bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive Epitope Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific T-Cell Responses Directed against the Entire Expressed HIV-1 Genome Demonstrate Broadly Directed Responses, but No Correlation to Viral Load
Authors: Addo M. M. , Yu X. G. , Rathod A. , Cohen D. , Eldridge R. L. , Strick D. , Johnston M. N. , Corcoran C. , Wurcel A. G. , Fitzpatrick C. A. , Feeney M. E. , Rodriguez W. R. , Basgoz N. , Draenert R. , Stone David R. , Brander C. , Goulder P. J. R. , Rosenberg E. S. , Altfeld M. , Walker B. D.
Published: January 2003

Cellular immune responses play a critical role in the control of human immunodeficiency virus type 1 (HIV-1); however, the breadth of these responses at the single-epitope level has not been comprehensively assessed. We therefore screened peripheral blood mononuclear cells (PBMC) from 57 individuals at different stages of HIV-1 infection for virus-specific T-cell responses using a matrix of 504 overlapping peptides spanning all expressed HIV-1 proteins in a gamma interferon-enzyme-linked immunospot (Elispot) assay. HIV-1-specific T-cell responses were detectable in all study subjects, with a median of 14 individual epitopic regions targeted per person (range, 2 to 42), and all 14 HIV-1 protein subunits were recognized. HIV-1 p24-Gag and Nef contained the highest epitope density and were also the most frequently recognized HIV-1 proteins. The total magnitude of the HIV-1-specific response ranged from 280 to 25,860 spot-forming cells (SFC)/10
6
PBMC (median, 4,245) among all study participants. However, the number of epitopic regions targeted, the protein subunits recognized, and the total magnitude of HIV-1-specific responses varied significantly among the tested individuals, with the strongest and broadest responses detectable in individuals with untreated chronic HIV-1 infection. Neither the breadth nor the magnitude of the total HIV-1-specific CD8
+
-T-cell responses correlated with plasma viral load. We conclude that a peptide matrix-based Elispot assay allows for rapid, sensitive, specific, and efficient assessment of cellular immune responses directed against the entire expressed HIV-1 genome. These data also suggest that the impact of T-cell responses on control of viral replication cannot be explained by the mere quantification of the magnitude and breadth of the CD8
+
-T-cell response, even if a comprehensive pan-genome screening approach is applied.
Replication of
Carnation Italian Ringspot Virus
Defective Interfering RNA in
Saccharomyces cerevisiae
Authors: Pantaleo Vitantonio , Rubino Luisa , Russo Marcello
Published: January 2003

Two plasmids from which the sequences coding for the 36- and 95-kDa proteins of
Carnation Italian ringspot virus
(CIRV) could be transcribed in vivo in the yeast
Saccharomyces cerevisiae
under the control of the ADH1 promoter and terminator were constructed. The two proteins, which constitute the viral replicase, were correctly translated and integrated into membranes of the yeast cells. An additional plasmid was introduced in yeasts expressing the CIRV replicase, from which a defective interfering (DI) RNA (DI-7 RNA) could be transcribed under the control of the GAL1 promoter and terminated by the
Tobacco ringspot virus
satellite ribozyme, which cleaved 19 nucleotides downstream of the 3′ end of DI RNA. The DI-7 RNA transcripts were amplified by the viral replicase as demonstrated by the restoration of the authentic 3′ end, the requirement of a specific
cis
-acting signal at this terminus, the preferential accumulation of molecules with the authentic 5′ terminus (AGAAA), the synthesis of head-to-tail dimers, the presence of negative strands, and the incorporation of 5-bromo-UTP. Additionally, transformation with a dimeric construct of DI-7 RNA led to the synthesis of monomers, mimicking the activity of the viral replicase in plant cells.
Human Immunodeficiency Virus Type 1 Nef-Mediated Downregulation of CD4 Correlates with Nef Enhancement of Viral Pathogenesis
Authors: Stoddart Cheryl A. , Geleziunas Romas , Ferrell Sharon , Linquist-Stepps Valerie , Moreno Mary E. , Bare Christopher , Xu Weiduan , Yonemoto Wes , Bresnahan Patricia A. , McCune Joseph M. , Greene Warner C.
Published: January 2003

