayer. The high degree of spatial uniformity of the crystals, formed by a soft nanoimprint technique, provides the ability to image binding events over large areas with micrometer spatial resolution. These features, together with compact form factors, low-cost fabrication procedures, simple readout apparatus, and ability for direct integration into microfluidic networks and arrays, suggest promise for these devices in label-free bioanalytical detection systems.
Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain
Authors: Anbanandam Asokan , Albarado Diana C. , Nguyen Catherine T. , Halder Georg , Gao Xiaolian , Veeraraghavan Sudha
Published: November 2006

Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. Our results provide a model for understanding the regulation of genome-wide gene expression during development by TEA/ATTS family of transcription factors.
Feasibility of cooling the Earth with a cloud of small spacecraft near the inner Lagrange point (L1)
Authors: Angel Roger
Published: November 2006

If it were to become apparent that dangerous changes in global climate were inevitable, despite greenhouse gas controls, active methods to cool the Earth on an emergency basis might be desirable. The concept considered here is to block 1.8% of the solar flux with a space sunshade orbited near the inner Lagrange point (L1), in-line between the Earth and sun. Following the work of J. Early [Early, JT (1989)
J Br Interplanet Soc
42:567–569], transparent material would be used to deflect the sunlight, rather than to absorb it, to minimize the shift in balance out from L1 caused by radiation pressure. Three advances aimed at practical implementation are presented. First is an optical design for a very thin refractive screen with low reflectivity, leading to a total sunshade mass of ≈20 million tons. Second is a concept aimed at reducing transportation cost to $50/kg by using electromagnetic acceleration to escape Earth's gravity, followed by ion propulsion. Third is an implementation of the sunshade as a cloud of many spacecraft, autonomously stabilized by modulating solar radiation pressure. These meter-sized “flyers” would be assembled completely before launch, avoiding any need for construction or unfolding in space. They would weigh a gram each, be launched in stacks of 800,000, and remain for a projected lifetime of 50 years within a 100,000-km-long cloud. The concept builds on existing technologies. It seems feasible that it could be developed and deployed in ≈25 years at a cost of a few trillion dollars, <0.5% of world gross domestic product (GDP) over that time.
Early modern humans from the Peştera Muierii, Baia de Fier, Romania
Authors: Soficaru Andrei , Doboş Adrian , Trinkaus Erik
Published: November 2006

The early modern human remains from the Peştera Muierii, Romania have been directly dated to ≈30,000 radiocarbon years before present (≈30 ka
14
C BP) (≈35 ka cal BP) (“calendrical” age; based on CalPal 2005) and augment a small sample of securely dated, European, pre-28 ka
14
C BP (≈32.5 ka cal BP) modern human remains. The Muierii fossils exhibit a suite of derived modern human features, including reduced maxillae with pronounced canine fossae, a narrow nasal aperture, small superciliary arches, an arched parietal curve, zygomatic arch above the auditory porous, laterally bulbous mastoid processes, narrow mandibular corpus, reduced anterior dentition, ventral-to-bisulcate scapular axillary border, and planoconcave tibial and fibular diaphyseal surfaces. However, these traits co-occur with contextually archaic and/or Neandertal features, including a moderately low frontal arc, a large occipital bun, a high coronoid process and asymmetrical mandibular notch, a more medial mandibular notch crest to condylar position, and a narrow scapular glenoid fossa. As with other European early modern humans, the mosaic of modern human and archaic/Neandertal features, relative to their potential Middle Paleolithic ancestral populations, indicates considerable Neandertal/modern human admixture. Moreover, the narrow scapular glenoid fossa suggests habitual movements at variance with the associated projectile technology. The reproductive and scapulohumeral functional inferences emphasize the subtle natures of behavioral contrasts between Neandertals and these early modern Europeans.
APhytophthora infestansCystatin-Like Protein Targets a Novel Tomato Papain-Like Apoplastic Protease
Authors: Tian Miaoying , Win Joe , Song Jing , van der Hoorn Renier , van der Knaap Esther , Kamoun Sophien
Published: November 2006

