bluuebunny/crossref_metadata_2025 huggingface dataset:
Histologic evaluation of demineralized freeze‐dried bone allografts in barrier membrane covered periodontal fenestration wounds and ectopic sites in dogs
Authors: Klepp Morten , Hinrichs James E. , Eastlund Ted , Schaffer Erwin M.
Published: June 2004

Background/Aim: The aim of this study was to investigate healing responses to demineralized freeze‐dried bone powder allografts in standardized periodontal fenestration defects, compared with subcutaneous wounds in a dog model.

Methods: Circular periodontal fenestration defects were created buccally at all four canines in 14 mongrel dogs. Each site received one of the following underneath a barrier membrane: (a) ethylene oxide (EO)‐sterilized demineralized freeze‐dried bone allografts (DFDBA), (b) heat‐treated DFDBA, (c) non‐sterilized DFDBA and (d) ungrafted control. Twelve of the 14 dogs had three subcutaneous chest wall pouches created and one of the three DFDBA materials placed in each. The animals were necropsied at 4 weeks. Histologic sections were prepared through the center of the fenestration sites in an apico‐coronal direction. Quantitative analysis using computer‐assisted imaging technique was performed. Subcutaneous implants were evaluated histologically and quantified for associated inflammatory cell infiltrate.

Results: Fenestration defects healed by partial osseous fill and cementum regeneration with formation of a periodontal ligament. The graft particles generally appeared isolated from the site of osteogenesis and covered by cementum‐like substance. Graft particles incorporated into newly formed bone at a distance from the root surface was the exception. No statistically significant differences in new bone formation were observed between treatment groups within animals, but significant inter‐animal variation was found (p<0.01). Quantities of retained graft particles were limited, and without cellular resorption. A bone augmentation effect was associated with the barrier in the majority of sites. No bone formation was evident at the subcutaneous sites where graft particles displayed distinctly modified surface zones and multinucleated giant cell resorption. Significantly more inflammatory infiltrate was associated with EO‐sterilized grafts compared with heat‐treated grafts (p=0.05).

Conclusion: Implantation of DFDBA neither enhanced osseous healing in periodontal fenestration defects, nor resulted in ectopic bone induction. DFDBA particles implanted in either periodontal fenestration or subcutaneous wounds evoked distinctly different healing responses.
Post‐transplant lymphoproliferative disorders presenting as gingival overgrowth in patients immunosuppressed with ciclosporin. A report of two cases
Authors: Rolland S.L. , Seymour R.A. , Wilkins B.S. , Parry G. , Thomason J.M.
Published: June 2004

Background:Post‐transplant lymphoproliferative disorder (PTLD) can occur in patients maintained on immunosuppressive therapy following transplantation. This paper describes two cases of PTLD occurring in gingival tissues, in patients receiving ciclosporin following cardiac transplantation.

Treatment:The lesions were localised to gingival tissues, mimicking ciclosporin‐induced gingival overgrowth. They were removed surgically and the ciclosporin dose reduced to help prevent recurrence.

Conclusion:The importance of histopathological examination of all tissue removed during routine gingivectomy procedures for ciclosporin‐induced gingival overgrowth is highlighted.
Evidence that hsp90 Is Involved in the Altered Interactions ofAcanthamoeba castellaniiVariants with Bacteria
Authors: Yan Ling , Cerny Ronald L. , Cirillo Jeffrey D.
Published: June 2004

There are many similarities between the interactions of environmental protozoa with pathogenic bacterial species and those observed in mammalian macrophages. Since single-celled protozoa predate mammalian hosts, it is likely that interactions in environmental biofilms have selected for many of the bacterial virulence mechanisms responsible for human disease. In order to better understand bacterial-phagocyte interactions, we developed a selection forAcanthamoeba castellaniivariants that are more resistant to killing by bacterial pathogens. We identified four amoebal clones that display decreased phagocytosis of bacteria but no difference in uptake of latex beads compared to wild-type amoebae. These amoebal variants display differences in cellular morphology, partial resistance to killing by bacteria, more bactericidal activity, and higher frequencies of lysosome fusion with the bacterial vacuole. Three proteins are present at lower levels in these variants than in wild-type amoebae, and matrix-assisted laser desorption ionization-time of flight mass spectrometry allowed identification of two of them as actin and hsp90. We found that specific inhibitors of hsp90 produce a similar phenotypic effect in macrophages. These data suggest that hsp90 plays a role in phagocytic and, possibly, bactericidal pathways that affect interactions of phagocytic cells with bacteria.
Novel Promoter Sequence Required for Manganese Regulation of Manganese Peroxidase Isozyme 1 Gene Expression in
Phanerochaete chrysosporium
Authors: Ma Biao , Mayfield Mary B. , Godfrey Bruce J. , Gold Michael H.
Published: June 2004

