bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and Antigenic Diversities of Major Immunoreactive Proteins in Globally DistributedEhrlichia canisStrains
Authors: Zhang Xiaofeng , Luo Tian , Keysary Avi , Baneth Gad , Miyashiro Simone , Strenger Carmela , Waner Trevor , McBride Jere W.
Published: May 2008

The extent of knowledge regarding the diversity of globally distributedEhrlichia canisstrains has been limited to information gained from a few evolutionarily conserved genes. In this study,E. canisstrains from the United States (strain Jake [US]), Brazil (strain São Paulo [BR]), and Israel (strain 611 [IS] and Ranana [IS-R]) were used to examine the antigenic and genetic diversities of four well-characterized major immunoreactive protein genes/proteins. gp36 and gp200 were the most divergent genes, and nucleotide substitutions in the gp36 tandem repeat region of the IS strain, but not the IS-R strain, resulted in two amino acid differences (S→P and P→T) in each nine-amino-acid repeat (epitope-containing region). DNA sequences of gp19 and gp140 were completely conserved in the US and BR strains, but differences were found in the Israeli strains, including two fewer tandem repeats in gp140 and a single amino acid substitution in gp19 from the IS strain.E. caniswhole-cell lysates from each isolate were examined by Western immunoblotting using sera from naturally infected dogs from each country, and four major immunoreactive proteins (gp19, gp36, gp140, and gp200) were identified in each strain using protein-specific antisera. The US and BR strains exhibited highly conserved immunoreactive protein profiles, while some differences were identified in the IS strain. Sera from naturally infected Israeli dogs confirmed gene sequencing information, which demonstrated two distinctE. canisstrains, defined by the gp36 gene. Conversely, gp19 was strongly reactive and present in allE. canisisolates. gp140 and gp200 were also present in all strains, although gp140 in the IS strain had two fewer tandem repeats and exhibited a smaller mass.
LDBio-Toxo II Immunoglobulin G Western Blot Confirmatory Test for Anti-
Toxoplasma
Antibody Detection
Authors: Franck Jacqueline , Garin Yves Jean-François , Dumon Henri
Published: May 2008

Tests commonly used for routine determination of anti-
Toxoplasma gondii
immunoglobulin G (IgG) antibodies show a high level of consistency. However, considerable variations between commercial screening tests are still observed in detecting antibodies present at low concentrations, leading to a number of discrepant and/or equivocal results. It is therefore important to use a reference test to confirm borderline results. In this study, we evaluated the use of a new qualitative test based on Western blot analysis—the LDBio-Toxo II IgG test—as a confirmatory test for at-risk patients. The study was performed retrospectively, using 569 serum samples with “low-positive” (2 to 32 international units) anti-
Toxoplasma
IgG levels from 375 patients. These samples were either sera collected during the routine screening of pregnant women, from patients with unrelated infections, or from immunocompromised patients or sequential sera taken from pregnant women with acquired
Toxoplasma
infection or from their newborns during follow-up. The LDBio-Toxo II IgG test was compared to several commercial tests commonly used for anti-
Toxoplasma
IgG screening. The Sabin-Feldman dye test was used as a reference test. In this study, the results of the LDBio-Toxo II IgG test appeared to be consistent with those of the dye test; the LDBio-Toxo II IgG test had a specificity of 100% and a sensitivity of 99.2%. Our findings suggest that the LDBio-Toxo II IgG test is a useful serological tool in cases in which the presence or absence of
Toxoplasma
antibodies needs to be reliably determined, for example, for the follow-up of pregnant women and their newborns or for subjects with immune deficiencies following human immunodeficiency virus infection, hematological malignancies, or transplantation.
Time to Blood Culture Positivity as a Marker for Catheter-Related Candidemia
Authors: Ben-Ami Ronen , Weinberger Miriam , Orni-Wasserlauff Ruth , Schwartz David , Itzhaki Avraham , Lazarovitch Tzipora , Bash Edna , Aharoni Yuval , Moroz Irina , Giladi Michael
Published: May 2008

Candida
spp. are important causes of nosocomial bloodstream infections. Around 80% of patients with candidemia have an indwelling central venous catheter (CVC). Determining whether the CVC is the source of candidemia has implications for patient management. We assessed whether the time to detection of
Candida
species in peripheral blood (time to positivity [TTP]) can serve as a marker for catheter-related candidemia. Prospective surveillance of
Candida
bloodstream infection was conducted in two medical centers. TTP was recorded by the BacT/Alert automated system. Sixty-four candidemia episodes were included. Fifty patients (78%) had an indwelling CVC. Thirteen patients (20.3%) had definite catheter-related candidemia. TTP was shorter for definite catheter-related candidemia (17.3 ± 2 h) than that for candidemia from other sources (38.2 ± 3 h;
P
< 0.001). A TTP cutoff of 30 h was 100% sensitive and 51.4% specific for catheter-related candidemia (area under the receiver-operator characteristic curve of 0.76). We conclude that TTP in peripheral blood is a sensitive but nonspecific marker for catheter-related candidemia and that a TTP of more than 30 h can help exclude an intravascular catheter as the possible source of candidemia.
Microbiological Characteristics, Presumptive Identification, and Antibiotic Susceptibilities of
Staphylococcus lugdunensis
Authors: Tan Thean Yen , Ng Siew Yong , He Jie
Published: May 2008