There is emerging evidence that the proteolytic machinery of plants plays important roles in defense against pathogens. The oomycete pathogen Phytophthora infestans, the agent of the devastating late blight disease of tomato (Lycopersicon esculentum) and potato (Solanum tuberosum), has evolved an arsenal of protease inhibitors to overcome the action of host proteases. Previously, we described a family of 14 Kazal-like extracellular serine protease inhibitors from P. infestans. Among these, EPI1 and EPI10 bind and inhibit the pathogenesis-related (PR) P69B subtilisin-like serine protease of tomato. Here, we describe EPIC1 to EPIC4, a new family of P. infestans secreted proteins with similarity to cystatin-like protease inhibitor domains. Among these, the epiC1 and epiC2 genes lacked orthologs in Phytophthora sojae and Phytophthora ramorum, were relatively fast-evolving within P. infestans, and were up-regulated during infection of tomato, suggesting a role during P. infestans-host interactions. Biochemical functional analyses revealed that EPIC2B interacts with and inhibits a novel papain-like extracellular cysteine protease, termed Phytophthora Inhibited Protease 1 (PIP1). Characterization of PIP1 revealed that it is a PR protein closely related to Rcr3, a tomato apoplastic cysteine protease that functions in fungal resistance. Altogether, this and earlier studies suggest that interplay between host proteases of diverse catalytic families and pathogen inhibitors is a general defense-counterdefense process in plant-pathogen interactions.
A Heat-Inducible Transcription Factor, HsfA2, Is Required for Extension of Acquired Thermotolerance in Arabidopsis
Authors: Charng Yee-yung , Liu Hsiang-chin , Liu Nai-yu , Chi Wen-tzu , Wang Chun-neng , Chang Shih-hsun , Wang Tsu-tsuen
Published: November 2006

The expression of heat shock proteins (Hsps) induced by nonlethal heat treatment confers acquired thermotolerance (AT) to organisms against subsequent challenges of otherwise lethal temperature. After the stress signal is removed, AT gradually decays, with decreased Hsps during recovery. AT of sufficient duration is critical for sessile organisms such as plants to survive repeated heat stress in their environment, but little is known regarding its regulation. To identify potential regulatory components, we took a reverse genetics approach by screening for Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutants that show decreased thermotolerance after a long recovery (2 d) under nonstress conditions following an acclimation heat treatment. Among the tested mutants corresponding to 48 heat-induced genes, only the heat shock transcription factor HsfA2 knockout mutant showed an obvious phenotype. Following pretreatment at 37°C, the mutant line was more sensitive to severe heat stress than the wild type after long but not short recovery periods, and this could be complemented by the introduction of a wild-type copy of the HsfA2 gene. Quantitative hypocotyl elongation assay also revealed that AT decayed faster in the absence of HsfA2. Significant reduction in the transcript levels of several highly heat-inducible genes was observed in HsfA2 knockout plants after 4 h recovery or 2 h prolonged heat stress. Immunoblot analysis showed that Hsa32 and class I small Hsp were less abundant in the mutant than in the wild type after long recovery. Our results suggest that HsfA2 as a heat-inducible transactivator sustains the expression of Hsp genes and extends the duration of AT in Arabidopsis.
The Exoribonuclease XRN4 Is a Component of the Ethylene Response Pathway inArabidopsis
Authors: Potuschak Thomas , Vansiri Amérin , Binder Brad M. , Lechner Esther , Vierstra Richard D. , Genschik Pascal
Published: November 2006

EXORIBONUCLEASE4 (XRN4), the Arabidopsis thaliana homolog of yeast XRN1, is involved in the degradation of several unstable mRNAs. Although a role for XRN4 in RNA silencing of certain transgenes has been reported, xrn4 mutant plants were found to lack any apparent visible phenotype. Here, we show that XRN4 is allelic to the unidentified components of the ethylene response pathway ETHYLENE-INSENSITIVE5/ACC-INSENSITIVE1 (EIN5/AIN1) and EIN7. xrn4 mutant seedlings are ethylene-insensitive as a consequence of the upregulation of EIN3 BINDING F-BOX PROTEIN1 (EBF1) and EBF2 mRNA levels, which encode related F-box proteins involved in the turnover of EIN3 protein, a crucial transcriptional regulator of the ethylene response pathway. Epistasis analysis placed XRN4/EIN5/AIN1 downstream of CTR1 and upstream of EBF1/2. XRN4 does not appear to regulate ethylene signaling via an RNA-INDUCED SILENCING COMPLEX–based RNA silencing mechanism but acts by independent means. The identification of XRN4 as an integral new component in ethylene signaling adds RNA degradation as another posttranscriptional process that modulates the perception of this plant hormone.
Sleep and the metabolic syndrome
Authors: Wolk Robert , Somers Virend K.
Published: November 2006

