bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic Analysis of Pathogenic and Attenuated Alcelaphine Herpesvirus 1
Authors: Dry Inga , Haig David M. , Inglis Neil F. , Imrie Lisa , Stewart James P. , Russell George C.
Published: March 2008

The gammaherpesvirus alcelaphine herpesvirus 1 (AlHV-1) causes malignant catarrhal fever in susceptible ungulates but infects its natural host, wildebeest, without obvious clinical signs. In tissue culture, AlHV-1 is initially predominantly cell associated and virulent but on extended culture becomes cell-free and attenuated. We wanted to determine what changes in protein composition had taken place during the transition from virulent to attenuated virus in culture. Purified virus preparations were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and proteins were analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry. Peptides were identified in serial gel slices by using MASCOT software to interrogate virus-specific and nonredundant sequence databases. Twenty-three AlHV-1-encoded proteins and six cellular proteins were identified in the attenuated and virulent viruses. Two polypeptides were detected in only the virulent virus preparations, while one other protein was found in only the attenuated virus. Two of these virus-specific proteins were identified by a single peptide, suggesting that these may be low-abundance virion proteins rather than markers of attenuation or pathogenesis. The results suggest that attenuation of AlHV-1 is not the result of gross changes in the composition of the virus particle but probably due to altered viral gene expression in the infected cell.
Vaccinia Virus A56/K2 Fusion Regulatory Protein Interacts with the A16 and G9 Subunits of the Entry Fusion Complex
Authors: Wagenaar Timothy R. , Ojeda Suany , Moss Bernard
Published: March 2008

Deletion of the A56R or K2L gene of vaccinia virus (VACV) results in the spontaneous fusion of infected cells to form large multinucleated syncytia. A56 and K2 polypeptides bind to one another (A56/K2) and together are required for interaction with the VACV entry fusion complex (EFC); this association has been proposed to prevent the fusion of infected cells. At least eight viral polypeptides comprise the EFC, but no information has been available regarding their interactions either with each other or with A56/K2. Utilizing a panel of recombinant VACVs designed to repress expression of individual EFC subunits, we demonstrated that A56/K2 interacted with two polypeptides: A16 and G9. Both A16 and G9 were required for the efficient binding of each to A56/K2, suggesting that the two polypeptides interact with each other within the EFC. Such an interaction was established by the copurification of A16 and G9 from infected cells under conditions in which a stable EFC complex failed to assemble and from detergent-treated lysates of uninfected cells that coexpressed A16 and G9. A recombinant VACV that expressed G9 modified with an N-terminal epitope tag induced the formation of syncytia, suggesting partial interference with the functional interaction of A56/K2 with the EFC during infection. These data suggest that A16 and G9 are physically associated within the EFC and that their interaction with A56/K2 suppresses spontaneous syncytium formation and possibly “fuse-back” superinfection of cells.
Importance of the Membrane-Perturbing Properties of the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 gp41 to Viral Fusion
Authors: Vishwanathan Sundaram A. , Hunter Eric
Published: March 2008

The membrane-proximal external region (MPER; K
665
WASLWNWFNITNWLWYIK
683
) of the human immunodeficiency virus type 1 (HIV-1) gp41 ectodomain plays a critical role in envelope glycoprotein-mediated fusion. In addition, the epitopes of important neutralizing antibodies (2F5, Z13, and 4E10) and the sequence of the peptide fusion inhibitor T20 overlap this conserved region. The MPER has an unusually high percentage of tryptophan residues that likely contribute to the membrane-disrupting nature of the region, which is predicted to adopt an α-helical conformation on membrane contact. We have investigated the membrane-disruptive requirements for this region using a panel of mutants that replace most of the MPER with antibacterial, membrane-active peptides. The results demonstrate that the mutant Envs were processed, transported, and expressed on the cell surface similar to wild type. Some of the mutant Envs induced moderate levels of cell-cell fusion, demonstrating that the region can accommodate the substitution of proline-rich foreign peptides while retaining significant biological function. In contrast, the incorporation into and stability of the mutated Envs in virions was reduced, consistent with the severely impaired viral entry observed for all the mutants. These data suggest that both structural (for Env incorporation) and functional (membrane disruption) constraints may contribute to the highly conserved nature of this region.
Infectivity Studies of Influenza Virus Hemagglutinin Receptor Binding Site Mutants in Mice
Authors: Meisner Jeffrey , Szretter Kristy J. , Bradley Konrad C. , Langley William A. , Li Zhu-Nan , Lee Byeong-Jae , Thoennes Sudha , Martin Javier , Skehel John J. , Russell Rupert J. , Katz Jacqueline M. , Steinhauer David A.
Published: March 2008

The replicative properties of influenza virus hemagglutinin (HA) mutants with altered receptor binding characteristics were analyzed following intranasal inoculation of mice. Among the mutants examined was a virus containing a Y98F substitution at a conserved position in the receptor binding site that leads to a 20-fold reduction in binding. This mutant can replicate as well as wild-type (WT) virus in MDCK cells and in embryonated chicken eggs but is highly attenuated in mice, exhibiting titers in lungs more than 1,000-fold lower than those of the WT. The capacity of the Y98F mutant to induce antibody responses and the structural locations of HA reversion mutations are examined.
Differential Response of Respiratory Dendritic Cell Subsets to Influenza Virus Infection
Authors: Hao Xueli , Kim Taeg S. , Braciale Thomas J.
Published: March 2008

