bluuebunny/crossref_metadata_2025 huggingface dataset:
Microfluidic Bubble Logic
Authors: Prakash Manu , Gershenfeld Neil
Published: February 2007

We demonstrate universal computation in an all-fluidic two-phase microfluidic system. Nonlinearity is introduced into an otherwise linear, reversible, low–Reynolds number flow via bubble-to-bubble hydrodynamic interactions. A bubble traveling in a channel represents a bit, providing us with the capability to simultaneously transport materials and perform logical control operations. We demonstrate bubble logic AND/OR/NOT gates, a toggle flip-flop, a ripple counter, timing restoration, a ring oscillator, and an electro–bubble modulator. These show the nonlinearity, gain, bistability, synchronization, cascadability, feedback, and programmability required for scalable universal computation. With increasing complexity in large-scale microfluidic processors, bubble logic provides an on-chip process control mechanism integrating chemistry and computation.
Ethanol for a Sustainable Energy Future
Authors: Goldemberg José
Published: February 2007

Renewable energy is one of the most efficient ways to achieve sustainable development. Increasing its share in the world matrix will help prolong the existence of fossil fuel reserves, address the threats posed by climate change, and enable better security of the energy supply on a global scale. Most of the “new renewable energy sources” are still undergoing large-scale commercial development, but some technologies are already well established. These include Brazilian sugarcane ethanol, which, after 30 years of production, is a global energy commodity that is fully competitive with motor gasoline and appropriate for replication in many countries.
Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production
Authors: Himmel Michael E. , Ding Shi-You , Johnson David K. , Adney William S. , Nimlos Mark R. , Brady John W. , Foust Thomas D.
Published: February 2007

Lignocellulosic biomass has long been recognized as a potential sustainable source of mixed sugars for fermentation to biofuels and other biomaterials. Several technologies have been developed during the past 80 years that allow this conversion process to occur, and the clear objective now is to make this process cost-competitive in today's markets. Here, we consider the natural resistance of plant cell walls to microbial and enzymatic deconstruction, collectively known as “biomass recalcitrance.” It is this property of plants that is largely responsible for the high cost of lignocellulose conversion. To achieve sustainable energy production, it will be necessary to overcome the chemical and structural properties that have evolved in biomass to prevent its disassembly.
Challenges in Engineering Microbes for Biofuels Production
Authors: Stephanopoulos Gregory
Published: February 2007

Economic and geopolitical factors (high oil prices, environmental concerns, and supply instability) have been prompting policy-makers to put added emphasis on renewable energy sources. For the scientific community, recent advances, embodied in new insights into basic biology and technology that can be applied to metabolic engineering, are generating considerable excitement. There is justified optimism that the full potential of biofuel production from cellulosic biomass will be obtainable in the next 10 to 15 years.
Don't Forget Long-Term Fundamental Research in Energy
Authors: Whitesides George M. , Crabtree George W.
Published: February 2007

Achieving a fundamental understanding of the phenomena that will underpin both global stewardship and future technologies in energy calls for a thoughtful balance between large-scale immediate solutions using existing technology and the fundamental research needed to provide better solutions in the 50-year period.
Avidity of the Immunoglobulin G Response to aNeisseria meningitidisGroup C Polysaccharide Conjugate Vaccine as Measured by Inhibition and Chaotropic Enzyme-Linked Immunosorbent Assays
Authors: Harris Shannon L. , Tsao How , Ashton Lindsey , Goldblatt David , Fernsten Philip
Published: February 2007

Antibody avidity, the strength of the multivalent interaction between antibodies and their antigens, is an important characteristic of protective immune responses. We have developed an inhibition enzyme-linked immunosorbent assay (ELISA) to measure antibody avidity for the capsular polysaccharide (PS) ofNeisseria meningitidisgroup C (MnC) and determined the avidity constants (KDs) for 100 sera from children immunized with an MnC PS conjugate vaccine. The avidity constants were compared to the avidity indices (AI) obtained for the same sera using a chaotropic ELISA protocol. After the primary immunization series, the geometric mean (GM)KDwas 674 nM and did not change in the months following immunization. However, the GM avidity did increase after the booster dose (GMKD, 414 nM 1 month after booster immunization). In contrast, the GM AI increased from an initial value of 118 after the primary immunization series to 147 6 months after the completion of the primary immunization series and then further increased to 178 after booster immunization. At the individual subject level, the avidity constant and AI correlated after the primary immunization series and after booster immunization but not prior to boosting. This work suggests that the AI, as measured by the chaotropic ELISA, in contrast to theKD, reflects changes that render antibody populations less susceptible to disruption by chaotropic agents without directly affecting the strength of the binding interactions.
Multicenter Evaluation of a Commercial PCR-Enzyme-Linked Immunosorbent Assay Diagnostic Kit (Onychodiag) for Diagnosis of Dermatophytic Onychomycosis
Authors: Savin C. , Huck S. , Rolland C. , Benderdouche M. , Faure O. , Noacco G. , Menotti J. , Candolfi E. , Pelloux H. , Grillot R. , Coupe S. , Derouin F.
Published: February 2007

