bluuebunny/crossref_metadata_2025 huggingface dataset:
Etching mechanisms of thin SiO2 exposed to Cl2 plasma
Authors: Petit-Etienne C. , Darnon M. , Vallier L. , Pargon E. , Cunge G. , Fouchier M. , Bodart P. , Haass M. , Brihoum M. , Joubert O. , Banna S. , Lill T.
Published: August 2011

Plasma etching is the most standard patterning technology used in micro- and nano-technologies. Chlorine-based plasmas are often used for silicon etching. However, the behavior of thin silicon oxide exposed to such a plasma is still not fully understood. In this paper, we investigate how a thin silicon oxide layer on silicon behaves when it is exposed to a Cl2 plasma. The authors show that chlorine atoms diffuse and/or Cl+ ions are implanted through the thin (<2.5 nm) oxide, leading to the formation of a SiClx interface layer between the two layers of Si and SiO2. Chlorine accumulates at the interface until the SiO2 is thin enough to release volatile SiClx species and the silicon begins to be etched.
Gallium nitride nanowire electromechanical resonators with piezoresistive readout
Authors: Gray Jason M. , Rogers Charles T. , Bertness Kris A. , Sanford Norman A.
Published: August 2011

The authors report on the fabrication, piezoresistive readout, and frequency response of doubly clamped c-axis gallium nitride nanowire (NW) resonators that show mechanical quality factors exceeding 10 000. The devices are fabricated using a combination of lithographic patterning and dielectrophoresis to suspend NWs across 10 μm gaps. An electrostatic gate induces NW vibration, which is electronically detected via NW piezoresistance. The naturally occurring range of NW diameters results in lowest beam resonances in the range of 9–36 MHz, consistent with a Young’s modulus of roughly 300 GPa. Mechanical quality factors, Q, as high as 26 000 under vacuum at 8 K are observed. Selective variation of NW temperature by local joule heating while maintaining cold mechanical clamps demonstrates the dominant role of the polycrystalline metallic end clamps in the room-temperature mechanical dissipation.
Dosimetry protocol for the preclinical trials in white‐beam minibeam radiation therapy
Authors: Prezado Y. , Martínez‐Rovira I. , Thengumpallil S. , Deman P.
Published: August 2011

Purpose:

In the quest of a curative radiotherapy treatment for gliomas, new delivery modes are being explored. At the Biomedical Beamline of the European Synchrotron Radiation Facility, a new spatially fractionated technique, called minibeam radiation therapy (MBRT), is under development. The aims of this work were to assess different dosimetric aspects and to establish a dosimetry protocol to be applied in the forthcoming animal (rat) studies in order to evaluate the therapeutic index of this new radiotherapy approach.

Methods:

Absolute dosimetry was performed with a thimble ionization chamber (PTW semiflex 31010) whose center was positioned at 2 g cm−2 depth. To translate the dose measured in broad beam configuration to the dose deposited with a minibeam, the scatter factors were used. Those were assessed by using the Monte Carlo simulations and verified experimentally with Gafchromic films and a Bragg Peak chamber. The comparison of the theoretical and experimental data were used to benchmark the calculations. Finally, the dose distributions in a rat phantom were evaluated by using the validated Monte Carlo calculations.

Results:

The absolute dosimetry in broad beam configuration was measured in reference conditions. The dose rate was in the range between 168 and 224 Gy/min, depending on the storage ring current. A scatter factor of 0.80 ± 0.04 was obtained. Percentage depth dose and lateral profiles were evaluated both in homogenous and heterogeneous slab phantoms. The general good agreement between Monte Carlo simulations and experimental data permitted the benchmark of the calculations. Finally, the peak doses in the rat head phantom were assessed from the measurements in reference conditions. In addition, the peak‐to‐valley dose ratio values as a function of depth in the rat head were evaluated.

Conclusions:

A new promising radiotherapy approach is being explored at the ESRF: Minibeam Radiation Therapy. To assess the therapeutic index of this new modality, in vivo experiments are being planned, for which an accurate knowledge of the dosimetry is essential. For that purpose, a complete set of measurements and Monte Carlo simulations was performed. The first dosimetry protocol for preclinical trials in minibeam radiation therapy was established. This protocol allows to have reproducibility in terms of dose for the different biological studies.
A modeling approach to predict acoustic nonlinear field generated by a transmitter with an aluminum lens
Authors: Fan Tingbo , Liu Zhenbo , Chen Tao , Li Faqi , Zhang Dong
Published: August 2011

Purpose:

In this work, the authors propose a modeling approach to compute the nonlinear acoustic field generated by a flat piston transmitter with an attached aluminum lens.

Methods:

In this approach, the geometrical parameters (radius and focal length) of a virtual source are initially determined by Snell's refraction law and then adjusted based on the Rayleigh integral result in the linear case. Then, this virtual source is used with the nonlinear spheroidal beam equation (SBE) model to predict the nonlinear acoustic field in the focal region.

Results:

To examine the validity of this approach, the calculated nonlinear result is compared with those from the Westervelt and (Khokhlov‐Zabolotskaya‐Kuznetsov) KZK equations for a focal intensity of 7 kW/cm2. Results indicate that this approach could accurately describe the nonlinear acoustic field in the focal region with less computation time.