The metabolic syndrome represents a clustering of several interrelated risk factors of metabolic origin that are thought to increase cardiovascular risk. It is still uncertain whether this clustering results from multiple underlying risk factors or whether it has a single cause. One metabolic abnormality that may underlie several clinical characteristics of the metabolic syndrome is insulin resistance. This review discusses the evidence that sleep disturbances (obstructive sleep apnoea, sleep deprivation and shift work) may independently lead to the development of both insulin resistance and individual clinical components of the metabolic syndrome. The converse may also be true, in that metabolic abnormalities associated with the metabolic syndrome and insulin resistance may potentially exacerbate sleep disorders. The notion that sleep disturbances exert detrimental metabolic effects may help explain the increasing prevalence of the metabolic syndrome and insulin resistance in the general population and may have important implications for population‐based approaches to combat the increasing epidemic of metabolic and cardiovascular disease.
Induction of cardioplegic arrest immediately activates the myocardial apoptosis signal pathway
Authors: Fischer Uwe M. , Cox Charles S. , Laine Glen A. , Mehlhorn Uwe , Bloch Wilhelm , Allen Steven J.
Published: November 2006

Myocardial ischemia-reperfusion, including cardioplegic arrest (CA), has been associated with cardiac apoptosis induction. However, the time course of apoptosis activation and the trigger mechanisms are still unclear. Because apoptosis inhibition may represent a novel therapeutic strategy for long-term myocardial preservation, we sought to investigate the time course of apoptosis signal-pathway induction during CA. As to method, Sprague-Dawley rats (300–350 g) were anesthetized, intubated, and mechanically ventilated. CA was initiated by infusion of ice-cold crystalloid solution (Custodiol, 10 ml/kg) into the aortic root, and hearts were rapidly excised and stored for 0, 30, 60, and 120 min in 0.9% sodium chloride solution (28°C). In controls, no CA was initiated before removal and storage at 28°C. In another group, calcium-rich cardioplegia was used, and an additional group received a caspase-8 inhibitor before CA induction. Left ventricular cytosolic extracts were isolated and investigated for the activity of caspase-3 and -6 (effector caspases) and caspase-8 and -9 (involved in extrinsic and intrinsic pathways of apoptosis induction). Fluorometric activity assays were performed by using specific substrates. As a result, activities of all tested caspases were significantly increased immediately after CA induction compared with controls. Administration of the caspase-8 inhibitor significantly reduced activities of all caspases. With calcium-rich cardioplegia, caspase activities were significantly lower compared with low-calcium CA. Control hearts also showed an increase of caspase activities during cold-storage ischemia without CA but had significantly different time courses compared with hearts with CA. In conclusion, our data show rapid apoptosis signal-pathway induction immediately following CA exposure. Thus apoptosis signal-pathway inhibition as a potential strategy for improved myocardial preservation would have the greatest effect when applied before CA exposure.
Downregulation of PCNA potentiates p21-mediated growth inhibition in response to hyperoxia
Authors: Gehen Sean C. , Vitiello Peter F. , Bambara Robert A. , Keng Peter C. , O'Reilly Michael A.
Published: November 2006