Dendritic cells (DC) are believed to play an important role in the initiation of innate and adaptive immune responses to infection, including respiratory tract infections, where respiratory DC (RDC) perform this role. In this report, we examined the susceptibilities of isolated murine RDC to influenza virus infection in vitro and the effect of the multiplicity of infection (MOI) on costimulatory ligand upregulation and inflammatory cytokine/chemokine production after infection. We found that the efficiency of influenza virus infection of RDC increased with increasing MOIs. Furthermore, distinct subpopulations of RDC differed in their susceptibilities to influenza virus infection and in the magnitude/tempo of costimulatory ligand expression. Additional characterization of the CD11c-positive (CD11c+) RDC revealed that the identifiable subsets of RDC differed in susceptibility to infection, with CD11c+CD103+DC exhibiting the greatest susceptibility, CD11c+CD11bhiDC exhibiting intermediate susceptibility, and CD11c+B220+plasmacytoid DC (pDC) exhibiting the least susceptibility to infection. A companion analysis of the in vivo susceptibilities of these RDC subsets to influenza virus revealed a corresponding infection pattern. The three RDC subsets displayed different patterns of cytokine/chemokine production in response to influenza virus infection in vitro: pDC were the predominant producers of most cytokines examined, while CD103+DC and CD11bhiDC produced elevated levels of the murine chemokine CXCL1 (KC), interleukin 12p40, and RANTES in response to influenza virus infection. Our results indicate that RDC are targets of influenza virus infection and that distinct RDC subsets differ in their susceptibilities and responses to infection.
Anticapsid Immunity Level, Not Viral Persistence Level, Correlates with the Progression of Theiler's Virus-Induced Demyelinating Disease in Viral P1-Transgenic Mice
Authors: Myoung Jinjong , Bahk Young Yil , Kang Hyun Seok , Dal Canto Mauro C. , Kim Byung S.
Published: March 2008

Intracranial infection of Theiler's murine encephalomyelitis virus (TMEV) induces demyelination and a neurological disease in susceptible SJL/J (SJL) mice that resembles multiple sclerosis. While the virus is cleared from the central nervous system (CNS) of resistant C57BL/6 (B6) mice, it persists in SJL mice. To investigate the role of viral persistence and its accompanying immune responses in the development of demyelinating disease, transgenic mice expressing the P1 region of the TMEV genome (P1-Tg) were employed. Interestingly, P1-Tg mice with the B6 background showed severe reductions in both CD4+and CD8+T-cell responses to capsid epitopes, while P1-Tg mice with the SJL background displayed transient reductions following viral infection. Reduced antiviral immune responses in P1-Tg mice led to >100- to 1,000-fold increases in viral persistence at 120 days postinfection in the CNS of mice with both backgrounds. Despite the increased CNS TMEV levels in these P1-Tg mice, B6 P1-Tg mice developed neither neuropathological symptoms nor demyelinating lesions, and SJL P1-Tg mice developed significantly less severe TMEV-induced demyelinating disease. These results strongly suggest that viral persistence alone is not sufficient to induce disease and that the level of T-cell immunity to viral capsid epitopes is critical for the development of demyelinating disease in SJL mice.
Structural and Nonstructural Protein Genome Regions of Eastern Equine Encephalitis Virus Are Determinants of Interferon Sensitivity and Murine Virulence
Authors: Aguilar Patricia V. , Adams A. Paige , Wang Eryu , Kang Wenli , Carrara Anne-Sophie , Anishchenko Michael , Frolov Ilya , Weaver Scott C.
Published: March 2008

Eastern equine encephalitis virus (EEEV) causes sporadic epidemics of human and equine disease in North America, but South American strains have seldom been associated with human neurologic disease or mortality, despite serological evidence of infection. In mice, most North American and South American strains of EEEV produce neurologic disease that resembles that associated with human and equine infections. We identified a South American strain that is unable to replicate efficiently in the brain or cause fatal disease in mice yet produces 10-fold higher viremia than virulent EEEV strains. The avirulent South American strain was also sensitive to human interferon (IFN)-α, -β, and -γ, like most South American strains, in contrast to North American strains that were highly resistant. To identify genes associated with IFN sensitivity and virulence, infectious cDNA clones of a virulent North American strain and the avirulent South American strain were constructed. Two reciprocal chimeric viruses containing swapped structural and nonstructural protein gene regions of the North American and South American strains were also constructed and found to replicate efficiently in vitro. Both chimeras produced fatal disease in mice, similar to that caused by the virulent North American strain. Both chimeric viruses also exhibited intermediate sensitivity to human IFN-α, -β, and -γ compared to that of the North American and South American strains. Virulence 50% lethal dose assays and serial sacrifice experiments further demonstrated that both structural and nonstructural proteins are important contributors to neurovirulence and viral tissue tropism. Together, the results of this study emphasize the complex and important influences of structural and nonstructural protein gene regions on EEEV virulence.
Herpes Simplex Virus Type 2 UL56 Interacts with the Ubiquitin Ligase Nedd4 and Increases Its Ubiquitination
Authors: Ushijima Yoko , Koshizuka Tetsuo , Goshima Fumi , Kimura Hiroshi , Nishiyama Yukihiro
Published: March 2008