Manganese peroxidase (MnP) is a major, extracellular component of the lignin-degrading system produced by the wood-rotting basidiomycetous fungus
Phanerochaete chrysosporium
. The transcription of MnP-encoding genes (
mnp
s) in
P. chrysosporium
occurs as a secondary metabolic event, triggered by nutrient-nitrogen limitation. In addition,
mnp
expression occurs only under Mn
2+
supplementation. Using a reporter system based on the enhanced green fluorescent protein gene (
egfp
), we have characterized the
P. chrysosporium mnp1
promoter by examining the effects of deletion, replacement, and translocation mutations on
mnp1
promoter-directed
egfp
expression. The 1,528-bp
mnp1
promoter fragment drives
egfp
expression only under Mn
2+
-sufficient, nitrogen-limiting conditions, as required for endogenous MnP production. However, deletion of a 48-bp fragment, residing 521 bp upstream of the translation start codon in the
mnp1
promoter, or replacement of this fragment with an unrelated sequence resulted in
egfp
expression under nitrogen limitation, both in the absence and presence of exogenous Mn
2+
. Translocation of the 48-bp fragment to a site 120 bp downstream of its original location resulted in Mn
2+
-dependent
egfp
expression under conditions similar to those observed with the wild-type
mnp1
promoter. These results suggest that the 48-bp fragment contains at least one Mn
2+
-responsive
cis
element. Additional promoter-deletion experiments suggested that the Mn
2+
element(s) is located within the 33-bp sequence at the 3′ end of the 48-bp fragment. This is the first promoter sequence containing a Mn
2+
-responsive element(s) to be characterized in any eukaryotic organism.
The Signal from the Initiation of Meiotic Recombination to the First Division of Meiosis
Authors: Malone Robert E. , Haring Stuart J. , Foreman Kelley E. , Pansegrau Morgan L. , Smith Sonja M. , Houdek Demelza R. , Carpp Lindsay , Shah Bijal , Lee KariAn E.
Published: June 2004

Two of the unique events that occur in meiosis are high levels of genetic recombination and the reductional division. Our previous work demonstrated that the
REC102
,
REC104
,
REC114
, and
RAD50
genes, required to initiate meiotic recombination in
Saccharomyces cerevisiae
, are needed for the proper timing of the first meiotic (MI) division. If these genes are absent, the MI division actually begins at an earlier time. This paper demonstrates that the meiotic recombination genes
MER2/REC107
,
SPO11
, and
MRE2
and the synaptonemal complex genes
HOP1
and
RED1
are also required for the normal delay of the MI division. A
rec103/ski8
mutant starts the MI division at the same time as in wild-type cells. Our data indicate no obvious correlation between the timing of premeiotic S phase and the timing of the first division in Rec
−
mutants. Cells with
rec102
or
rec104
mutations form MI spindles before wild-type cells, suggesting that the initiation signal acts prior to spindle formation. Neither
RAD9
nor
RAD24
is needed to transduce the signal, which delays the first division. The timing of the MI division in
RAD24
mutants indicates that the pachytene checkpoint is not active in Rec
+
cells and suggests that the coordination between recombination and the MI division in wild-type cells may occur primarily due to the initiation signal. Finally, at least one of the targets of the recombination initiation signal is the
NDT80
gene, a transcriptional regulator of middle meiotic gene expression required for the first division.
The Kip3-Like Kinesin KipB Moves along Microtubules and Determines Spindle Position during Synchronized Mitoses in
Aspergillus nidulans
Hyphae
Authors: Rischitor Patricia E. , Konzack Sven , Fischer Reinhard
Published: June 2004

Kinesins are motor proteins which are classified into 11 different families. We identified 11 kinesin-like proteins in the genome of the filamentous fungus
Aspergillus nidulans
. Relatedness analyses based on the motor domains grouped them into nine families. In this paper, we characterize KipB as a member of the Kip3 family of microtubule depolymerases. The closest homologues of KipB are
Saccharomyces cerevisiae
Kip3 and
Schizosaccharomyces pombe
Klp5 and Klp6, but sequence similarities outside the motor domain are very low. A disruption of
kipB
demonstrated that it is not essential for vegetative growth.
kipB
mutant strains were resistant to high concentrations of the microtubule-destabilizing drug benomyl, suggesting that KipB destabilizes microtubules.
kipB
mutations caused a failure of spindle positioning in the cell, a delay in mitotic progression, an increased number of bent mitotic spindles, and a decrease in the depolymerization of cytoplasmic microtubules during interphase and mitosis. Meiosis and ascospore formation were not affected. Disruption of the
kipB
gene was synthetically lethal in combination with the temperature-sensitive mitotic kinesin motor mutation
bimC4
, suggesting an important but redundant role of KipB in mitosis. KipB localized to cytoplasmic, astral, and mitotic microtubules in a discontinuous pattern, and spots of green fluorescent protein moved along microtubules toward the plus ends.
Multiple Functionally Redundant Signals Mediate Targeting to the Apicoplast in the Apicomplexan Parasite
Toxoplasma gondii
Authors: Harb Omar S. , Chatterjee Bithi , Fraunholz Martin J. , Crawford Michael J. , Nishi Manami , Roos David S.
Published: June 2004