Prolonged exposure to hyperoxia inhibits cell proliferation in G1via increased expression of p21. While p21 inhibits proliferating cell nuclear antigen (PCNA)-dependent DNA synthesis, it can also directly lower PCNA abundance; however, it is unclear whether loss of PCNA contributes to growth arrest. Here, we investigate how PCNA loss affects ability of p21 to exert G1growth arrest of lung epithelial cells exposed to hyperoxia. In A549 cells that express p21 and growth arrest in G1during hyperoxia, small interfering RNA (siRNA) knockdown of p21 led to G1checkpoint bypass, increased cell death, and restoration of PCNA expression. Conditional overexpression of the PCNA binding domain of p21 in H1299 cells that do not normally express p21, or exposure to hyperoxia, caused a time-dependent loss of PCNA. Titrating PCNA levels using siRNA to approximate the low amount observed in cells expressing p21 resulted in S phase arrest. While lowering PCNA by itself caused S phase arrest, the combination of hyperoxia and siRNA against PCNA dramatically reduced PCNA abundance resulting in G1arrest. G1growth arrest was markedly enhanced upon the addition of p21 to these cells. Our findings suggest a model in which reducing expression of the abundant protein PCNA allows the less abundant protein p21 to be more effective at suppressing the processivity functions of remaining PCNA, thereby fully exerting the G1checkpoint. Given that high p21 expression is often associated with lower PCNA abundance, our findings are suggestive of a global growth inhibitory mechanism involving p21-mediated PCNA suppression.
Cardiovascular and lung inflammatory effects induced by systemically administered diesel exhaust particles in rats
Authors: Nemmar Abderrahim , Al-Maskari Sultan , Ali Badreldin H. , Al-Amri Issa S.
Published: November 2006

Pollution by particulates has consistently been associated with increased cardiorespiratory morbidity and mortality. It has been suggested that ultrafine particles, of which diesel exhaust particles (DEP) are significant contributors, are able to translocate from the airways into the bloodstream in vivo. In the present study, we assessed the effect of systemic administration of DEP on cardiovascular and respiratory parameters. DEP were administered into the tail vein of rats, and heart rate, blood pressure, blood platelet activation, and lung inflammation were studied 24 h later. Doses of 0.02, 0.1, or 0.5 mg DEP/kg (8, 42, or 212 μg DEP/rat) induced a significant decrease of heart rate and blood pressure compared with saline-treated rats. Although the number of platelets was not affected, all the doses of DEP caused a shortening of the bleeding time. Similarly, in addition to triggering lung edema, the bronchoalveolar lavage analysis revealed the presence of neutrophil influx in DEP-treated rats in a dose-dependent manner. We conclude that the presence of DEP in the systemic circulation leads not only to cardiovascular and haemostatic changes but it also triggers pulmonary inflammation.
Proproliferative phenotype of pulmonary microvascular endothelial cells
Authors: Solodushko Victor , Fouty Brian
Published: November 2006

Endothelial cells perform a number of important functions including release of vasodilators, control of the coagulation cascade, and restriction of solutes and fluid from the extravascular space. Regulation of fluid balance is of particular importance in the microcirculation of the lung where the loss of endothelial barrier function can lead to alveolar flooding and life-threatening hypoxemia. Significant heterogeneity exists between endothelial cells lining the microcirculation and cells from larger pulmonary arteries, however, and these differences may be relevant in restoring barrier function following vascular injury. Using well-defined populations of rat endothelial cells harvested from the pulmonary microcirculation [pulmonary microvascular endothelial cells (PMVEC)] and from larger pulmonary arteries [pulmonary artery endothelial cells (PAEC)], we compared their growth characteristics in low serum conditions. Withdrawal of serum inhibited proliferation and induced G0/G1arrest in PAEC, whereas PMVEC failed to undergo G0/G1arrest and continued to proliferate. Consistent with this observation, PMVEC had an increased cdk4 and cdk2 kinase activity with hyperphosphorylated (inactive) retinoblastoma (Rb) relative to PAEC as well as a threefold increase in cyclin D1 protein levels; overexpression of the cdk inhibitors p21Cip1/Waf1and p27Kip1induced G0/G1arrest. While serum withdrawal failed to induce G0/G1arrest in nonconfluent PMVEC, confluence was associated with hypophosphorylated Rb and growth arrest; loss of confluence led to resumption of growth. These data suggest that nonconfluent PMVEC continue to proliferate independently of growth factors. This proliferative characteristic may be important in restoring confluence (and barrier function) in the pulmonary microcirculation following endothelial injury.
The evolutionary continuum from lung development to homeostasis and repair
Authors: Torday J. S. , Rehan V. K.
Published: November 2006