The
nef
gene products encoded by human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus type 1 (SIV-1) increase viral loads in infected hosts and accelerate clinical progression to AIDS. Nef exhibits a spectrum of biological activities, including the ability to downregulate surface expression of CD4 and major histocompatibility complex (MHC) class I antigens, to alter the state of T-cell activation, and to enhance the infectivity of viral particles. To determine which of these in vitro functions most closely correlates with the pathogenic effects of Nef in vivo, we constructed recombinant HIV-1 NL4-3 viruses carrying mutations within the
nef
gene that selectively impair these functions. These mutant viruses were evaluated for pathogenic potential in severe combined immunodeficiency (SCID) mice implanted with human fetal thymus and liver (SCID-hu Thy/Liv mice), in which virus-mediated depletion of thymocytes is known to be Nef dependent. Disruption of the polyproline type II helix (Pxx)
4
within Nef (required for binding of Hck and p21-activated kinase-like kinases, downregulation of MHC class I, and enhancement of HIV-1 infectivity in vitro but dispensable for CD4 downregulation) did not impair thymocyte depletion in virus-infected Thy/Liv human thymus implants. Conversely, three separate point mutations in Nef that compromised its ability to downregulate CD4 attenuated thymocyte depletion while not diminishing viral replication. These findings indicate that the functional ability of Nef to downregulate CD4 and not MHC class I downregulation, Hck or PAK binding, or (Pxx)
4
-associated enhancement of infectivity most closely correlates with Nef-mediated enhancement of HIV-1 pathogenicity in vivo. Nef-mediated CD4 downregulation merits consideration as a new target for the development of small-molecule inhibitors.
Virus Replication in Engineered Human Cells That Do Not Respond to Interferons
Authors: Young D. F. , Andrejeva L. , Livingstone A. , Goodbourn S. , Lamb R. A. , Collins P. L. , Elliott R. M. , Randall R. E.
Published: January 2003

The V protein of the paramyxovirus simian virus 5 blocks interferon (IFN) signaling by targeting STAT1 for proteasome-mediated degradation. Here we report on the isolation of human cell lines that express the V protein and can no longer respond to IFN. A variety of viruses, particularly slow-growing wild-type viruses and vaccine candidate viruses (which are attenuated due to mutations that affect virus replication, virus spread, or ability to circumvent the IFN response), form bigger plaques and grow to titers that are increased as much as 10- to 4,000-fold in these IFN-nonresponsive cells. We discuss the practical applications of using such cells in vaccine development and manufacture, virus diagnostics and isolation of newly emerging viruses, and studies on host cell tropism and pathogenesis.
Cytomegalovirus-Mediated Upregulation of Chemokine Expression Correlates with the Acceleration of Chronic Rejection in Rat Heart Transplants
Authors: Streblow Daniel N. , Kreklywich Craig , Yin Qiang , De La Melena V. T. , Corless Christopher L. , Smith Patricia A. , Brakebill Christina , Cook Judith W. , Vink Cornelis , Bruggeman Cathrien A. , Nelson Jay A. , Orloff Susan L.
Published: January 2003

Cytomegalovirus (CMV) infections have been shown to dramatically affect solid organ transplant graft survival in both human and animal models. Recently, it was demonstrated that rat CMV (RCMV) infection accelerates the development of transplant vascular sclerosis (TVS) in both rat heart and small bowel graft transplants. However, the mechanisms involved in this process are still unclear. In the present study, we determined the kinetics of RCMV-accelerated TVS in a rat heart transplant model. Acute RCMV infection enhances the development of TVS in rat heart allografts, and this process is initiated between 21 and 24 days posttransplantation. The virus is consistently detected in the heart grafts from day 7 until day 35 posttransplantation but is rarely found at the time of graft rejection (day 45 posttransplantation). Grafts from RCMV-infected recipients had upregulation of chemokine expression compared to uninfected controls, and the timing of this increased expression paralleled that of RCMV-accelerated neointimal formation. In addition, graft vessels from RCMV-infected grafts demonstrate the increased infiltration of T cells and macrophages during periods of highest chemokine expression. These results suggest that CMV-induced acceleration of TVS involves the increased graft vascular infiltration of inflammatory cells through enhanced chemokine expression.
The E6 and E7 Proteins of the Cutaneous Human Papillomavirus Type 38 Display Transforming Properties
Authors: Caldeira Sandra , Zehbe Ingeborg , Accardi Rosita , Malanchi Ilaria , Dong Wen , Giarrè Marianna , de Villiers Ethel-Michele , Filotico Raffaele , Boukamp Petra , Tommasino Massimo
Published: January 2003

Several studies have suggested the involvement of cutaneous human papillomaviruses (HPVs) in the development of nonmelanoma skin cancers. Here we have characterized the in vitro properties of E7 proteins of three cutaneous HPV types, 10, 20, and 38, which are frequently detected in skin specimens. We show that HPV38 E7 is able to inactivate the tumor suppressor pRb and induces loss of G
1
/S transition control, a key event in carcinogenesis. In contrast, HPV10 and HPV20 E7 proteins do not display these in vitro transforming activities. We also show that the two early proteins E6 and E7 of HPV38 are sufficient to corrupt the cell cycle and senescence programs in primary cells, inducing active and long-lasting proliferation of primary human keratinocytes, the natural host cells. Our study shows that E6 and E7 of this cutaneous HPV type have transforming activity in primary human cells, suggesting a role for HPV38 infection in skin carcinogenesis. In further support of such a role, we detected HPV38 DNA in approximately 50% of nonmelanoma skin cancers, but only in 10% of healthy skin specimens (
P
< 0.001).
The Promyelocytic Leukemia Protein Does Not Mediate Foamy Virus Latency In Vitro
Authors: Meiering Christopher D. , Linial Maxine L.
Published: January 2003