Most species of the protozoan phylum Apicomplexa harbor an endosymbiotic organelle—the apicoplast—acquired when an ancestral parasite engulfed a eukaryotic plastid-containing alga. Several hundred proteins are encoded in the parasite nucleus and are posttranslationally targeted to the apicoplast by a distinctive bipartite signal. The N-terminal 20 to 30 amino acids of nucleus-encoded apicoplast targeted proteins function as a classical signal sequence, mediating entry into the secretory pathway. Cleavage of the signal sequence exposes a transit peptide of variable length (50 to 200 amino acids) that is required for directing proteins to the apicoplast. Although these peptides are enriched in basic amino acids, their structural and functional characteristics are not well understood, which hampers the identification of apicoplast proteins that may constitute novel chemotherapeutic targets. To identify functional domains for a model apicoplast transit peptide, we generated more than 80 deletions and mutations throughout the transit peptide of
Toxoplasma gondii
ferredoxin NADP
+
reductase (TgFNR) and examined the ability of these altered transit peptides to mediate proper targeting and processing of a fluorescent protein reporter. These studies revealed the presence of numerous functional domains. Processing can take place at multiple sites in the protein sequence and may occur outside of the apicoplast lumen. The TgFNR transit peptide contains at least two independent and functionally redundant targeting signals, each of which contains a subdomain that is required for release from or proper sorting within the endoplasmic reticulum. Certain deletion constructs traffic to multiple locations, including the apicoplast periphery, the rhoptries, and the parasitophorous vacuole, suggesting a common thread for targeting to these specialized compartments.
Lipid Raft Polarization Contributes to Hyphal Growth in
Candida albicans
Authors: Martin Stephen W. , Konopka James B.
Published: June 2004

The polarization of sterol- and sphingolipid-enriched domains (lipid rafts) has been linked to morphogenesis and cell movement in diverse cell types. In the yeast
Saccharomyces cerevisiae
, a dramatic polarization of sterol-rich domains to the shmoo tip was observed in pheromone-induced cells (M. Bagnat and K. Simons, Proc. Natl. Acad. Sci. USA
99:
14183-14188, 2002). We therefore examined whether plasma membrane lipid polarization contributes to the ability of the fungal pathogen
Candida albicans
to grow in a highly polarized manner to form hyphae. Interestingly, staining with filipin revealed that membrane sterols were highly polarized to the leading edge of growth during all stages of hyphal growth. Budding and pseudohyphal cells did not display polarized staining. Filipin staining was also enriched at septation sites in hyphae, where colocalization with septin proteins was observed, suggesting a role for the septins in forming a boundary domain. Actin appeared to play a role in sterol polarization and hyphal morphogenesis in that both were disrupted by low concentrations of latrunculin A that did not prevent budding. Furthermore, blocking either sphingolipid biosynthesis with myriocin or sterol biosynthesis with ketoconazole resulted in a loss of ergosterol polarization and caused abnormal hyphal morphogenesis, suggesting that lipid rafts are involved. Since hyphal growth is required for the full virulence of
C. albicans
, these results suggest that membrane polarization may contribute to the pathogenesis of this organism.
Hph1p and Hph2p, Novel Components of Calcineurin-Mediated Stress Responses in
Saccharomyces cerevisiae
Authors: Heath Victoria L , Shaw Sidney L. , Roy Sharmili , Cyert Martha S.
Published: June 2004

Calcineurin is a Ca
2+
- and calmodulin-dependent protein phosphatase that plays a key role in animal and yeast physiology. In the yeast
Saccharomyces cerevisiae
, calcineurin is required for survival during several environmental stresses, including high concentrations of Na
+
, Li
+
, and Mn
2+
ions and alkaline pH. One role of calcineurin under these conditions is to activate gene expression through its regulation of the Crz1p transcription factor. We have identified Hph1p as a novel substrate of calcineurin.
HPH1
(
YOR324C
) and its homolog
HPH2
(
YAL028W
) encode tail-anchored integral membrane proteins that interact with each other in the yeast two-hybrid assay and colocalize to the endoplasmic reticulum. Hph1p and Hph2p serve redundant roles in promoting growth under conditions of high salinity, alkaline pH, and cell wall stress. Calcineurin modifies the distribution of Hph1p within the endoplasmic reticulum and is required for full Hph1p activity in vivo. Furthermore, calcineurin directly dephosphorylates Hph1p and interacts with it through a sequence motif in Hph1p, PVIAVN. This motif is related to calcineurin docking sites in other substrates, such as NFAT and Crz1p, and is required for regulation of Hph1p by calcineurin. In contrast, Hph2p neither interacts with nor is dephosphorylated by calcineurin. Ca
2+
-induced Crz1p-mediated transcription is unaffected in
hph1
Δ
hph2
Δ mutants, and genetic analyses indicate that
HPH1/HPH2
and
CRZ1
act in distinct pathways downstream of calcineurin. Thus, Hph1p and Hph2p are components of a novel Ca
2+
- and calcineurin-regulated response required to promote growth under conditions of high Na
+
, alkaline pH, and cell wall stress.
Functional Unit of the RNA Polymerase II C-Terminal Domain Lies within Heptapeptide Pairs
Authors: Stiller John W. , Cook Matthew S.
Published: June 2004

Unlike all other RNA polymerases, the largest subunit (RPB1) of eukaryotic DNA-dependent RNA polymerase II (RNAP II) has a C-terminal domain (CTD) comprising tandemly repeated heptapeptides with the consensus sequence Y-S-P-T-S-P-S. The tandem structure, heptad consensus, and most key functions of the CTD are conserved between yeast and mammals. In fact, all metazoans, fungi, and green plants examined to date, as well as the nearest protistan relatives of these multicellular groups, contain a tandemly repeated CTD. In contrast, the RNAP II largest subunits from many other eukaryotic organisms have a highly degenerate C terminus or show no semblance of the CTD whatsoever. The reasons for intense stabilizing selection on CTD structure in certain eukaryotes, and its apparent absence in others, are unknown. Here we demonstrate, through in vivo genetic complementation, that the essential functional unit of the yeast CTD is contained within pairs of heptapeptides. Insertion of a single alanine residue between diheptads has little phenotypic effect, while increasing the distance between diheptads produces a mostly quantitative effect on yeast cell growth. We further explore structural constraints on the CTD within an evolutionary context and propose selective mechanisms that could maintain a global tandem structure across hundreds of millions of years of eukaryotic evolution.
Hemoglobin Regulates Expression of an Activator of Mating-Type Locus α Genes in
Candida albicans
Authors: Pendrak Michael L. , Yan S. Steve , Roberts David D.
Published: June 2004