A functional, developmental, and comparative biological approach is probably the most effective way for arranging gene regulatory networks (GRNs) in their biological contexts. Evolutionary developmental biology allows comparison of GRNs during development across phyla. For lung evolution, the parathyroid hormone-related protein (PTHrP) GRN exemplifies a continuum from ontogeny to phylogeny, homeostasis, and repair. PTHrP signaling between the lung endoderm and mesoderm stimulates lipofibroblast differentiation by downregulating the myofibroblast Wnt signaling pathway and upregulating the protein kinase A-dependent cAMP signaling pathway, inducing the lipofibroblast phenotype. Leptin secreted by the lipofibroblast, in turn, binds to its receptor on the alveolar type II cell, stimulating surfactant synthesis to ensure alveolar homeostasis. Failure of the PTHrP/PTHrP receptor signaling mechanism causes transdifferentiation of lipofibroblasts to myofibroblasts, which are the hallmark for lung fibrosis. We have shown that by targeting peroxisome proliferator-activated receptor γ, the downstream target for lipofibroblast PTHrP signaling, we can prevent lung fibrosis. We speculate that the recapitulation of the myofibroblast phenotype during transdifferentiation is consistent with lung injury as lung evolution in reverse. Repair recapitulates ontogeny because it is programmed to express the cross talk between epithelium and mesoderm through evolution. This model demonstrates how epithelial-mesenchymal cross talk, when seen as a recapitulation of ontogeny and phylogeny (in both a forward and reverse direction), predicts novel, effective diagnostic and therapeutic targets.
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
Authors: Malig Rodrigo , Varela Cristian , Agosin Eduardo , Melo Francisco
Published: November 2006

Background

In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE). The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome.

Results

We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T) priming to internal poly-(A) regions during reverse transcription.

Conclusion

We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.
Unusual patterns of Monteggia fracture-dislocation
Authors: Kazakos Constantinos J , Galanis Vasilios G , Verettas Dennis-Alexander J , Dimitrakopoulou Alexandra , Polychronidis Alexandros , Simopoulos Constantinos
Published: November 2006

Background

High-energy trauma may result in uncommon open injuries around the elbow joint. The management of these injuries can be difficult.

Case description

Fourteen patients were treated between 1999 and 2003 and their injuries consisted of Monteggia fracture-dislocations combined with segmental fractures of the ulna or fractures of the forearm bones and/or various more complex trauma such as neural injuries, bone comminution and severe soft tissue injuries around the elbow. Eight of them (57%) were multiply injured with severe additional injuries. All patients underwent surgery within first 4–6 hours. Internal fixation, external fixation or a combination of both methods were used to stabilize fractures while open wounds had secondary closure.

Results

Additional operations were required in 6 patients. The functional results according to the Mayo Elbow Performance Index were excellent or good in eleven patients, and fair or poor in the remaining three. The patients with fair and poor results had suffered from severe neural and soft tissue trauma and/or multiple fractures of the upper extremity.

Conclusion

These injuries should be treated as an emergency. The surgeon should apply any available method that can provide stability to the bone fragments and safe handling of the soft tissues giving priority to internal fixation of the fractures. Severe osseous, soft tissue and neural trauma affect the functional results of the elbow region.
Effects of Graphene Layer Size on the Adsorption of Fluids on Graphitized Thermal Carbon Black. A Computer Simulation Study
Authors: Luangkiattikhun P. , Wongkoblap A. , Do D.D.
Published: November 2006

The adsorption of Lennard-Jones fluids (argon and nitrogen) onto a graphitized thermal carbon black surface was studied with a Grand Canonical Monte Carlo Simulation (GCMC). The surface was assumed to be finite in length and composed of three graphene layers. When the GCMC simulation was used to describe adsorption on a graphite surface, an over-prediction of the isotherm was consistently observed in the pressure regions where the first and second layers are formed. To remove this over-prediction, surface mediation was accounted for to reduce the fluid–fluid interaction.

Do and co-workers have introduced the so-called surface-mediation damping factor to correct the over-prediction for the case of a graphite surface of infinite extent, and this approach has yielded a good description of the adsorption isotherm. In this paper, the effects of the finite size of the graphene layer on the adsorption isotherm and how these would affect the extent of the surface mediation were studied. It was found that this finite-surface model provides a better description of the experimental data for graphitized thermal carbon black of high surface area (i.e. small crystallite size) while the infinite-surface model describes data for carbon black of very low surface area (i.e. large crystallite size).
Design and Behavior of Enlarged End Flange (EEF) Steel Moment-Frame Connections
Authors: Hsiao J. Kent , Coupar Matthew S.
Published: November 2006