Conclusions:

The proposed modeling approach is shown to accurately describe the nonlinear acoustic field in the focal region. Compared with the Westervelt equation, the computation time of this approach is significantly reduced. It might also be applicable for the widely used concave focused transmitter with a large aperture angle.
Circumstellar Material in Type Ia Supernovae via Sodium Absorption Features
Authors: Sternberg A. , Gal-Yam A. , Simon J. D. , Leonard D. C. , Quimby R. M. , Phillips M. M. , Morrell N. , Thompson I. B. , Ivans I. , Marshall J. L. , Filippenko A. V. , Marcy G. W. , Bloom J. S. , Patat F. , Foley R. J. , Yong D. , Penprase B. E. , Beeler D. J. , Prieto C. Allende , Stringfellow G. S.
Published: August 2011

Most of the progenitors of type Ia supernovae in nearby spiral galaxies may be white dwarf−normal star binary systems.
The Structure of the Kinesin-1 Motor-Tail Complex Reveals the Mechanism of Autoinhibition
Authors: Kaan Hung Yi Kristal , Hackney David D. , Kozielski Frank
Published: August 2011

A tail domain autoinhibits a dimeric kinesin by preventing relative movement of the two motor domains.
A Synthetic Nickel Electrocatalyst with a Turnover Frequency Above 100,000 s
−1
for H
2
Production
Authors: Helm Monte L. , Stewart Michael P. , Bullock R. Morris , DuBois M. Rakowski , DuBois Daniel L.
Published: August 2011

Precisely shaped basic ligands protect highly reactive protons and electrons to help accelerate catalytic hydrogen formation.
Epidermal Electronics
Authors: Kim Dae-Hyeong , Lu Nanshu , Ma Rui , Kim Yun-Soung , Kim Rak-Hwan , Wang Shuodao , Wu Jian , Won Sang Min , Tao Hu , Islam Ahmad , Yu Ki Jun , Kim Tae-il , Chowdhury Raeed , Ying Ming , Xu Lizhi , Li Ming , Chung Hyun-Joong , Keum Hohyun , McCormick Martin , Liu Ping , Zhang Yong-Wei , Omenetto Fiorenzo G. , Huang Yonggang , Coleman Todd , Rogers John A.
Published: August 2011

Electronic systems with physical properties matched to the human epidermis can be used in clinical monitoring.
Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi
Authors: Rosling Anna , Cox Filipa , Cruz-Martinez Karelyn , Ihrmark Katarina , Grelet Gwen-Aëlle , Lindahl Björn D. , Menkis Audrius , James Timothy Y.
Published: August 2011

Cultivation and cloning allow phylogenetic placement of a prominent fungal lineage.
Nicotinic Acetylcholine Receptor β2 Subunits in the Medial Prefrontal Cortex Control Attention
Authors: Guillem Karine , Bloem Bernard , Poorthuis Rogier B. , Loos Maarten , Smit August B. , Maskos Uwe , Spijker Sabine , Mansvelder Huibert D.
Published: August 2011

An important molecular mechanism involved in cognition has been unraveled.
Ribosome Assembly Factors Prevent Premature Translation Initiation by 40
S
Assembly Intermediates
Authors: Strunk Bethany S. , Loucks Cherisse R. , Su Min , Vashisth Harish , Cheng Shanshan , Schilling Justin , Brooks Charles L. , Karbstein Katrin , Skiniotis Georgios
Published: August 2011

Ribosome assembly factors block multiple steps in translation initiation.
Cool Vibrations
Authors: Meystre Pierre
Published: August 2011

The ability to cool mechanical systems to ultralow temperatures will enable a new generation of sensitive detectors.
Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis
Authors: Kiers E. Toby , Duhamel Marie , Beesetty Yugandhar , Mensah Jerry A. , Franken Oscar , Verbruggen Erik , Fellbaum Carl R. , Kowalchuk George A. , Hart Miranda M. , Bago Alberto , Palmer Todd M. , West Stuart A. , Vandenkoornhuyse Philippe , Jansa Jan , Bücking Heike
Published: August 2011

Plants and their associated fungi reward partners that offer the best resources to sustain mutualism in complex systems.
A Simple Type of Wood in Two Early Devonian Plants
Authors: Gerrienne Philippe , Gensel Patricia G. , Strullu-Derrien Christine , Lardeux Hubert , Steemans Philippe , Prestianni Cyrille
Published: August 2011

The earliest evolution of wood occurred in plants of surprisingly small stature.
An Electronic Second Skin
Authors: Ma Zhenqiang
Published: August 2011

Small, flexible devices that attach to the skin without adhesives or gels monitor physiological signals.
Determining Sexual Identity
Authors: Van Doren Mark
Published: August 2011

In
Drosophila
, expression of the
Sex lethal
gene feminizes male germ cells.
Altruistic Wasps?
Authors: Gadagkar Raghavendra
Published: August 2011

Is the widely invoked theory of kin selection necessary to explain the apparent altruism in social wasp colonies?
Figuring Out What the Debt Agreement Means for Science
Authors: Mervis Jeffrey
Published: August 2011

Research advocates say their initial response to the Budget Control Act of 2011 is one of cautious optimism about the immediate future—and apprehension about the longer-term prospects.
The Legacy of the Three Gorges Dam
Authors: Stone Richard
Published: August 2011

The travails of the Three Gorges Dam are a cautionary tale for Laos and its Southeast Asian neighbors as they wrestle with the pros and cons of damming the lower Mekong River.
Th1/Th2 Cytokine Profile in Patients Coinfected with HIV and Leishmania in Brazil
Authors: Rodrigues Maria Zilma Andrade , Grassi Maria Fernanda Rios , Mehta Sanjay , Zhang Xing-Quan , Gois Luana Leandro , Schooley Robert T. , Badaro Roberto
Published: August 2011

To evaluate the effects of HIV on immune responses in cutaneous leishmaniasis (CL), we quantified cytokine levels from plasma and stimulated peripheral blood mononuclear cells (PBMCs) from individuals infected with HIV and/or CL. Gamma interferon (IFN-γ) and interleukin 13 (IL-13) levels and the ratio of IFN-γ to IL-10 produced in response to stimulation with solubleLeishmaniaantigens were significantly lower in HIV-Leishmania-coinfected patients than in CL-monoinfected patients.
Analyzing Multiclonality of Staphylococcus aureus in Clinical Diagnostics Using
spa
-Based Denaturing Gradient Gel Electrophoresis
Authors: Matussek Andreas , Stark Lisa , Dienus Olaf , Aronsson Joakim , Mernelius Sara , Löfgren Sture , Lindgren Per-Eric
Published: August 2011