Phenotypic switching from the white to the opaque phase is a necessary step for mating in the pathogenic fungus
Candida albicans
. Suppressing switching during vascular dissemination of the organism may be advantageous, because opaque cells are more susceptible to host defenses. A repressor of white-opaque switching,
HBR1
(hemoglobin response gene 1), was identified based on its specific induction following growth in the presence of exogenous hemoglobin. Deletion of a single
HBR1
allele allowed opaque phase switching and mating competence, accompanied by a lack of detectable
MTL
α1 and α2 gene expression and enhanced
MTL
a
1
gene expression. Conversely, overexpression of Hbr1p or exposure to hemoglobin increased
MTL
α
gene expression. The
a
1/α2 repressed target gene
CAG1
was derepressed in the same mutant in a hemoglobin-sensitive manner. Regulation of
CAG1
by hemoglobin required an intact
MTL
a
1
gene. Several additional Mtlp targets were perturbed in
HBR1
mutants in a manner consistent with commitment to an
a
mating phenotype, including
YEL007w
,
MF
α,
HST6
, and
RAM2.
Therefore, Hbr1 is part of a host factor-regulated signaling pathway that controls white-opaque switching and mating in the absence of allelic deletion at the
MTL
locus.
Overexpression of Sphingosine-1-Phosphate Lyase or Inhibition of Sphingosine Kinase in
Dictyostelium discoideum
Results in a Selective Increase in Sensitivity to Platinum-Based Chemotherapy Drugs
Authors: Min Junxia , Stegner Andrew L. , Alexander Hannah , Alexander Stephen
Published: June 2004

The efficacy of the chemotherapy drug cisplatin is often limited due to resistance of the tumors to the drug, and increasing the potency of cisplatin without increasing its concentration could prove beneficial. A previously characterized
Dictyostelium discoideum
mutant with increased resistance to cisplatin was defective in the gene encoding sphingosine-1-phosphate (S-1-P) lyase, which catalyzes the breakdown of S-1-P, an important regulatory molecule in cell function and development and in the regulation of cell fate. We hypothesized that the increased resistance to cisplatin was due to an elevation of S-1-P and predicted that lowering levels of S-1-P should increase sensitivity to the drug. We generated three strains that stably overexpress different levels of the S-1-P lyase. The overexpressor strains have reduced growth rate and, confirming the hypothesis, showed an expression-dependent increase in sensitivity to cisplatin. Consistently, treating the cells with
d
-erythro-
N
,
N
,-dimethylsphingosine, a known inhibitor of sphingosine kinase, increased the sensitivity of mutant and parent cells to cisplatin, while addition of exogenous S-1-P or 8-Br-cyclic AMP made the cells more resistant to cisplatin. The increased sensitivity of the overexpressors to cisplatin was also observed with the cisplatin analog carboplatin. In contrast, the response to doxorubicin, 5-flurouracil, or etoposide was unaffected, indicating that the involvement of the sphingolipid metabolic pathway in modulating the response to cisplatin is not part of a global genotoxic stress response. The augmented sensitivity to cisplatin appears to be the result of an intracellular signaling function of S-1-P, because
D. discoideum
does not appear to have endothelial differentiation growth (EDG/S1P) receptors. Overall, the results show that modulation of the sphingolipid pathway at multiple points can result in increased sensitivity to cisplatin and has the potential for increasing the clinical usefulness of this important drug.
The Circadian RNA-Binding Protein CHLAMY 1 Represents a Novel Type Heteromer of RNA Recognition Motif and Lysine Homology Domain-Containing Subunits
Authors: Zhao Bin , Schneid Claudia , Iliev Dobromir , Schmidt Eva-Maria , Wagner Volker , Wollnik Franziska , Mittag Maria
Published: June 2004

The RNA-binding protein CHLAMY 1 from
Chlamydomonas reinhardtii
binds specifically to UG
(≥7)
repeat sequences situated in the 3′ untranslated regions of several mRNAs. Its binding activity is controlled by the circadian clock. The biochemical purification and characterization of CHLAMY 1 revealed a novel type of RNA-binding protein. It includes two different subunits (named C1 and C3), whose interaction appears necessary for RNA binding. One of them (C3) belongs to the proteins of the CELF (CUG-BP-ETR-3-like factors) family and thus bears three RNA recognition motif domains. The other is composed of three lysine homology domains and a protein-protein interaction domain (WW). The subunits C1 and C3 have theoretical molecular masses of 45 and 52 kDa, respectively, and are present in nearly equal amounts during the circadian cycle. At the beginning of the subjective night, both can be found in protein complexes of 100 to 160 kDa. However, during subjective day when binding activity of CHLAMY 1 is low, the C1 subunit in addition is present in a high-molecular-mass protein complex of more than 680 kDa. These data indicate posttranslational control of the circadian binding activity of CHLAMY 1. Notably, the C3 subunit shows significant homology to the rat CUG-binding protein 2. Anti-C3 antibodies can recognize the rat homologue, which can also be found in a protein complex in this vertebrate.
Analysis ofDrosophila proboscipediamutant alleles
Authors: Tayyab I , Hallahan H M , Percival-Smith A
Published: June 2004