Spumaviruses, commonly called foamy viruses, are complex retroviruses that establish life-long persistent infections in the absence of accompanying pathology. Depending upon cell type, infection of cells in tissue culture cells can result in either lytic replication, persistence, or latency. The cellular factors that mediate foamy virus (FV) latency are poorly understood. In this study we show that the only known inhibitor of FV replication, the promyelocytic leukemia protein (PML), which binds the FV transactivator (Tas), does not play an important role in FV latency in vitro. We found no significant differences in PML levels in cells that supported lytic replication compared to those that were latently infected. Furthermore, endogenous PML levels did not change following exposure to phorbol myristate acetate (PMA), which induces FV replication. We demonstrated that FV replication proceeded in the presence of substantial levels of PML, both in fully permissive cells and during reactivation of latent FV. Endogenous PML did not efficiently colocalize with Tas, even after upregulation by alpha interferon (IFN-α) treatment. IFN-α did, however, partially suppress the reactivation of latent FV by PMA. Finally, depletion of endogenous PML by small interfering RNA did not promote activation of FV in cells that responded to PMA treatment. Taken together, these data indicate that endogenous PML does not play an important role in mediating FV latency.
Frequency and Phenotype of Circulating Vα24/Vβ11 Double-Positive Natural Killer T Cells during Hepatitis C Virus Infection
Authors: Lucas Michaela , Gadola Stephan , Meier Ute , Young Neil T. , Harcourt Gillian , Karadimitris Anastasios , Coumi Nikki , Brown Dave , Dusheiko Geoff , Cerundolo Vincenzo , Klenerman Paul
Published: January 2003

Natural killer T (NKT) cells are thought to be involved in innate responses against infection. We investigated one specific type of NKT cell, Vα24/Vβ11 double positive, in hepatitis C virus (HCV) infection. Lower frequencies of this population were detected in the blood of HCV PCR-positive patients than in controls. Unlike Vα24/Vβ11 NKT cells found in blood, those in the liver appeared to be recently activated.
Recognition of a Novel Stage of Betaherpesvirus Latency in Human Herpesvirus 6
Authors: Kondo Kazuhiro , Sashihara Junji , Shimada Kazuya , Takemoto Masaya , Amo Kiyoko , Miyagawa Hiromi , Yamanishi Koichi
Published: January 2003

Latency-associated transcripts of human herpesvirus 6 (H6LTs) (K. Kondo et al. J. Virol.
76:
4145-4151, 2002) were maximally expressed at a fairly stable intermediate stage between latency and reactivation both in vivo and in vitro. H6LTs functioned as sources of immediate-early protein 1 at this stage, which up-regulated the viral reactivation.
Fine Mapping of a
cis
-Acting Sequence Element in Yellow Fever Virus RNA That Is Required for RNA Replication and Cyclization
Authors: Corver Jeroen , Lenches Edith , Smith Kayla , Robison R. Aaron , Sando Trisha , Strauss Ellen G. , Strauss James H.
Published: January 2003

We present fine mapping of a
cis
-acting nucleotide sequence found in the 5′ region of yellow fever virus genomic RNA that is required for RNA replication. There is evidence that this sequence interacts with a complementary sequence in the 3′ region of the genome to cyclize the RNA. Replicons were constructed that had various deletions in the 5′ region encoding the capsid protein and were tested for their ability to replicate. We found that a sequence of 18 nucleotides (residues 146 to 163 of the yellow fever virus genome, which encode amino acids 9 to 14 of the capsid protein) is essential for replication of the yellow fever virus replicon and that a slightly longer sequence of 21 nucleotides (residues 146 to 166, encoding amino acids 9 to 15) is required for full replication. This region is larger than the core sequence of 8 nucleotides conserved among all mosquito-borne flaviviruses and contains instead the entire sequence previously proposed to be involved in cyclization of yellow fever virus RNA.
In a Subset of Subjects on Highly Active Antiretroviral Therapy, Human Immunodeficiency Virus Type 1 RNA in Plasma Decays from 50 to <5 Copies per Milliliter, with a Half-Life of 6 Months
Authors: Di Mascio Michele , Dornadula Geethanjali , Zhang Hui , Sullivan Julie , Xu Yan , Kulkosky Joseph , Pomerantz Roger J. , Perelson Alan S.
Published: January 2003

Three of five virally suppressed human immunodeficiency virus type I (HIV-1)-infected patients treated with highly active antiretroviral therapy and followed intensively with a supersensitive reverse transcriptase PCR assay with a lower limit of quantitation of 5 copies/ml showed statistically significant viral load decays below 50 copies/ml, with half-lives of 5 to 8 months and a mean of 6 months. This range of half-lives is consistent with the estimated half-life of the latent HIV-1 reservoir in the peripheral blood. Those patients without decay of viral load in plasma may have significant cryptic HIV-1 residual replication.
High-Frequency Phenotypic Reversion and Pathogenicity of an Acyclovir-Resistant Herpes Simplex Virus Mutant
Authors: Griffiths Anthony , Coen Donald M.
Published: January 2003

