bluuebunny/crossref_metadata_2025 huggingface dataset:
Primary Immunodeficiencies: A Field in Its Infancy
Authors: Casanova Jean-Laurent , Abel Laurent
Published: August 2007

A paradigm shift is occurring in the field of primary immunodeficiencies, with revision of the definition of these conditions and a considerable expansion of their limits. Inborn errors of immunity were initially thought to be confined to a few rare, familial, monogenic, recessive traits impairing the development or function of one or several leukocyte subsets and resulting in multiple, recurrent, opportunistic, and fatal infections in infancy. A growing number of exceptions to each of these conventional qualifications have gradually accumulated. It now appears that most individuals suffer from at least one of a multitude of primary immunodeficiencies, the dissection of which is helping to improve human medicine while describing immunityin natura.
Division of Labor with a Workforce of One: Challenges in Specifying Effector and Memory T Cell Fate
Authors: Reiner Steven L. , Sallusto Federica , Lanzavecchia Antonio
Published: August 2007

In the course of the immune response against microbes, naïve T cells proliferate and generate varied classes of effector cells, as well as memory cells with distinct properties and functions. Owing to recent technological advances, some of the most imposing questions regarding effector and memory T cell differentiation are now becoming experimentally soluble: How many classes of antigen-specific T cells exist, and how malleable are they in their fate and in their functional state? How might a spectrum of cell fates be imparted to the clonal descendants of a single lymphocyte? Where, when, and how does pathogen-associated information refine the instruction, selection, and direction of newly activated T cells as they perform their tasks in different locations and times? Some surprising new glimpses ahead on these subjects and other yet-unanswered questions are discussed.
Epigenetic Flexibility Underlying Lineage Choices in the Adaptive Immune System
Authors: Kioussis Dimitris , Georgopoulos Katia
Published: August 2007

Although fundamental models have emerged in recent years describing how chromatin and transcription regulation interface with one another in the developing immune system, the order of events and their biological impact are still being resolved. Recent advances have provided a flexible, rather than static, view of chromatin regulation to reveal how both positive and negative forces work concomitantly to establish specific chromatin structures and regulate gene expression. The challenge will now be to explore new epigenetic models and validate them during lymphocyte development, with the ultimate goal of unraveling the long-sought mechanisms that support the emerging complexity of the adaptive immune response.
Just Another Bomb?
Authors: Krige John
Published: August 2007

Five Days in August
. How World War II Became a Nuclear War.
By Michael D. Gordin
. Princeton University Press, Princeton, NJ, 2007. 225 pp. $24.95, £14.95. ISBN 9780691128184.

Gordin centers this short, intriguing reconsideration of the role of the atomic bomb in ending the second world war on the military, strategic, and political aspects of the history.
Assessment of Cross-Reactivity between
Mycobacterium bovis
and
M. kansasii
ESAT-6 and CFP-10 at the T-Cell Epitope Level
Authors: Vordermeier H. Martin , Brown Jemma , Cockle Paul J. , Franken Willeke P. J. , Arend Sandra M. , Ottenhoff Tom H. M. , Jahans Keith , Hewinson R. Glyn
Published: August 2007

Cross-reactivity between
Mycobacterium kansasii
ESAT-6 and CFP-10 homologues and their
M. bovis
counterparts can confound the interpretation of immunodiagnostic tests for tuberculosis.
M. kansasii
is a nontuberculous mycobacterial species cultured from skin test-positive cattle in Great Britain. Using peptides derived from
M. bovis
and
M. kansasii
ESAT-6 and CFP-10 regions that differ between these species, we investigated the species specificity and cross-reactivity at the level of individual bovine T-cell epitopes. Our results demonstrated that all peptides tested are fully cross-reactive, with the exception of one ESAT-6-derived peptide that harbored an
M. bovis
-specific epitope(s) when it was recognized in the context of bovine leukocyte antigen (BoLA)-DQ but that was cross-reactive with its
M. kansasii
homologues when it was restricted by BoLA-DR. This observation further highlights that prediction of species specificity by comparing sequence identity/homology alone is not sufficient and that individuals with diverse major histocompatibility complex constellations need to be tested to characterize the cross-reactivity or species specificity of peptide-based reagents.
USA300 Genotype Community-Associated Methicillin-Resistant
Staphylococcus aureus
as a Cause of Surgical Site Infections
Authors: Patel Mukesh , Kumar Ritu A. , Stamm Alan M. , Hoesley Craig J. , Moser Stephen A. , Waites Ken B.
Published: August 2007

Community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) strains are increasingly recovered from nosocomial settings. We conducted a retrospective study of surgical site infections (SSI) during 2004 and 2005 to determine the prevalence of CA-MRSA; 57% of MRSA strains tested belonged to the USA300 genotype. CA-MRSA has become a prominent cause of SSI at our institution.
Sequential Linezolid-Resistant
Staphylococcus epidermidis
Isolates with G2576T Mutation
Authors: Hong Tao , Li Xiangyang , Wang Jie , Sloan Cynthia , Cicogna Cristina
Published: August 2007

We report on an analysis of sequential isolates of
Staphylococcus epidermidis
from cultures of blood obtained from a patient with acute myeloid leukemia while the patient was receiving linezolid treatment. All 12 isolates had a linezolid MIC of 32 μg/ml. A 420-bp domain V region of the 23S rRNA gene from all isolates was amplified, and their nucleotide sequences were determined. A G2576T mutation was identified in all isolates. It was estimated that 67% of the 23S rRNA genes carried this mutation. This is the first report of the failure of linezolid treatment for
Staphylococcus epidermidis
bacteremia associated with a G2576T mutation in an immunocompromised patient.
The Interaction of APOBEC3G with Human Immunodeficiency Virus Type 1 Nucleocapsid Inhibits tRNA
3
Lys
Annealing to Viral RNA
Authors: Guo Fei , Cen Shan , Niu Meijuan , Yang Yiliang , Gorelick Robert J. , Kleiman Lawrence
Published: August 2007