We prospectively evaluated a new PCR-enzyme-linked immunosorbent assay kit (Onychodiag; BioAdvance, France) for the diagnosis of dermatophytic onychomycosis by testing nail samples from 438 patients with suspected onychomycosis and from 108 healthy controls in three independent laboratories. In two laboratories, samples were collected by trained mycologists as close as possible to the lesions (proximal samples). In one laboratory, samples were collected by other physicians. All samples were processed by conventional mycological techniques and by Onychodiag, blindly to the mycological results. An additional distal sample, collected by clipping the nail plate, was obtained from 75 patients and tested with Onychodiag alone. In patients with culture-proven dermatophytic onychomycosis, the sensitivity of Onychodiag was 83.6% (87.9% including the gray zone) and ranged from 75 to 100% according to the laboratory and the sampling conditions. The specificity was 100% when healthy subjects were considered true negative controls. Onychodiag was positive on 68 patient samples that were sterile or yielded nondermatophyte species in culture. Based on the results of Onychodiag for mycologically proven positive samples and true-negative samples, these results were considered true positives, and the poor performance of mycology on these samples was attributed to inconvenient sampling conditions or to contaminants. When tested on distal samples, Onychodiag was positive in 49/53 (92%) cases of proven dermatophytic onychomycosis. Finally, with either proximal or distal samples, Onychodiag provided a diagnosis of dermatophytic onychomycosis within 24 to 48 h after sampling, and its sensitivity was close to that of mycological techniques applied to proximal samples.
Epidemiologic Analysis of Reactivated Cytomegalovirus Antigenemia in Patients with Cancer
Authors: Han Xiang Y.
Published: February 2007

The epidemiologic features of reactivated cytomegalovirus (CMV) antigenemia were studied among 4,382 cancer patients who were cared for and tested at the University of Texas M. D. Anderson Cancer Center from 2001 to 2004. The effects of stem cell transplant (SCT) status, underlying disease, age, sex, ethnicity, and antibody status (prior to CMV exposure) on the incidence of CMV antigenemia were determined; and the CMV burdens were quantified. Antigenemia occurred in 9.3% of patients with non-SCT (
n
= 2511), 12.0% with autologous SCT (
n
= 582), and 39.1% with allogeneic SCT (
n
= 1289). Non-SCT patients with lymphoid tumors had a significantly higher rate of antigenemia than those with myeloid tumors (13.6% versus 3.9%) (
P
< 0.001); however, after allogeneic SCT, the underlying diseases had little effect, except for multiple myeloma (56.8%) (
P
= 0.014). Among the allogeneic SCT recipients, higher CMV antigenemia rates were also associated with female sex, older age, and positivity for pre-SCT CMV antibody. Depending on the underlying disease and its associated initial CMV risk, allogeneic SCT increased the risk by 2.6- to 29.6-fold (overall, 4.0-fold). With or without SCT, Asians had the highest CMV antigenemia rates and burdens, followed by blacks, Hispanics, and whites, and these partially correlated with antibody prevalence. Among the 808 patients with antigenemia, the circulating peak CMV burden was significantly higher among non-SCT patients (geometric mean, 18.7 positive cells per 10
6
leukocytes) than among allogeneic SCT patients (geometric mean, 7.7 positive cells per 10
6
leukocytes) or autologous SCT patients (geometric mean, 7.0 positive cells per 10
6
leukocytes) who underwent monitoring for CMV. Together, these results allow stratification of CMV risks and suggest a substantial CMV reactivation among non-SCT cancer patients and, thus, the need for better diagnosis and control.
Evaluation of VITEK 2 and RapID Yeast Plus Systems for Yeast Species Identification: Experience at a Large Clinical Microbiology Laboratory
Authors: Sanguinetti Maurizio , Porta Rosaria , Sali Michela , La Sorda Marilena , Pecorini Giovanni , Fadda Giovanni , Posteraro Brunella
Published: February 2007

A total of 750 clinical yeast isolates were evaluated by two identification systems, VITEK 2 and RapID Yeast Plus, using sequence analysis of the rRNA gene internal transcribed spacer regions as the reference method. The VITEK 2 and RapID systems correctly identified 737 (98.2%) and 716 (95.5%) isolates, respectively.
Selective Depletion of High-Avidity Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD8
+
T Cells after Early HIV-1 Infection
Authors: Lichterfeld Mathias , Yu Xu G. , Mui Stanley K. , Williams Katie L. , Trocha Alicja , Brockman Mark A. , Allgaier Rachel L. , Waring Michael T. , Koibuchi Tomohiko , Johnston Mary N. , Cohen Daniel , Allen Todd M. , Rosenberg Eric S. , Walker Bruce D. , Altfeld Marcus
Published: February 2007

Human immunodeficiency virus type 1 (HIV-1)-specific CD8
+
T cells in early infection are associated with the dramatic decline of peak viremia, whereas their antiviral activity in chronic infection is less apparent. The functional properties accounting for the antiviral activity of HIV-1-specific CD8
+
T cells during early infection are unclear. Using cytokine secretion and tetramer decay assays, we demonstrated in intraindividual comparisons that the functional avidity of HIV-1-specific CD8
+
T cells was consistently higher in early infection than in chronic infection in the presence of high-level viral replication. This change of HIV-1-specific CD8
+
T-cell avidity between early and chronic infections was linked to a substantial switch in the clonotypic composition of epitope-specific CD8
+
T cells, resulting from the preferential loss of high-avidity CD8
+
T-cell clones. In contrast, the maintenance of the initially recruited clonotypic pattern of HIV-1-specific CD8
+
T cells was associated with low-level set point HIV-1 viremia. These data suggest that high-avidity HIV-1-specific CD8
+
T-cell clones are recruited during early infection but are subsequently lost in the presence of persistent high-level viral replication.
Superinfection Exclusion in Cells Infected with Hepatitis C Virus
Authors: Tscherne Donna M. , Evans Matthew J. , von Hahn Thomas , Jones Christopher T. , Stamataki Zania , McKeating Jane A. , Lindenbach Brett D. , Rice Charles M.
Published: February 2007