A double-guanine-insertion mutation within a run of guanines in the herpes simplex virus gene encoding thymidine kinase (TK) was previously found in an acyclovir-resistant clinical isolate. This mutation was engineered into strain KOS, and stocks were generated from single plaques. Plaque autoradiography revealed that most plaques in such stocks exhibited low levels of TK activity, while ∼3% of plaques exhibited high levels of TK activity, indicating a remarkably high frequency of phenotypic reversion. This virus was able to reactivate from latency in mouse ganglia; a fraction of the reactivating virus expressed a high level of TK activity due to an additional G insertion, suggesting that the observed genetic instability contributed to pathogenicity.
Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers
Authors: Nagy E D , Molnár-Láng M , Linc G , Láng L
Published: January 2003

Five wheatbarley translocations in a wheat background were characterized through the combination of cytogenetic and molecular genetic approaches. The wheat chromosome segments involved in the translocations were identified using sequential GISH and two-colour FISH with the probes pSc119.2 and pAs1. The barley chromatin in these lines was identified using SSR markers. A total of 45 markers distributed over the total barley genome were selected from a recently published linkage map of barley and tested on the translocation lines. The following translocations were identified: 2DS.2DL1HS, 3HS.3BL, 6BS.6BL4HL, 4D5HS, and 7DL.7DS5HS. Wheatbarley disomic and ditelosomic addition lines for the chromosomes 3HS, 4H, 4HL, 5H, 5HL, and 6HS were used to determine the correct location of 21 markers and the position of the centromere. An intragenomic translocation breakpoint was detected on the short arm of the barley chromosome 5H with the help of SSR marker analysis. Physical mapping of the SSR markers on chromosomes 1H and 5H was carried out using the intragenomic and the interspecific translocation breakpoints, as well as the centromere, as physical landmarks.Key words: wheat-barley translocations, sequential GISH and FISH, SSR markers, physical mapping.
Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs
Authors: Murray J , Larsen J , Michaels T E , Schaafsma A , Vallejos C E , Pauls K P
Published: January 2003

A set of 79 previously mapped bean (Phaseolus vulgaris) genomic (Bng) clones were partially sequenced. BLAST database searches detected homologies between 59 of these clones and genes from a variety of plants, especially Arabidopsis thaliana. Some matches in the database to the Bng clones included a putative P-glycoprotein  ABC transporter from Arabidopsis, an early nodulin-binding protein (ENBP1) from Medicago truncatula, a lon-protease protein from spinach, a branched-chain amino-acid aminotransferase from Arabidopis, and a vacuolar sorting receptor (BP-80) from Pisum sativum. Additional matches were found for genes involved in isoprenoid biosynthesis, sulfur metabolism, proline biosynthesis, and floral development. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs). Polymorphisms were detected for six of the STSs.Key words: CAPS, SSR, molecular markers, gene identification.
Heterologous nuclear and chloroplast microsatellite amplification and variation in tea,Camellia sinensis
Authors: Kaundun Shiv Shankhar , Matsumoto Satoru
Published: January 2003

The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species. Key words: tea, Camellia sinensis, SSR, microsatellites, genetic diversity.
Mutations in wheat showing altered field resistance to yellow and brown rust
Authors: Boyd L A , Smith P H , Wilson A H , Minchin P N
Published: January 2003

Intensive screening of a small population of mutagenised wheat lines revealed a large number of lines with altered resistance to both yellow and brown rust. The parental cultivar Guardian has an intermediate level of adult plant resistance to this disease; mutants were therefore isolated that showed either enhanced resistance or enhanced susceptibility to yellow rust. Seven lines were identified that gave an altered yellow rust disease phenotype as adult plants under both field and greenhouse conditions. Simultaneous field testing for brown rust infection identified two of these lines as having increased resistance to brown rust.Key words: Disease resistance, mutants, wheat, yellow rust.
Genetic factors controllingwhitegene expression of the transposonAR4-24at a telomere inDrosophila melanogaster
Authors: Balasov M L
Published: January 2003

The position effect of the AR4-24 P[white, rosy] transposon was studied at cytological position 60F. Three copies of the transposon (within ~50-kb region) resulted in a spatially restricted pattern of white variegation. This pattern was modified by temperature and by removal of the Y chromosome, suggesting that it was due to classical heterochromatin-induced position effect variegation (PEV). In contrast with classical PEV, extra dose of the heterochromatin protein 1 (HP1) suppressed white variegation and one dose enhanced it. The effect of Pc-G, trx-G, and other PEV suppressors was also tested. It was found that E(Pc)1, TrlR85, and mutations of Su(z)2C relieve AR4-24- silencing and z1enhances it. To explain the results obtained with these modifiers, it is proposed that PEV and telomeric position effect can counteract each other at this particular cytological site.Key words: position effect variegation, heterochromatin protein 1, Drosophila melanogaster.
Geographic structure of genetic variation in the widespread woodland grassMilium effusumL. A comparison between two regions with contrasting history and geomorphology
Authors: Tyler Torbjörn
Published: January 2003

Allozyme variation in the forest grass Milium effusum L. was studied in 2123 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.Key words: Milium effusum, allozymes, geographic differentiation, population fragmentation, allelic richness.
An isoleucine to leucine mutation in acetyl-CoA carboxylase confers herbicide resistance in wild oat
Authors: Christoffers Michael J , Berg Michelle L , Messersmith Calvin G
Published: January 2003