This study validated abbreviated methods for the presumptive identification of
Staphylococcus lugdunensis
and studied the antibiotic susceptibilities of 106 isolates. The combination of positive responses to ornithine and pyrrolidonyl arylamidase identified all
S. lugdunensis
isolates. Resistance to penicillin and methicillin was detected in 27 and 5% of isolates, respectively.
Difficulties in Diagnosing Group O Human Immunodeficiency Virus Type 1 Acute Primary Infection
Authors: Henquell Cécile , Jacomet Christine , Antoniotti Odile , Chaib Abdelhak , Regagnon Christel , Brunet Sylvie , Peigue-Lafeuille Hélène , Barin Francis
Published: May 2008

We report a rare case of acute human immunodeficiency virus (HIV) type 1 group O infection in a French Caucasian woman. Her sexual partner was secondarily diagnosed with HIV infection, and transmission was confirmed by phylogenetic analysis. The unequal performance of many of the serologic and molecular assays commercially available leads to delays in diagnosis and affects patient management.
Real-Time PCR Method for Detection of Zygomycetes
Authors: Hata D. Jane , Buckwalter Seanne P. , Pritt Bobbi S. , Roberts Glenn D. , Wengenack Nancy L.
Published: May 2008

Zygomycete infections can be devastating in immunocompromised hosts. Difficulties in the histopathologic differentiation of this class from other filamentous fungi (e.g.,
Aspergillus
spp.,
Fusarium
spp.) may lead to delays in diagnosis and initiation of appropriate treatment, thereby significantly affecting patient outcome. A real-time PCR assay was developed to detect species of the zygomycete genera
Absidia
,
Apophysomyces
,
Cunninghamella
,
Mucor
,
Rhizopus
, and
Saksenaea
in culture and tissue samples. Primers and fluorescence resonance energy transfer hybridization probes were designed to detect a 167-bp conserved region of the multicopy zygomycete cytochrome
b
gene. A plasmid containing target sequence from
Mucor racemosus
was constructed as a positive control. The analytical sensitivity of the assay is 10 targets/μl, and a specificity panel consisting of other filamentous fungi, yeasts (
Candida
spp.), and bacteria demonstrated no cross-reactivity in the assay. The clinical sensitivity and specificity of the assay from culture isolates were 100% (39/39) and 92% (59/64), respectively. Sensitivity and specificity determined using a limited number of fresh tissue specimens were both 100% (2/2). The sensitivity seen with formalin-fixed, paraffin-embedded tissues was 56% (35/62), and the specificity was 100% (19/19). The speed, sensitivity, and specificity of the PCR assay indicate that it is useful for the rapid and accurate detection of zygomycetes.
Cross-Reactive Human Immunodeficiency Virus Type 1-Neutralizing Human Monoclonal Antibody That Recognizes a Novel Conformational Epitope on gp41 and Lacks Reactivity against Self-Antigens
Authors: Zhang Mei-Yun , Vu Bang K. , Choudhary Anil , Lu Hong , Humbert Michael , Ong Helena , Alam Munir , Ruprecht Ruth M. , Quinnan Gerald , Jiang Shibo , Montefiori David C. , Mascola John R. , Broder Christopher C. , Haynes Barton F. , Dimitrov Dimiter S.
Published: May 2008

Broadly cross-reactive human immunodeficiency virus (HIV)-neutralizing antibodies are infrequently elicited in infected humans. The two best-characterized gp41-specific cross-reactive neutralizing human monoclonal antibodies, 4E10 and 2F5, target linear epitopes in the membrane-proximal external region (MPER) and bind to cardiolipin and several other autoantigens. It has been hypothesized that, because of such reactivity to self-antigens, elicitation of 2F5 and 4E10 and similar antibodies by vaccine immunogens based on the MPER could be affected by tolerance mechanisms. Here, we report the identification and characterization of a novel anti-gp41 monoclonal antibody, designated m44, which neutralized most of the 22 HIV type 1 (HIV-1) primary isolates from different clades tested in assays based on infection of peripheral blood mononuclear cells by replication-competent virus but did not bind to cardiolipin and phosphatidylserine in an enzyme-linked immunosorbent assay and a Biacore assay nor to any protein or DNA autoantigens tested in Luminex assays. m44 bound to membrane-associated HIV-1 envelope glycoproteins (Envs), to recombinant Envs lacking the transmembrane domain and cytoplasmic tail (gp140s), and to gp41 structures containing five-helix bundles and six-helix bundles, but not to N-heptad repeat trimers, suggesting that the C-heptad repeat is involved in m44 binding. In contrast to 2F5, 4E10, and Z13, m44 did not bind to any significant degree to denatured gp140 and linear peptides derived from gp41, suggesting a conformational nature of the epitope. This is the first report of a gp41-specific cross-reactive HIV-1-neutralizing human antibody that does not have detectable reactivity to autoantigens. Its novel conserved conformational epitope on gp41 could be helpful in the design of vaccine immunogens and as a target for therapeutics.
Mutational Analysis of Plant Cap-Binding Protein eIF4E Reveals Key Amino Acids Involved in Biochemical Functions and Potyvirus Infection
Authors: German-Retana Sylvie , Walter Jocelyne , Doublet Bénédicte , Roudet-Tavert Geneviève , Nicaise Valérie , Lecampion Cécile , Houvenaghel Marie-Christine , Robaglia Christophe , Michon Thierry , Le Gall Olivier
Published: May 2008