Superinfection exclusion is the ability of an established virus infection to interfere with infection by a second virus. In this study, we found that Huh-7.5 cells acutely infected with hepatitis C virus (HCV) genotype 2a (chimeric strain J6/JFH) and cells harboring HCV genotype 1a, 1b, or 2a full-length or subgenomic replicons were resistant to infection with cell culture-produced HCV (HCVcc). Replicon-containing cells became permissive for HCVcc infection after treatment with an HCV-specific protease inhibitor. With the exception of cells harboring a J6/JFH-FLneo replicon, infected or replicon-containing cells were permissive for HCV pseudoparticle (HCVpp) entry, demonstrating a postentry superinfection block downstream of primary translation. The surprising resistance of J6/JFH-FLneo replicon-containing cells to HCVpp infection suggested a defect in virus entry. This block was due to reduced expression of the HCV coreceptor CD81. Further analyses indicated that J6/JFH may be toxic for cells expressing high levels of CD81, thus selecting for a CD81
low
population. CD81 down regulation was not observed in acutely infected cells, suggesting that this may not be a general mechanism of HCV superinfection exclusion. Thus, HCV establishes superinfection exclusion at a postentry step, and this effect is reversible by treatment of infected cells with antiviral compounds.
Induction of Natural Killer Cell Responses by Ectromelia Virus Controls Infection
Authors: Parker April Keim , Parker Scott , Yokoyama Wayne M. , Corbett John A. , Buller R. Mark L.
Published: February 2007

Natural killer (NK) cells play a pivotal role in the innate immune response to viral infections, particularly murine cytomegalovirus (MCMV) and human herpesviruses. In poxvirus infections, the role of NK cells is less clear. We examined disease progression in C57BL/6 mice after the removal of NK cells by both antibody depletion and genetic means. We found that NK cells were crucial for survival and the early control of virus replication in spleen and to a lesser extent in liver in C57BL/6 mice. Studies of various knockout mice suggested that γδ T cells and NKT cells are not important in the C57BL/6 mousepox model and CD4
+
and CD8
+
T cells do not exhibit antiviral activity at 6 days postinfection, when the absence of NK cells has a profound effect on virus titers in spleen and liver. NK cell cytotoxicity and/or gamma interferon (IFN-γ) secretion likely mediated the antiviral effect needed to control virus infectivity in target organs. Studies of the effects of ectromelia virus (ECTV) infection on NK cells demonstrated that NK cells proliferate within target tissues (spleen and liver) and become activated following a low-dose footpad infection, although the mechanism of activation appears distinct from the ligand-dependent activation observed with MCMV. NK cell IFN-γ secretion was detected by intracellular cytokine staining transiently at 32 to 72 h postinfection in the lymph node, suggesting a role in establishing a Th1 response. These results confirm a crucial role for NK cells in controlling an ECTV infection.
Molecular Characterization of the Rhesus Rhadinovirus (RRV) ORF4 Gene and the RRV Complement Control Protein It Encodes
Authors: Mark Linda , Spiller O. Brad , Okroj Marcin , Chanas Simon , Aitken Jim A. , Wong Scott W. , Damania Blossom , Blom Anna M. , Blackbourn David J.
Published: February 2007

The diversity of viral strategies to modulate complement activation indicates that this component of the immune system has significant antiviral potential. One example is the Kaposi's sarcoma-associated herpesvirus (KSHV) complement control protein (KCP), which inhibits progression of the complement cascade. Rhesus rhadinovirus (RRV), like KSHV, is a member of the subfamilyGammaherpesvirinaeand currently provides the only in vivo model of KSHV pathobiology in primates. In the present study, we characterized the KCP homologue encoded by RRV, RRV complement control protein (RCP). Two strains of RRV have been sequenced to date (H26-95 and 17577), and the RCPs they encode differ substantially in structure: RCP from strain H26-95 has four complement control protein (CCP) domains, whereas RCP from strain 17577 has eight CCP domains. Transcriptional analyses of the RCP gene (ORF4, referred to herein asRCP) in infected rhesus macaque fibroblasts mapped the ends of the transcripts of both strains. They revealed that H26-95 encodes a full-length, unsplicedRCPtranscript, while 17577RCPgenerates a full-length unspliced mRNA and two alternatively spliced transcripts. Western blotting confirmed that infected cells express RCP, and immune electron microscopy disclosed this protein on the surface of RRV virions. Functional studies of RCP encoded by both RRV strains revealed their ability to suppress complement activation by the classical (antibody-mediated) pathway. These data provide the foundation for studies into the biological significance of gammaherpesvirus complement regulatory proteins in a tractable, non-human primate model.
Duplicated Sequence Motif in the Long Terminal Repeat of Maedi-Visna Virus Extends Cell Tropism and Is Associated with Neurovirulence
Authors: Óskarsson Thórdur , Hreggvidsdóttir Hulda S. , Agnarsdóttir Gudrún , Matthíasdóttir Sigrídur , Ogmundsdóttir Margrét H. , Jónsson Stefán R. , Georgsson Gudmundur , Ingvarsson Sigurdur , Andrésson Ólafur S. , Andrésdóttir Valgerdur
Published: February 2007