We present a novel denaturing gradient gel electrophoresis (DGGE) method which characterizes multiclonal communities of
Staphylococcus aureus
. The
spa
PCR-based DGGE method simultaneously separates strains that differ in only one base, thereby revealing multiclonal colonization and infections.
Rapid and Accurate Identification of Human-Associated Staphylococci by Use of Multiplex PCR
Authors: Hirotaki Shintaro , Sasaki Takashi , Kuwahara-Arai Kyoko , Hiramatsu Keiichi
Published: August 2011

Although staphylococci are identified by phenotypic analysis in many clinical laboratories, these results are often incorrect because of phenotypic variation. Genetic analysis is necessary for definitive species identification. In the present study, we developed a simple multiplex-PCR (M-PCR) for species identification of human-associated staphylococci, which were as follows:
Staphylococcus aureus
,
S. capitis
,
S. caprae
,
S. epidermidis
,
S. haemolyticus
,
S. hominis
,
S. lugdunensis
,
S. saprophyticus
, and
S. warneri
. This method was designed on the basis of nucleotide sequences of the thermonuclease (
nuc
) genes that were universally conserved in staphylococci except the
S. sciuri
group and showed moderate sequence diversity. In order to validate this assay, 361 staphylococcal strains were studied, which had been identified at the species levels by sequence analysis of the
hsp60
genes. In consequence, M-PCR demonstrated a sensitivity of 100% and a specificity of 100%. By virtue of simplicity and accuracy, this method will be useful in clinical research.
Loop-Mediated Isothermal Amplification Assay for Detection of Haemophilus influenzae Type b in Cerebrospinal Fluid
Authors: Kim Dong Wook , Kilgore Paul Evan , Kim Eun Jin , Kim Soon Ae , Anh Dang Duc , Seki Mitsuko
Published: August 2011

Haemophilus influenzaetype b (Hib) is one of the leading causes of meningitis in developing countries. To establish and evaluate a novel loop-mediated isothermal amplification (LAMP) assay for Hib, we designed a LAMP primer set targeting the Hib-specific capsulation locus. LAMP detected 10 copies of purified DNA in a 60-min reaction. This indicated that the detection limit of LAMP was >100-fold lower than the detection limits of both a PCR for the detection ofbexAand a nested PCR for Hib (Hib PCR). NoH. influenzae, other than Hib or control bacteria, was detected. Linear determination ranged from 10 to 1,000,000 microorganisms per reaction mixture using real-time turbidimetry. We evaluated the Hib LAMP assay using a set of 52 randomly selected cerebrospinal fluid (CSF) specimens obtained from children with suspected meningitis. For comparison, the CSF specimens were tested using a conventional Hib PCR assay. Hib was detected in 30 samples using LAMP and in 22 samples using the Hib PCR assay. The Hib PCR showed a clinical sensitivity of 73.3% and a clinical specificity of 100% relative to the Hib LAMP assay. These results suggest that further development and evaluation of the Hib LAMP will enhance the global diagnostic capability for Hib detection.
Evaluation of Pooling Strategies for Acute HIV-1 Infection Screening Using Nucleic Acid Amplification Testing
Authors: Sullivan Timothy J. , Patel Pragna , Hutchinson Angela , Ethridge Steven F. , Parker Monica M.
Published: August 2011

A 128-member specimen pooling scheme for acute HIV infection (AHI) detection was evaluated using 21 AHI specimens (range, 1,520 to 500,000 copies/ml) previously identified by RNA testing of 16-member plasma pools. HIV-1 RNA was detectable in 128-member pools for all 21 specimens; however, one pool created from a specimen with 1,827 copies/ml was nonreactive in one of three replicates.
Validation of a Low-Cost Human Papillomavirus Genotyping Assay Based on PGMY PCR and Reverse Blotting Hybridization with Reusable Membranes
Authors: Estrade C. , Menoud P.-A. , Nardelli-Haefliger D. , Sahli R.
Published: August 2011

The genotyping of human papillomaviruses (HPV) is essential for the surveillance of HPV vaccines. We describe and validate a low-cost PGMY-based PCR assay (PGMY-CHUV) for the genotyping of 31 HPV by reverse blotting hybridization (RBH). Genotype-specific detection limits were 50 to 500 genome equivalents per reaction. RBH was 100% specific and 98.61% sensitive using DNA sequencing as the gold standard (n= 1,024 samples). PGMY-CHUV was compared to the validated and commercially available linear array (Roche) on 200 samples. Both assays identified the same positive (n= 182) and negative samples (n= 18). Seventy-six percent of the positives were fully concordant after restricting the comparison to the 28 genotypes shared by both assays. At the genotypic level, agreement was 83% (285/344 genotype-sample combinations; κ of 0.987 for single infections and 0.853 for multiple infections). Fifty-seven of the 59 discordant cases were associated with multiple infections and with the weakest genotypes within each sample (P< 0.0001). PGMY-CHUV was significantly more sensitive for HPV56 (P= 0.0026) and could unambiguously identify HPV52 in mixed infections. PGMY-CHUV was reproducible on repeat testing (n= 275 samples; 392 genotype-sample combinations; κ of 0.933) involving different reagents lots and different technicians. Discordant results (n= 47) were significantly associated with the weakest genotypes in samples with multiple infections (P< 0.0001). Successful participation in proficiency testing also supported the robustness of this assay. The PGMY-CHUV reagent costs were estimated at $2.40 per sample using the least expensive yet proficient genotyping algorithm that also included quality control. This assay may be used in low-resource laboratories that have sufficient manpower and PCR expertise.
Characterization of Structural Features and Diversity of Variable-Region Determinants of Related Quaternary Epitopes Recognized by Human and Rhesus Macaque Monoclonal Antibodies Possessing Unusually Potent Neutralizing Activities
Authors: Krachmarov Chavdar , Lai Zhong , Honnen William J. , Salomon Aidy , Gorny Miroslaw K. , Zolla-Pazner Susan , Robinson James , Pinter Abraham
Published: August 2011