Human immunodeficiency virus type 1 (HIV-1) containing human APOBEC3G (hA3G) has a reduced ability to produce viral DNA in newly infected cells. At least part of this hA3G-facilitated inhibition is due to a cytidine deamination-independent reduction in the ability to initiate reverse transcription. HIV-1 nucleocapsid (NCp7) is required both for the incorporation of hA3G into virions and for the annealing between viral RNA and tRNA
3
Lys
, the primer tRNA for reverse transcription. Herein we present evidence that the interaction of hA3G with nucleocapsid is required for the inhibition of reverse transcription initiation. A tRNA
3
Lys
priming complex was produced in vitro by the NCp7-facilitated annealing of tRNA
3
Lys
to synthetic viral RNA in the absence or presence of hA3G. The effect of hA3G on the annealing of tRNA
3
Lys
to viral RNA and the ability of tRNA
3
Lys
to initiate reverse transcription was measured. Our results show the following. (i) Electrophoretic band shift and primer binding site assays show that hA3G reduces the annealing of tRNA
3
Lys
44 and 60%, respectively, but does not disrupt the annealed complex once formed. (ii) hA3G inhibits tRNA
3
Lys
priming 70 to 80%. (iii) Inhibition of tRNA
3
Lys
priming by hA3G requires an interaction between hA3G and NCp7 during annealing. Thus, annealing of tRNA
3
Lys
is insensitive to hA3G inhibition when facilitated by a zinc finger mutant of NCp7 unable to interact with hA3G. NCp7-independent annealing of DNA to viral RNA also is insensitive to hA3G inhibition. These results indicate that hA3G does not sterically block tRNA
3
Lys
annealing by binding to viral RNA. Annealing and priming are not affected by another RNA binding protein, QKI-6.
Equine Herpesvirus 1 Enters Cells by Two Different Pathways, and Infection Requires the Activation of the Cellular Kinase ROCK1
Authors: Frampton Arthur R. , Stolz Donna B. , Uchida Hiroaki , Goins William F. , Cohen Justus B. , Glorioso Joseph C.
Published: August 2007

Equine herpesvirus type 1 (EHV-1), a member of the
Alphaherpesviridae
, displays a broad host range in vitro, allowing for detailed study of the mechanisms of productive infection, including attachment and entry, in various cell culture systems. Previously, we showed that EHV-1 infects Chinese hamster ovary (CHO-K1) cells even though these cells do not express a known alphaherpesvirus entry receptor. In this report, we show by electron microscopy and an infectious recovery assay that entry into CHO-K1 cells occurs via an endocytic or phagocytic mechanism, while entry into equine dermal (ED) or rabbit kidney (RK13) cells occurs by direct fusion at the cell surface. In both cases (endocytic/phagocytic or direct fusion), entry leads to productive infection. Using drugs that inhibit clathrin-dependent or caveola-dependent endocytosis, we showed that EHV-1 entry into CHO-K1 cells does not require clathrin or caveolae. We also show that EHV-1 infection requires the activation of cell signaling molecules. In particular, we demonstrate that activation of the serine/threonine Rho kinase ROCK1 is critical for infection. Inhibition of this kinase by drugs or overexpression of a negative regulator of ROCK1 significantly blocked EHV-1 infection. These results show that EHV-1 can enter disparate cell types by at least two distinct mechanisms and that productive infection is dependent upon the activation of ROCK1.
Incorporation of High Levels of Chimeric Human Immunodeficiency Virus Envelope Glycoproteins into Virus-Like Particles
Authors: Wang Bao-Zhong , Liu Weimin , Kang Sang-Moo , Alam Munir , Huang Chunzi , Ye Ling , Sun Yuliang , Li Yingying , Kothe Denise L. , Pushko Peter , Dokland Terje , Haynes Barton F. , Smith Gale , Hahn Beatrice H. , Compans Richard W.
Published: August 2007

The human immunodeficiency virus (HIV) envelope (Env) protein is incorporated into HIV virions or virus-like particles (VLPs) at very low levels compared to the glycoproteins of most other enveloped viruses. To test factors that influence HIV Env particle incorporation, we generated a series of chimeric gene constructs in which the coding sequences for the signal peptide (SP), transmembrane (TM), and cytoplasmic tail (CT) domains of HIV-1 Env were replaced with those of other viral or cellular proteins individually or in combination. All constructs tested were derived from HIV type 1 (HIV-1) Con-S ΔCFI gp145, which itself was found to be incorporated into VLPs much more efficiently than full-length Con-S Env. Substitution of the SP from the honeybee protein mellitin resulted in threefold-higher chimeric HIV-1 Env expression levels on insect cell surfaces and an increase of Env incorporation into VLPs. Substitution of the HIV TM-CT with sequences derived from the mouse mammary tumor virus (MMTV) envelope glycoprotein, influenza virus hemagglutinin, or baculovirus (BV) gp64, but not from Lassa fever virus glycoprotein, was found to enhance Env incorporation into VLPs. The highest level of Env incorporation into VLPs was observed in chimeric constructs containing the MMTV and BV gp64 TM-CT domains in which the Gag/Env molar ratios were estimated to be 4:1 and 5:1, respectively, compared to a 56:1 ratio for full-length Con-S gp160. Electron microscopy revealed that VLPs with chimeric HIV Env were similar to HIV-1 virions in morphology and size and contained a prominent layer of Env spikes on their surfaces. HIV Env specific monoclonal antibody binding results showed that chimeric Env-containing VLPs retained conserved epitopes and underwent conformational changes upon CD4 binding.
The Structure of a Putative Scaffolding Protein of Immature Poxvirus Particles as Determined by Electron Microscopy Suggests Similarity with Capsid Proteins of Large Icosahedral DNA Viruses
Authors: Hyun Jae-Kyung , Coulibaly Fasséli , Turner Adrian P. , Baker Edward N. , Mercer Andrew A. , Mitra Alok K.
Published: August 2007