Maedi-visna virus (MVV) is a lentivirus of sheep causing chronic inflammatory disease of the lungs (maedi) and the nervous system (visna). We have previously shown that a duplicated sequence in the long terminal repeat (LTR) of MVV is a determinant of cell tropism. Here, we demonstrate that deletion of a CAAAT sequence from either one of the repeats resulted in poor virus growth in sheep choroid plexus cells. A duplication in the LTR encompassing the CAAAT sequence was found in four neurological field cases that were sequenced, but no duplication was present in the LTRs from seven maedi cases; one maedi isolate was mixed. These results indicate that the duplication in the LTR is associated with neurovirulence.
TopBP1 Regulates Human Papillomavirus Type 16 E2 Interaction with Chromatin
Authors: Donaldson Mary M. , Boner Winifred , Morgan Iain M.
Published: February 2007

Human papillomavirus type 16 (HPV16) E2 regulates transcription from and replication of the viral genome, in association with viral and cellular factors. HPV16 E2 interacts functionally with TopBP1, a cellular protein essential for the initiation of cellular, and potentially viral, DNA replication. This report demonstrates that the absence of TopBP1 results in the redistribution of HPV16 E2 into an alternative cellular protein complex, resulting in enhanced affinity for chromatin. This redistribution does not significantly alter the ability of HPV16 E2 to either activate or repress transcription. We also show colocalization of both proteins on chromatin at late stages of mitosis, suggesting that TopBP1 could be the mitotic chromatin receptor for HPV16 E2. The possible significance of the results for the regulation of the viral life cycle is discussed.
Model for T-Antigen-Dependent Melting of the Simian Virus 40 Core Origin Based on Studies of the Interaction of the Beta-Hairpin with DNA
Authors: Kumar Anuradha , Meinke Gretchen , Reese Danielle K. , Moine Stephanie , Phelan Paul J. , Fradet-Turcotte Amélie , Archambault Jacques , Bohm Andrew , Bullock Peter A.
Published: February 2007

The interaction of simian virus 40 (SV40) T antigen (T-ag) with the viral origin has served as a model for studies of site-specific recognition of a eukaryotic replication origin and the mechanism of DNA unwinding. These studies have revealed that a motif termed the “beta-hairpin” is necessary for assembly of T-ag on the SV40 origin. Herein it is demonstrated that residues at the tip of the “beta-hairpin” are needed to melt the origin-flanking regions and that the T-ag helicase domain selectively assembles around one of the newly generated single strands in a manner that accounts for its 3′-to-5′ helicase activity. Furthermore, T-ags mutated at the tip of the “beta-hairpin” are defective for oligomerization on duplex DNA; however, they can assemble on hybrid duplex DNA or single-stranded DNA (ssDNA) substrates provided the strand containing the 3′ extension is present. Collectively, these experiments indicate that residues at the tip of the beta-hairpin generate ssDNA in the core origin and that the ssDNA is essential for subsequent oligomerization events.
PATJ, a Tight Junction-Associated PDZ Protein, Is a Novel Degradation Target of High-Risk Human Papillomavirus E6 and the Alternatively Spliced Isoform 18 E6*
Authors: Storrs Carina H. , Silverstein Saul J.
Published: February 2007

The E6 protein from high-risk human papillomavirus types interacts with and degrades several PDZ domain-containing proteins that localize to adherens junctions or tight junctions in polarized epithelial cells. We have identified the tight junction-associated multi-PDZ protein PATJ (PALS1-associated TJ protein) as a novel binding partner and degradation target of high-risk types 16 and 18 E6. PATJ functions in the assembly of the evolutionarily conserved CRB-PALS1-PATJ and Par6-aPKC-Par3 complexes and is critical for the formation of tight junctions in polarized cells. The ability of type 18 E6 full-length to bind to, and the subsequent degradation of, PATJ is dependent on its C-terminal PDZ binding motif. We demonstrate that the spliced 18 E6* protein, which lacks a C-terminal PDZ binding motif, associates with and degrades PATJ independently of full-length 18 E6. Thus, PATJ is the first binding partner that is degraded in response to both isoforms of 18 E6. The ability of E6 to utilize a non-E6AP ubiquitin ligase for the degradation of several PDZ binding partners has been suggested. We also demonstrate that 18 E6-mediated degradation of PATJ is not inhibited in cells where E6AP is silenced by shRNA. This suggests that the E6-E6AP complex is not required for the degradation of this protein target.
Processing of RNAs of the Family
Avsunviroidae
in
Chlamydomonas reinhardtii
Chloroplasts
Authors: Molina-Serrano Diego , Suay Loreto , Salvador María L. , Flores Ricardo , Daròs José-Antonio
Published: February 2007

The family
Avsunviroidae
comprises four viroid species with the ability to form hammerhead ribozymes that mediate self-cleavage of the multimeric plus and minus strands resulting from replication in the chloroplast through a symmetric rolling-circle mechanism. Research on these RNAs is restricted by their host range, which is limited to the plants wherein they were initially identified and some closely related species. Here we report cleavage and ligation in transplastomic
Chlamydomonas reinhardtii
expressing plus- and minus-strand dimeric transcripts of representative members of the family
Avsunviroidae
. Despite the absence of viroid RNA-RNA transcription, the
C. reinhardtii
-based system can be used to address intriguing questions about viroid RNA processing and, in particular, about the cellular factors involved in cleavage and ligation.
An Affinity-Enhanced Neutralizing Antibody against the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 gp41 Recognizes an Epitope between Those of 2F5 and 4E10
Authors: Nelson Josh D. , Brunel Florence M. , Jensen Richard , Crooks Emma T. , Cardoso Rosa M. F. , Wang Meng , Hessell Ann , Wilson Ian A. , Binley James M. , Dawson Philip E. , Burton Dennis R. , Zwick Michael B.
Published: February 2007