The eukaryotic translation initiation factor 4E (eIF4E) (the cap-binding protein) is involved in natural resistance against several potyviruses in plants. In lettuce, the recessive resistance genesmo11andmo12againstLettuce mosaic virus(LMV) are alleles coding for forms of eIF4E unable, or less effective, to support virus accumulation. A recombinant LMV expressing the eIF4E of a susceptible lettuce variety from its genome was able to produce symptoms inmo11ormo12varieties. In order to identify the eIF4E amino acid residues necessary for viral infection, we constructed recombinant LMV expressing eIF4E with point mutations affecting various amino acids and compared the abilities of these eIF4E mutants to complement LMV infection in resistant plants. Three types of mutations were produced in order to affect different biochemical functions of eIF4E: cap binding, eIF4G binding, and putative interaction with other virus or host proteins. Several mutations severely reduced the ability of eIF4E to complement LMV accumulation in a resistant host and impeded essential eIF4E functions in yeast. However, the ability of eIF4E to bind a cap analogue or to fully interact with eIF4G appeared unlinked to LMV infection. In addition to providing a functional mutational map of a plant eIF4E, this suggests that the role of eIF4E in the LMV cycle might be distinct from its physiological function in cellular mRNA translation.
Humanized Monoclonal Antibodies Derived from Chimpanzee Fabs Protect against Japanese Encephalitis Virus In Vitro and In Vivo
Authors: Goncalvez Ana P. , Chien Cheng-Hsin , Tubthong Kamolchanok , Gorshkova Inna , Roll Carrie , Donau Olivia , Schuck Peter , Yoksan Sutee , Wang Sy-Dar , Purcell Robert H. , Lai Ching-Juh
Published: May 2008

Japanese encephalitis virus (JEV)-specific Fab antibodies were recovered by repertoire cloning from chimpanzees initially immunized with inactivated JE-VAX and then boosted with attenuated JEV SA14-14-2. From a panel of 11 Fabs recovered by different panning strategies, three highly potent neutralizing antibodies, termed Fabs A3, B2, and E3, which recognized spatially separated regions on the virion, were identified. These antibodies reacted with epitopes in different domains: the major determinant for Fab A3 was Lys179(domain I), that for Fab B2 was Ile126(domain II), and that for Fab E3 was Gly302(domain III) in the envelope protein, suggesting that these antibodies neutralize the virus by different mechanisms. Potent neutralizing antibodies reacted with a low number of binding sites available on the virion. These three Fabs and derived humanized monoclonal antibodies (MAbs) exhibited high neutralizing activities against a broad spectrum of JEV genotype strains. Demonstration of antibody-mediated protection of JEV infection in vivo is provided using the mouse encephalitis model. MAb B2 was most potent, with a 50% protective dose (ED50) of 0.84 μg, followed by MAb A3 (ED50of 5.8 μg) and then MAb E3 (ED50of 24.7 μg) for a 4-week-old mouse. Administration of 200 μg/mouse of MAb B2 1 day after otherwise lethal JEV infection protected 50% of mice and significantly prolonged the average survival time compared to that of mice in the unprotected group, suggesting a therapeutic potential for use of MAb B2 in humans.
Intersubunit Disulfide Isomerization Controls Membrane Fusion of Human T-Cell Leukemia Virus Env
Authors: Li Kejun , Zhang Shujing , Kronqvist Malin , Wallin Michael , Ekström Maria , Derse David , Garoff Henrik
Published: May 2008

Human T-cell leukemia virus (HTLV-1) Env carries a typical disulfide isomerization motif, C
225
XXC, in the C-terminal domain SU. Here we have tested whether this motif is used for isomerization of the intersubunit disulfide of Env and whether this rearrangement is required for membrane fusion. We introduced the C225A and C228A mutations into Env and found that the former but not the latter mutant matured into covalently linked SU-TM complexes in transfected cells. Next, we constructed a secreted Env ectodomain and showed that it underwent incubation-dependent intersubunit disulfide isomerization on target cells. However, the rearrangement was blocked by the C225A mutation, suggesting that C
225
carried the isomerization-active thiol. Still, it was possible to reduce the intersubunit disulfide of the native C225A ectodomain mutant with dithiothreitol (DTT). The importance of the CXXC-mediated disulfide isomerization for infection was studied using murine leukemia virus vectors pseudotyped with wild-type or C225A HTLV-1 Env. We found that the mutant Env blocked infection, but this could be rescued with DTT. The fusion activity was tested in a fusion-from-within assay using a coculture of rat XC target and transfected BHK-21 effector cells. We found that the mutation blocked polykaryon formation, but this could be reversed with DTT. Similar DTT-reversible inhibition of infection and fusion was observed when a membrane-impermeable alkylator was present during the infection/fusion incubation. We conclude that the fusion activity of HTLV-1 Env is controlled by an SU CXXC-mediated isomerization of the intersubunit disulfide. Thus, this extends the applicability of the isomerization model from gammaretroviruses to deltaretroviruses.
Qualitative and Quantitative Characteristics of Rotavirus-Specific CD8 T Cells Vary Depending on the Route of Infection
Authors: Jiang Janina Q. , He Xiao-Song , Feng Ningguo , Greenberg Harry B.
Published: May 2008