Wild oat (Avena fatua L.) populations resistant to herbicides that inhibit acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) represent an increasingly important weed control problem. The objective of this study was to determine the ACCase mutation responsible for herbicide resistance in a well-studied wild oat biotype (UM1). A 2039-bp region encompassing the carboxybiotin and acetyl-CoA binding domains of multifunctional plastidic ACCase was analyzed. DNA sequences representing three plastidic ACCase gene loci were isolated from both the resistant UM1 and a herbicide-susceptible biotype, consistent with the hexaploid nature of wild oat. Only one nonsynonymous point mutation was found among the resistant wild oat sequences, inferring an isoleucine to leucine substitution. The position of this substitution corresponds to residue 1769 of wheat (Triticum aestivum L.) plastidic ACCase (GenBank accession No. AF029895). Analysis of an F2 population derived from a cross between a herbicide-resistant and a susceptible biotype confirmed co-segregation of herbicide resistance with the mutated ACCase. We conclude that the isoleucine to leucine mutation is responsible for herbicide resistance in UM1 wild oat based on a comparison of the substitution site across species and ACCase types. While isoleucine is conserved among plastidic ACCases of herbicide-susceptible grasses, leucine is found in plastidic and cytosolic forms of multifunctional herbicide-resistant ACCase.Key words: acetyl-CoA carboxylase, herbicide resistance, mutation, wild oat.
Polytene chromosome maps of the melon flyBactrocera cucurbitae(Diptera: Tephritidae)
Authors: Shahjahan Reza M , Yesmin Farzana
Published: January 2003

Standard photographic maps of the polytene chromosomes are presented for the melon fly Bactrocera cucurbitae, a serious pest of fleshy fruits and vegetables. Five larval salivary gland polytene chromosomes (10 polytene arms) were isolated, and their characteristic features and landmarks have been recognized. Banding patterns of each of the polytene arms are presented, where variation in band intensity and puffs appear to reflect fundamental differences in chromosomes. The whole polytene genome has been typically mapped by dividing it into 100 sections and the subsections were lettered. The mitotic chromosomes of larval brain ganglia are also examined, five pairs of autosomes and an XX/XY sex chromosome pair. In addition, a heterochromatic mass corresponding to the sex chromosomes are observed in the polytene nuclei of salivary gland tissue. This investigation showed that B. cucurbitae has excellent cytological material for polytene chromosome analysis and proved to be very useful for obtaining more detailed genetic information on the pest's natural populations.Key words: Bactrocera cucurbitae, salivary gland, banding patterns, polytene maps.
Rapid microsatellite analysis using discontinuous polyacrylamide gel electrophoresis
Authors: White E , Sahota R , Edes S
Published: January 2003

A method for screening large numbers of samples for microsatellites using discontinuous, non-denaturing polyacrylamide gels and rapid fluorescent gel staining is described. Disc electrophoresis on slab gels provides high-resolution of PCR products. It is useful for collecting population data once microsatellite loci have been characterized.Key words: microsatellite, discontinuous polyacrylamide gel electrophoresis, non-denaturing
Two different genes encoding acetylcholinesterase existing in cotton aphid (Aphis gossypii)
Authors: Li Fei , Han Zhao-Jun
Published: January 2003

Two acetylcholinesterase (AChE) genes, Ace1 and Ace2, have been cloned from cotton aphid, Aphis gossypii Glover, using the rapid amplification of cDNA ends (RACE) technique. To the best of our knowledge, this should be the first direct molecular evidence that multiple AChE genes exist in insects. The Ace1 gene was successfully amplified along its full length of 2371 bp. The open reading frame is 2031 bp long and encodes 676 amino acids (GenBank accession No. AF502082). The Ace2 gene was amplified as a mega-fragment of 2130 bp lacking part of 5'-end untranslated region (UTR). The open reading frame is 1992 bp long and ecodes a protein of 664 amino acids (GenBank accession No. AF502081). Both genes have the conserved amino acids and features shared by the AChE family, but share only 35% identity in amino acid sequence. The Ace1 gene is highly homologous to the AChE gene of Schizaphis graminum (AF321574) with 95% identity, and Ace2 to that of Myzus persicae (AF287291) with 92% identity. Phylogenetic analysis showed that the two cloned AChEs of A. gossypii are different in evolution. The phylogenetic tree generated by the PHYLIP program package inferred that AChE2 of A. gossypii is a more ancestral form of AChE. Homology modeling of structures using Torpedo californica (2ACE_) andDrosophila melanogaster (1Q09:A) native acetylcholinesterase structure as main template indicated that the two AChEs ofAphis gossypii might have different three-dimensional structures. Alternative splicing of Ace1 near the 5'-end resulting in two proteins differing by the presence or absence of a fragment of four amino acids is also reported.Key words: Aphis gossypii Glover, acetylcholinesterase, gene clone, homology modeling, alternative splicing, phylogenetic analysis.
Ribosomal DNA variation in the grasshopper,Dichroplus elongatus
Authors: Clemente M , Remis M I , Vilardi J C
Published: January 2003