The membrane-proximal external region (MPER) of human immunodeficiency virus type 1 (HIV-1) gp41 bears the epitopes of two broadly neutralizing antibodies (Abs), 2F5 and 4E10, making it a target for vaccine design. A third Ab, Fab Z13, had previously been mapped to an epitope that overlaps those of 2F5 and 4E10 but only weakly neutralizes a limited set of primary isolates. Here, libraries of Fab Z13 variants displayed on phage were engineered and affinity selected against an MPER peptide and recombinant gp41. A high-affinity variant, designated Z13e1, was isolated and found to be ∼100-fold improved over the parental Fab not only in binding affinity for the MPER antigens but also in neutralization potency against sensitive HIV-1. Alanine scanning of MPER residues 664 to 680 revealed that N671 and D674 are crucial for peptide recognition as well as for the neutralization of HIV-1 by Z13e1. Ab competition studies and truncation of MPER peptides indicate that Z13e1 binds with high affinity to an epitope between and overlapping with those of 2F5 and 4E10, with the minimal peptide epitope WASLWNWFDITN. Still, Z13e1 remained about an order of magnitude less potent than 4E10 against several isolates of pseudotyped HIV-1. The sum of our molecular analyses with Z13e1 suggests that the segment on the MPER of gp41 between the 2F5 and 4E10 epitopes is exposed on the functional envelope trimer but that access to the specific Z13e1 epitope within this segment is limited. Thus, the ability of MPER-bearing immunogens to elicit potent HIV-1-neutralizing Abs may depend in part on recapitulating the particular constraints that the functional envelope trimer imposes on the segment of the MPER to which Z13e1 binds.
Cytosolic Activation of Cathepsins Mediates Parvovirus H-1-Induced Killing of Cisplatin and TRAIL-Resistant Glioma Cells
Authors: Di Piazza Matteo , Mader Carmen , Geletneky Karsten , Herrero y Calle Marta , Weber Ekkehard , Schlehofer Jörg , Deleu Laurent , Rommelaere Jean
Published: February 2007

Gliomas are often resistant to the induction of apoptotic cell death as a result of the development of survival mechanisms during astrocyte malignant transformation. In particular, the overexpression of Bcl-2-family members interferes with apoptosis initiation by DNA-damaging agents (e.g., cisplatin) or soluble death ligands (e.g., TRAIL). Using low-passage-number cultures of glioma cells, we have shown that parvovirus H-1 is able to induce death in cells resistant to TRAIL, cisplatin, or both, even when Bcl-2 is overexpressed. Parvovirus H-1 triggers cell death through both the accumulation of lysosomal cathepsins B and L in the cytosol of infected cells and the reduction of the levels of cystatin B and C, two cathepsin inhibitors. The impairment of either of these effects protects glioma cells from the viral lytic effect. In normal human astrocytes, parvovirus H-1 fails to induce a killing mechanism. In vivo, parvovirus H-1 infection of rat glioma cells intracranially implanted into recipient animals triggers cathepsin B activation as well. This report identifies for the first time cellular effectors of the killing activity of parvovirus H-1 against malignant brain cells and opens up a therapeutic approach which circumvents their frequent resistance to other death inducers.
Characterization of a Replication-Competent, Integrase-Defective Human Immunodeficiency Virus (HIV)/Simian Virus 40 Chimera as a Powerful Tool for the Discovery and Validation of HIV Integrase Inhibitors
Authors: Daelemans Dirk , Lu Richard , De Clercq Erik , Engelman Alan
Published: February 2007

Integrase is actively studied as an antiviral target, but many inhibitors selected from biochemical screens fail to inhibit human immunodeficiency virus (HIV) replication or primarily affect off-site targets. Here we develop and validate a replication-competent, simian virus 40-HIV integrase mutant chimera as a novel tool to classify the mechanism of action of potential integrase inhibitors. Whereas the mutant was more susceptible than the wild type to entry, reverse transcriptase, and protease inhibitors, it specifically resisted the action of integrase inhibitor L-870,810. We furthermore demonstrate inhibition of integration by GS-9137 and GS-9160 and off-site targeting by the 6-aminoquinolone antibiotic WM-5.
Chlorine atom initiated reactions of selected tropospheric halocarbons — Kinetic and product studies
Authors: Garib Anisha , Timerghazin Qadir K , Ariya Parisa A
Published: February 2007

Halogens are suggested as important atmospheric oxidants in the marine boundary layer. The room-temperature kinetics of the chlorine-initiated reactions of three biogenic brominated hydrocarbons and four anthropogenic chlorinated ethenes was investigated by gas chromatography with flame ionization detection (GC–FID) at a pressure of 1 atm (1 atm = 101.325 kPa) in air, using the relative rate technique. The rate constants (× 1013cm3molecule–1s–1) for CH2Br2, CHBr2Cl, and CHBr3reactions at 298 ± 2 K were found to be 4.25 ± 0.65, 2.03 ± 0.31, and 2.81 ± 0.41, respectively, using methane as a reference compound. Room temperature rate constants (±1011cm3molecule–1s–1) obtained for 1,1-dichloroethene, cis-dichloroethene, trans-dichloroethene, and trichloroethene using ethene as a reference are 13.4 ± 3.3, 9.1 ± 2.3, 7.4 ± 1.8, and 7.7 ± 1.9, respectively. The rate constants of chlorine-atom reactions with various hydrocarbons obtained in this work and taken from literature were correlated with corresponding rate constants of the OH radical available in the literature. The temperature dependences for the reactions of chlorine atoms with chlorinated ethenes were studied within the 298–358 K range. The corresponding Arrhenius expressions for the rate constants are (cm3molecule–1s–1): ln k = (–25.26 ± 0.17) – (758 ± 55)/T for 1,1-dichloroethene, ln k = (–25.79 ± 0.10) – (799 ± 34)/T for cis-dichloroethene, ln k = (–26.74 ± 0.09) – (1018 ± 28)/T for trans-dichloroethene, and ln k = (–26.10 ± 0.26) – (846 ± 83)/T for trichloroethene. In addition, product studies for the chlorine-initiated gas phase oxidation reactions of CHBr3and CHBr2Cl were performed using gas chromatography with mass spectrometric detection (GC–MS). The only identified product for the reaction of CHBr3with Cl reaction was COBr2, while for the CHBr2Cl + Cl reaction, COBrCl and COCl2were observed, indicating the possibility of halogen atom release. The atmospheric implications of the results obtained are discussed.Key words: tropospheric reactions, kinetics, chlorine atoms, chlorinated hydrocarbons, brominated hydrocarbons.
Synthesis and coordination chemistry of the diamido-arsine ligand [NAsN] (NAsN = PhAs(CH2SiMe2NPh)2))
Authors: Carmichael Christopher D , Shaver Michael P , Fryzuk Michael D
Published: February 2007

