bluuebunny/crossref_metadata_2025 huggingface dataset:
Preferential Use of CXCR4 by R5X4 Human Immunodeficiency Virus Type 1 Isolates for Infection of Primary Lymphocytes
Authors: Yi Yanjie , Shaheen Farida , Collman Ronald G.
Published: January 2005

Coreceptor specificity of human immunodeficiency virus type 1 (HIV-1) strains is generally defined in vitro in cell lines expressing CCR5 or CXCR4, but lymphocytes and macrophages are the principal targets in vivo. CCR5-using (R5) variants dominate early in infection, but strains that use CXCR4 emerge later in a substantial minority of subjects. Many or most CXCR4-using variants can use both CXCR4 and CCR5 (R5X4), but the pathways that are actually used to cause infection in primary cells and in vivo are unknown. We examined several R5X4 prototype and primary isolates and found that they all were largely or completely restricted to CXCR4-mediated entry in primary lymphocytes, even though lymphocytes are permissive for CCR5-mediated entry by R5 strains. In contrast, in primary macrophages R5X4 isolates used both CCR5 and CXCR4. The R5X4 strains were also more sensitive than R5 strains to CCR5 blocking, suggesting that interactions between the R5X4 strains and CCR5 are less efficient. These results indicate that coreceptor phenotyping in transformed cells does not necessarily predict utilization in primary cells, that variability exists among HIV-1 isolates in the ability to use CCR5 expressed on lymphocytes, and that many or most strains characterized as R5X4 are functionally X4 in primary lymphocytes. Less efficient interactions between R5X4 strains and CCR5 may be responsible for the inability to use CCR5 on lymphocytes, which express relatively low CCR5 levels. Since isolates that acquire CXCR4 utilization retain the capacity to use CCR5 on macrophages despite their inability to use it on lymphocytes, these results also raise the possibility that a CCR5-mediated macrophage reservoir is required for sustained infection in vivo.
Capped RNA Transcripts of Full-Length cDNA Clones of Swine Hepatitis E Virus Are Replication Competent When Transfected into Huh7 Cells and Infectious When Intrahepatically Inoculated into Pigs
Authors: Huang Y. W. , Haqshenas G. , Kasorndorkbua C. , Halbur P. G. , Emerson S. U. , Meng X. J.
Published: January 2005

Swine hepatitis E virus (swine HEV), the first animal strain of HEV to be isolated, is a zoonotic agent. We report here the construction and in vitro and in vivo characterizations of infectious cDNA clones of swine HEV. Eight overlapping fragments spanning the entire genome were amplified by reverse transcription-PCR and assembled into a full-length cDNA clone, clone C, which contained 14 mutations compared to the consensus sequence of swine HEV. RNA transcripts from clone C were not infectious, as determined by intrahepatic inoculation into pigs and by in vitro transfection of Huh7 cells. Multiple site-based site-directed mutagenesis was performed to generate three new cDNA clones (pSHEV-1, pSHEV-2, and pSHEV-3) which differed from each other. The transfection of capped RNA transcripts into human liver Huh7 cells resulted in the synthesis of both ORF2 capsid and ORF3 proteins, indicating that the cDNA clones were replication competent. Each of the three clones resulted in active swine HEV infections after the intrahepatic inoculation of pigs with capped RNA transcripts. The patterns of seroconversion, viremia, and fecal virus shedding for pigs inoculated with RNA transcripts from clones pSHEV-2 and pSHEV-3 were similar to each other and to those for pigs inoculated with wild-type swine HEV, suggesting that the nucleotide differences between these two cDNA clones were not critical for replication. Pigs inoculated with RNA transcripts from clone pSHEV-1, which contained three nonsilent mutations in the ORF2 capsid gene, had a delayed appearance of seroconversion and fecal virus shedding and had undetectable viremia. The availability of these infectious cDNA clones affords us an opportunity to understand the mechanisms of cross-species infection by constructing chimeric human and swine HEVs.
Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event
Authors: Vijgen Leen , Keyaerts Els , Moës Elien , Thoelen Inge , Wollants Elke , Lemey Philippe , Vandamme Anne-Mieke , Van Ranst Marc
Published: January 2005

Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10−4nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.
Efficient Inhibition of Hepatitis B Virus Infection by Acylated Peptides Derived from the Large Viral Surface Protein
Authors: Gripon Philippe , Cannie Isabelle , Urban Stephan
Published: January 2005