The FEMA-350 indicates that the expected location of the plastic hinge for the frame beams with the Reduced Beam Section (RBS) connections is valid only for beams with gravity loads representing a small portion of the total flexural demand. In order to overcome the limitation of the gravity loads, the Enlarged End Flange (EEF) connection is proposed. In EEF connections, side plates are welded to the beam flanges near the beam ends. This paper presents a hand-calculated design example and the suggested connection details of a beam with the EEF connection. A study of the flexural strength and the interstory drift angular rotations of a total of five EEF beam-to-column connections, with beam sizes ranging from W24 × 94 up to W36 × 182, using the nonlinear static finite element approach is also summarized in this paper. The study concludes that the EEF connection is recommended for use in an ordinary moment frame system with wide bay widths.
The Modification of Strength Reduction Factors for MDOF Effect
Authors: Zhai Chang-Hai , Xie Li-Li
Published: November 2006

This paper focuses on the modification of SDOF system strength reduction factors to suit MDOF systems. Firstly, an approach to calculation of the modification factors is presented and a method of determining storey ductility of structures with incremental dynamic analysis is introduced. Then, the modifications of the strength reduction factors to take account of MDOF effect are investigated for four RC frame structures strictly designed according to the Chinese seismic code subjected to 80 earthquake ground motions. The ductility level, structural period and site conditions effects on the modification factors are discussed and a simplified expression to estimate the modification factors is presented, which is a function of the structural period and the ductility level. It is concluded that the modification factors are primarily affected by the ductility level and structural periods and the inverse of the modification factors increases apparently with increasing ductility level and structural period. It also appears that the site conditions have little effect on the modification factors.
Design of Gold Nanoparticles for Magnetic Resonance Imaging
Authors: Debouttière P.‐J. , Roux S. , Vocanson F. , Billotey C. , Beuf O. , Favre‐Réguillon A. , Lin Y. , Pellet‐Rostaing S. , Lamartine R. , Perriat P. , Tillement O.
Published: November 2006

Improving the sensitivity of magnetic resonance imaging (MRI), a powerful non‐invasive medical imaging technique, requires the development of novel contrast agents with a higher efficiency than gadolinium chelates such as DTPA:Gd (DTPA: diethylenetriaminepentaacetic acid) that are currently used for clinical diagnosis. To achieve this objective, the strategy that we have explored involves the use of gold nanoparticles as carriers for gadolinium chelates. These nanoparticles are obtained by reducing a gold salt in the presence of a dithiolated derivative of DTPA. Characterization of these particles by transmission electron microscopy (TEM), X‐ray diffraction (XRD), thermogravimetric analysis (TGA), colorimetric titration, and X‐ray photoelectron spectroscopy (XPS) reveals the presence of a multilayered shell containing about 150 ligands on 2–2.5 nm sized particles. These particles exhibit a high relaxivity (r1 = 585 mM–1 s–1 as compared to 3.0 mM–1 s–1 for DTPA:Gd), rendering them very attractive as contrast agents for MRI.
Projections of somatosensory cortex and frontal eye fields onto incertotectal neurons in the cat
Authors: Perkins Eddie , Warren Susan , Lin Rick C.‐S. , May Paul J.
Published: November 2006

The goal of this study was to determine whether the input‐output characteristics of the zona incerta (ZI) are appropriate for it to serve as a conduit for cortical control over saccade‐related activity in the superior colliculus. The study utilized the neuronal tracers wheat germ agglutinin‐horseradish peroxidase (WGA‐HRP) and biotinylated dextran amine (BDA) in the cat. Injections of WGA‐HRP into primary somatosensory cortex (SI) revealed sparse, widespread nontopographic projections throughout ZI. In addition, region‐specific areas of more intense termination were present in ventral ZI, although strict topography was not observed. In comparison, the frontal eye fields (FEF) also projected sparsely throughout ZI, but terminated more heavily, medially, along the border between the two sublaminae. Furthermore, retrogradely labeled incertocortical neurons were observed in both experiments. The relationship of these two cortical projections to incertotectal cells was also directly examined by retrogradely labeling incertotectal cells with WGA‐HRP in animals that had also received cortical BDA injections. Labeled axonal arbors from both SI and FEF had thin, sparsely branched axons with numerous en passant boutons. They formed numerous close associations with the somata and dendrites of WGA‐HRP‐labeled incertotectal cells. In summary, these results indicate that both sensory and motor cortical inputs to ZI display similar morphologies and distributions. In addition, both display close associations with incertotectal cells, suggesting direct synaptic contact. From these data, we conclude that inputs from somatosensory and FEF cortex both play a role in controlling gaze‐related activity in the superior colliculus by way of the inhibitory incertotectal projection. Anat Rec Part A, 2006. © 2006 Wiley‐Liss, Inc.
Kleine Geschichte der Schnee‐ und Windlastannahmen im 19. Jahrhundert
Authors: Holzer Stefan M.
Published: November 2006