The preparation and characterization of the diamido-arsine ligand [NAsN]Li2(THF) (1) (where NAsN = PhAs(CH2SiMe2NPh)2), the protonated ligand precursor [NAsN]H2 (2), and its coordination chemistry with tantalum is presented. The complex [NAsN]TaMe3 (3) can be synthesized from 1 and TaMe3Cl2. Hydrogenation of 3 did not produce the desired tetrahydride ([NAsN]Ta)2(µ-H)4, instead, activation of Ta–N bonds in the complex produced a modest yield of the free ligand 2. In an attempt to understand the unusual reactivity of 3, a density functional theory investigation of the model complexes 'NAsN'Li2(OMe2)2 (4) and 'NAsN'TaMe3 (5) (where 'NAsN' = MeAs(CH2SiH2NMe)2) and their phosphine analogs 'NPN'Li2(OMe2) (7), 'NPN'TaMe3 (8), and a related niobium complex 'NPN'NbMe3 (10) (where 'NPN' = MeP(CH2SiH2NMe)2) was undertaken. The difference between the chemistry supported by the As and P ligands originates from the poor binding of As to Ta in these systems and is likely due to a mismatch of the soft As donor and the hard Ta(V) metal centre.Key words: arsine ligand, tridentate, tantalum, hydrogenation, DFT calculations.
THE ABELIAN FIBRATION ON THE HILBERT CUBE OF A K3 SURFACE OF GENUS 9
Authors: ILIEV ATANAS , RANESTAD KRISTIAN
Published: February 2007

In this paper we construct an abelian fibration over P3on the Hilbert cube of the primitive K3 surface of genus 9. After the abelian fibration constructed by Hassett and Tschinkel on the Hilbert square on the primitive K3 surface of genus 5, this is the second example where the abelian fibration is constructed directly on [Formula: see text]. The recent more general result of Sawon proves the existence of an abelian fibration on the Hilbert scheme [Formula: see text] of a primitive K3 surface S of degree 2g - 2 = m2(2n - 2). Our example provides an alternative proof in the case m = 2, n = 3. Furthermore we identify the general fiber with the Hilbert scheme of twisted cubic curves in a Fano 3-fold of genus 9, and interpret the addition law on this variety.
THE ADAPTED COMPLEXIFICATION OF AN ELLIPSOID
Authors: AGUILAR RAUL M.
Published: February 2007

We show that an n-dimensional real ellipsoid in ℝn+1 with the induced Riemannian metric does not admit an unbounded adapted complexification in the sense of Lempert/Szőke and Guillemin/Stenzel, unless it is a round sphere. In other words, an ellipsoid whose (maximal) Grauert tube has infinite radius must be a round sphere. For the proof we take advantage of the integrability of the geodesic flow and use a classical theorem on umbilic geodesics. We carry out an extension of this result to Liouville metrics elsewhere.
FLUCTUATIONS OF THE MODAL ARRIVAL TIMES DUE TO LINEAR INTERNAL WAVES: APPLICATION TO INVERSION
Authors: BOUCHAGE GERALDINE , TAROUDAKIS MICHAEL I.
Published: February 2007

It is well known that internal waves in the ocean are an important source of environmental variability which has serious effects in the structure of an acoustic field due to a known source. When measurements of the acoustic field form the input data for an inversion procedure aiming at the recovery of the environmental parameters, the information they carry on includes the internal wave effects. It is therefore natural to assume that neglecting the effects of the internal waves in an inversion procedure based on acoustic field measurements, errors are induced in the inversion. The paper deals with this problem and addresses the case of inversion schemes using travel time information of an acoustic signal. Using a statistical 2D model of the internal waves, based on the Garrett and Munk spectrum, the spatial and temporal evolution of the internal waves field as well as the fluctuations of the sound speed profile is estimated for a characteristic shallow-water environment. Considering a sound speed anomaly in the water column as the oceanographic feature to be recovered, the paper studies the influence of the internal waves field on the modal travel time information obtained through the propagation of a tomographic signal through this environment. The sound speed anomaly denoted as "current" is described by a suitable Gaussian function. Using an analytical expression based on a perturbation approach, the difference in the modal arrival times calculated for a background environment and a perturbed one (considering that the sound speed perturbations are due either to a current or to the summation of a current and of the internal waves field) was calculated for each propagating mode of the waveguide. These calculations led to the conclusion that the internal waves have a non-negligible impact on the arrival times and that the maximum amplitude of a current can be under- or overestimated of several meters per second when these waves are not taken into account in the inversion method, whereas they are present in the oceanic medium.
EFFECT OF HORIZONTAL INHOMOGENEITY OF THE OCEAN ON INTERFERENCE OF NEAR-AXIAL WAVES IN LONG-RANGE ACOUSTIC PROPAGATION
Authors: GRIGORIEVA NATALIE S. , FRIDMAN GREGORY M.
Published: February 2007