Orf virus, the prototype parapoxvirus, is responsible for contagious ecthyma in sheep and goats. The central region of the viral genome codes for proteins highly conserved among vertebrate poxviruses and which are frequently essential for viral proliferation. Analysis of the recently published genome sequence of orf virus revealed that among such essential proteins, the protein orfv075 is an orthologue of D13, the rifampin resistance gene product critical for vaccinia virus morphogenesis. Previous studies showed that D13, arranged as “spicules,” is necessary for the formation of vaccinia virus immature virions, a mandatory intermediate in viral maturation. We have determined the three-dimensional structure of recombinant orfv075 at ∼25-Å resolution by electron microscopy of two-dimensional crystals. orfv075 organizes as trimers with a tripod-like main body and a propeller-like smaller domain. The molecular envelope of orfv075 shows unexpectedly good agreement to that of a distant homologue, VP54, the major capsid protein of
Paramecium bursaria Chlorella
virus type 1. Our structural analysis suggests that orfv075 belongs in the double-barreled capsid protein family found in many double-stranded DNA icosahedral viruses and supports the hypothesis that the nonicosahedral poxviruses and the large icosahedral DNA viruses are evolutionarily related.
Commitment to Apoptosis in CD4
+
T Lymphocytes Productively Infected with Human Immunodeficiency Virus Type 1 Is Initiated by Lysosomal Membrane Permeabilization, Itself Induced by the Isolated Expression of the Viral Protein Nef
Authors: Laforge Mireille , Petit Frederic , Estaquier Jérôme , Senik Anna
Published: August 2007

Primary CD4
+
T lymphocytes, supporting in vitro human immunodeficiency virus type 1 (HIV-1) replication, are destined to die by apoptosis. We explored the initial molecular events that act upstream from mitochondrial dysfunction in CD4
+
T lymphocytes exposed to the HIV-1
LAI
strain. We tracked by immunofluorescence the cells expressing the p24 viral antigen and used Percoll density gradients to isolate a nonapoptotic CD4
+
T-cell subset with a high inner mitochondrial transmembrane potential (ΔΨm) but no outer mitochondrial membrane (OMM) rupture. In most p24
+
(but not bystander p24
−
) cells of this subset, the lysosomes were undergoing limited membrane permeabilization, allowing the lysosomal efflux of cathepsins (Cat) to the cytosol. This was also induced by HIV-1 isolates from infected patients. Using pepstatin A to inhibit Cat-D enzymatic activity and Cat-D small interfering RNA to silence the
Cat-D
gene, we demonstrate that once released into the cytosol, Cat-D induces the conformational change of Bax and its insertion into the OMM. Inhibition of Cat-D activity/expression also conferred a transient survival advantage upon productively HIV-1-infected cells, indicating that Cat-D is an early death factor. The transfection of activated CD4
+
T lymphocytes with a Nef expression vector rapidly induced the permeabilization of lysosomes and the release of Cat-D, with these two events preceding OMM rupture. These results reveal a previously undocumented mechanism in which Nef acts as an internal cytopathic factor and strongly suggest that this viral protein may behave similarly in the context of productive HIV-1 infection in CD4
+
T lymphocytes.
Human Immunodeficiency Virus Type 1 Derivative with 7% Simian Immunodeficiency Virus Genetic Content Is Able To Establish Infections in Pig-Tailed Macaques
Authors: Igarashi Tatsuhiko , Iyengar Ranjini , Byrum Russel A. , Buckler-White Alicia , Dewar Robin L. , Buckler Charles E. , Lane H. Clifford , Kamada Kazuya , Adachi Akio , Martin Malcolm A.
Published: August 2007

A human immunodeficiency virus type 1 (HIV-1) derivative (HIVNL-DT5R) containing sequences encoding a 7-amino-acid segment of CA and the entirevifgene from simian immunodeficiency virus (SIV) was previously shown to establish spreading infections in cultured macaque peripheral blood mononuclear cells. To assess its replicative and disease-inducing properties in vivo, HIVNL-DT5Rwas inoculated into pig-tailed macaques. HIVNL-DT5Rgenerated plasma viremia in all five of the monkeys and elicited humoral responses against all of the HIV-1 structural proteins but did not cause CD4+T-lymphocyte depletion or clinical disease. Additional adaptation will be required to optimize infectivity in vivo.
Frequent Transmission of Immunodeficiency Viruses among Bobcats and Pumas
Authors: Franklin S. P. , Troyer J. L. , Terwee J. A. , Lyren L. M. , Boyce W. M. , Riley S. P. D. , Roelke M. E. , Crooks K. R. , VandeWoude S.
Published: August 2007