We report an RFLP analysis of ribosomal DNA variation in natural populations of the grasshopper, Dichroplus elongatus, previously analyzed for mitochondrial DNA variation. DNA samples were digested with five restriction enzymes, BamHI, EcoRI, HindIII, PstI, andXbaI.BamHI was the only enzyme that showed no variation. The remaining enzymes showed fragment size variation at both intra- and interpopulation levels. Stepwise regression analysis revealed that the average number of length variants per individual is significantly associated with altitude. Moreover, the same analysis indicated that the frequency of some restriction variants exhibits a significant regression on both geographic and climatic variables. The intra- and interpopulation variability of rDNA was analysed by Lynch's and Hedrick's similarity indices using presence or absence of a fragment and band intensities, respectively. The corresponding neighbour-joining (N-J) trees based on Lynch's and Hedrick's genetic distances resulted in similar topologies. However, these trees were not in agreement with the N-J dendrogram obtained from mtDNA data previously reported by Clemente et al. (2000). The disagreement between mtDNA and rDNA phenograms along with the observed correlation between rDNA variability and geographical and climatic variables suggest some form of selection, besides genetic drift and migration, is involved in the pattern of rDNA variation.Key words: Dichroplus elongatus, ribosomal DNA, RFLP, environmental variables.
Chloroplast microsatellite polymorphisms inVitisspecies
Authors: Arroyo-García Rosa , Lefort Francois , Andrés María Teresa de , Ibáñez Javier , Borrego Joaquín , Jouve Nicolas , Cabello Felix , Martínez-Zapater José Miguel
Published: January 2003

The use of consensus chloroplast microsatellites primers for dicotyledonous chloroplast genomes revealed the existence of intra and interspecific length variation within the genus Vitis. Three chloroplast microsatellite loci were found to be polymorphic in samples of Vitis vinifera, Vitis berlandieri, Vitis riparia, and Vitis rupestris out of a total of 10 consensus primer pairs tested. These polymorphisms were always due to a variable number of mononucleotide residues within A and (or) T stretches in the amplified regions. Chloroplast microsatellite polymorphisms were used to demonstrate the maternal inheritance of chloroplast in V. vinifera and to characterise the chloroplast haplotypes present in wine grape cultivars of this species grown in Spain and Greece. The different distribution of haplotype frequencies in the two ends of the Mediterranean growth area suggests the existence of independent domestication events for grapevine.Key words: Vitis, grapevine, chloroplast microsatellites, chloroplast haplotypes, chloroplast inheritance, grapevine domestication.
Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences
Authors: Nishikawa Tomotaro , Salomon Björn , Komatsuda Takao , von Bothmer Roland , Kadowaki Koh-ichi
Published: January 2003

The genus Hordeum consists of three cytotypes (2x, 4x, and 6x). Its reproductive isolation has been incomplete between closely related species and hence the genetic relationship is reticulate and complex. We used 32 taxa of Hordeum and three chloroplast DNA sequences, matK, atpBrbcL, and trnLtrnF, in the current study. Molecular phylogenetic analysis based on sequence data of the three chloroplast DNA regions clearly demonstrated genetic relationships among taxa and origin of polypoids. The formation of H. secalinum likely involved hybridization between Hordeum marinum subsp. marinum and a Eurasian diploid possessing the H genome. The formation of hexaploid Hordeum brachyantherum involved hybridization between tetraploid H. brachyantherum and diploid H. marinum subsp. gussoneanum. The formation of three tetraploids, H. brachyantherum, Hordeum jubatum, and Hordeum guatemalense, probably involved hybridization between H. brachyantherum subsp. californicum and an altered H genome diploid. The formation of Hordeum arizonicum involved the two taxa Hordeum pusillum and H. jubatum.Key words: chloroplast DNA, phylogeny, Hordeum, barley.
An original mutation in soybean (Glycine max(L.) Merrill) involving degeneration of the generative cell and causing male sterility
Authors: Bione Nilton Cesar Pires , Pagliarini Maria Suely , Almeida Leones Alves de
Published: January 2003

A spontaneous mutation causing male sterility has been detected in line BR97-17739 from the soybean breeding program conducted by Embrapa  National Soybean Research Center. Meiotic division and male gametophyte development were analyzed in 10 male-sterile, female-fertile plants. Meiotic process had few irregularities related to chromosome segregation and affected about 2% of tetrads. Despite the high frequency of normal microspores, pollen sterility was total. After callose dissolution, microspores were released into the anther loculle and interphase nucleus was displaced from the center to one side of the cell. Displacement continued throughout normal microspore mitosis (PMI). After telophase, the hemispherical phragmoplast marked the place of cytokinesis. A typical generative cell, adjacent to the plasma membrane, and the vegetative one, containing most of the cytoplasm, were formed. In spite of the well-formed generative cell, pollen mitosis (PMII) failed to occur. The generative cell degenerated and was completely destroyed. The 3:1 segregation for male sterility in this line and its progenies indicate that a single recessive gene controls mutation.Key words: soybean, microsporogenesis, microgametogenesis, mutation, male sterility, generative cell.
Length and sequence heterogeneity in 5S rDNA ofPopulus deltoides
Authors: Negi Madan S , Rajagopal Jyothi , Chauhan Neeti , Cronn Richard , Lakshmikumaran Malathi
Published: January 2003