When the source and receiver are located close to the depth of the waveguide axis, there exist cusped caustics repeatedly along the axis. A description of the propagation of energy along the waveguide axis in terms of geometrical acoustics is not valid in neighborhoods of cusped caustics, because in these neighborhoods the waves associated with individual ray paths interfere with one another. Neighborhoods of interference grow with range, and at long distances they overlap. This results in the formation of a diffractive (as opposed to ray, i.e., geometrical acoustics) component of the field — the axial wave — that propagates along the sound-channel axis. In this paper, the integral representation of the axial wave obtained before for an arbitrary deep-water waveguide in a three-dimensional range-independent medium is generalized to a range-dependent ocean. The integral representation of the axial wave is derived with the use of solutions of the homogeneous Helmholtz equation concentrated near the sound-channel axis and which decrease exponentially outside a narrow strip containing the axis. The observed time-of-arrival patterns from a number of long-range ocean acoustic propagation experiments show early geometrical-like arrivals followed by a crescendo of energy that propagates along the sound-channel axis and is not resolved into individual arrivals. The practical application of the developed analytic expression for the sound field near the axis of an ocean type waveguide is the discrimination of noninterfering (resolved) and interfering (nonresolved) arrivals. In this paper, the axial wave is simulated for a deterministic model of a range-dependent medium, where the range-dependence results for such things as change in geographic location. The model is based on the information about sound-speed profiles as a function of range between the source and receiving array for the AET experiment. The sound source frequency is taken equal to 75Hz. The propagation range is 3250 km.
Intracellular distribution of the lysyl oxidase propeptide in osteoblastic cells
Authors: Guo Ying , Pischon Nicole , Palamakumbura Amitha H. , Trackman Philip C.
Published: February 2007

Lysyl oxidase plays a critical role in the formation of the extracellular matrix, and its activity is required for the normal maturation and cross-linking of collagen and elastin. An 18-kDa lysyl oxidase propeptide (LOPP) is generated from 50-kDa prolysyl oxidase by extracellular proteolytic cleavage during the biosynthesis of active 30-kDa lysyl oxidase enzyme. The fate and the functions of the LOPP are largely unknown, although intact LOPP was previously observed in osteoblast cultures. We investigated the spatial localization of molecular forms of lysyl oxidase, including LOPP in proliferating and differentiating osteoblasts, by using confocal immunofluorescence microscopy and Western blots of cytoplasmic and nuclear extracts. In the present study, a stage-dependent intracellular distribution of LOPP in the osteoblastic cell was observed. In proliferating osteoblasts, LOPP epitopes were principally associated with the Golgi and endoplasmic reticulum, and mature lysyl oxidase epitopes were found principally in the nucleus and perinuclear region. In differentiating cells, LOPP and mature lysyl oxidase immunostaining showed clear colocalization with the microtubule network. The subcellular distribution of LOPP and its temporal and physical association with microtubules were confirmed by Western blot and far Western blot studies. We also report that N-glycosylated and nonglycosylated LOPP are present in MC3T3-E1 cell cultures. We conclude that LOPP has a stage-dependent intracellular distribution in osteoblastic cells. Future studies are needed to investigate whether the LOPP associations with microtubules or the osteoblast nucleus have functional effects for osteoblast differentiation and bone formation.
Neutral Na-amino acid cotransport is differentially regulated by glucocorticoids in the normal and chronically inflamed rabbit small intestine
Authors: Sundaram Uma , Wisel Sheik , Coon Steven
Published: February 2007

Neutral Na-amino acid cotransport by system ATB0[e.g., Na-alanine cotransport (NAcT)] is an important means of assimilation of amino acids in the intestine. NAcT is inhibited during chronic intestinal inflammation by an alteration in the affinity for the amino acid. How glucocorticoids, a standard of treatment for diseases characterized by chronic intestinal inflammation, may affect NAcT during chronic enteritis is not known. Thus we first demonstrated that methylprednisolone (MP) stimulated NAcT in the normal intestine. The mechanism of stimulation was secondary to an increase in cotransporter numbers without an alteration in the affinity for the amino acid. Treatment with MP reversed the reduction in NAcT in villus cells from the chronically inflamed intestine. MP also alleviated the decrease in Na-K-ATPase activity in villus cells during chronic enteritis. However, MP treatment reversed the NAcT inhibition in villus cell brush border membrane vesicles from the inflamed intestine, which suggested an effect of MP at the level of the cotransporter itself. Kinetic studies demonstrated that the reversal of NAcT inhibition by MP was secondary to restoration in the affinity for the amino acid without a change in the Vmax. Unaltered steady-state mRNA and immunoreactive protein levels of NAcT also indicated that the number of cotransporters was unchanged after MP treatment in the chronically inflamed intestine. These results indicated that MP reversed NAcT inhibition in the chronically inflamed intestine by restoring the affinity of the transporter for the amino acid while it stimulated NAcT in the normal intestine by increasing the cotransporter numbers. Therefore, MP differentially regulates NAcT in the normal and chronically inflamed intestine.
Ghrelin selectively reduces mechanosensitivity of upper gastrointestinal vagal afferents
Authors: Page Amanda J. , Slattery James A. , Milte Catherine , Laker Rhianna , O'Donnell Tracey , Dorian Camilla , Brierley Stuart M. , Blackshaw L. Ashley
Published: February 2007