The herpes simplex virus UL56 gene is conserved among most members of the
Alphaherpesvirinae
family and plays a critical role in viral pathogenicity in vivo. The HSV-2 UL56 protein (UL56) is a C-terminally anchored type II membrane protein that is predicted to be inserted into the virion envelope, leaving its N-terminal domain in the tegument. UL56 interacts with KIF1A and UL11. Here we report that UL56 also interacts with the ubiquitin ligase Nedd4 and increases its ubiquitination. Nedd4 was identified as a UL56-interacting protein by a yeast two-hybrid screen. UL56 bound to Nedd4 via its PY motifs. Nedd4 was phosphorylated and degraded in wild-type HSV-2-infected cells but not in cells infected with a UL56-deficient mutant. Ubiquitination assays revealed that UL56 increased ubiquitinated Nedd4, which was actively degraded in infected cells. UL56 also caused a decrease in Nedd4 protein levels and the increased ubiquitination in cotransfected cells. However, UL56 itself was not ubiquitinated, despite its interaction with Nedd4. Based on these findings, we propose that UL56 regulates Nedd4 in HSV-2-infected cells, although deletion of UL56 had no apparent effect on viral growth in vitro.
Recruitment of Antigen-Presenting Cells to the Site of Inoculation and Augmentation of Human Immunodeficiency Virus Type 1 DNA Vaccine Immunogenicity by In Vivo Electroporation
Authors: Liu Jinyan , Kjeken Rune , Mathiesen Iacob , Barouch Dan H.
Published: March 2008

In vivo electroporation (EP) has been shown to augment the immunogenicity of plasmid DNA vaccines, but its mechanism of action has not been fully characterized. In this study, we show that in vivo EP augmented cellular and humoral immune responses to a human immunodeficiency virus type 1 Env DNA vaccine in mice and allowed a 10-fold reduction in vaccine dose. This enhancement was durable for over 6 months, and re-exposure to antigen resulted in anamnestic effector and central memory CD8
+
T-lymphocyte responses. Interestingly, in vivo EP also recruited large mixed cellular inflammatory infiltrates to the site of inoculation. These infiltrates contained 45-fold-increased numbers of macrophages and 77-fold-increased numbers of dendritic cells as well as 2- to 6-fold-increased numbers of B and T lymphocytes compared to infiltrates following DNA vaccination alone. These data suggest that recruiting inflammatory cells, including antigen-presenting cells (APCs), to the site of antigen production substantially improves the immunogenicity of DNA vaccines. Combining in vivo EP with plasmid chemokine adjuvants that similarly recruited APCs to the injection site, however, did not result in synergy.
Role of the Membrane-Spanning Domain of Human Immunodeficiency Virus Type 1 Envelope Glycoprotein in Cell-Cell Fusion and Virus Infection
Authors: Shang Liang , Yue Ling , Hunter Eric
Published: March 2008

The membrane-spanning domain (MSD) of the human immunodeficiency virus type 1 (HIV-1) gp41 glycoprotein is critical for its biological activity. Previous C-terminal truncation studies have predicted an almost invariant core structure of 12 amino acid residues flanked by basic amino acids in the HIV-1 MSD that function to anchor the glycoprotein in the lipid bilayer. To further understand the role of specific amino acids within the MSD core, we initially replaced the core region with 12 leucine residues and then constructed recovery-of-function mutants in which specific amino acid residues (including a GGXXG motif) were reintroduced. We show here that conservation of the MSD core sequence is not required for normal expression, processing, intracellular transport, and incorporation into virions of the envelope glycoprotein (Env). However, the amino acid composition of the MSD core does influence the ability of Env to mediate cell-cell fusion and plays a critical role in the infectivity of HIV-1. Replacement of conserved amino acid residues with leucine blocked virus-to-cell fusion and subsequent viral entry into target cells. This restriction could not be released by C-terminal truncation of the gp41 glycoprotein. These studies imply that the highly conserved core residues of the HIV Env MSD, in addition to serving as a membrane anchor, play an important role in mediating membrane fusion during viral entry.
Ataxia Telangiectasia-Mutated Damage-Signaling Kinase- and Proteasome-Dependent Destruction of Mre11-Rad50-Nbs1 Subunits in Simian Virus 40-Infected Primate Cells
Authors: Zhao Xiaorong , Madden-Fuentes Ramiro J. , Lou Becky X. , Pipas James M. , Gerhardt Jeannine , Rigell Christopher J. , Fanning Ellen
Published: March 2008

Although the mechanism of simian virus 40 (SV40) DNA replication has been extensively investigated with cell extracts, viral DNA replication in productively infected cells utilizes additional viral and host functions whose interplay remains poorly understood. We show here that in SV40-infected primate cells, the activated ataxia telangiectasia-mutated (ATM) damage-signaling kinase, γ-H2AX, and Mre11-Rad50-Nbs1 (MRN) assemble with T antigen and other viral DNA replication proteins in large nuclear foci. During infection, steady-state levels of MRN subunits decline, although the corresponding mRNA levels remain unchanged. A proteasome inhibitor stabilizes the MRN complex, suggesting that MRN may undergo proteasome-dependent degradation. Analysis of mutant T antigens with disrupted binding to the ubiquitin ligase CUL7 revealed that MRN subunits are stable in cells infected with mutant virus or transfected with mutant viral DNA, implicating CUL7 association with T antigen in MRN proteolysis. The mutant genomes produce fewer virus progeny than the wild type, suggesting that T antigen-CUL7-directed proteolysis facilitates virus propagation. Use of a specific ATM kinase inhibitor showed that ATM kinase signaling is a prerequisite for proteasome-dependent degradation of MRN subunits as well as for the localization of T antigen and damage-signaling proteins to viral replication foci and optimal viral DNA replication. Taken together, the results indicate that SV40 infection manipulates host DNA damage-signaling to reprogram the cell for viral replication, perhaps through mechanisms related to host recovery from DNA damage.
Simultaneous Tracking of Capsid, Tegument, and Envelope Protein Localization in Living Cells Infected with Triply Fluorescent Herpes Simplex Virus 1
Authors: Sugimoto Ken , Uema Masashi , Sagara Hiroshi , Tanaka Michiko , Sata Tetsutaro , Hashimoto Yasuhiro , Kawaguchi Yasushi
Published: March 2008