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (π) estimates that are less than 0.15% of those obtained for class 2 spacers (π = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.Key words: 5S rDNA, Populus, repetitive DNA, microsatellite, sequence heterogeneity.
Development of an AFLP-based linkage map and localization of QTLs for seed fatty acid content in condiment mustard (Brassica juncea)
Authors: Lionneton E , Ravera S , Sanchez L , Aubert G , Delourme R , Ochatt S
Published: January 2003

A genetic linkage map of Brassica juncea based on AFLP and RAPD markers was constructed using 131 F1-derived doubled-haploid (DH) plants from a cross between two mustard lines. The map included 273 markers (264 AFLP, 9 RAPD) arranged on 18 linkage groups, and covered a total genetic distance of 1641 cM; 18.3% of the AFLP markers showed a segregation distortion (P < 0.01). The markers with biased segregation were clustered on seven linkage groups. QTLs for oil contents, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), eicosenoic acid (20:1), and erucic acid (22:1), were mapped on the AFLP linkage map. Correlation studies among fatty acids in the DH population and the localization of QTLs involved in their control indicated that a major gene located on linkage group (LG) 2 controlled the elongation step of erucic acid.Key words: Brassica juncea, doubled haploid, AFLP genetic linkage map, fatty acids, QTL.
LOW-TEMPERATURE SERIES EXPANSIONS FOR SQUARE-LATTICE ISING MODEL WITH FIRST AND SECOND NEIGHBOUR INTERACTIONS
Authors: KAO YEE MOU , CHEN MALL , LIN KEH YING
Published: January 2003

We have calculated the low-temperature series expansions of the spontaneous magnetization and the zero-field susceptibility of the square-lattice ferromagnetic Ising model with first-neighbour interaction J1 and second-neighbour interaction J2 to the 30th and 26th order respectively by computer. Our results extend the previous calculations by Lee and Lin to six more orders. We use the Padé approximants to estimate the critical exponents and the critical temperature for different ratios of R = J2/J1. The estimated critical temperature as a function of R agrees with the estimation by Oitmaa from high-temperature series expansions.
CHARGE-ORDERED CE-TYPE AND A-TYPE STATES IN HALF-DOPED MANGANITES
Authors: SHU ZHENGHUANG , DONG J. M. , XING D. Y.
Published: January 2003

According to the characteristics of the magnetic structures of the CE phase and the A phase for half-doped manganites, a two-dimensional model based on double exchange via degenerate eg orbitals as well as the Coulomb interaction and the superexchange interaction has been proposed to discuss the two phases on an equal footing. It is explained why the CE phase is usually easier to be realized for many half-doped manganites, while the A phase occasionally occurs. Moreover, our numerical calculations show that the two phases at x = 0.5 are not spin-canted, which is in good agreement with experimental observations.
PHASE STABILITY OF ALKALI METALS UNDER PRESSURE: PERTURBATIVE AND NON-PERTURBATIVE TREATMENTS
Authors: MUJIBUR RAHMAN S. M. , ALI ISSAM , BHUIYAN G. M. , ZIAUDDIN AHMED A. Z.
Published: January 2003

We have investigated the structural phase stability of crystalline alkali metals under external pressure in terms of their pair potentials, structural free energies, thermomechanical properties viz. the elastic constants and the density-of-sates [DOS] at the Fermi level. The pair potentials are calculated using amenable model potentials, the structural energies and the elastic constants are calculated in terms of the effective pair potentials and the DOS for the systems are calculated by employing the augmented-spherical-waves [ASW] method. The matching between the minima of the pair potentials and the relative positions of the first few lattice vectors of the relevant structures gives a qualitative impression on the relative stability of a crystal phase. Similarly the appearance of a minimum in the energy difference curves between relevant crystal structures manifests a relatively stable structure. On the contrary, a maximum in the bulk modulus indicates a stable structure; these maximum-minimum criteria are controlled by the profile of the effective pair interactions of the constituent atoms. If the relevant lattice vectors are populated in and around the minimum of the respective pair potential the corresponding bulk modulus shows a maximum trend. The same situation gives rise to a minimum in the free energy. Both of these tendencies favor a particular crystalline phase against other relevant structures. Similarly a maximum in the DOS curves gives rise to a minimum in the energy curve manifesting a stable structure. The population of electronic states plays the responsible role here. To treat the two entirely different methods, namely, the perturbative pseudopotential theory and the non-perturbative ASW method on the same footing, we have used the same metallic density in both the methods for the respective element. The calculated results show a qualitative trend in support of the observed structures for these elemental systems.
DIFFUSION IN PERIODIC INTERACTING SYSTEMS: QUASI-ELASTIC SPECTRUM IN BISTABLE POTENTIALS
Authors: MAZROUI M. , JAOUAD A. , EL ARROUM L. , BOUGHALEB Y. , FERRANDO R.
Published: January 2003