Proboscipedia (PB) is a HOX protein required for adult maxillary palp and proboscis formation. To identify domains of PB important for function, 21 pb point mutant alleles were sequenced. Twelve pb alleles had DNA sequence changes that encode an altered PB protein product. The DNA sequence changes of these 12 alleles fell into 2 categories: missense alleles that effect the PB homeodomain (HD), and nonsense or frameshift alleles that result in C-terminal truncations of the PB protein. The phenotypic analysis of the pb homeobox missense alleles suggests that the PB HD is required for maxillary palp and proboscis development and pb – Sex combs reduced (Scr) genetic interaction. The phenotypic analysis of the pb nonsense or frameshift alleles suggests that the C-terminus is an important region required for maxillary palp and proboscis development and pb–Scr genetic interaction. PB and SCR do not interact directly with one another in a co-immunoprecipitation assay and in a yeast two-hybrid analysis, which suggests the pb–Scr genetic interaction is not mediated by a direct interaction between PB and SCR.Key words: proboscipedia, Sex combs reduced, Hox genes, mutant analysis, Drosophila body plan, appendage development.
Stress-induced expression in wheat of the Arabidopsis thaliana DREB1A gene delays water stress symptoms under greenhouse conditions
Authors: Pellegrineschi Alessandro , Reynolds Matthew , Pacheco Mario , Brito Rosa Maria , Almeraya Rosaura , Yamaguchi-Shinozaki Kazuko , Hoisington David
Published: June 2004

One of the major environmental factors limiting plant productivity is lack of water. This is especially true for the major cereals maize, rice, and wheat, which demonstrate a range of susceptibility to moisture deficit. Although conventional breeding and marker-assisted selection are being used to develop varieties more tolerant to water stress, these methods are time and resource consuming and germplasm dependent. Genetic engineering is attractive because of its potential to improve abiotic stress tolerance more rapidly. Transcription factors have been shown to produce multiple phenotypic alterations, many of which are involved in stress responses. DREB1A, a transcription factor that recognizes dehydration response elements, has been shown in Arabidopsis thaliana to play a crucial role in promoting the expression of drought-tolerance genes. In our efforts to enhance drought tolerance in wheat, the A. thaliana DREB1A gene was placed under control of a stress-inducible promoter from the rd29A gene and transferred via biolistic transformation into bread wheat. Plants expressing the DREB1A gene demonstrated substantial resistance to water stress in comparison with checks under experimental greenhouse conditions, manifested by a 10-day delay in wilting when water was withheld.Key words: Wheat transformation, MPB Bobwhite 26, DREB1A, rd29 promoter, moisture stress tolerance.
The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2
Authors: Alvares Lúcia E , Wuyts Jan , Van de Peer Yves , Silva Eduardo P , Coutinho Luiz L , Brison Olivier , Ruiz Itamar R.G
Published: June 2004

The nucleotide sequence of the rDNA 18S region isolated from diploid and tetraploid species of the amphibian Odontophrynus americanus was determined and used to predict the secondary structure of the corresponding 18S rRNA molecules. Comparison of the primary and secondary structures for the 2n and 4n species confirmed that these species are very closely related. Only three nucleotide substitutions were observed, accounting for 99% identity between the 18S sequences, whereas several changes were detected by comparison with the Xenopus laevis 18S sequence (96% identity). Most changes were located in highly variable regions of the molecule. A noticeable feature of the Odontophrynus 18S rRNA was the presence of unusual extra sequences in the V2 region, between helices 9 and 11. These extra sequences do not fit the model for secondary structure predicted for vertebrate 18S rRNA.Key words: Odontophrynus americanus, Amphibia, polyploidy, 18S ribosomal DNA, molecular evolution.
Analysis of phylogenetic relationship among five mulberry (Morus) species using molecular markers
Authors: Vijayan K , Srivastava P P , Awasthi A K
Published: June 2004

Species identification in mulberry (Morus) continues to be a point of great debate among scientists despite the number of criteria such as floral characters, wood, and leaf anatomical and biochemical characters used to identify the species within this genus. However, no consensus system of classification has emerged. Hence, an investigation was undertaken with inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers to find out the possibility of using these DNA markers to confirm the identity of genotypes in a particular species. Fifteen ISSR and 15 RAPD primers generated 86% and 78% polymorphism, respectively, among 19 mulberry genotypes. The polymorphism among the species varied from 50% to 57% in ISSR markers and 31% to 53% in RAPD markers. Similarity coefficients were higher among the genotypes of M. latifolia, M. bombycis and M. alba. Cluster analyses separated genotypes of M. laevigata and M. indica from those of the other species. Population structure analysis of these species further showed high genetic differentiation coefficients (GST), high heterozygosity between two species (DST), and total heterozygosity among populations (Ht) coupled with considerably low gene flow (Nm) when M. laevigata was paired with other species. Based on these parameters and the result of cluster analysis it is concluded that M. laevigata can be considered as a separate species of mulberry, whereas the other four species may be grouped together and treated as subspecies.Key words: Morus species, genetic marker, ISSR, RAPD, DNA polymorphism, genetic flow.
QTL analysis of quantitative resistance toPhytophthora infestans(late blight) in tomato and comparisons with potato
Authors: Brouwer Douglas J , Jones Elizabeth S , Clair Dina A. St
Published: June 2004