We report here the construction of a triply fluorescent-tagged herpes simplex virus 1 (HSV-1) expressing capsid protein VP26, tegument protein VP22, and envelope protein gB as fusion proteins with monomeric yellow, red, and cyan fluorescent proteins, respectively. The recombinant virus enabled us to monitor the dynamics of these capsid, tegument, and envelope proteins simultaneously in the same live HSV-1-infected cells and to visualize single extracellular virions with three different fluorescent emissions. In Vero cells infected by the triply fluorescent virus, multiple cytoplasmic compartments were found to be induced close to the basal surfaces of the infected cells (the adhesion surfaces of the infected cells on the solid growth substrate). Major capsid, tegument, and envelope proteins accumulated and colocalized in the compartments, as did marker proteins for the
trans
-Golgi network (TGN) which has been implicated to be the site of HSV-1 secondary envelopment. Moreover, formation of the compartments was correlated with the dynamic redistribution of the TGN proteins induced by HSV-1 infection. These results suggest that HSV-1 infection causes redistribution of TGN membranes to form multiple cytoplasmic compartments, possibly for optimal secondary envelopment. This is the first real evidence for the assembly of all three types of herpesvirus proteins—capsid, tegument, and envelope membrane proteins—in TGN.
Cross-Recognition of Avian H5N1 Influenza Virus by Human Cytotoxic T-Lymphocyte Populations Directed to Human Influenza A Virus
Authors: Kreijtz J. H. C. M. , de Mutsert G. , van Baalen C. A. , Fouchier R. A. M. , Osterhaus A. D. M. E. , Rimmelzwaan G. F.
Published: March 2008

Since the number of human cases of infection with avian H5N1 influenza viruses is ever increasing, a pandemic outbreak caused by these viruses is feared. Therefore, in addition to virus-specific antibodies, there is considerable interest in immune correlates of protection against these viruses, which could be a target for the development of more universal vaccines. After infection with seasonal influenza A viruses of the H3N2 and H1N1 subtypes, individuals develop virus-specific cytotoxic T-lymphocyte responses, which are mainly directed against the relatively conserved internal proteins of the virus, like the nucleoprotein (NP). Virus-specific cytotoxic T lymphocytes (CTL) are known to contribute to protective immunity against infection, but knowledge about the extent of cross-reactivity with avian H5N1 influenza viruses is sparse. In the present study, we evaluated the cross-reactivity with H5N1 influenza viruses of polyclonal CTL obtained from a group of well-defined HLA-typed study subjects. To this end, the recognition of synthetic peptides representing H5N1 analogues of known CTL epitopes was studied. In addition, the ability of CTL specific for seasonal H3N2 influenza virus to recognize the NP of H5N1 influenza virus or H5N1 virus-infected cells was tested. It was concluded that, apart from some individual epitopes that displayed amino acid variation between H3N2 and H5N1 influenza viruses, considerable cross-reactivity exists with H5N1 viruses. This preexisting cross-reactive T-cell immunity in the human population may dampen the impact of a next pandemic.
Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungus
Authors: Park K.-C. , Kwon S.-J. , Kim P.-H. , Bureau T. , Kim N.-S.
Published: March 2008

Whole copies of the polygalacturonase (PG) genes from rice ( Oryza sativa subsp. japonica) and a filamentous fungus ( Aspergillus oryzae ) were isolated. The orthologs of the rice PGs were also retrieved from other plant species. The 106 plant PGs analyzed were divided into 5 clades, A, B, C, D, and E. The fungus PGs were classified into 3 clades, of which one formed a loose cluster with clade E of the plant PGs. Four domain motifs (I, II, III, IV) were identified in all PGs. Motifs II and III were split by introns such as G/DDC and CGPGHGIS/IGSLG, respectively. In plant PGs there were 446 introns in total and 3.98 introns per gene. Intron phase distribution was 65.5% for phase 0, 19.7% for phase 1, and 14.8% for phase 2 in plant PGs. In the PGs of A. oryzae there were 37 introns of phase 0 (59.5%), phase 1 (24.3%), and phase 2 (16.2%), with 2.47 introns per gene. The 5 clades of plant PGs were divided into 3 basic gene structure lineages. Intron positions and phases were conserved among the PGs in the first 2 lineages. The third lineage consisted of PGs of clade E, which also carried highly conserved introns at different positions from other PGs. Intron positions were not as highly conserved in fungus PGs as in plant PGs. The introns in the current PGs have been present since before the divergence of monocots from dicots. The results obtained show that differential losses of introns created gene diversity, which was followed by segmental and tandem duplication in plant PGs.
Identification of two genes for resistance to Triticum isolates of Magnaporthe oryzae in wheat
Authors: Zhan S. W. , Mayama S. , Tosa Y.
Published: March 2008