With the exception of human immunodeficiency virus (HIV), which emerged in humans after cross-species transmissions of simian immunodeficiency viruses from nonhuman primates, immunodeficiency viruses of the family
Lentiviridae
represent species-specific viruses that rarely cross species barriers to infect new hosts. Among the
Felidae
, numerous immunodeficiency-like lentiviruses have been documented, but only a few cross-species transmissions have been recorded, and these have not been perpetuated in the recipient species. Lentivirus seroprevalence was determined for 79 bobcats (
Lynx rufus
) and 31 pumas (
Puma concolor
) from well-defined populations in Southern California. Partial genomic sequences were subsequently obtained from 18 and 12 seropositive bobcats and pumas, respectively. Genotypes were analyzed for phylogenic relatedness and genotypic composition among the study set and archived feline lentivirus sequences. This investigation of feline immunodeficiency virus infection in bobcats and pumas of Southern California provides evidence that cross-species infection has occurred frequently among these animals. The data suggest that transmission has occurred in multiple locations and are most consistent with the spread of the virus from bobcats to pumas. Although the ultimate causes remain unknown, these transmission events may occur as a result of puma predation on bobcats, a situation similar to that which fostered transmission of HIV to humans, and likely represent the emergence of a lentivirus with relaxed barriers to cross-species transmission. This unusual observation provides a valuable opportunity to evaluate the ecological, behavioral, and molecular conditions that favor repeated transmissions and persistence of lentivirus between species.
The Coronavirus Spike Protein Induces Endoplasmic Reticulum Stress and Upregulation of Intracellular Chemokine mRNA Concentrations
Authors: Versteeg Gijs A. , van de Nes Paula S. , Bredenbeek Peter J. , Spaan Willy J. M.
Published: August 2007

Murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS) coronavirus (CoV) are two of the best-studied representatives of the family
Coronaviridae
. During CoV infection, numerous cytokines and chemokines are induced in vitro and in vivo. Human interleukin 8 and its mouse functional counterpart, CXCL2, are early-expressed chemokines. Here we show that SARS-CoV and MHV induce endoplasmic reticulum (ER) stress and Cxcl2 mRNA transcription during infection in vitro. Expression of the viral spike protein significantly induced ER stress and Cxcl2 mRNA upregulation, while expression of the other structural genes did not. Additional experiments with UV-inactivated virus, cell-cell fusion-blocking antibodies, and an MHV mutant with a defect in spike protein maturation demonstrated that spike-host interactions in the ER are responsible for the induction of ER stress and subsequent Cxcl2 mRNA transcription. Despite significant increases in levels of Cxcl2 mRNA and functional nucleus-to-cytoplasm RNA transport, no CXCL2 protein was released into the medium from MHV-infected cells. Yet Sendai virus-infected cells showed substantial Cxcl2 mRNA induction and a simultaneous increase in levels of secreted CXCL2 protein. Our results demonstrate that expression of CoV spike proteins induces ER stress, which could subsequently trigger innate immune responses. However, at that point in infection, translation of host mRNA is already severely reduced in infected cells, preventing the synthesis of CXCL2 and ER stress proteins despite their increased mRNA concentrations.
Probing the Flavivirus Membrane Fusion Mechanism by Using Monoclonal Antibodies
Authors: Stiasny Karin , Brandler Samantha , Kössl Christian , Heinz Franz X.
Published: August 2007

In this study, we investigated in a flavivirus model (tick-borne encephalitis virus) the mechanisms of fusion inhibition by monoclonal antibodies directed to the different domains of the fusion protein (E) and to different sites within each of the domains by using in vitro fusion assays. Our data indicate that, depending on the location of their binding sites, the monoclonal antibodies impaired early or late stages of the fusion process, by blocking the initial interaction with the target membrane or by interfering with the proper formation of the postfusion structure of E, respectively. These data provide new insights into the mechanisms of flavivirus fusion inhibition by antibodies and their possible contribution to virus neutralization.
Suppression of Viral Replication by Stress-Inducible GADD34 Protein via the Mammalian Serine/Threonine Protein Kinase mTOR Pathway
Authors: Minami Kahori , Tambe Yukihiro , Watanabe Ryosuke , Isono Takahiro , Haneda Masataka , Isobe Ken-ichi , Kobayashi Toshiyuki , Hino Okio , Okabe Hidetoshi , Chano Tokuhiro , Inoue Hirokazu
Published: August 2007

GADD34 is a protein that is induced by a variety of stressors, including DNA damage, heat shock, nutrient deprivation, energy depletion, and endoplasmic reticulum stress. Here, we demonstrated that GADD34 induced by vesicular stomatitis virus (VSV) infection suppressed viral replication in wild-type (WT) mouse embryo fibroblasts (MEFs), whereas replication was enhanced in GADD34-deficient (GADD34-KO) MEFs. Enhanced viral replication in GADD34-KO MEFs was reduced by retroviral gene rescue of GADD34. The level of VSV protein expression in GADD34-KO MEFs was significantly higher than that in WT MEFs. Neither phosphorylation of eIF2α nor cellular protein synthesis was correlated with viral replication in GADD34-KO MEFs. On the other hand, phosphorylation of S6 and 4EBP1, proteins downstream of mTOR, was suppressed by VSV infection in WT MEFs but not in GADD34-KO MEFs. GADD34 was able to associate with TSC1/2 and dephosphorylate TSC2 at Thr1462. VSV replication was higher in TSC2-null cells than in TSC2-expressing cells, and constitutively active Akt enhanced VSV replication. On the other hand, rapamycin, an mTOR inhibitor, significantly suppressed VSV replication in GADD34-KO MEFs. These findings demonstrate that GADD34 induced by VSV infection suppresses viral replication via mTOR pathway inhibition, indicating that cross talk between stress-inducible GADD34 and the mTOR signaling pathway plays a critical role in antiviral defense.
Alterations in Receptor Binding Properties of Recent Human Influenza H3N2 Viruses Are Associated with Reduced Natural Killer Cell Lysis of Infected Cells
Authors: Owen Rachel E. , Yamada Eriko , Thompson Catherine I. , Phillipson Louisa J. , Thompson Clare , Taylor Elizabeth , Zambon Maria , Osborn Helen M. I. , Barclay Wendy S. , Borrow Persephone
Published: August 2007