Quantitative trait loci (QTLs) for resistance to Phytophthora infestans (late blight) were mapped in tomato. Reciprocal backcross populations derived from cultivated Lycopersicon esculentum × wild Lycopersicon hirsutum (BC-E, backcross to L. esculentum; BC-H, backcross to L. hirsutum) were phenotyped in three types of replicated disease assays (detached-leaflet, whole-plant, and field). Linkage maps were constructed for each BC population with RFLPs. Resistance QTLs were identified on all 12 tomato chromosomes using composite interval mapping. Six QTLs in BC-E (lb1a, lb2a, lb3, lb4, lb5b, and lb11b) and two QTLs in BC-H (lb5ab and lb6ab) were most consistently detected in replicated experiments or across assay methods. Lycopersicon hirsutum alleles conferred resistance at all QTLs except lb2a. Resistance QTLs coincided with QTLs for inoculum droplet dispersal on leaves, a trait in L. hirsutum that may contribute to resistance, and dispersal was mainly associated with leaf resistance. Some P. infestans resistance QTLs detected in tomato coincided with chromosomal locations of previously mapped R genes and QTLs for resistance to P. infestans in potato, suggesting functional conservation of resistance within the Solanaceae.Key words: late blight, tomato, Lycopersicon hirsutum, QTL mapping, disease resistance, potato.
EST derived PCR-based markers for functional gene homologues in cotton
Authors: Chee Peng W , Rong Junkang , Williams-Coplin Dawn , Schulze Stefan R , Paterson Andrew H
Published: June 2004

We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for developing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs amplified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the corresponding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis.Key words: Gossypium arboreum, cotton, expressed sequence tag, PCR, known-function genes.
QTL affecting soluble carbohydrate concentrations in stored onion bulbs and their association with flavor and health-enhancing attributes
Authors: Havey Michael J , Galmarini Claudio R , Gökçe Ali Fuat , Henson Cynthia
Published: June 2004

Onion bulbs accumulate fructans, a type of soluble carbohydrate associated with lower rates of colorectal cancers. Higher fructan concentrations in bulbs are correlated with higher pungency, longer dormancy, and greater onion-induced antiplatelet activity (OIAA). We analyzed replicated field trials of a segregating family for types and concentrations of soluble carbohydrates in onion bulbs 90 days after harvest. Means were adjusted using dry weight as the covariant to reveal highly significant (P < 0.001) differences among parents and families for glucose, fructose, sucrose, and the fructans 1-kestose, neokestose, and (6G,1)-nystose. Fructan concentrations showed significant (P < 0.05) phenotypic correlations with each other and with sucrose, pungency, and OIAA. These observations are consistent with the hypothesis that onion bulbs accumulating fructans take up or retain less water, concentrating both soluble carbohydrates and thiosulfinates responsible for pungency and OIAA. Interval mapping of family means from the covariant analyses revealed regions on linkage groups A and D significantly (LOD > 2.68) affecting soluble carbohydrate concentrations. The enzyme catalyzing the first step of fructan polymerization, 1-sucrose-sucrose fructosyltransferase (1-SST), mapped independently of these genomic regions. One region on linkage group D near an acid-invertase gene was significantly (LOD = 3.45) associated with sucrose concentrations. This study reveals that the accumulation of sucrose in stored onion bulbs may allow for the combination of sweeter flavor with significant OIAA.Key words: quantitative trait locus, fructans, thiosulfinates, reducing sugars.
Reply to the comment by Salamini et al. on "AFLP data and the origins of domesticated crops"
Authors: Allaby Robin G , Brown Terence A
Published: June 2004

We reiterate the key points of a previous paper that showed that neighbor-joining analysis of AFLP datasets can produce erroneous results. The critical question, whether the datasets used to infer the origins of einkorn, barley, and the hulled and hard tetraploid wheats display sufficient linkage to avoid the artifacts that we observed, is not adequately answered by Salamini et al.Key words: AFLPs, crop domestication, einkorn wheat, barley, tetraploid wheat.
MINKOWSKI BRANE IN ASYMPTOTIC dS5 SPACETIME WITHOUT FINE-TUNING
Authors: CHANG ZHE , CHEN SHAO-XIA , HUANG XIN-BING
Published: June 2004

We discuss properties of a three-brane in an asymptotic five-dimensional de Sitter spacetime. It is found that a Minkowski solution can be obtained without fine-tuning. In the model, the tiny observed positive cosmological constant is interpreted as a curvature of five-dimensional manifold, but the Minkowski spacetime, where we live, is a natural three-brane perpendicular to the fifth coordinate axis.
BOUND STATE WAVE FUNCTIONS THROUGH THE QUANTUM HAMILTON–JACOBI FORMALISM
Authors: RANJANI S. SREE , GEOJO K. G. , KAPOOR A. K. , PANIGRAHI P. K.
Published: June 2004

The bound state wave functions for a wide class of exactly solvable potentials are found by utilizing the quantum Hamilton–Jacobi formalism of Leacock and Padgett. It is shown that, exploiting the singularity structure of the quantum momentum function, until now used only for obtaining the bound state energies, one can straightforwardly find both the eigenvalues and the corresponding eigenfunctions. After demonstrating the working of this approach through a few solvable examples, we consider Hamiltonians, which exhibit broken and unbroken phases of supersymmetry. The natural emergence of the eigenspectra and the wave functions, in both unbroken and the algebraically nontrivial broken phase, demonstrates the utility of this formalism.
CURVATONS IN THE MINIMALLY SUPERSYMMETRIC STANDARD MODEL
Authors: ENQVIST KARI
Published: June 2004