A screening of common wheat cultivars revealed that Triticum aestivum ‘Thatcher’ was resistant to Triticum isolates of Magnaporthe oryzae , whereas T. aestivum ‘Chinese Spring’ was susceptible. When F2 seedlings from a cross between ‘Thatcher’ and ‘Chinese Spring’ were inoculated with the Triticum isolates, resistant and susceptible seedlings segregated in a 15:1 ratio, suggesting that the resistance of ‘Thatcher’ was conditioned by two major genes. An inoculation test of ‘Chinese Spring’ substitution lines carrying individual chromosomes from ‘Thatcher’ indicated that these genes, designated Rmg2 and Rmg3, were located on chromosomes 7A and 6B.
Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bambooIHBT Publication No. 0732.
Authors: Sharma R. K. , Gupta P. , Sharma V. , Sood A. , Mohapatra T. , Ahuja P. S.
Published: March 2008

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics ( Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice ( Oryza sativa ) and sugarcane ( Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii ). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.
Identification and mapping of a third blackleg resistance locus inBrassica napusderived fromB. rapasubsp.sylvestris
Authors: Yu Fengqun , Lydiate Derek J. , Rimmer S. Roger
Published: March 2008

The spectrum of resistance to isolates of Leptosphaeria maculans and the map location of a new blackleg resistance gene found in the canola cultivar Brassica napus ‘Surpass 400’ are described. Two blackleg resistance genes, LepR1 and LepR2, from B. rapa subsp. sylvestris and introgressed in B. napus were identified previously. ‘Surpass 400’ also has blackleg resistance introgressed from B. rapa subsp. sylvestris. Using 31 diverse isolates of L. maculans, the disease reaction of ‘Surpass 400’ was compared with those of the resistant breeding lines AD9 (which contains LepR1), AD49 (which contains LepR2), and MC1-8 (which contains both LepR1 and LepR2). The disease reaction on ‘Surpass 400’ was different from those observed on AD9 and MC1-8, indicating that ‘Surpass 400’ carries neither LepR1 nor both LepR1 and LepR2 in combination. Disease reactions of ‘Surpass 400’ to most of the isolates tested were indistinguishable from those of AD49, which suggested ‘Surpass 400’ might contain LepR2 or a similar resistance gene. Classical genetic analysis of F1and BC1plants showed that a dominant allele conferred resistance to isolates of L. maculans in ‘Surpass 400’. The resistance gene, which mapped to B. napus linkage group N10 in an interval of 2.9 cM flanked by microsatellite markers sR12281a and sN2428Rb and 11.7 cM below LepR2, was designated LepR3. A 9 cM region of the B. napus genome containing LepR3 was found to be syntenic with a segment of Arabidopsis chromosome 5.
Gene amelioration demonstrated: the journey of nascent genes in bacteria
Authors: Marri Pradeep Reddy , Golding G. Brian
Published: March 2008

Gene amelioration is the hypothesis that genes acquired via lateral gene transfer will, over time, acquire the molecular characteristics of the host genome. Species for which multiple strains have been sequenced permit a demonstration that this hypothesis is correct. We use 7 sequenced genomes of Streptococcus pyogenes and 6 sequenced genomes of Staphylococcus aureus to illustrate the action of amelioration on these genomes.
Evidence of hexaploid karyotype in shortnose sturgeon
Authors: Fontana Francesco , Congiu Leonardo , Mudrak Vincent A. , Quattro Joseph M. , Smith Theodore I.J. , Ware Kent , Doroshov Serge I.
Published: March 2008

A karyotype analysis by several staining techniques was carried out on triplicate samples of the shortnose sturgeon, Acipenser brevirostrum . The chromosome number was found to be 2n = 372 ± 6. A representative karyotype of 374 chromosomes was composed of 178 metacentrics/submetacentrics and 196 telocentrics/acrocentrics and microchromosomes. The signals of fluorescent in situ hybridization (FISH) with a HindIII satellite DNA probe were visible on 14 chromosomes. The signals obtained with a PstI satellite DNA probe appeared on 12 chromosomes. The FISH with a 5S rDNA probe revealed fluorescent signals on 6 chromosomes. These last results, compared with 2 signals in species with about 120 chromosomes and 4 in species with 240, support the hypothesis that A. brevirostrum is a hexaploid species, probably of hybrid origin. Based on these results, we propose a model explaining speciation events occurring in sturgeons by hybridization, genome duplication, and diploidization.
The recent evolution of a pseudogene: diversity and divergence of a mitochondria-localized small heat shock protein inArabidopsis thaliana
Authors: Waters Elizabeth R. , Nguyen Suzan L. , Eskandar Raheleh , Behan Jennifer , Sanders-Reed Zipporah
Published: March 2008