CD8 T-cell response provides an important defense against rotavirus, which infects a variety of systemic locations in addition to the gut. Here we investigated the distribution, phenotype, and function of rotavirus-specific CD8 T cells in multiple organs after rotavirus infection initiated via the intranasal, oral, or intramuscular route. The highest level of virus-specific CD8 T cells was observed in the Peyer's patches of orally infected mice and in the lungs of intranasally infected animals. Very low levels of virus-specific CD8 T cells were detected in peripheral blood or spleen irrespective of the route of infection. Rotavirus-specific CD8 T cells from Peyer's patches of orally infected mice expressed high levels of CCR9, while CXCR6 and LFA-1 expression was associated with virus-specific CD8 T cells in lungs of intranasally infected mice. Oral infection induced the highest proportion of gamma interferon
−
CD107a/b
+
CD8 T cells in Peyer's patches. When equal numbers of rotavirus-specific CD8 T cells were transferred into Rag-1 knockout mice chronically infected with rotavirus, the donor cells derived from Peyer's patches of orally infected mice were more efficient than those derived from lungs of intranasally infected animals in clearing intestinal infection. These results suggest that different routes of infection induce virus-specific CD8 T cells with distinct homing phenotypes and effector functions as well as variable abilities to clear infection.
Biodistribution and Safety Profile of Recombinant Adeno-Associated Virus Serotype 6 Vectors following Intravenous Delivery
Authors: Stone Daniel , Liu Ying , Li Zong-Yi , Strauss Robert , Finn Eric E. , Allen James M. , Chamberlain Jeffrey S. , Lieber André
Published: May 2008

Recombinant adeno-associated virus vectors based on serotype 6 (rAAV6) efficiently transduce skeletal muscle after intravenous administration and have shown efficacy in the mdx model of muscular dystrophy. As a prelude to future clinical studies, we investigated the biodistribution and safety profile of rAAV6 in mice. Although it was present in all organs tested, rAAV6 was sequestered mainly in the liver and spleen. rAAV6 had a minimal effect on circulating blood cells and caused no apparent hepatotoxicity or coagulation activation. rAAV6 caused some neutrophil infiltration into the liver, with a transient elevation in cytokine and chemokine transcription/secretion. In summary, rAAV6 induces transient toxicity that subsides almost completely within 72 h and causes no significant side effects.
R5X4 Viruses Are Evolutionary, Functional, and Antigenic Intermediates in the Pathway of a Simian-Human Immunodeficiency Virus Coreceptor Switch
Authors: Tasca Silvana , Ho Siu-Hong , Cheng-Mayer Cecilia
Published: May 2008

To examine the pathway of the coreceptor switching of CCR5-using (R5) virus to CXCR4-using (X4) virus in simian-human immunodeficiency virus SHIV
SF162P3N
-infected rhesus macaque BR24, analysis was performed on variants present at 20 weeks postinfection, the time when the signature gp120 V3 loop sequence of the X4 switch variant was first detected by PCR. Unexpectedly, circulating and tissue variants with His/Ile instead of the signature X4 V3 His/Arg insertions predominated at this time point. Phylogenetic analysis of the sequences of the C2 conserved region to the V5 variable loop of the envelope (Env) protein showed that viruses bearing HI insertions represented evolutionary intermediates between the parental SHIV
SF162P3N
and the final X4 HR switch variant. Functional analyses demonstrated that the HI variants were phenotypic intermediates as well, capable of using both CCR5 and CXCR4 for entry. However, the R5X4 intermediate virus entered CCR5-expressing target cells less efficiently than the parental R5 strain and was more sensitive to both CCR5 and CXCR4 inhibitors than either the parental R5 or the final X4 virus. It was also more sensitive than the parental R5 virus to antibody neutralization, especially to agents directed against the CD4 binding site, but not as sensitive as the late X4 virus. Significantly, the V3 loop sequence that determined CXCR4 use also conferred soluble CD4 neutralization sensitivity. Collectively, the data illustrate that, similar to human immunodeficiency virus type 1 (HIV-1) infection in individuals, the evolution from CCR5 to CXCR4 usage in BR24 transitions through an intermediate phase with reduced virus entry and coreceptor usage efficiencies. The data further support a model linking an open envelope gp120 conformation, better CD4 binding, and expansion to CXCR4 usage.
Cellular Proteins PML and Daxx Mediate an Innate Antiviral Defense Antagonized by the Adenovirus E4 ORF3 Protein
Authors: Ullman Amanda J. , Hearing Patrick
Published: May 2008

The adenovirus (Ad) E4 ORF3 protein is both necessary and sufficient to reorganize a nuclear subdomain, the PML nuclear body (PML-NB), from punctate structures into elongated nuclear tracks. PML-NB disruption is recapitulated by a variety of DNA viruses that encode proteins responsible for compromising PML-NB integrity through different mechanisms. PML-NB disruption has been correlated with the antagonism of both innate and intrinsic immune responses. The E4 ORF3 protein is required for adenoviral DNA replication in the interferon (IFN)-induced antiviral state. This may reflect the fact that PML itself, in addition to several other PML-NB proteins, is encoded by an interferon-stimulated gene. Here, we demonstrate that reorganization of the PML-NB by E4 ORF3 antagonizes an innate antiviral response mediated by both PML and Daxx. Reduction of either of these proteins is sufficient to restore the replicative capacity of virus with the E4 ORF3 protein deleted in the IFN-induced antiviral state. Further, we provide evidence that both the HSV1 ICP0 and HCMV IE1 proteins, which disrupt PML-NBs by mechanistically distinct strategies, behave in a manner functionally analogous to E4 ORF3 with respect to antagonizing the IFN-induced antiviral state. In addition, we assert that this innate antiviral strategy mediated by PML and Daxx does not involve transcriptional repression. While early gene transcription is modestly diminished in the absence of E4 ORF3 protein expression, this reduction does not affect early protein function. We propose that, in addition to its ability to repress gene expression, the PML-NB participates in additional innate immune activities.
Transcription Factor YY1 and Its Associated Acetyltransferases CBP and p300 Interact with Hepatitis Delta Antigens and Modulate Hepatitis Delta Virus RNA Replication
Authors: Huang Wen-Hung , Mai Ru-Tsun , Wu Lee Yan-Hwa
Published: May 2008