The lack of an appropriate in vitro infection system for the major human pathogen hepatitis B virus (HBV) has prevented a molecular understanding of the early infection events of HBV. We used the novel HBV-infectible cell line HepaRG and primary human hepatocytes to investigate the interference of infection by HBV envelope protein-derived peptides. We found that a peptide consisting of the authentically myristoylated N-terminal 47 amino acids of the pre-S1 domain of the large viral envelope protein (L protein) specifically prevented HBV infection, with a 50% inhibitory concentration (IC
50
) of 8 nM. The replacement of myristic acid with other hydrophobic moieties resulted in changes in the inhibitory activity, most notably by a decrease in the IC
50
to picomolar concentrations for longer unbranched fatty acids. The obstruction of HepaRG cell susceptibility to HBV infection after short preincubation times with the peptides suggested that the peptides efficiently target and inactivate a receptor at the hepatocyte surface. Our data both shed light on the molecular mechanism of HBV entry into hepatocytes and provide a basis for the development of potent hepadnaviral entry inhibitors as a novel therapeutic concept for the treatment of hepatitis Β.
Computational Design of Antiviral RNA Interference Strategies That Resist Human Immunodeficiency Virus Escape
Authors: Leonard Joshua N. , Schaffer David V.
Published: January 2005

Recently developed antiviral strategies based upon RNA interference (RNAi), which harnesses an innate cellular system for the targeted down-regulation of gene expression, appear highly promising and offer alternative approaches to conventional highly active antiretroviral therapy or efforts to develop an AIDS vaccine. However, RNAi is faced with several challenges that must be overcome to fully realize its promise. Specifically, it degrades target RNA in a highly sequence-specific manner and is thus susceptible to viral mutational escape, and there are also challenges in delivery systems to induce RNAi. To aid in the development of anti-human immunodeficiency virus (anti-HIV) RNAi therapies, we have developed a novel stochastic computational model that simulates in molecular-level detail the propagation of an HIV infection in cells expressing RNAi. The model provides quantitative predictions on how targeting multiple locations in the HIV genome, while keeping the overall RNAi strength constant, significantly improves efficacy. Furthermore, it demonstrates that delivery systems must be highly efficient to preclude leaving reservoirs of unprotected cells where the virus can propagate, mutate, and eventually overwhelm the entire system. It also predicts how therapeutic success depends upon a relationship between RNAi strength and delivery efficiency and uniformity. Finally, targeting an essential viral element, in this case the HIV TAR region, can be highly successful if the RNAi target sequence is correctly selected. In addition to providing specific predictions for how to optimize a clinical therapy, this system may also serve as a future tool for investigating more fundamental questions of viral evolution.
Identification of the Membrane-Active Regions of the Severe Acute Respiratory Syndrome Coronavirus Spike Membrane Glycoprotein Using a 16/18-Mer Peptide Scan: Implications for the Viral Fusion Mechanism
Authors: Guillén Jaime , Pérez-Berná Ana J. , Moreno Miguel R. , Villalaín José
Published: January 2005

We have identified the membrane-active regions of the severe acute respiratory syndrome coronavirus (SARS CoV) spike glycoprotein by determining the effect on model membrane integrity of a 16/18-mer SARS CoV spike glycoprotein peptide library. By monitoring the effect of this peptide library on membrane leakage in model membranes, we have identified three regions on the SARS CoV spike glycoprotein with membrane-interacting capabilities: region 1, located immediately upstream of heptad repeat 1 (HR1) and suggested to be the fusion peptide; region 2, located between HR1 and HR2, which would be analogous to the loop domain of human immunodeficiency virus type 1; and region 3, which would correspond to the pretransmembrane region. The identification of these membrane-active regions, which are capable of modifying the biophysical properties of phospholipid membranes, supports their direct role in SARS CoV-mediated membrane fusion, as well as facilitating the future development of SARS CoV entry inhibitors.
Human Immunodeficiency Virus Type 1 Vectors with Alphavirus Envelope Glycoproteins Produced from Stable Packaging Cells
Authors: Strang Blair L. , Takeuchi Yasuhiro , Relander Thomas , Richter Johan , Bailey Ranbir , Sanders David A. , Collins Mary K. L. , Ikeda Yasuhiro
Published: January 2005