In this study we examined the evolution of the genes for three organelle-localized small heat shock proteins in Arabidopsis thaliana : the chloroplast-localized (CP) protein HSP21 and two mitochondria-localized (MT) proteins, HSP23.5 and HSP23.6. We found that the CP protein and one of the MT proteins, HSP23.6, are evolving under purifying selection to maintain function. In contrast, the gene for HSP23.5, the other MT protein, is highly variable within A. thaliana, and in some accessions or ecotypes this gene may be a pseudogene. HSP23.5 and HSP23.6 are related via a segmental duplication event, and the presence of orthologs of each gene in other species within the Brassicaceae indicates that the duplication generating HSP23.5 and HSP23.6 may have occurred as much as 20 million years ago. This is considerably longer than the 4 million year half-life of gene duplicates (functional genes as well as pseudogenes) reported by some studies. Our results are consistent with the prediction that after gene duplication one gene duplicate can be maintained for some time under relaxed selection while it accumulates random mutations. By capturing a pseudogene in the making our study provides important information on how pseudogenes are formed.
Development of a Brassica seed cDNA microarray
Authors: Xiang Daoquan , Datla Raju , Li Fengling , Cutler Adrian , Malik Meghna R. , Krochko Joan E. , Sharma Nirmala , Fobert Pierre , Georges Fawzy , Selvaraj Gopalan , Tsang Ed , Klassen Darrin , Koh Chushin , Deneault Jean-Sebastien , Nantel Andre , Nowak Jacek , Keller Wilf , Bekkaoui Faouzi
Published: March 2008

Brassica species represent several important crops including canola ( Brassica napus ). Understanding of genetic elements that contribute to seed-associated functions will impact future improvements in the canola crop. Brassica species share a very close taxonomic and molecular relationship with Arabidopsis thaliana. However, there are several subtle but distinct seed-associated agronomic characteristics that differ among the oil seed crop species. To address these, we have generated 67 535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10 642 unigenes for the preparation of a targeted seed cDNA array. A set of 10 642 PCR primer pairs was designed and corresponding amplicons were produced for spotting, along with relevant controls. Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. The microarray was also tested with specific RNA targets from embryos, germinating seeds, and leaf tissues. The hybridizations, signal intensities, and overall quality of these slides were consistent and reproducible. Additionally, there are 429 ESTs represented on the array that show no homology with any A. thaliana annotated gene or any gene in the Brassica genome databases or other plant databases; however, all of these probes hybridized to B. napus transcripts, indicating that the array also will be useful in defining expression patterns for genes so far unique to Brassica species.
Structure and evolution of the mitochondrial control region of the pollen beetleMeligethes thalassophilus(Coleoptera: Nitidulidae)
Authors: Mancini Emiliano , De Biase Alessio , Mariottini Paolo , Bellini Alessandro , Audisio Paolo
Published: March 2008

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the pollen beetle Meligethes thalassophilus is described. This mtDNA CR represents the longest sequenced for beetles so far, since the entire nucleotide sequence ranges from ~5000 to ~5500 bp. The CR of M. thalassophilus is organized in three distinct domains: a conserved domain near the tRNAIlegene, a variable domain flanking the 12S rRNA gene, and a relatively large central tandem array made up of a variable number of ~170 bp repeats that is responsible for the intraspecific length variation observed. Like other CRs found in insects, the M. thalassophilus CR contains two long homopolymeric runs that may be involved in mtDNA replication. Furthermore, conserved stem-and-loop structures in the repetitive domain were identified and their possible role in generating length variation is examined. Intraspecific comparison of the tandem repeat elements of M. thalassophilus suggests mechanisms of concerted evolution leading to homogenization of the repetitive region. The utility of such an array of tandem repeats as a genetic marker for assessing population-level variability and evolutionary relationships among populations is discussed. Finally, the technical difficulties found in isolating the mtDNA CR in beetles are remarked upon.
SPIN-DEPENDENCE OF THERMODYNAMIC QUANTITIES AROUND A HOROWITZ–STROMINGER BLACK HOLE
Authors: LI GU-QIANG
Published: March 2008

Making use of the brick wall method, we investigate the energy density, entropy density, pressure, and state equation for a perfect relativistic gas with spin s = 1/2, 1, 3/2, 2 around a Horowitz–Strominger black hole (HSBH). We show that there exists an additional spin-dependent term in the expression of these thermodynamic quantities except the leading term which is the same as that in flat spacetime.
GRAVITINO PRODUCTION IN AN INFLATIONARY UNIVERSE AND IMPLICATIONS FOR LEPTOGENESIS
Authors: RANGARAJAN RAGHAVAN , SAHU NARENDRA
Published: March 2008

Models of leptogenesis are constrained by the low reheat temperature at the end of reheating associated with the gravitino bound. However, a detailed view of reheating, in which the maximum temperature during reheating, T max , can be orders of magnitude higher than the reheat temperature, allows for the production of heavy Majorana neutrinos needed for leptogenesis. But then one must also consider the possibility of enhanced gravitino production in such scenarios. In this paper we consider gravitino production during reheating, its dependence on T max , and its relevance for leptogenesis. Earlier analytical studies of the gravitino abundance have only considered gravitino production in the post-reheating radiation dominated era. We find that the gravitino abundance generated during reheating is comparable to that generated after reheating. This lowers the upper bound on the reheat temperature by a factor of 4/3.
EFFECTS OF UNIVERSAL EXTRA DIMENSIONS ON HIGGS SIGNALS AT LHC
Authors: RAI SANTOSH KUMAR
Published: March 2008