Hepatitis delta virus (HDV) is a pathogenic RNA virus with a plant viroid-like genome structure. HDV encodes two isoforms of delta antigen (HDAg), the small and large forms of HDAg (SHDAg and LHDAg), which are essential for HDV RNA replication and virion assembly, respectively. Replication of HDV RNA depends on host cellular transcription machinery, and the exact molecular mechanism for HDV RNA replication is still unclear. In this study, we demonstrated that both isoforms of HDAg interact with transcription factor YY1 (Yin Yang 1) in vivo and in vitro. Their interaction domains were identified as the middle region encompassing the RNA binding domain of HDAg and the middle GA/GK-rich region and the C-terminal zinc-finger region of YY1. Results of sucrose gradient centrifugation analysis indicated the cosedimentation of the majority of SHDAg and a portion of the LHDAg with YY1 and its associated acetyltransferases CBP (CREB-binding protein) and p300 as a large nuclear complex in vivo. Furthermore, exogenous expression of YY1 or CBP/p300 in HDV RNA replication system showed an enhancement of HDV RNA replication. Interestingly, the acetyltransferase activity of p300 is important for this enhancement. Moreover, SHDAg could be acetylated in vivo, and treatment with cellular deacetylase inhibitor elevated the replication of HDV RNA and acetylation of SHDAg. All together, our results reveal that HDAg interacts with cellular transcription factor YY1 and its associated acetyltransferases CBP and p300 in a large nuclear complex, which in turn modulates the replication of HDV RNA.
A comparative study of leaf thickness among southern Appalachian hardwoods
Authors: Carpenter Stanley B. , Smith Naomi D.
Published: May 2008

A linear displacement transducer was used to measure the leaf thickness of sun and shade leaves collected from trees growing in the mountain and eastern coalfield region of Kentucky. Leaf thickness measurements are presented for 64 southern Appalachian forest species which occupy all strata of the forest communities. Leaf thickness varied from 117.1 μm in Hydrangea arborescans to 473.9 μm in Ilex opaca. In all species sun leaves were thicker than shade leaves. Species considered tolerant of shade had significantly thicker sun and shade leaves than intolerant species when shrubs were included. When shrubs were excluded the sun and shade leaves of tolerant species were thinner than sun and and shade leaves of intolerant species. For all species including shrubs, sun leaf thickness for the tolerant, medium, and intolerant classes averaged 220.1, 183.5, and 213.3 μm, respectively. Although there appeared to be differences in leaf thickness between species inhabiting xeric and mesic sites, these differences were not statistically significant. Variation in sun leaf thickness within the genus Quercus ranged from 130.6 μm in Quercus alba to 306.5 μm in Quercus stellata. Shrub species generally had the thickest leaf blades.
Enzymes of asparagine catabolism in the developing maize endosperm
Authors: Misra S. , Oaks A. , Joy K. W. , McLimont M.
Published: May 2008

Asparaginase and asparagine transaminase (asparagine-pyruvate and asparagine-α-ketoglutarate) activities have been identified in maize endosperm. In each case there is a low level of activity at day 5, an increase to a maximum, and finally a decline in activity. The peaks for the transaminase activities (asparagine-pyruvate, 241 nmol∙h−1∙endosperm−1, and asparagine-α-ketoglutarate, 223 nmol∙h−1∙endosperm−1) were somewhat later in time than the peak in asparaginase activity (349 nmol∙h−1∙endosperm−1). The initial increase coincides with the increase in zein protein in the endosperm. Both the levels of activity at each stage of development and Km for asparagine (about 10 mM) suggest that either reaction could be responsible for the degradation of asparagine in maize endosperm. The degradation of asparagine in developing seeds is apparently not as significant a reaction in Zea mays as it is in Lupinus or Pisum.
Control of cambial activity and dormancy in Picea sitchensis by indol-3-ylacetic and abscisic acids
Authors: Little C. H. A. , Wareing P. F.
Published: May 2008