A series of potently neutralizing monoclonal antibodies (MAbs) that target quaternary epitopes on the native Env trimer have recently been described. A common feature shared by these antibodies is the critical involvement of sites in both the V2 and V3 variable domains in antibody recognition. In this study the gp120 variable-region determinants were mapped for eight rhesus macaque monoclonal antibodies (RhMAbs) possessing potently neutralizing activity specific for a quaternary target in SF162 Env and compared to those originally identified for human MAb 2909. These studies showed that determinants for the epitopes defined by the RhMAbs differed in both the V2 (positions 160, 167, and 169) and V3 (positions 313 and 315) regions from 2909, and in a number of cases, from each other. Attempts to reconstitute expression of these epitopes on the cell surface by cotransfecting Envs containing either the V2 or the V3 determinant of the epitope were not successful, suggesting that these epitopes were expressed on individual protomers in a trimer-dependent manner. Several of the V2 positions found to be critical for expression of these quaternary epitopes also significantly affected exposure and neutralization sensitivity of targets in the V3 and CD4-binding domains. These results demonstrated a considerable diversity in the fine structure of this class of epitopes and further suggested a potentially important relationship between the expression of such quaternary epitopes and V1/V2-mediated masking of immunodominant epitopes.
Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection
Authors: Ganusov Vitaly V. , Goonetilleke Nilu , Liu Michael K. P. , Ferrari Guido , Shaw George M. , McMichael Andrew J. , Borrow Persephone , Korber Bette T. , Perelson Alan S.
Published: August 2011

HIV-1 often evades cytotoxic T cell (CTL) responses by generating variants that are not recognized by CTLs. We used single-genome amplification and sequencing of complete HIV genomes to identify longitudinal changes in the transmitted/founder virus from the establishment of infection to the viral set point at 1 year after the infection. We found that the rate of viral escape from CTL responses in a given patient decreases dramatically from acute infection to the viral set point. Using a novel mathematical model that tracks the dynamics of viral escape at multiple epitopes, we show that a number of factors could potentially contribute to a slower escape in the chronic phase of infection, such as a decreased magnitude of epitope-specific CTL responses, an increased fitness cost of escape mutations, or an increased diversity of the CTL response. In the model, an increase in the number of epitope-specific CTL responses can reduce the rate of viral escape from a given epitope-specific CTL response, particularly if CD8+T cells compete for killing of infected cells or control virus replication nonlytically. Our mathematical framework of viral escape from multiple CTL responses can be used to predict the breadth and magnitude of HIV-specific CTL responses that need to be induced by vaccination to reduce (or even prevent) viral escape following HIV infection.
Inhibition of RIG-I-Mediated Signaling by Kaposi's Sarcoma-Associated Herpesvirus-Encoded Deubiquitinase ORF64
Authors: Inn Kyung-Soo , Lee Sun-Hwa , Rathbun Jessica Y. , Wong Lai-Yee , Toth Zsolt , Machida Keigo , Ou Jing-Hsiung James , Jung Jae U.
Published: August 2011

Virus infection triggers interferon (IFN)-mediated innate immune defenses in part through viral nucleic acid interactions. However, the immune recognition mechanisms by which the host identifies incoming DNA viruses are still elusive. Here, we show that increased levels of Kaposi's sarcoma-associated herpesvirus (KSHV) persistency are observed in retinoic acid-inducible gene I (RIG-I)-deficient cells and that KSHV ORF64, a tegument protein with deubiqutinase (DUB) activity, suppresses RIG-I-mediated IFN signaling by reducing the ubiquitination of RIG-I, crucial for its activation. This study suggests that RIG-I plays a potential role in sensing KSHV infection and that KSHV ORF64 DUB counteracts RIG-I signaling.
Differential Processing of Nuclear Pore Complex Proteins by Rhinovirus 2A Proteases from Different Species and Serotypes
Authors: Watters Kelly , Palmenberg Ann C.
Published: August 2011