A major focus at the Large Hadron Collider (LHC) will be on Higgs boson studies and it would be an interesting prospect to simultaneously probe for physics beyond the Standard Model in the Higgs signals. In this work we show as to what extent, the effects of universal extra dimension (UED) can be isolated at the LHC through the Higgs signals. By doing a detailed study of the different uncertainties involved in the measurement of the rates for the process pp →h →γγ, we estimate the extent to which these uncertainties can mask the effects of the contributions coming from UED.
GHOSTS AND TACHYONS IN THE FIFTH DIMENSION
Authors: POSPELOV MAXIM
Published: March 2008

We present several solutions for the five-dimensional gravity models in the presence of bulk ghosts and tachyons to argue that these "troublesome" fields can be a useful model-building tool. The ghost-like signature of the kinetic term for a bulk scalar creates a minimum in the scale factor, removing the necessity for a negative tension brane in models with the compactified fifth dimension. It is shown that the model with the positive tension branes and a ghost field in the bulk leads to the radion stabilization. The bulk scalar with the variable sign kinetic term can be used to model both positive and negative tension branes of a finite width in the compact dimension. Finally, we present several ghost and tachyon field configurations in the bulk that lead to the localization of gravity in four dimensions, including one solution with the Gaussian profile for the metric, gμν(y) = ημν exp {-αy2}, which leads to a stronger localization of gravity than the Randall–Sundrum model.
ANALYTIC EQUATION OF STATE AND THERMODYNAMIC PROPERTIES FOR FCC C70 SOLID BASED ON THE ANALYTIC MEAN FIELD APPROACH
Authors: WEI YANG , SUN JIU-XUN , WANG LI-GUO , TIAN RONG-GANG
Published: March 2008

The analytic expressions for equation of state and internal energy for the poly-exponential solid have been derived based on the analytic mean-field potential (AMFP) method. The formalism is applied to the fcc C 70 solid. One set of potential parameters are determined through fitting the experimental compression data1 of C 70 up to 1 GPa and at temperature 365 K. The difference between the well depth for C 70 molecules and that for C 60 molecules is fairly small. The thermo-physical properties including the isothermals, thermal expansivity, isochoric heat capacity, Helmholtz free energy and internal energy have been calculated and analyzed. The theoretical results are in good agreement with the experimental data of C 70 solid available. Based on the results of our calculations, we may also predict the behaviors of C 70 at extreme conditions.
ACCELERATING THE REVIVAL OF A TRAPPED-ION SYSTEM
Authors: SHE L. , LI J. M. , GAO K. L.
Published: March 2008

We propose a method to accelerate the revival of ion Rabi oscillation in a trapped ion system. Suitable manipulation of the frequency of the driven laser field permits us to switch from Jaynes–Cummings to off-resonant interaction. The combination of Jaynes–Cummings model and the off-resonant model induces some interesting characteristics of the ion-trap system, particularly the accelerated revival of the population of trapped ions. The amplitude of this revival is sensitive to the change of the laser frequency.
ANALYTICAL APPROXIMATIONS TO THE l-WAVE SOLUTIONS OF THE SCHRÖDINGER EQUATION WITH A HYPERBOLIC POTENTIAL
Authors: DONG SHISHAN , MIRANDA S. G. , ENRIQUEZ F. M. , DONG SHI-HAI
Published: March 2008

The bound-state solutions of the Schrödinger equation for a hyperbolic potential with the centrifugal term are presented approximately. It is shown that the solutions can be expressed by the hypergeometric function 2F1(a, b; c; z). To show the accuracy of our results, we calculate the energy levels numerically for arbitrary quantum numbers n and l. It is found that the results are in good agreement with those obtained by other methods for short-range potential. Two special cases for l = 0 and σ = 1 are also studied briefly.
MINIMAL CONSISTENT SUBSET FOR HYPER SURFACE CLASSIFICATION METHOD
Authors: HE QING , ZHAO XIU-RONG , SHI ZHONG-ZHI
Published: March 2008

Hyper Surface Classification (HSC), which is based on Jordan Curve Theorem in Topology, has proven to be a simple and effective method for classifying a larger database in our previous work. To select a representative subset from the original sample set, the Minimal Consistent Subset (MCS) of HSC is studied in this paper. For HSC method, one of the most important features of MCS is that it has the same classification model as the entire sample dataset, and can totally reflect its classification ability. From this point of view, MCS is the best way of sampling from the original dataset for HSC. Furthermore, because of the minimum property of MCS, every single deletion or multiple deletions from it will lead to a reduction in generalization ability, which can be exactly predicted by the proposed formula in this paper.
COMPETITIVE ANALYSIS FOR THE MOST RELIABLE PATH PROBLEM WITH ONLINE AND FUZZY UNCERTAINTIES
Authors: MA WEI-MIN , TANG SHAO-HUA , WANG KE
Published: March 2008

Based on some results of the fuzzy network computation and competitive analysis, the Online Fuzzy Most Reliable Path Problem (OFRP), which is one of the most important problems in network optimization with uncertainty, has been originally proposed by our team. In this paper, the preliminaries about fuzzy and the most reliable path and competitive analysis are given first. Following that, the mathematical model of OFRP, in which two kinds of uncertainties, namely online and fuzzy, are combined to be considered at the same time, is established. Then some online fuzzy algorithms are developed to address the OFRP and the rigorous proofs of the competitive analysis are given in detail. Finally, some possible research directions of the OFRP are discussed and the conclusions are drawn.
A PRESENTATION OF THE DUAL SYMMETRIC INVERSE MONOID
Authors: EASDOWN DAVID , EAST JAMES , FITZGERALD D. G.
Published: March 2008