The combined gas chromatography – mass spectrometry (GCMS) technique of single-ion current monitoring was used to measure indol-3-ylacetic acid (IAA) and abscisic acid (ABA) levels in diffusible, acidic, and conjugated fractions obtained from the cambial region of Sitka spruce (1) during the annual cycle of cambial activity and dormancy in trees reared under natural and controlled environmental conditions, and (2) after debudding, girdling, defoliating, applying exogenous IAA, droughting, or changing the photoperiod. Seasonal changes occurred in the level of IAA and ABA in each fraction, but not obviously and consistently in conjunction with specific changes in cambial activity and dormancy. Debudding and girdling halted tracheid production, decreased the radial enlargement of the last-formed tracheids, and abruptly reduced the content of IAA and ABA in the diffusible and acidic fractions without affecting the ABA level in the conjugated fraction. Applying exogenous IAA to debudded shoots maintained tracheid production and differentiation, and largely prevented the decrease in IAA and ABA content. Elevating the internal water stress inhibited apical and cambial growth, increased the contents of diffusible, acidic, and conjugated ABA, and decreased diffusible and acidic IAA levels; the foliar concentrations of acidic IAA, acidic ABA, and conjugated ABA were similarly altered. Short-day photoperiod induced apical and cambial dormancy and reduced the levels of diffusible and acidic IAA and diffusible, acidic, and conjugated ABA; the decline in hormone content occurred mainly after the cambium ceased activity. Exogenous IAA could not prevent the cambium from ceasing activity under natural field conditions or short-day photoperiod. It is concluded that (1) there is an intrinsic seasonal pattern of change in IAA and ABA levels in the cambial region, governed primarily by seasonal changes in foliar hormone production; (2) this pattern is readily and variously perturbed by changes in the environment, particularly by factors affecting the internal water stress; (3) the evidence accumulated to date casts doubt on a role for ABA in controlling cambial dormancy; (4) cambial activity and the completion of the springtime transition from quiescence to activity depend on a continuous supply of basipetally transported IAA; (5) the changeover from activity to rest at the end of the cambial growing period is due to the development of an inability to respond to IAA, not to a deficiency in IAA supply; and (6) the transition from rest to quiescence during the cambial dormant period involves regaining the ability to respond to IAA.
Somatic hybridization between Nicotiana rustica and N. tabacum. IV. Analysis of nuclear and chloroplast genome expression in somatic hybrids
Authors: Douglas G. C. , Wetter L. R. , Keller W. A. , Setterfield G.
Published: May 2008

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBPCase) from 14 Nicotiana rustica + N. tabacum somatic hybrid plants was isolated and subjected to isoelectric focussing after carboxymethylation. The resulting polypeptide banding pattern for the nuclear-encoded small subunit of the enzyme showed bands derived from both parental species whereas the banding pattern for the plastid-encoded large subunit showed bands characteristic of N. rustica or N. tabacum but not both species. Eleven plants expressed the chloroplast genome of N. rustica and three expressed N. tabacum chloroplast genes.
Mucronate hyphopodia of Meliolaceae are phialides
Authors: Hughes S. J.
Published: May 2008

Preparations of colonies of some species of Appendiculella, Asteridiella, Irenopsis, and Meliola in lactic acid – fast green FCF show that mucronate hyphopodia are phialides producing hyaline nonseptate conidia (? spermatia).
Some rare plant collections, including three new records for Canada, from Cathedral Provincial Park, southern British Columbia
Authors: Douglas George W. , Ratcliffe Marilyn J.
Published: May 2008

Three new vascular plant records for the Canadian flora are reported. In addition, three other species of interest are discussed
Crown architecture of Larix laricina saplings: shoot preformation and neoformation and their relationships to shoot vigour
Authors: Remphrey W. R. , Powell G. R.
Published: May 2008

Resting buds from five locations on long shoots in each of six crown positions were compared for 30 Larix laricina (Du Roi) K. Koch saplings. At each locus, bud sizes, numbers of bud scales and preformed leaf primordia (basal and axial for long-shoot buds), and apical widths were positively related to parent-shoot length. Along individual shoots, (i) terminal and lateral long-shoot buds contained fewer basal-leaf primordia than the more proximal short-shoot buds; (ii) terminal buds contained the most bud scales and axial-leaf primordia; and (iii) numbers of bud scales increased, while numbers of axial-leaf primordia generally decreased, basipetally among lateral buds. Comparison of bud leaf content with leaves on elongated shoots by regression showed that numbers of preformed and neoformed leaves increased with shoot length, but numbers of neoformed leaves did so to a greater degree. Internode lengths, numbers of leaves per lateral bud produced, and leaf lengths were greater on neoformed than on preformed shoot segments. Because of their capacity for neoformed growth following preformed growth and because of increases in internode lengths among all axial leaves, shoots from subjacent lateral buds replaced experimentally decapitated tree leaders (terminal buds) in one season, with little or no loss of height growth.
Seasonal variation in the chemical constituents of the brown algae Macrocystis integrifolia and Nereocystis luetkeana
Authors: Rosell Karl-Gunnar , Srivastava Lalit M.
Published: May 2008

Ash, mannitol, alginate content, and inclusion levels of 27 inorganic elements in the brown algae Macrocystis integrifolia and Nereocystis luetkeana were monitored monthly over a period of 2 years. In addition, the composition and viscosity of the alginate were determined. Potassium, sodium, calcium, magnesium and phosphorus were the major elements present. Others, in decreasing amounts, included iodide, strontium, boron, iron, arsenic, aluminum, zinc, barium, manganese, copper, and cobalt. Some of these elements were accumulated to high concentrations in the thallus when compared with their concentrations in seawater. Marked seasonal variations were observed for potassium and phosphate, with high levels in winter and low levels in summer. Boron and iodide showed a reverse trend. Among the major elements, sodium, calcium, and magnesium showed no seasonal variations. Most of the inorganic elements, except potassium, were more abundant in the blade compared with the stipe. Leaching experiments with organic and inorganic solvents suggested that the alkali metals, sodium and potassium, were present mostly as inorganic salts, while divalent cations, calcium, magnesium, and strontium, were probably bound to alginic acid. Organic solvents did not leach appreciable quantities of the inorganic elements. The ash content in both algae was minimum (24%) in summer and maximum (49%) during winter, mainly because of the higher concentration of potassium in winter. Nereocystis showed higher values of ash than Macrocystis, and ash content was slightly higher in the stipe than in the blade tissues. The mannitol content ranged from 2 to 16% and alginate content from 19 to 31% of dry weight, both compounds showing higher values during the summer. Far more mannitol was present in the blade than in the stipe tissue, whereas the alginic acid content was slightly higher in the stipe than in the blade tissue. The mannuronate–guluronate ratio of alginate varied between 1.2 and 1.7 and the viscosity between 800 and 2000 cps.
Studies on the inflorescence of wild oats (Avena fatua). Morphology and anatomy of the awn in relation to its movement
Authors: Raju M. V. S.
Published: May 2008