Natural killer (NK) cell recognition of influenza virus-infected cells involves hemagglutinin (HA) binding to sialic acid (SA) on activating NK receptors. SA also acts as a receptor for the binding of influenza virus to its target host cells. The SA binding properties of H3N2 influenza viruses have been observed to change during circulation in humans: recent isolates are unable to agglutinate chicken red blood cells and show reduced affinity for synthetic glycopolymers representing SA-α-2,3-lactose (3′SL-PAA) and SA-α-2,6-N-acetyl lactosamine (6′SLN-PAA) carbohydrates. Here, NK lysis of cells infected with human H3N2 influenza viruses isolated between 1969 and 2003 was analyzed. Cells infected with recent isolates (1999 to 2003) were found to be lysed less effectively than cells infected with older isolates (1969 to 1996). This change occurred concurrently with the acquisition of two new potential glycosylation site motifs in HA. Deletion of the potential glycosylation site motif at 133 to 135 in HA1 from a recent isolate partially restored the agglutination phenotype to a recombinant virus, indicating that the HA-SA interaction is inhibited by the glycosylation modification. Deletion of either of the recently acquired potential glycosylation sites from HA led to increased NK lysis of cells infected with recombinant viruses carrying modified HA. These results indicate that alterations in HA glycosylation may affect NK cell recognition of influenza virus-infected cells in addition to virus binding to host cells.
Replication-Competent Herpes Simplex Virus 1 Isolates Selected from Cells Transfected with a Bacterial Artificial Chromosome DNA Lacking Only the U
L
49 Gene Vary with Respect to the Defect in the U
L
41 Gene Encoding Host Shutoff RNase
Authors: Sciortino Maria Teresa , Taddeo Brunella , Giuffrè-Cuculletto Maria , Medici Maria Antonietta , Mastino Antonio , Roizman Bernard
Published: August 2007

To generate a null U
L
49 gene mutant of herpes simplex virus 1 (HSV-1), we deleted from the viral DNA, encoded as a bacterial artificial chromosome (BAC), the U
L
49 open reading frame and, in a second step, restored it. Upon transfection into Vero cells, the BAC-ΔU
L
49 DNA yielded foci of degenerated cells that could not be expanded and a few replication-competent clones. The replication-competent viral clones derived from independent transfections yielded viruses that expressed genes with some delay, produced smaller plaques, and gave lower yields than wild-type virus. A key finding is that the independently derived replication-competent viruses lacked the virion host shutoff (
vhs
) activity expressed by the RNase encoded by the U
L
41 gene. One mutant virus expressed no
vhs
protein, whereas two others, derived from independent transfections, produced truncated
vhs
proteins consistent with the spontaneous in-frame deletion. In contrast, cells infected with the virus recovered upon transfection of the BAC-U
L
49R DNA (R-U
L
49) accumulated a full-length
vhs
protein, indicating that in the parental BAC-ΔU
L
49 DNA, the U
L
41 gene was intact. We conclude that expression of the
vhs
protein in the absence of U
L
49 protein is lethal, a conclusion bolstered by the evidence reported elsewhere that in transfected cells
vhs
requires both VP16 and VP22, the product of U
L
49, to be neutralized.
Construction of a Doxycycline-Dependent Simian Immunodeficiency Virus Reveals a Nontranscriptional Function of Tat in Viral Replication
Authors: Das Atze T. , Klaver Bep , Harwig Alex , Vink Monique , Ooms Marcel , Centlivre Mireille , Berkhout Ben
Published: August 2007

In the quest for an effective vaccine against human immunodeficiency virus (HIV), live attenuated virus vaccines have proven to be very effective in the experimental model system of simian immunodeficiency virus (SIV) in macaques. However, live attenuated HIV vaccines are considered unsafe for use in humans because the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. As an alternative approach, we earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (DOX). Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient DOX administration. Since the effectiveness and safety of such a conditionally live AIDS vaccine should be tested in macaques, we constructed a similar DOX-dependent SIVmac239 variant in which the Tat-TAR (
trans
-
a
cting
r
esponsive) transcription control mechanism was functionally replaced by the DOX-inducible Tet-On regulatory mechanism. Moreover, this virus can be used as a tool in SIV biology studies and vaccine research because both the level and duration of replication can be controlled by DOX administration. Unexpectedly, the new SIV variant required a wild-type Tat protein for replication, although gene expression was fully controlled by the incorporated Tet-On system. This result suggests that Tat has a second function in SIV replication in addition to its role in the activation of transcription.
The higher plant PII signal transduction protein: structure, function and properties
Authors: Moorhead Greg B.G. , Ferrar Tony S. , Chen Yan M. , Mizuno Yutaka , Smith Catherine S. , Ng Kenneth K.S. , Muench Douglas G. , Lohmeier-Vogel Elke
Published: August 2007