Human rhinoviruses (HRVs) from the HRV-A, HRV-B, and HRV-C species use encoded proteases, 2A
pro
and 3C
pro
, to process their polyproteins and shut off host cell activities detrimental to virus replication. Reactions attributed to 2A
pro
include cleavage of eIF4G-I and -II to inhibit cellular mRNA translation and cleavage of select nucleoporin proteins (Nups) within nuclear pore complexes (NPCs) to disrupt karyopherin-dependent nuclear-cytoplasmic transport and signaling. Sequence diversity among 2A
pro
proteases from different HRV clades, even within species, suggested individual viruses might carry out these processes with unique mechanistic signatures. Six different recombinant 2A
pro
proteases (A16, A89, B04, B14, Cw12, and Cw24) were compared for their relative substrate preferences and cleavage kinetics using eIF4G from cellular extracts and Nups presented in native (NPC) or recombinant formats. The enzyme panel attacked these substrates with different rates or processing profiles, mimicking the preferences observed during natural infection (A16 and B14). For eIF4G, all 2A
pro
proteases cleaved at similar sites, but the comparative rates were species specific (HRV-A > HRV-C ≫ HRV-B). For Nup substrates, 5 of the 6 enzymes had unique product profiles (order of Nup selection) or reacted at different sites within Nup62, Nup98, and Nup153. Only A16 and A89 behaved similarly in most assays. Since each type of karyopherin receptor prefers particular Nups or uses a limited cohort of binding motifs within those Nups, the consequences of individual 2A
pro
avidities could profoundly affect relative viral replication levels, intracellular signaling, or extracellular signaling, all of which are underlying triggers for different host immune responses.
Novel Adenoviruses in Wild Primates: a High Level of Genetic Diversity and Evidence of Zoonotic Transmissions
Authors: Wevers Diana , Metzger Sonja , Babweteera Fred , Bieberbach Marc , Boesch Christophe , Cameron Kenneth , Couacy-Hymann Emmanuel , Cranfield Mike , Gray Maryke , Harris Laurie A. , Head Josephine , Jeffery Kathryn , Knauf Sascha , Lankester Felix , Leendertz Siv Aina J. , Lonsdorf Elizabeth , Mugisha Lawrence , Nitsche Andreas , Reed Patricia , Robbins Martha , Travis Dominic A. , Zommers Zinta , Leendertz Fabian H. , Ehlers Bernhard
Published: August 2011

Adenoviruses (AdVs) broadly infect vertebrate hosts, including a variety of nonhuman primates (NHPs). In the present study, we identified AdVs in NHPs living in their natural habitats, and through the combination of phylogenetic analyses and information on the habitats and epidemiological settings, we detected possible horizontal transmission events between NHPs and humans. Wild NHPs were analyzed with a pan-primate AdV-specific PCR using a degenerate nested primer set that targets the highly conserved adenovirus DNA polymerase gene. A plethora of novel AdV sequences were identified, representing at least 45 distinct AdVs. From the AdV-positive individuals, 29 nearly complete hexon genes were amplified and, based on phylogenetic analysis, tentatively allocated to all known human AdV species (Human adenovirus AtoHuman adenovirus G[HAdV-A to -G]) as well as to the only simian AdV species (Simian adenovirus A[SAdV-A]). Interestingly, five of the AdVs detected in great apes grouped into the HAdV-A, HAdV-D, HAdV-F, or SAdV-A clade. Furthermore, we report the first detection of AdVs in New World monkeys, clustering at the base of the primate AdV evolutionary tree. Most notably, six chimpanzee AdVs of species HAdV-A to HAdV-F revealed a remarkably close relationship to human AdVs, possibly indicating recent interspecies transmission events.
The Breadth of Antiviral Activity of Apobec3DE in Chimpanzees Has Been Driven by Positive Selection
Authors: Duggal Nisha K. , Malik Harmit S. , Emerman Michael
Published: August 2011

The Apobec3 family of cytidine deaminases can inhibit the replication of retroviruses and retrotransposons. Human and chimpanzee genomes encode seven
Apobec3
paralogs; of these,
Apobec3DE
has the greatest sequence divergence between humans and chimpanzees. Here we show that even though human and chimpanzee Apobec3DEs are very divergent, the two orthologs similarly restrict long terminal repeat (LTR) and non-LTR retrotransposons (MusD and Alu, respectively). However, chimpanzee Apobec3DE also potently restricts two lentiviruses, human immunodeficiency virus type 1 (HIV-1) and the simian immunodeficiency virus (SIV) that infects African green monkeys (SIVagmTAN), unlike human Apobec3DE, which has poor antiviral activity against these same viruses. This difference between human and chimpanzee Apobec3DE in the ability to restrict retroviruses is not due to different levels of Apobec3DE protein incorporation into virions but rather to the ability of Apobec3DE to deaminate the viral genome in target cells. We further show that
Apobec3DE
rapidly evolved in chimpanzee ancestors approximately 2 to 6 million years ago and that this evolution drove the increased breadth of chimpanzee Apobec3DE antiviral activity to its current high activity against some lentiviruses. Despite a difference in target specificities between human and chimpanzee Apobec3DE, Apobec3DE is likely to currently play a role in host defense against retroelements in both species.
Targeting the Human Papillomavirus E6 and E7 Oncogenes through Expression of the Bovine Papillomavirus Type 1 E2 Protein Stimulates Cellular Motility
Authors: Morrison Monique A. , Morreale Richard J. , Akunuru Shailaja , Kofron Matthew , Zheng Yi , Wells Susanne I.
Published: August 2011

Expression of the high-risk human papillomavirus (HPV) E6 and E7 oncogenes is essential for the initiation and maintenance of cervical cancer. The repression of both was previously shown to result in activation of their respective tumor suppressor targets, p53 and pRb, and subsequent senescence induction in cervical cancer cells. Consequently, viral oncogene suppression is a promising approach for the treatment of HPV-positive tumors. One well-established method of E6/E7 repression involves the reexpression of the viral E2 protein which is usually deleted in HPV-positive cancer cells. Here, we show that, surprisingly, bovine papillomavirus type 1 (BPV1) E2 but not RNA interference-mediated E6/E7 repression in HPV-positive cervical cancer cells stimulates cellular motility and invasion. Migration correlated with the dynamic formation of cellular protrusions and was dependent upon cell-to-cell contact. While E2-expressing migratory cells were senescent, migration was not a general feature of cellular senescence or cell cycle arrest and was specifically observed in HPV-positive cervical cancer cells. Interestingly, E2-expressing cells not only were themselves motile but also conferred increased motility to admixed HeLa cervical cancer cells. Together, our data suggest that repression of the viral oncogenes by E2 stimulates the motility of E6/E7-targeted cells as well as adjacent nontargeted cancer cells, thus raising the possibility that E2 expression may unfavorably increase the local invasiveness of HPV-positive tumors.
Human and Rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H Demonstrate a Conserved Capacity To Restrict Vif-Deficient HIV-1
Authors: Hultquist Judd F. , Lengyel Joy A. , Refsland Eric W. , LaRue Rebecca S. , Lackey Lela , Brown William L. , Harris Reuben S.
Published: August 2011