Die extremen Wetterereignisse der letzten Jahre haben die atmosphärischen Lasteinwirkungen auf Bauwerke zurück ins Bewußtsein gebracht. Während die Entwicklung der Lastannahmen für Wind und Schnee im 20. Jahrhundert recht bekannt sein dürfte, findet man wenige Informationen über die “Frühgeschichte” der Lastansätze. Im vorliegenden Beitrag wird die frühe Entwicklung der Lastannahmen im allgemeinen skizziert und insbesondere die Einführung der Schnee‐ und Windlast in die statische Berechnung untersucht. Anschließend wird die Geschichte der Schnee‐ und Windlastannahmen bis ins frühe 20. Jahrhundert verfolgt.
The role of women's self‐injury support‐groups: a grounded theory
Authors: Corcoran Jennifer , Mewse Avril , Babiker Gloria
Published: November 2006

Research evidence suggests that services are struggling to adequately address the increasing incidence of self‐injury and the needs of women who self‐injure, while national self‐injury support‐groups across the UK appear to be growing in number. Despite their reported value, evidence regarding the role of self‐injury support‐groups in women's management of their self‐injury is lacking although government policy and official guidelines are advocating the incorporation of support‐groups into self‐injury services. Seven semi‐structured interviews were conducted and analysed using Grounded Theory to investigate the role of three UK self‐injury support‐groups in women's management of self‐injury and associated difficulties. Empowerment‐as‐process emerged as the core theme of self‐injury support‐groups, mediated through experiences of belonging, sharing, autonomy, positive feeling and change. Findings are discussed in relation to relevant theory and research, followed by critical evaluation and implications of the study. Copyright © 2006 John Wiley & Sons, Ltd.
Mercury binding on activated carbon
Authors: Padak Bihter , Brunetti Michael , Lewis Amanda , Wilcox Jennifer
Published: November 2006

Density functional theory has been employed for the modeling of activated carbon (AC) using a fused‐benzene ring cluster approach. Oxygen functional groups have been investigated for their promotion of effective elemental mercury binding on AC surface sites. Lactone and carbonyl functional groups yield the highest mercury binding energies. Further, the addition of halogen atoms has been considered to the modeled surface, and has been found to increase the AC's mercury adsorption capacity. The mercury binding energies increase with the addition of the following halogen atoms, F > Cl > Br > I, with the fluorine addition being the most promising halogen for increasing mercury adsorption. © 2006 American Institute of Chemical Engineers Environ Prog, 2006
Isolation of optically pure (−)‐linalyl acetate from clary sage, Salvia dominica L., Lavender and Lavandin
Authors: Ravid Uzi , Putievsky Eli , Bassat Michal , Ikan Raphael , Weinstein Vera
Published: November 2006

Optically pure (—)‐linalyl acetate was isolated from the essential oils of the plants clary sage, Salvia dominica L., lavender and lavandin belonging to the Labiatae family. 1H‐NMR of synthetic racemic and natural (—)‐linalyl acetate in the presence of various molar ratios of a chiral lanthanide shift reagent Eu(hfc)3 was performed.
The essential oils of some rosemary cultivars
Authors: Tucker Arthur O. , Maciarello Michael J.
Published: November 2006