The PII carbon/nitrogen sensing protein was discovered in Escherichia coli (Migula 1895) Castellani and Chalmers 1919, over 40 years ago. Orthologues have been discovered in three kingdoms of life making it one of the most ancient and conserved signaling proteins known. Recent advances in the field have established its primary binding partner in plants as N-acetyl glutamate kinase and the crystal structure has revealed features unique to plants that likely contribute to its function in vivo. Here, we review the properties, function, and novel structural features of this chloroplast-localized metabolic sensor of higher plants.
Population differentiation of the lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana) complex in Alberta: growth, survival, and responses to climate
Authors: Rweyongeza Deogratias M. , Dhir Narinder K. , Barnhardt Leonard K. , Hansen Christine , Yang Rong-Cai
Published: August 2007

Growth and survival of 33 populations from a species complex involving interior lodgepole pine ( Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) and jack pine ( Pinus banksiana Lamb.) and their natural hybrids in Alberta were evaluated at ages 5, 10, and 15 years in eight test sites across Alberta. We determined population differentiations by estimating Mahalanobis distances between populations from the canonical discriminant analysis of the total variability and by calculating dissimilarity indexes between populations from the quadratic regression of overall growth and survival on the overall climate. The grouping of the populations based on the Mahalanobis distances showed that most jack pine populations could be separated from lodgepole and hybrid populations, but no further subdivision was possible to distinguish lodgepole from hybrid populations. This clustering pattern was remarkably similar to the grouping based on molecular markers as shown in our earlier study. This pattern of grouping is best explained by a clear elevational demarcation between jack pine at low elevations and lodgepole pine and hybrids at midrange and high elevations. The grouping of the populations based on the dissimilarity indexes revealed a somewhat contrasting pattern; most lodgepole pine populations were in one group, whereas jack pine and hybrid populations were mixed up in the other group. The two contrasting patterns of grouping suggest that nonclimatic factors such as edaphic preference and habitat disturbances are also important in determining population distributions and niche spaces in the lodgepole – jack pine complex.
THE UPPER BOUND ON THE LIGHTEST HIGGS MASS IN THE NMSSM REVISITED
Authors: ELLWANGER ULRICH , HUGONIE CYRIL
Published: August 2007

We update the upper bound on the lightest CP-even Higgs mass in the NMSSM, which is given as a function of tan β and λ. It is pointed out that large values of tan β, with λ not too small, imply a large value for the MSSM-like parameter MA. We include the available one- and two-loop corrections to the NMSSM Higgs masses, and constraints from the absence of Landau singularities below the GUT scale as well as from the stability of the NMSSM Higgs potential. For m top varying between 171.4 and 178 GeV, squark masses of 1 TeV and maximal mixing the upper bound is assumed near tan β ~ 2 and varies between 139.9 and 141.4 GeV.
COSMIC RAYS FROM THE KNEE TO THE SECOND KNEE: 1014 TO 1018eV
Authors: HÖRANDEL JÖRG R.
Published: August 2007

The energies of cosmic rays, fully ionized charged nuclei, extend over a wide range up to 1020 eV. A particularly interesting energy region spans from 1014 to 1018 eV, where the all-particle energy spectrum exhibits two interesting structures, the "knee" and the "second knee". An explanation of these features is thought to be an important step in understanding the origin of the high-energy particles. Recent results of air shower experiments in this region are discussed. Special attention is drawn to explain the principle of air shower measurements — a simple Heitler model of (hadronic) air showers is developed.
THEORY OF TRANSPORT PROCESSES AND THE METHOD OF THE NONEQUILIBRIUM STATISTICAL OPERATOR
Authors: KUZEMSKY A. L.
Published: August 2007

The aim of this paper is to provide better understanding of a few approaches that have been proposed for treating nonequilibrium (time-dependent) processes in statistical mechanics with the emphasis on the interrelation between theories. The ensemble method, as it was formulated by Gibbs, has great generality and broad applicability to equilibrium statistical mechanics. Different macroscopic environmental constraints lead to different types of ensembles, with particular statistical characteristics. In the present work, the statistical theory of nonequilibrium processes which is based on nonequilibrium ensemble formalism is discussed. We also outline the reasoning leading to some other useful approaches to the description of the irreversible processes. The kinetic approach to dynamic many-body problems, which is important from the point of view of the fundamental theory of irreversibility, is alluded to. Appropriate references are made to papers dealing with similar problems arising in other fields. The emphasis is on the method of the nonequilibrium statistical operator (NSO) developed by Zubarev. The NSO method permits one to generalize the Gibbs ensemble method to the nonequilibrium case and to construct a nonequilibrium statistical operator which enables one to obtain the transport equations and calculate the transport coefficients in terms of correlation functions, and which, in the case of equilibrium, goes over to the Gibbs distribution. Although some space is devoted to the formal structure of the NSO method, the emphasis is on its utility. Applications to specific problems such as the generalized transport and kinetic equations, and a few examples of the relaxation and dissipative processes, which manifest the operational ability of the method, are considered.
DIELECTRIC RELAXATION IN COMPLEX PEROVSKITE BaFe1/2Sb1/2O3
Authors: DUTTA A. , SINHA T. P.
Published: August 2007

The complex perovskite oxide barium iron antimonate, BaFe 1/2 Sb 1/2 O 3 (BFS) is synthesized by a solid-state reaction technique for the first time. The X-ray diffraction of the sample at room temperature shows a monoclinic phase. The field dependences of dielectric response and the loss tangent of the sample are measured in a frequency range from 50 Hz to 1 MHz and in a temperature range from 143 to 463 K. An analysis of the loss factor with frequency is performed by the scaling behavior of the dielectric loss spectra. The frequency dependence of the loss peaks are found to obey the Arrhenius law with an activation energy ≃0.81 eV . The scaling behavior of the dielectric loss spectra suggests that the distribution of relaxation times is temperature-independent. The frequency-dependent electrical data are also analyzed in the framework of conductivity and electric modulus formalisms. The scaling behavior of the imaginary electric modulus shows the temperature-independent nature of the distribution of relaxation times. All these formalisms resulted in the qualitative similarities in the relaxation time. The relationship between relaxation parameters and electrical conduction indicates the hopping motion of electrons from Fe(II) to Fe(III) ions in BFS.
ANTI-SYNCHRONIZATION OF THREE-DIMENSIONAL AUTONOMOUS CHAOTIC SYSTEMS VIA ACTIVE CONTROL
Authors: WANG XINGYUAN , WANG YONG
Published: August 2007