Successful intracellular pathogens must evade or neutralize the innate immune defenses of their host cells and render the cellular environment permissive for replication. For example, to replicate efficiently in CD4
+
T lymphocytes, human immunodeficiency virus type 1 (HIV-1) encodes a protein called viral infectivity factor (Vif) that promotes pathogenesis by triggering the degradation of the retrovirus restriction factor APOBEC3G. Other APOBEC3 proteins have been implicated in HIV-1 restriction, but the relevant repertoire remains ambiguous. Here we present the first comprehensive analysis of the complete, seven-member human and rhesus APOBEC3 families in HIV-1 restriction. In addition to APOBEC3G, we find that three other human APOBEC3 proteins, APOBEC3D, APOBEC3F, and APOBEC3H, are all potent HIV-1 restriction factors. These four proteins are expressed in CD4
+
T lymphocytes, are packaged into and restrict Vif-deficient HIV-1 when stably expressed in T cells, mutate proviral DNA, and are counteracted by HIV-1 Vif. Furthermore, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H of the rhesus macaque also are packaged into and restrict Vif-deficient HIV-1 when stably expressed in T cells, and they are all neutralized by the simian immunodeficiency virus Vif protein. On the other hand, neither human nor rhesus APOBEC3A, APOBEC3B, nor APOBEC3C had a significant impact on HIV-1 replication. These data strongly implicate a combination of four APOBEC3 proteins—APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H—in HIV-1 restriction.
Resistance of Human Immunodeficiency Virus Type 1 to a Third-Generation Fusion Inhibitor Requires Multiple Mutations in gp41 and Is Accompanied by a Dramatic Loss of gp41 Function
Authors: Eggink Dirk , Bontjer Ilja , Langedijk Johannes P. M. , Berkhout Ben , Sanders Rogier W.
Published: August 2011

HIV-1 entry into target cells requires the fusion of viral and cellular membranes. This process is an attractive target for therapeutic intervention, and a first-generation fusion inhibitor, T20 (Enfuvirtide; Fuzeon), was approved for clinical use in 2003. Second-generation (T1249) and third-generation (T2635) fusion inhibitors with improved stability and potency were developed. Resistance to T20 and T1249 usually requires one or two amino acid changes within the binding site. We studied the
in vitro
evolution of resistance against T2635. After 6 months of culturing, a multitude of resistance mutations was identified in all gp41 subdomains, but no single mutation provided meaningful T2635 resistance. In contrast, multiple mutations within gp41 were required for resistance, and this was accompanied by a dramatic loss of viral infectivity. Because most of the escape mutations were situated outside the T2635 binding site, a decrease in drug target affinity cannot account for most of the resistance. T2635 resistance is likely to depend on altered kinetics of six-helix bundle formation, thus limiting the time window for T2635 to interfere with membrane fusion. Interestingly, the loss of virus infectivity caused by T2635 resistance mutations in gp41 was partially compensated for by a mutation at the base of the V3 domain in gp120. Thus, escape from the third-generation HIV-1 fusion inhibitor T2635 is mechanistically distinct from resistance against its predecessors T20 and T1249. It requires the accumulation of multiple mutations in gp41, is accompanied with a dramatic loss of gp41 function, and induces compensatory mutations in gp120.
Membrane Integration of Poliovirus 2B Viroporin
Authors: Martínez-Gil Luis , Bañó-Polo Manuel , Redondo Natalia , Sánchez-Martínez Silvia , Nieva José Luis , Carrasco Luis , Mingarro Ismael
Published: August 2011

Virus infections can result in a variety of cellular injuries, and these often involve the permeabilization of host membranes by viral proteins of the viroporin family. Prototypical viroporin 2B is responsible for the alterations in host cell membrane permeability that take place in enterovirus-infected cells. 2B protein can be localized at the endoplasmic reticulum (ER) and the Golgi complex, inducing membrane remodeling and the blockade of glycoprotein trafficking. These findings suggest that 2B has the potential to integrate into the ER membrane, but specific information regarding its biogenesis and mechanism of membrane insertion is lacking. Here, we report experimental results of
in vitro
translation-glycosylation compatible with the translocon-mediated insertion of the 2B product into the ER membrane as a double-spanning integral membrane protein with an N-/C-terminal cytoplasmic orientation. A similar topology was found when 2B was synthesized in cultured cells. In addition, the
in vitro
translation of several truncated versions of the 2B protein suggests that the two hydrophobic regions cooperate to insert into the ER-derived microsomal membranes.
Conformation-Selective Methylation of Geminivirus DNA
Authors: Paprotka T. , Deuschle K. , Metzler V. , Jeske H.
Published: August 2011

Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially.
The compressibility of sodium tungsten bronzes
Authors: Vondrák Jiří , Zámečník Jozef
Published: August 2011

The linear compressibility of cubic sodium tungsten bronze NaxWO3 (x = 0.72) is (-8.56 ± 0.54) . 1012 Pa-1; the linear compressibility of type I tetragonal bronze (x = 0.46) is (-20.2 ± 1.3) . 1012 Pa-1 parallel to the a axis and (+4.17 ± 1.9) . 1012 Pa-1 parallel to the c axis. The compressibility of cubic bronze decreases somewhat with increasing pressure (in the range 0-250 mPa). The compressibility was directly measured optically.
2-Chloro-7-fluoro- and 2-chloro-3,7-difluoro-11-[4-(4-fluoroaralkyl)piperazino]-10,11-dihydrodibenzo-[b,f]thiepins and related compounds; Long acting tranquillizers
Authors: Bártl Václav , Metyšová Jiřina , Protiva Miroslav
Published: August 2011