Mechanism of ion transport in periodic interacting systems is investigated by employing the Fokker–Planck approach. This is done through an investigation of the quasielastic peak in the dynamic structure factor S(q, ω). Its half width at half maximum (hwhm) exhibits an oscillatory behavior as a function of the scattering wave-vectors q, reflecting the role of correlations among diffusing particles. All calculations are performed at low temperature and at high friction limit.
KOLMOGOROV CONSTANT IN LARGE SPACE DIMENSIONS
Authors: NANDY MALAY K.
Published: January 2003

A large d (space dimension) expansion together with the ∊-expansion is implemented to calculate the Kolmogorov constant from the energy equation of Kraichnan's direct-interaction approximation using the Heisenberg's eddy-viscosity approximation and Kraichnan's distant-interaction algorithm. The Kolmogorov constant C is found to be C = C0 d1/3 in the leading order of a 1/d expansion. This is consistent with Fournier, Frisch, and Rose. The constant C0 evaluated in the above scheme, is found to be C0 = (16/27)1/3.
HIGH-TEMPERATURE SUSCEPTIBILITY SERIES FOR SQUARE-LATTICE ISING MODEL WITH FIRST AND SECOND NEIGHBOUR INTERACTIONS
Authors: LIN KEH YING , CHEN MALL
Published: January 2003

We have calculated the high-temperature series expansion of the zero-field susceptibility of the square-lattice Ising model with first and second neighbour interactions to the 20th order by computer. Our results extend the previous calculation by Hsiao and Lin to two more orders. We use the Padé approximants to estimate the critical exponent γ and the critical temperature. Our result 1.747 < γ < 1.753 supports the universality conjecture that all two-dimensional Ising models have the same critical exponent γ = 1.75.
TRIPARTITE ENTANGLED STATE REPRESENTATION AND ITS APPLICATION IN QUANTUM TELEPORTATION
Authors: FAN HONGYI , JIANG NIANQUAN , LU HAILIANG
Published: January 2003

We set up a tripartite entangled state representation |p, χ2, χ3> in three-mode Fock space which is composed of the common eigenvectors of three particles' relative coordinates X1 - X2 and X1 - X3 as well as the total momentum P1 + P2 + P3. The Schmidt decomposition of |p, χ2, χ3 > is made and its application in quantum teleporting a two-particle entangled state or a two-mode squeezed state is analyzed.
LANDAU GHOSTS AND ANTI-GHOSTS IN CONDENSED MATTER AND HIGH DENSITY HADRONIC MATTER
Authors: SIVASUBRAMANIAN S. , WIDOM A. , SRIVASTAVA Y. N.
Published: January 2003

It is observed that the "ghost" (originally discovered by Landau in quantum electro-dynamics) and its counterparts in other theories are indeed ubiquitous as they occur in a one-loop approximation to any conventional (unbroken) gauge theory. The mechanism is first exposed in its generality via the Dyson equation and a simple but explicit example in condensed matter is provided through the static Clausius–Mossotti equation and its dynamic counterpart, the Lorenz–Lorentz equation. The physical phase transition phenomenon associated with it is found to be super-radiance. We verify quantitatively that water (and many other polar liquids) are indeed super-radiant at room temperature. In quantum chromo-dynamics on the other hand, we encounter, thanks to asymptotic freedom, an "anti-ghost" which is closely associated with color confinement. Thus, in QCD, free quarks and glue exist in a super-radiant phase and hadronic matter exists in the normal one.
POSSIBILISTIC ENTROPIES AND THE COMPRESSION OF POSSIBILISTIC DATA
Authors: SGARRO ANDREA , DINU LIVIU PETRIŞOR
Published: January 2003

We re-take the possibilistic model for information sources recently put forward by the first author, as opposed to the standard probabilistic models of information theory. Based on an interpretation of possibilistic source coding inspired by utility functions, we define a notion of possibilistic entropy for a suitable class of interactive possibilistic sources, and compare it with the possibilistic entropy of stationary non-interactive sources. Both entropies have a coding-theoretic nature, being obtained as limit values for the rates of optimal compression codes. We list properties of the two entropies, which might support their use as measures of "possibilistic ignorance".
FACILITY LOCATION SELECTION USING FUZZY TOPSIS UNDER GROUP DECISIONS
Authors: CHU TA-CHUNG
Published: January 2003

This work presents a fuzzy TOPSIS model under group decisions for solving the facility location selection problem, where the ratings of various alternative locations under different subjective attributes and the importance weights of all attributes are assessed in linguistic values represented by fuzzy numbers. The objective attributed are transformed into dimensionless indices to ensure compatibility with the linguistic ratings of the subjective attributes. Furthermore, the membership function of the aggregation of the ratings and weights for each alternative location versus each attribute can be developed by interval arithmetic and α-cuts of fuzzy numbers. The ranking method of the mean of the integral values is applied to help derive the ideal and negative-ideal fuzzy solutions to complete the proposed fuzzy TOPSIS model. Finally, a numerical example demonstrates the computational process of the proposed model.