The mature awn of wild oats (Avena fatua L.) is geniculate consisting of a proximal twisted portion and a distal subulate awl; the awl is placed at right angles to the proximal part. The proximal part of the awn can untwist upon wetting with water and twist upon drying. The awl by itself cannot twist or untwist, but it can rotate along with the proximal part of the awn. It can, however, act as a brace causing the wild oat lemma-covered caryopsis to turn in the opposite direction dislodging it from the spikelet. The proximal part untwists on wetting to become straight when the two ridges of the awn, wide adaxial and narrow abaxial, become obvious and remain superimposed alternating with adjacent furrows. The two ridges internally are joined by a vertically extending thin sheet, three to four cells thick, called the connective. The ridges and the connective in a mature dry awn contain unlignified, thick-walled fiber cells which are individually capable of twisting upon drying and untwisting upon wetting. The short fiber cells of the connective, especially the ones centrally situated, undergo longitudinal compression with little or no twisting. The more peripherally placed fiber cells are long and tend to twist extensively and (or) form helices. The extent of longitudinal compression owing to the loss of water decreases in cells from the center to the periphery, but the twisting of cells increases. These differences in the pattern of shrinkage between central and peripheral cells of the awn result in a change of form of the awn from a straight to a geniculate condition.
Structural, chemical, and permeability changes following wounding in onion roots
Authors: Moon G. J. , Peterson Carol A. , Peterson R. L.
Published: May 2008

Onion roots were wounded by scoring them with a needle 80 to 120 mm proximal to the root tip. Cells in the region of the wound were studied immediately after wounding and daily for the next 6 days. By the 2nd day, cortical cells near the wound had produced pit callose and deposited suberin in their walls and air spaces. The amount of suberin deposited increased until 4 days after wounding. No suberin lamellae were observed in cortical cell walls, but histochemical tests and acid digestion confirmed the presence of suberin within the existing wall. Intercellular air spaces adjacent to the wound were totally occluded with an electron-dense material which had characteristics of suberin. Penetration studies using Calcofluor white M2R, a fluorescent apoplastic dye, showed that the wound was completely sealed 4 days after wounding. Thus, in response to wounding, nonlamellar suberin was deposited in the cortical cell walls and air spaces surrounding the wound and was continuous with the suberin present in the normal hypodermis, forming a complete apoplastic barrier.
Decomposition of natural litter mixtures in a deciduous forest
Authors: Dwyer Lianne M. , Merriam Gray
Published: May 2008

Decomposition rates were measured for four litter mixtures, including mixed species and ages, representing common herbaceous litter and canopy leaf litter in a Canadian deciduous forest. Quantitative changes were expressed as monthly exponential weight loss rates based on measurements from a 6-month and from a 16-month period. Monthly loss rates of herbaceous litter were up to 11 times those of mixed-age canopy leaf mixtures (calculated over 6 months), and the loss rate for mixed-age canopy leaf litter calculated over 6 months was more than 3 times that monitored over 16 months. Similarly, qualitative changes, estimated as monthly arithmetic organic loss and lignin gain rates, were generally more rapid for herbaceous litter than for canopy litter, and mixed-age canopy litter had a faster rate of change calculated over 6 months compared with that estimated over the 16-month period. Following the initial rapid release of nutrients, decomposition slows and becomes more dependent on the availability and distribution of decomposer organisms. We hypothesize that an undisturbed litter layer provides the microenvironments required by these decomposers and that a spatial variability in decomposition therefore arises only as a result of spatial variability in litter distribution or disturbance (e.g., by wind) of the litter layer.
Penicillin inhibition of release of lateral buds of gram (Cicer arietinum) seedlings from apical dominance
Authors: Sen Monidipa , Bhattacharya Subires , Mukherji S.
Published: May 2008

The effect of penicillin on apical dominance was investigated in gram (Cicer arietinum L.) seedlings. Application of penicillin to the decapitated stump was found to reestablish apical dominance in preventing the growth of lateral buds. Penicillin was seen to mimic auxin action in this system. Penicillin inhibition of lateral bud growth was relieved by the simultaneous application of antiauxins like 2,3,5-triiodobenzoic acid and maleic hydrazide. An increase in auxin-synthesizing capacity of the treated tissue has been suggested as the possible mode of action of penicillin in the regulation of lateral bud growth.
Identifying faces across variations in lighting
Authors: Tarr Michael J. , Georghiades Athinodoros S. , Jackson Cullen D.
Published: May 2008

Humans have the ability to identify objects under varying lighting conditions with extraordinary accuracy. We investigated the behavioral aspects of this ability and compared it to the performance of the illumination cones (IC) model of Belhumeur and Kriegman [1998]. In five experiments, observers learned 10 faces under a small subset of illumination directions. We then tested observers' recognition ability under different illuminations. Across all experiments, recognition performance was found to be dependent on the distance between the trained and tested illumination directions. This effect was modulated by the nature of the trained illumination directions. Generalizations from frontal illuminations were different than generalizations from extreme illuminations. Similarly, the IC model was also sensitive to whether the trained images were near-frontal or extreme. Thus, we find that the nature of the images in the training set affects the accuracy of an object's representation under variable lighting for both humans and the model. Beyond this general correspondence, the microstructure of the generalization patterns for both humans and the IC model were remarkably similar, suggesting that the two systems may employ related algorithms.
Security analysis of cryptographically controlled access to XML documents
Authors: Abadi Martín , Warinschi Bogdan
Published: May 2008