This paper analyzes anti-synchronization of three-dimensional autonomous chaotic systems and achieves the anti-synchronization of a class of three-dimensional autonomous chaotic systems, i.e., Lorenz system, Chen system, and Lü system with one another via active control. Numerical simulations are demonstrated to verify the effectiveness of the proposed method.
PHOTOEXCITED CARRIER LIFETIME IN DIRECT AND INDIRECT BAND GAP CRYSTALS ON THE Z-SCAN TECHNIQUE AT 532 nm
Authors: GAUR ARUN , SHARMA D. K. , SINGH K. S. , SINGH NAGESHWAR
Published: August 2007

The photoexcited carrier lifetime in ZnSe and CdSe (direct band gap crystals) and CdI 2 and PbI 2 (indirect band gap crystals) has been investigated by the use of a single beam Z-scan technique at 532 nm. The carrier lifetime (τ) is determined to be (1.7 ± 0.5) ns in the case of direct band gap and (1.2 ± 0.03) ps in the case of indirect band gap crystals. Lower values of τ in the case of indirect band gap crystals can be attributed to the reduction in value of the carrier density (N).
INTERPRETATION OF SEISMIC SIGNALS FOR TSUNAMIGENIC EARTHQUAKES
Authors: CHEW SOON-HOE , KUENZA KARMA
Published: August 2007

Tsunami can cause severe damage to properties and loss of many human lives. Tsunami is often related to earthquakes. Within a close proximity and with similar magnitude, some earthquakes produce very severe tsunamis, e.g. the December 2004 Sumatra earthquake, and others produce very minor or insignificant wave height increase, e.g. the March 2005 Sumatra earthquake. Thus, the study of tsunamigenesis of earthquakes, i.e., whether an earthquake will generate significant tsunami, is critical to the prevention or minimization of damage due to tsunami. In this study, the seismic signals from earthquakes were analyzed in order to determine tsunamigenesis more accurately. Fast Fourier Transform (FFT) of the seismic signals of the earthquakes was performed for a number of historical earthquake records of both tsunamigenic and non-tsunamigenic earthquakes of similar magnitude and epicenter distance. The results showed that tsunamigenic earthquakes have lower amplitude in the high frequency range (0.15–0.3 Hz) as compared to non-tsunamigenic earthquakes. Preliminary wavelet analysis of these earthquakes also revealed that the intensity pattern of tsunamigenic and non-tsunamigenic earthquake was similar to the findings from FFT. Both techniques lead to the conclusion that the long period signal and the depletion of high frequency energy revealed in the seismic signal may well indicate the tsunamigenic potential of the earthquakes. Thus the techniques that analyze the frequency content of the seismic signals have a great potential to complement the existing Pacific Tsunami Warning System, which only takes the magnitude of earthquake as the determining factor in predicting the generation of tsunami.
Methodology for the Characterization of Parallel-Plates Electrochemical Reactor
Authors: Velasco Guillermo , Gutierrez Sivia , Alatorre Ordaz Alejandro , Rodríguez-Torres Israel
Published: August 2007

This work presents a methodology for characterizing parallel- plates electrochemical reactors, which allows obtaining precise knowledge about the operation of the unit. Flow distribution is analyzed by injecting a dye at the inlet of the reactor and is followed by a digital video-camera. This has produced knowledge about several parameters such as solution mixing in the diffuser, inter-electrode separation (gap) and linear flow velocity in the reaction chamber of the reactor. Residence time distribution was studied by injecting an electrochemical tracer (Fe(CN)63-) at the inlet and its detection at the reactor outlet. It was found that at certain linear velocities there are stagnant volumes. Mass transport analysis and polarization curves were obtained with redox systems of fast charge transfer (Fe(CN)63- / Fe(CN)64-). Current distribution was obtained using a segmented electrode and the same redox system. An improved transport was observed when the linear velocity is increased.
Effect of Dichromate Added to the Electrolyte on Reduction of Hypochlorite Ion on SS400 Cathode
Authors: Hayashida Toshikazu , Hatano Satoshi , Kuniyone Atsushi , Morimitsu Masatsugu , Inaba Minoru , Tasaka Akimasa
Published: August 2007

Kinetic study of ClO- reduction on the cathode has been carried out in catholytes composed of 80 g/l-NaCl, 1.0 wt%- NaClO and x g/l-dichromate (x = 0, 3.0, and 5.0) at temperatures such as 30, 40, and 50{degree sign}C by galvanostatic method. The rate constant of reduction of ClO- (k2) on the SS400 steel cathode was sharply decreased in the dichromate concentration of 5.0 g/l at every temperature. And the activation energy of ClO- reduction (E(k2)) was increased in the dichromate concentration of 5.0 g/l. SEM observation and XPS analysis revealed that a thin layer of chromium trihydroxide was formed on the cathode surface after electrolysis. From these results, it is considered that reduction of ClO- was suppressed by addition of dichromate and that the formed Cr(OH)3 layer may prevent ClO- from reduction on the cathode.
Electrochemical Syntheses of Sodium Percarbonate in Aqueous Solution
Authors: Ruiz Edgar J. , Meas Y. , Ortega Raúl , Jurado José L.
Published: August 2007