Curvaton is an effectively massless field whose energy density during inflation is negligible but which later becomes dominant. This is a novel mechanism to generate the scale invariant perturbations. We discuss the possibility that the curvaton could be found among the fields of the minimally supersymmetric standard model (MSSM), which contains a number of flat directions along which the renormalizable potential vanishes. The requirements of late domination and the absence of damping of the perturbations pick out essentially a unique candidate for the MSSM curvaton. One must also require that inflation takes place in a hidden sector. If the inflaton energy density can be radiated into extra dimensions, many constraints can be relaxed, and the simplest flat direction consisting of the Higgses Hu and Hd would provide a working example of an MSSM curvaton.
COMMENT ON "NONCOMMUTATIVITY AS A POSSIBLE ORIGIN OF THE ULTRAHIGH-ENERGY COSMIC RAY AND THE TEV PHOTON PARADOXES"
Authors: ZACHOS COSMAS
Published: June 2004

A Lorentz-noninvariant modification of the kinematic dispersion law was proposed in Ref. 1, claimed to be derivable from q-deformed noncommutative theory, and argued to evade ultrahigh energy threshold anomalies (trans-GKZ-cutoff cosmic rays and TeV-photons) by raising the respective thresholds. It is pointed out that such dispersion laws do not follow from deformed oscillator systems, and the proposed dispersion law is invalidated by tachyonic propagation, as well as photon instability, in addition to the process considered.
RECENT PROGRESS IN RECONSTRUCTING QUANTUM STATES OF ELECTROMAGNETIC FIELDS
Authors: ZHANG ZHI-MING
Published: June 2004

The reconstruction of quantum states of electromagnetic fields is an active research field in modern physics. This paper presents a brief review on this issue. Our review includes the theoretical proposals and experimental measurements on the reconstruction of quantum states of traveling fields and cavity fields. For traveling fields and cavity fields, we discuss the one-mode, two-mode, and multi-mode cases, respectively.
VARIOUS FACETS OF CHALKER–CODDINGTON NETWORK MODEL
Authors: KAGALOVSKY VICTOR , HOROVITZ BARUCH , AVISHAI YSHAI
Published: June 2004

We briefly discuss various applications of the Chalker–Coddington network model, starting with the original one, proposed to describe inter-plateaux transition in the integer quantum Hall effect (IQHE). Next, we present generalization appropriate for the IQHE allowing to include spin, and conclude with recent applications to dirty superconductors. We then describe how numerical calculations on an open network produce data for the localization length behavior in the metal-insulator transition, whereas calculations on the closed system allow elucidation of various levels statistics. We also discuss how numerical algorithm for systems with additional symmetries is modified in order to improve the accuracy. Finally, results for the nearest-neighbor spacing distribution in dirty superconductors are presented.
DIRECT OPTICAL ABSORPTION IN CYLINDRICAL QUANTUM DOT
Authors: SARKISYAN H. A.
Published: June 2004

Direct optical absorption of light in cylindrical quantum dot was theoretically investigated. Analytical expressions for light absorption coefficients were found for two regimes of size quantization: strong and weak. The corresponding selection rules for optical transitions are defined. The expressions for absorption threshold frequencies are found. The obtained results are compared with the case of light direct optical absorption in spherical quantum dot.
DETECTION OF SPIN INJECTION EFFICIENCY BY TUNNELING MAGNETORESISTANCE
Authors: MA JUN , SUN JIE , WANG JUN
Published: June 2004

To detect the spin injection efficiency η from a ferromagnet metal (FM) to a semiconductor (SC) in an FM/SC tunnel junction, we propose to introduce another similar single junction to form an FM/SC/FM double tunnel junction, and to measure its tunneling magnetoresistance ( TMR ). It is found that there is an approximate relation TMR = η2 in the sequential tunneling region and at low bias voltage. As the thickness of the middle SC layer is decreased to the extent so that the size of the entire structure is smaller than the electronic coherence length, both coherent tunneling conductance and resonant TMR exhibit oscillating behavior.
MULTIPHASE GENETIC PROGRAMMING: A CASE STUDY IN SUMO MANEUVER EVOLUTION
Authors: LIU JIMING , ZHANG SHIWU
Published: June 2004

In this paper, we describe a new evolutionary computation approach, called multiphase genetic programming (MPGP). The special features of this approach lie in its variable-granularity representations of chromosomes and their corresponding genetic operations. In the paper, we provide an overview of the MPGP approach as well as details on how the sumo maneuver evolution experiments are carried out and how the MPGP-based case study differs from others.
UNDERSTANDING IN THE SHAPE UNDERSTANDING SYSTEM
Authors: LES ZBIGNIEW , LES MAGDALENA
Published: June 2004