The dual symmetric inverse monoid [Formula: see text] is the inverse monoid of all isomorphisms between quotients of an n-set. We give a monoid presentation of [Formula: see text] and, along the way, establish criteria for a monoid to be inverse when it is generated by completely regular elements.
Alternative Medicine: Definition, Scope and Challenges
Authors: Eskinazi Daniel , Mindes Janet
Published: March 2008

This article reveals the rational Definition of Alternative medicine by knowing its challenges and scopes.
Shifting Paradigm: From Conventional to Alternative Medicines — An Introduction on Traditional Indian Medicines
Authors: Grover J. K. , Vats V.
Published: March 2008

This article delivers an Introduction on Indian Traditional Medicine.
Analysis of Battery Safety and Hazards' Risk Mitigation
Authors: Ashtiani Cyrus
Published: March 2008

For several years now, there has been a strong drive in the automotive industry to displace the NiMH batteries in Hybrid Electric Vehicles (HEV) with lighter, more durable, more powerful and potentially less expensive Li-Ion batteries. These efforts have been hampered mostly by the concerns over the safety of the Li-Ion batteries. Such concerns have been overblown by merely focusing on abusive testing without paying equal attention to assessing the risk posed by such batteries in the event of a mishap. History shows that the automotive industry has been very successful in managing the risk posed by gasoline, a highly combustible fluid with an energy density 100 times more than the most energy-dense of advance batteries. This paper discusses a methodology developed for the risk assessment of advance batteries. Although the focus here is on the batteries used in hybrid, electric, or plug-in vehicles, the methodology itself, called Hazard Modes & Risk Mitigation Analysis (HMRMA), is quite general and can be used in other applications for batteries as well as for other components & parts that maybe considered hazardous. In addition, the methodology quantifies the risk associated with each hazard and becomes a valuable design tool to develop the most effective way of reducing the risk.
In-Situ Thermal Investigation of LiMn2O4/Li4Ti5O12 Lithium Ion Cells
Authors: Joachin Humberto H. , Amiruddin Shabab , Li Bing , Kaun Thomas D. , Amine Khalil , Prakash Jai
Published: March 2008

Two spinel structures, LiMn2O4 as cathode and Li4Ti5O12 as anode, were studied as a promising chemistry for lithium-ion batteries. Both materials were studied for its electrochemical performance and heat generated during cycling by IMC at 25oC. Both electrodes exhibited good reversible capacities. Their thermal behaviors during cycling were similar in half cells and most of their heat develops at the end of the charge and discharge processes. Also, the heat generated by a LiMn2O4/Li4Ti5O12 cell was estimated using the individual heat generated by LiMn2O4 and Li4Ti5O12 materials.
Abuse Response of 18650 Li-Ion Cells with Different Cathodes Using EC:EMC/LiPF6 and EC:PC:DMC/LiPF6 Electrolytes
Authors: Roth E. Peter
Published: March 2008

Lithium-Ion batteries are being considered as a high-energy density replacement for Nickel Metal Hydride (NiMH) batteries in Hybrid Electric Vehicles (HEVs) and in the new Plug-In Hybrids (PHEVs). Although these cells can result in significant reduction in weight and volume, they have several safety related issues that still need to be addressed. We report here on the thermal response of Li-ion cells specifically assembled in our laboratory to test new materials, electrolytes and additives. Improvements in the thermal abuse tolerance of cells are reported and discussed in terms of the need for overall battery system safety.
Identification of the Source of Evolved Gas in Li-Ion Batteries by Using 13C-Labeled Solvents
Authors: Onuki Masamichi , Sakata Yuuichi , Yanagidate Miwa , Otake Yumiko , Kinoshita Shinichi , Ue Makoto , Deguchi Masaki
Published: March 2008

Gas evolution in lithium-ion batteries at elevated temperature is a big problem to be solved for practical usage. In order to elucidate the mechanism of gas evolution, we employed 13C-labeled ethylene carbonate (13C-EC) and diethyl carbonate (13C-DEC) as solvent components. Evolved CO2 during storage were analyzed by GC/AED technique to determine the isotopic ratio. The relative proportions of the CO2 derived from EC, DEC, and non-solvent were determined to be 52%, 11%, and 37%, respectively. The main source of CO2 was found to be EC. Further storage tests with a single electrode showed that CO2 evolution also occurs from cathode components.
Effect of Nanostructured Surface of Light Metals on Hydroxyapatite Coating
Authors: Ono Sachiko , Kiyotake Atsushi , Asoh Hidetaka
Published: March 2008

Hydroxyapatite coating by alternative dipping method on light metals such as Al, Mg and Ti having porous surface was studied with focusing on the morphology and composition of the surface layer. HAp coating is significantly enhanced by porous substrates having a pore size of 10 nm ~ 30 nm, i.e., mesoporous range. Incorporated electrolyte species into the substrates assist the precipitation of HAp in the following order: Sulfuric acid ≧ NaOH > Oxalic acid > Phosphoric acid. Plate-like deposit was formed on Mg substrate having thin natural oxide or defective anodic films. However, no deposit was found on chemically etched surface. Thus, it was clarified that the meso-porous size as well as incorporated anions of porous substrate strongly affected to the HAp coating.