Some promising recent schemes for XML access control employ encryption for implementing security policies on published data, avoiding data duplication. In this article, we study one such scheme, due to Miklau and Suciu [2003]. That scheme was introduced with some intuitive explanations and goals, but without precise definitions and guarantees for the use of cryptography (specifically, symmetric encryption and secret sharing). We bridge this gap in the present work. We analyze the scheme in the context of the rigorous models of modern cryptography. We obtain formal results in simple, symbolic terms close to the vocabulary of Miklau and Suciu. We also obtain more detailed computational results that establish security against probabilistic polynomial-time adversaries. Our approach, which relates these two layers of the analysis, continues a recent thrust in security research and may be applicable to a broad class of systems that rely on cryptographic data protection.
Minimum-weight triangulation is NP-hard
Authors: Mulzer Wolfgang , Rote Günter
Published: May 2008

A triangulation of a planar point set
S
is a maximal plane straight-line graph with vertex set
S
. In the
minimum-weight triangulation
(MWT) problem, we are looking for a triangulation of a given point set that minimizes the sum of the edge lengths. We prove that the decision version of this problem is NP-hard, using a reduction from PLANAR 1-IN-3-SAT. The correct working of the gadgets is established with computer assistance, using dynamic programming on polygonal faces, as well as the β-skeleton heuristic to certify that certain edges belong to the minimum-weight triangulation.
Improving SDRAM access energy efficiency for low-power embedded systems
Authors: Trajkovic Jelena , Veidenbaum Alexander V. , Kejariwal Arun
Published: May 2008

DRAM (dynamic random-access memory) energy consumption in low-power embedded systems can be very high, exceeding that of the data cache or even that of the processor. This paper presents and evaluates a scheme for reducing the energy consumption of SDRAM (synchronous DRAM) memory access by a combination of techniques that take advantage of SDRAM energy efficiencies in bank and row access. This is achieved by using small, cachelike structures in the memory controller to prefetch an additional cache block(s) on SDRAM reads and to combine block writes to the same SDRAM row. The results quantify the SDRAM energy consumption of MiBench applications and demonstrate significant savings in SDRAM energy consumption, 23%, on average, and reduction in the energy-delay product, 44%, on average. The approach also improves performance: the CPI is reduced by 26%, on average.
Accurate and fast system-level power modeling
Authors: Varma Ankush , Debes Eric , Kozintsev Igor , Klein Paul , Jacob Bruce
Published: May 2008

Accurate and fast system modeling is central to the rapid design space exploration needed for embedded-system design. With fast, complex SoCs playing a central role in such systems, system designers have come to require MIPS-range simulation speeds and near-cycle accuracy. The sophisticated simulation frameworks that have been developed for high-speed system performance modeling do not address power consumption, although it is a key design constraint. In this paper, we define a simulation-based methodology for extending system performance modeling frameworks to also include power modeling. We demonstrate the use of this methodology with a case study of a real, complex embedded system, comprising the Intel XScale embedded microprocessor, its WMMX SIMD co processor, L1 caches, SDRAM, and the on-board address and data buses. We describe detailed power models for each of these components and validate them against physical measurements from hardware, demonstrating that such frameworks enable designers to model both power and performance at high speeds without sacrificing accuracy. Our results indicate that the power estimates obtained are accurate within 5% of physical measurements from hardware, while simulation speeds consistently exceed a million instructions per second (MIPS).
Compile-time and instruction-set methods for improving floating- to fixed-point conversion accuracy
Authors: Aamodt Tor M. , Chow Paul
Published: May 2008

This paper proposes and evaluates compile time and instruction-set techniques for improving the accuracy of signal-processing algorithms run on fixed-point embedded processors. These techniques are proposed in the context of a profile guided floating- to fixed-point compiler-based conversion process. A novel fixed-point scaling algorithm (IRP) is introduced that exploits correlations between values in a program by applying fixed-point scaling, retaining as much precision as possible without causing overflow. This approach is extended into a more aggressive scaling algorithm (IRP-SA) by leveraging the modulo nature of 2's complement addition and subtraction to discard most significant bits that may not be redundant sign-extension bits. A complementary scaling technique (IDS) is then proposed that enables the fixed-point scaling of a variable to be parameterized, depending upon the context of its definitions and uses. Finally, a novel instruction-set enhancement—fractional multiplication with internal left shift(FMLS)—is proposed to further leverage interoperand correlations uncovered by the IRP-SA scaling algorithm. FMLS preserves a different subset of the full product's bits than traditional fractional fixed-point or integer multiplication. On average, FMLS combined with IRP-SA improves accuracy on processors with uniform bitwidth register architectures by the equivalent of 0.61 bits of additional precision for a set of signal-processing benchmarks (up to 2 bits). Even without employing FMLS, the IRP-SA scaling algorithm achieves additional accuracy over two previous fixed-point scaling algorithms by averages of 1.71 and 0.49 bits. Furthermore, as FMLS combines multiplication with a scaling shift, it reduces execution time by an average of 9.8%. An implementation of IDS, specialized to single-nested loops, is found to improve accuracy of a lattice filter benchmark by the equivalent of more than 16-bits of precision.