Twenty‐three named cultivars of Rosmarinus officinalis L. were examined. These cultivars, derived from five botanical varieties, show wide ranges in the leading components: 0.06–57.45% α‐pinene, 3.55–42.69% 1,8‐cineole, 0.20–56.45% camphor, 0.66–21.03% bornyl acetate, and 0.40–14.69% borneol. They may be grouped into six chemical groups: (1) α‐pinene > 1,8‐cineole, (2) 1,8‐cineole > α‐pinene, (3) α‐pinene > camphor + camphene > 1,8‐cineole, (4) camphor + camphene > α‐pinene > 1,8‐cineole, (5) camphor + camphene > 1,8‐cineole > α‐pinene, and (6) borneol + bornyl acetate > camphor.
Additional neutral volatiles from litchi (Litchi chinensis sonn.) fruit
Authors: Fröhlich O. , Schreier P.
Published: November 2006

The volatiles from fresh litchi (Litchi chinensis Sonn.) fruit pulp were separated by standard controlled high‐vacuum distillation with subsequent solvent extraction (pentane‐dichloromethane, 2:1) and silica gel liquid chromatography pre‐separation using a pentane‐diethyl ether gradient. Polar fruit constituents were separated by chloroform extraction and subsequent liquid‐liquid distribution. The concentrates were analysed by capillary gas chromatography (HRGC) and coupled HRGC techniques, i.e. on‐line capillary gas chromatography‐mass spectrometry using electron impact and chemical ionization mode (HRGC‐EI/CI‐MS) as well as capillary gas chromatography‐Fourier transform infrared spectroscopy (HRGC‐FTIR). These techniques revealed the occurrence of 34 aroma components, not previously reported as litchi fruit constituents.
The volatile fraction of Senecio glaucus subsp. Coronopifolius
Authors: De Pooter H. L. , De Buyck L. F. , Schamp N. M. , Aboutabl E. , De Bruyn A. , Husain S. Z.
Published: November 2006

The volatile constituents of Senecio glaucus subsp. coronopifolius (Maire Alexander) were investigated by capillary GC‐MS of the essential oil obtained by steam distillation and of the headspace. Out of more than 80 volatiles, 30 components, accounting for 90% of the oil, were identified by their Kováts indices on stabilized OV‐1 columns and mass spectral data. Chief components of the oil are: myrcene (24%) and dehydrofukinone (I) (21%). (I) was isolated and characterized by UV, IR, 1H‐NMR, 13C‐NMR and MS. The oil smells apricot‐like, while the odour of the intact plant is herbaceous, spicy and floral fruity. (I) is the character impact compound of the oil.
Antibacterial activities of essential oils from Turkish spices and citrus
Authors: Kivanç Merih , Akgül Attila
Published: November 2006

The bacteriostatic and bactericidal activities of 22 essential oils (anise, calamint, celery, coriander, cornmint, cumin, dill, fennel, Laser, laurel, lemon peel, lemon leaf, orange peel, oregano, parsley, rosemary, sage, savory, tarragon, thyme, wild thyme, and Ziziphora) from Turkish spice and citrus plants against seven bacteria (Aerobacter aerogenes, Bacillus subtilis, Escherichia coli, Proteus vulgaris, Pseudomonas aeruginosa, Staphylococcus albus, and Staphylococcus aureus) were evaluated.

The results showed that the essential oils tested varied in their antibacterial activity. Anise, celery, coriander, parsley, and sage were inactive or had little activity; while cornmint, cumin, laurel, lemon peel, orange, oregano, and Ziziphora were active against all tested bacteria to a variable extent. S. aureus and P. vulgaris were the most sensitive organisms, while P. aeruginosa was the most resistant except towards thyme oil. Fifteen essential oils had MBC lower than MIC and only seven were at about the same level. The results also showed that the bacteriostatic data obtained by agar diffusion and serial dilution methods were not always comparable; therefore, in testing the biostatic effects of essential oils it is advisable to carry out both techniques.
Essential oil isolates from the australian flora. Part 2
Authors: Southwell Ian A.
Published: November 2006

The sources of several additional isolates of interest from : ralian flora are listed along with details of yield, isolation procedure and use.
Composition of the volatile oil of Minthostachys glabrescens epl.
Authors: Svendsen A. Baerheim , Scheffer J. J. C. , Looman A.
Published: November 2006

Gas chromatographic analysis of the steam volatile oil of inthostachys glabrescens Epl. showed the presence of a large number of components, 36 of which comprised 95% of the oil. The major components were pulegone (45%) and menthone (18%). The identity of the components was checked by GC‐MS.