Understanding is based on a large number of highly varied abilities called intelligence that can be measured. In this paper understanding abilities of the shape understanding system (SUS) are tested based on the adoption of the intelligence tests. The SUS tests are formulated as the tasks given to the system and performance of SUS is compared with the human performance of these tasks. The main novelty of the presented method is that the process of understanding is related to the visual concept represented as a symbolic name of the possible classes of shape. The visual concept is one of the ingredients of the concept of the visual object (the phantom concept) that makes it possible to perform different tasks that are characteristic for the visual understanding. The presented results are part of the research aimed at developing the shape understanding method able to perform the complex visual tasks connected with visual thinking. The shape understanding method is implemented as the shape understanding system (SUS).
STILL IMAGE SEGMENTATION TOOLS FOR OBJECT-BASED MULTIMEDIA APPLICATIONS
Authors: MEZARIS VASILEIOS , KOMPATSIARIS IOANNIS , STRINTZIS MICHAEL G.
Published: June 2004

In this paper, a color image segmentation algorithm and an approach to large-format image segmentation are presented, both focused on breaking down images to semantic objects for object-based multimedia applications. The proposed color image segmentation algorithm performs the segmentation in the combined intensity–texture–position feature space in order to produce connected regions that correspond to the real-life objects shown in the image. A preprocessing stage of conditional image filtering and a modified K-Means-with-connectivity-constraint pixel classification algorithm are used to allow for seamless integration of the different pixel features. Unsupervised operation of the segmentation algorithm is enabled by means of an initial clustering procedure. The large-format image segmentation scheme employs the aforementioned segmentation algorithm, providing an elegant framework for the fast segmentation of relatively large images. In this framework, the segmentation algorithm is applied to reduced versions of the original images, in order to speed-up the completion of the segmentation, resulting in a coarse-grained segmentation mask. The final fine-grained segmentation mask is produced with partial reclassification of the pixels of the original image to the already formed regions, using a Bayes classifier. As shown by experimental evaluation, this novel scheme provides fast segmentation with high perceptual segmentation quality.
KAUFFMAN–HARARY CONJECTURE HOLDS FOR MONTESINOS KNOTS
Authors: ASAEDA MARTA M. , PRZYTYCKI JÓZEF H. , SIKORA ADAM S.
Published: June 2004

The Kauffman–Harary conjecture states that for any reduced alternating diagram K of a knot with a prime determinant p, every non-trivial Fox p-coloring of K assigns different colors to its arcs. We generalize this conjecture by stating it in terms of homology of the double cover of S3. In this way we extend the scope of the conjecture to all prime alternating links of arbitrary determinants. We first prove the Kauffman–Harary conjecture for pretzel knots and then we generalize our argument to show the generalized Kauffman–Harary conjecture for all Montesinos links. Finally, we discuss on the relation between the conjecture and Menasco's work on incompressible surfaces in exteriors of alternating links.
SURGERY n-TRIVIALITY AND COMPANION TORI
Authors: KALFAGIANNI E.
Published: June 2004

We define a knot K to be surgery n-trivial if there exists a collection of m-disjoint crossing circles for K such that twisting along any 0<m≤n of them turns K into the unknot. We use techniques from the theory of sutured 3-manifolds to study the question of whether, in the case that K is a non-trivial satellite, these crossing circles can be chosen to be disjoint from a companion torus of K. We show that if the twists are taken to have order bigger than one the answer to this question is yes. As a consequence of this we show that, under the hypothesis that the twists used have order bigger than one, the only knot that is surgery n-trivial for all n∈N, is the unknot.
A CLASS OF 3-COMPLEXES WITH INFINITE CYCLIC FUNDAMENTAL GROUP
Authors: BEDENIKOVIC TONY
Published: June 2004

Let D be a clasp disk in S3 with n singularities and let U be a regular neighborhood of D. Say D bounds the knot Γ. We show that the 3-complex X=(U\Γ)∪ c * Bd(U) 3-deforms to [Formula: see text]. In particular, π1(X)=ℤ for all 3-complexes X constructed in this manner. We observe that each X in this class corresponds to an unknotting scheme for the participating knot Γ.
WebBIS: AN INFRASTRUCTURE FOR AGILE INTEGRATION OF WEB SERVICES
Authors: MEDJAHED BRAHIM , BENATALLAH BOUALEM , BOUGUETTAYA ATHMAN , ELMAGARMID AHMED
Published: June 2004

The Web is changing the way organizations are conducting their business. Businesses are rushing to provide modular applications, called Web services, that can be programmatically accessed through the Web. Despite the tremendous developments achieved so far, one of the most important, yet untapped potential, is the use of Web services as facilitators for inter-organizational cooperation. This promising concept, known as Web service composition, is gaining momentum as the potential silver bullet for the envisioned Semantic Web. The development of such integrated services has so far been ad hoc, time-consuming, and requires extensive low-level programming efforts. In this paper, we present WebBIS (Web Base of Internet-accessible Services), a generic framework for composing and managing Web services. We combine the object-oriented and active rules paradigms for such a task. We also provide a ontology-based framework for organizing the Web service space. We finally propose a peer-to-peer mechanism for reporting, propagating, and reacting to changes in Web services.
AN AUTOMATA-BASED APPROACH TO CSCW VERIFICATION
Authors: PAPADOPOULOS CONSTANTINOS
Published: June 2004

Software development for computer-supported cooperative work (CSCW) is a notoriously difficult task, involving often concurrent processes which are bound up with rigid timing constraints. To cope effectively with this difficulty, we propose in this paper the use of abstract finite-state models. The utility of these models is illustrated by encoding a CSCW system that we have built into finite-state automata, specifying in them a number of desired properties with temporal logic, and verifying these properties with model checking. By incorporating timing constraints into this process, we also gain insight into the usability of our system in real cooperative scenarios.