The present research is focused on electrochemical production of sodium percarbonate as both the 2Na2CO3.3H2O2 form and the Na2C2O6 formulation. The routes to these two electrochemical syntheses from carbonate solution proceed through oxygen reduction at the cathode and electrochemical oxidation of water at the anode, respectively. We have studied each of these reactions separately, potentiostatically for the cathodic reaction and galvanostatically for the anodic side. In both cases, the effects of experimental conditions, such the addition of a stabilizer or the use of a cation-permeable membrane, have been investigated; products were analyzed for % active oxygen content in dry samples according standard methods.
Studies on Sodium Borohydride for Energy Systems
Authors: Sequeira Cesar A. , Pardal Tiago C. , Santos Diogo M. , Condeco Jose A. , Franco Marta W. , Goncalves Marta C.
Published: August 2007

This paper describes a process for synthesising a sodium borohydride solution using a two-compartment electrolytic cell with conversion of borate ions to borohydride ions. This occurs in the catholyte to produce the sodium borohydride solution from which the borohydride material may be extracted. The electrolyte carrier may be an aqueous or a non-aqueous solution, namely a room-temperature ionic liquid. Novel permselective membrane separators are considered. The borohydride stepwise hydrolysis is analysed and proposals are advanced to minimise the resulting hydrogen generation. It is disclosed that sodium borohydride may be used for reversible hydrogen storage, for fuel of direct borohydride fuel cells (DBFC), for high power density cells, and for other relevant energy systems with multifunctional applications, namely in spacecraft.
Analysis of the Use of Copper Electrode in a Filter-Press Electrochemical Reactor for the Electrochemical Reduction of Cr(VI)
Authors: Velasco Guillermo , Gutiérrez Silvia , Rodriguez Israel
Published: August 2007

In this work, the Cr(VI) electrochemical reduction by Cyclic Voltammetry (CV) and Linear Sweep Voltammetry (LSV), in acidic solutions and on a copper electrode, was studied. Cr(VI) reduction occurs in one step by a diffusive process at -230 mV / Ag/AgCl. The results obtained by LSV suggest a mass- transfer control for Cr(VI) reduction. The diffusion coefficient obtained for Cr(VI) was DHCrO4- = 1.1x10-5 cm2 s-1. The polarization curves obtained in a Filter-Press Electrochemical Reactor (FPER) corroborate the mechanism obtained with smaller electrodes and this allowed determining the best electrolysis voltage (2.0 V). The electrolysis showed conversions up to 70% in 60 min for solutions with 110 ppm of Cr (VI) in batch recycle mode.
Nanoparticle-Metallopolymer Assemblies: Luminescent Properties
Authors: Dennany Lynn , Forster Robert J.
Published: August 2007

The unique optical, electric and magnetic properties of nanoparticles continue to drive intense research in fields including sensor development. Combining smart luminescent polymers with nanoparticles is attractive because the combination ought to lead to unique photonic properties. Previous studies have shown that metallopolymers can be utilized to control the size of the nanoparticles by altering the mole fraction of metallopolymer to nanoparticle during the growth of the nanoparticle. Luminescence properties of these materials have been probed and reveal that the nanoparticles lead to enhanced emission presumably through interaction of the luminescent centres with the plasmon of the Au nanoparticles. This contribution also investigates if the mole fraction of metallopolymer to nanoparticle, that produces the optimal luminescent enhancement, is translated into metallopolymer-Au nanoparitcle composites. Several analytical applications are possible one of which may be increased sensitivity of established sensors, by utilizing composite films of this nature that possess enhanced luminescent properties.
Single Molecule Detection Surface-Enhanced Raman Scattering Substrates by Electroless Synthesis of Ag Nanoparticles on Nanostructured Silicon Films
Authors: Kalkan A. K.
Published: August 2007

Surface-enhanced Raman scattering (SERS) substrates have been demonstrated through electroless reduction of silver on nanostructured Si films. At low analyte concentrations (10−9 - 10−10 M), the SERS signal shows temporal and sudden spectral fluctuations characteristic of single molecules (SM). When this intermittent SERS radiation is monitored with a CCD video- camera, blinking bright spots are observed attributable to SERS emission from SMs finding ultrahigh SERS gain sites. The laser, once focused on the SERS substrate, is found to induce Ostwald ripening and concomitant formation of aggregates, which are essential for SM detection. Unlike the previous single molecule SERS demonstrations, which have employed citrate-reduced nanoparticles, it is not necessary to incubate the Ag in analyte solution for hours. Instead, single molecule SERS signal is observed immediately after the spotting of the analyte. This is likely due to the absence of any chemical agents on the Ag nanoparticle surfaces allowing quick analyte adsorption.
Numerical Simulation of Corrosion Cells by the Method of Fundamental Solution
Authors: Barrios Carlos P. , Almeraya-Calderon Facundo , Nuñez-Jaquez Rosa Elba , Gaona Citalli , Martínez-Villafañe Alberto , Chacon Nava Jose
Published: August 2007

In this paper is presented the application of the Method of Fundamental Solution (MFS) to obtain the solution of Laplace equation with linear boundary conditions to describe the distribution of potentials in corrosion cells. The results obtained by this method are compared with another numerical method, in this case finite element. As case of study takes the interior problem analyzed by McCafferty (1). In which two concentric electrodes placed in bottom of a cylindrical container, creating a galvanic cell. The results obtained by the MFS present a good agreement with the calculated by finite element.