Substitution reactions of 2,11-dichloro-7-fluoro-(seriesa) and 2,11-dichloro-3,7-difluoro-10,11-dihydrodibenzo[b,f]thiepin (seriesb) with 1-(4-fluorobenzyl)piperazine, 1-[2-(4-fluorophenyl)-ethyl]piperazine, 1-[2-(4-fluorophenoxy)ethyl]piperazine, 1-[2-(4-fluorophenylthio)ethyl]piperazine, 1-[3-(4-fluorobenzoyl)propyl]piperazine and 1-[4,4-bis-(4-fluorophenyl)butyl]piperazine gave the title compounds Ia,b-VIa,b. Compounds of the series a are little toxic, have low cataleptic activity and display a relatively high central depressant activity, being fully developed only after 4 h and persisting until the 3rd-7th day after the oral administration. Compounds of series b are less active and the protracted depressant effects are shown only by substances IIIb and Vb.
Mechanismus der Photo-Umlagerung von Benzylarylethern
Authors: Timpe Hans-Joachim , Dietrich Reinhard , Böckelmann Jürgen , Friedel Ingrid , Bögel Horst , Haucke Günther
Published: August 2011

Aus Absorptions- und Emissionsspektren konnten die ES- und ET-Werte einiger Benzylarylether bestimmt werden. Die Photo-Claisen-Umlagerung dieser Ether erfolgt aus dem S1-Zustand, wie durch Sensibilisierungs- und Löschexperimente mit aromatischen Kohlenwasserstoffen bzw. Diacetyl bewiesen wurde. Bei der Photolyse werden primär Benzyl- und Phenoxyradikale gebildet, deren Entstehen durch Spin-Trapping-Experimente bewiesen wurde. Die Spaltung der Ether geschieht mit hohen Quantenausbeuten, die wenig von Substituenten sowohl im Phenoxy- als auch im Benzylteil der Ether beeinflußt werden. In protischen Lösungsmitteln steigen die Werte geringfügig an. Die Quantenausbeuten für die Reaktionsprodukte wurden ebenfalls bestimmt; deren Summe ergibt die Größe für den Etherabbau. Die Produktverteilung bei der Photolyse einiger p-substituierter Ether legt nahe, daß die Benzylradikale auch in p-Stellung der Phenoxyradikale angreifen. Es wird ein allgemeiner Mechanismus diskutiert und kinetisch modelliert. Dadurch werden die Geschwindigkeitskonstanten einiger Teilschritte zugänglich und wahrscheinlich gemacht, daß die Radikale auch zum Ether rekombinieren.
Reduction of 1-isoquinolyl-dimethylmethanol and 1-(1-isoquinolyl)cyclohexanol
Authors: Ferles Miloslav , Šputová Michaela , Tegza Marian
Published: August 2011

Reduction of alcohols Ia and IIa with zinc and formic acid afforded 1-isopropylisoquinoline (Ib) and 1-cyclohexylisoquinoline (IIb), respectively, reduction with sodium in 1-butanol led to the 1,2,3,4-tetrahydroisoquinoline derivatives III, IV and Va and electrolytical reduction gave 1-isopropyl-1,2,3,4-tetrahydroisoquinoline (Vd) and the 1-cyclohexyl derivative Ve, respectively.
Synthesis of oxytocin, arginine-vasopressin and its deamino-analogue using 2,4,6-trimethylbenzyl group for protection of the cysteine sulfur
Authors: Brtník František , Krojidlo Milan , Barth Tomislav , Jošt Karel
Published: August 2011

Preparation of oxytocin, arginine-vasopressin and its deamino-analogue serves as an example of use of 2,4,6-trimethylbenzyl group for protection of the cysteine sulfur atom in the peptide synthesis. This modified benzyl group is sufficiently stable under conditions of solvolytic removal of common amino-protecting groups and it can be cleaved off under mild conditions with liquid hydrogen fluoride or trifluoromethanesulfonic acid.
Viscosity of binary and tertinary liquid nonelectrolyte mixtures. Comparison of correlation equations and analysis of viscosity curves
Authors: Škubla Pavol
Published: August 2011

The derived equations for correlation of viscosity of binary and ternary mixtures were tested and compared with those of McAllister, Chandramouli and Laddha. Testing on a large number of experimental data revealed that the equations for correlation of viscosity of binary mixtures are approximately as accurate as the equation of McAllister. On adding another coefficient, the relative deviations are lowered by 26-40%. Equations for correlation of viscosity of ternary mixtures are about as accurate as the equation of Chandramouli and Laddha. Analysis of viscosity curves of binary mixtures revealed a correlation between their form and the chemical nature of the components of the mixture.
Investigation of subtilisin digest of pepsin chain between half-cystines II and III
Authors: Kostka Vladimír
Published: August 2011

Aminoethylated hog pepsin was subjected to tryptic digestion and the longest fragment, arising from cleavage at S-(β-aminoethyl)-cysteine residue No II and III was isolated from the digest. This fragment was subjected to additional cleavage with subtilisin and the digest resolved into crude fractions by chromatography on Dowex 1. The isolation and final purification of the peptides was carried out by paper electrophoreses and paper chromatography. By these methods 55 peptides were obtained which were subjected to sequential analysis by stepwise degradation. The amino acid sequences of these peptides and their position in the pepsin chain are given. These sequences provided overlaps for peptides obtained by hydrolysis of this part of the pepsin chain by other enzymes.
Potential noncataleptic neuroleptic agents: 2,4-Dichloro- and 2,4,8-trichloro-10-piperazino-10,11-dihydrodibenzo[b,f]thiepins
Authors: Valenta Vladimír , Dlabač Antonín , Protiva Miroslav
Published: August 2011