Ghrelin is a peptide released from gastric endocrine cells that has an orexigenic effect via a vagal pathway. Here we determine the effect of ghrelin on mechanosensitivity of upper-intestinal vagal afferent fibers in ferret and mouse. The responses of gastroesophageal vagal afferents to graded mechanical stimulation were determined in vitro before and during application of ghrelin to their peripheral endings. Three types of vagal afferent were tested: tension receptors responding to circumferential tension, mucosal receptors responding only to mucosal stroking, and tension/mucosal (TM) receptors in ferret esophagus that responded to both stimuli. In the mouse, ghrelin did not significantly affect the response of mucosal receptors to mucosal stroking with calibrated von Frey hairs. However, it significantly reduced responses of tension receptors to circumferential tension ( P < 0.005; two-way ANOVA) by up to 40%. This inhibition was reversed by the ghrelin receptor antagonist [d-Lys-3]-growth hormone-releasing peptide (GHRP)-6. In the ferret, ghrelin significantly reduced the response of mucosal and TM receptors to mucosal stroking with calibrated von Frey hairs. Surprisingly, ghrelin did not significantly alter the response to circumferential tension in either tension or TM receptors. RT-PCR analysis indicated that both ghrelin and its receptor are expressed in vagal afferent cell bodies in mouse nodose ganglia. In conclusion, ghrelin selectively inhibits subpopulations of mechanically sensitive gastroesophageal vagal afferents; there is also potential for ghrelin release from vagal afferents. However, the subpopulation of afferents inhibited differs between species. These data have broad implications for ghrelin's role in food intake regulation and reflex control of gastrointestinal function.
Alix (AIP1) is a vasopressin receptor (V2R)-interacting protein that increases lysosomal degradation of the V2R
Authors: Yi Xianhua , Bouley Richard , Lin Herbert Y. , Bechoua Shaliha , Sun Tian-xiao , del Re Elisabetta , Shioda Toshi , Raychowdhury Malay K. , Lu Hua A. J. , Abou-Samra Abdul B. , Brown Dennis , Ausiello Dennis A.
Published: February 2007

The vasopressin type 2 receptor (V2R) is a G protein-coupled receptor that plays a central role in renal water reabsorption. Termination of ligand (vasopressin) stimulation is an important physiological regulatory event, but few proteins that interact with the V2R during downregulation after vasopressin (VP) binding have been identified. Using yeast two-hybrid screening of a human kidney cDNA library, we show that a 100-kDa protein called ALG-2-interacting protein X (Alix) interacts with the last 29 amino acids of the V2R COOH terminus. This was confirmed by pull-down assays using a GST-V2R-COOH-tail fusion protein. Alix was immunolocalized in principal cells of the kidney, which also express the V2R. The function of the Alix-V2R interaction was studied by transfecting Alix into LLC-PK1epithelial cells expressing V2R-green fluorescent protein (GFP). Under basal conditions, V2R-GFP localized mainly at the plasma membrane. On VP treatment, V2R-GFP was internalized into perinuclear vesicles in the nontransfected cells. In contrast, V2R-GFP fluorescence was virtually undetectable 2 h after exposure to VP in cells that coexpressed Alix. Western blotting using an anti-GFP antibody showed marked degradation of the V2R after 2 h in the presence of VP and Alix, a time point at which little or no degradation was detected in the absence of Alix. In contrast, little or no degradation of the parathyroid hormone receptor was detectable in the presence or absence of Alix and/or the PTH ligand. The VP-induced disappearance of V2R-GFP was abolished by chloroquine, a lysosomal degradation inhibitor, but not by MG132, a proteosome inhibitor. These data suggest that Alix increases the rate of lysosomal degradation of V2R and may play an important regulatory role in the VP response by modulating V2R downregulation.
Motor Strategies Used by Rats Spinalized at Birth to Maintain Stance in Response to Imposed Perturbations
Authors: Giszter Simon F. , Davies Michelle R. , Graziani Virginia
Published: February 2007

Some rats spinalized P1/P2 achieve autonomous weight-supported locomotion and quiet stance as adults. We used force platforms and robot-applied perturbations to test such spinalized rats ( n = 6) that exhibited both weight-supporting locomotion and stance, and also normal rats ( n = 8). Ground reaction forces in individual limbs and the animals' center of pressure were examined. In normal rats, both forelimbs and hindlimbs participated actively to control horizontal components of ground reaction forces. Rostral perturbations increased forelimb ground reaction forces and caudal perturbations increased hindlimb ground reaction forces. Operate rats carried 60% body weight on the forelimbs and had a more rostral center of pressure placement. The pattern in normal rats was to carry significantly more weight on the hindlimbs in quiet stance (roughly 60%). The strategy of operate rats to compensate for perturbations was entirely in forelimbs; as a result, the hindlimbs were largely isolated from the perturbation. Stiffness magnitude of the whole body was measured: its magnitude was hourglass shaped, with the principal axis oriented rostrocaudally. Operate rats were significantly less stiff—only 60–75% of normal rats' stiffness. The injured rats adopt a stance strategy that isolates the hindlimbs from perturbation and may thus prevent hindlimb loadings. Such loadings could initiate reflex stepping, which we observed. This might activate lumbar pattern generators used in their locomotion. Adult spinalized rats never achieve independent hindlimb weight-supported stance. The stance strategy of the P1 spinalized rats differed strongly from the behavior of intact rats and may be difficult for rats spinalized as adults to master.