3,5-Dichloro-2-iodobenzoic acid (IV), prepared from 3,5-dichloroanthranilic acid (III), was transformed in 5 steps into the diphenyl sulfide-2-acetic acids IXab. Cyclization resulted in ketones XVab which were processed in further 3 steps into the title compounds Iab and IIa. These products are mild tranquilizers devoid of cataleptic and antiapomorphine activity.
Purification and characterization of alcohol dehydrogenase from pig liver
Authors: Pařízek Radim , Kovář Jan , Skurský Ladislav
Published: August 2011

Alcohol dehydrogenase from pig liver was purified from a tissue homogenate under conditions of enzyme protection in a complex with NADH and isobutyramide and further by chromatography on ion-exchange celluloses and Sephadex G-100. pH 8 and an addition of dithiotreitol was found most effective for stabilization of the enzyme. Electrophoretic behavior revealed the existence of at least 4 isoenzymes with variable relative amounts of 3 minor components. Using a titration of the enzyme by NADH in the presence of isobutyramide the concentration of active sites and turnover number of the enzyme were determined. The basic kinetic characteristics show that the pig enzyme is less active than that of the horse origin, whereas its affinity to coenzymes and substrates is comparable. Pig alcohol dehydrogenase can be inhibited by inhibitors active against other animal alcohol dehydrogenases.
Half-wave potentials of quinone methides in dimethylformamide: Substituent effects
Authors: Krupička Josef , Koutek Bohumír , Musil Lubomír , Pavlíčková Libuše , Souček Milan
Published: August 2011

Half-wave potentials of two series of quinone methides A have been determined in 0.1M tetrabutylammonium perchlorate in dimethylformamide. the first series (type I; 14 compounds) contained fuchsones substituted in positions 2 and 2,6 of the quinonoid ring, the second series (type II and III; 17 compounds) consisted of 2,6-ditert-butylquinone methides, with substituents at the exocyclic C(7) carbon atom. Properties of the first polarographic wave proved that in both series the reaction is one-electron, reversible, diffusion-controlled process. Linear free energy relationship was found between E1/2 and dual substituent constants σI and σR. Statistical analysis of linear free energy relationship for 2- and 2,6-substituted derivatives proved absence of steric factor in transmission of electronic substituent effect. The experimental results were interpreted on the basis of LUMO energies and spin densities, calculated by the HMO method.
Calculation of isokinetic temperature of non-catalyzed hydrolysis of substituted 3-(N-methylcarbamoyl)-1,3-diphenyltriazenes
Authors: Pytela Oldřich , Večeřa Miroslav , Vetešník Pavel
Published: August 2011

Temperature dependence of kinetics of non-catalyzed hydrolysis of substituted 3-(N-methylcarbamoyl)-1,3-diphenyltriazines has been measured. An optimized calculation method has been suggested for calculation of the isokinetic temperature and the experimental data have been evaluated. In all the cases it has been found that the hypothesis of common intersection of the straight lines log k vs1/T is rejected at the significance level α = 0.05, but, within approximate validity of the isokinetic hypothesis the isokinetic relation can be considered to be fulfilled in the given reaction series. The change of the reaction constant ρ connected with the change of the reaction mechanism shows a statistically significant correspondence with the change of the isokinetic temperature.
Alkaloids from Papaver oreophilum F. J. RUPR
Authors: Věžník František , Táborská Eva , Slavík Jiří
Published: August 2011

In addition to the konwn alkaloids from Papaver oreophilum F. J. RUPR., i.e. oridine, mecambridine, isocorydine, protopine, oreodine, rhoeadine, nuciferine, isooridine (oridine-2), oridine-3, alkaloid PO-5 (R-K, alborine) and trace alkaloids rhoeagenine, oreogenine, isorhoeadine, papaverrubines A, D and E, sanguinarine, N-methyloridine and coptisine, we isolated from the aerial part or from the roots the following further alkaloids: allocryptopine and - from the quaternary fraction - menisperine and magnoflorine (3.6%), which is the main alkaloid in the roots. Further corydine and trace amounts of papaverrubine C, chelirubine, berberine, corysamine and probably O-methyloridine and O,N-dimethyloridine were also detected. It was shown that oridine-3 was identical with the hydrochloride of isooridine.
Crystal and molecular structure of the nickel(II) chelate of salicylidenethiosemicarbazone ammine - C8H7N3OSNi.NH3
Authors: Gyepes Eduard , Pavelčík František , Beňo Anton
Published: August 2011

The nickel(II) chelate of salicylidenethiosemicarbazone ammine-C8H7N3OSNi.NH3 crystallizes in a monoclinic system. The lattice parameters are: a = 6.857(2), b = 9.763(2), c = 15.340(4) .10-10 m, β = 90.34(2)° and the volume of the unit cell V = 1027(1) . 10-30 m3; the specific weight was measured as dm = 1.76 Mg m-3 and calculated as dc = 1.74 Mg m-3. The number of formula units in the unit cell, Z = 4, and the symmetry space group is P21/c.
Kinetics of hydrolysis of peroxodisulphate ions in acidic medium to peroxomonosulphuric acid
Authors: Balej Jan , Thumová Milada
Published: August 2011

The rate of hydrolysis of S2O82- ions in acidic medium to peroxomonosulphuric acid was measured at 20 and 30 °C. The composition of the starting solution corresponded to the anolyte flowing out from an electrolyser for production of this acid or its ammonium salt at various degrees of conversion and starting molar ratios of sulphuric acid to ammonium sulphate. The measured data served to calculate the rate constants at both temperatures on the basis of the earlier proposed mechanism of the hydrolysis, and their dependence on the ionic strength was studied.