Alphavirus glycoproteins have broad host ranges. Human immunodeficiency virus type 1 (HIV-1) vectors pseudotyped with their glycoproteins could extend the range of tissues that can be transduced in both humans and animal models. Here, we established stable producer cell lines for HIV vectors pseudotyped with alphavirus Ross River virus (RRV) and Semliki Forest virus (SFV) glycoproteins E2E1. RRV E2E1-stable clones could routinely produce high-titer pseudotyped vectors for at least 5 months. SFV E2E1-stable clones, however, produced relatively low titers. We examined the properties of RRV E2E1-pseudotyped vectors [HIV-1(RRV)] and compared them with amphotropic murine leukemia virus Env- and vesicular stomatitis virus glycoprotein G-pseudotyped vectors. HIV-1(RRV) displayed a number of characteristics which would be advantageous in ex vivo and in vivo experiments, including resistance to inactivation by heat-labile components in fresh human sera and thermostability at 37°C. Upon single-step concentration by ultracentrifugation of HIV-1(RRV), we could achieve vector stocks with titers up to 6 × 10
7
IU/ml. HIV-1(RRV) efficiently transduced cells from several different species, including murine primary dendritic cells, but failed to transduce human and murine T cells as well as human hematopoietic stem cells (HSC). These results indicate that HIV-1(RRV) could be used in a number of applications including animal model experiments and suggest that expression of RRV cellular receptors is limited or absent in certain cell types such as T cells and human HSC.
Genetic Composition of Human Immunodeficiency Virus Type 1 in Cerebrospinal Fluid and Blood without Treatment and during Failing Antiretroviral Therapy
Authors: Strain M. C. , Letendre S. , Pillai S. K. , Russell T. , Ignacio C. C. , Günthard H. F. , Good B. , Smith D. M. , Wolinsky S. M. , Furtado M. , Marquie-Beck J. , Durelle J. , Grant I. , Richman D. D. , Marcotte T. , McCutchan J. A. , Ellis R. J. , Wong J. K.
Published: January 2005

Human immunodeficiency virus (HIV) infection of the central nervous system (CNS) is a significant cause of morbidity. The requirements for HIV adaptation to the CNS for neuropathogenesis and the value of CSF virus as a surrogate for virus activity in brain parenchyma are not well established. We studied 18 HIV-infected subjects, most with advanced immunodeficiency and some neurocognitive impairment but none with evidence of opportunistic infection or malignancy of the CNS. Clonal sequences of C2-V3 env and population sequences of pol from HIV RNA in cerebrospinal fluid (CSF) and plasma were correlated with clinical and virologic variables. Most (14 of 18) subjects had partitioning of C2-V3 sequences according to compartment, and 9 of 13 subjects with drug resistance exhibited discordant resistance patterns between the two compartments. Regression analyses identified three to seven positions in C2-V3 that discriminated CSF from plasma HIV. The presence of compartmental differences at one or more of the identified positions in C2-V3 was highly associated with the presence of discordant resistance (P= 0.007), reflecting the autonomous replication of HIV and the independent evolution of drug resistance in the CNS. Discordance of resistance was associated with severity of neurocognitive deficits (P= 0.07), while low nadir CD4 counts were linked both to the severity of neurocognitive deficits and to discordant resistance patterns (P= 0.05 and 0.09, respectively). These observations support the study of CSF HIV as an accessible surrogate for HIV virions in the brain, confirm the high frequency of discordant resistance in subjects with advanced disease in the absence of opportunistic infection or malignancy of the CNS, and begin to identify genetic patterns in HIVenvassociated with adaptation to the CNS.
Characterization of Snakehead Rhabdovirus Infection in Zebrafish (
Danio rerio
)
Authors: Phelan Peter E. , Pressley Meagan E. , Witten P. Eckhard , Mellon Mark T. , Blake Sharon , Kim Carol H.
Published: January 2005

The zebrafish,
Danio rerio
, has become recognized as a valuable model for the study of development, genetics, and toxicology. Recently, the zebrafish has been recognized as a useful model for infectious disease and immunity. In this study, the pathogenesis and antiviral immune response of zebrafish to experimental snakehead rhabdovirus (SHRV) infection was characterized. Zebrafish 24 h postfertilization to 30 days postfertilization were susceptible to infection by immersion in 10
6
50% tissue culture infective doses (TCID
50
) of SHRV/ml, and adult zebrafish were susceptible to infection by intraperitoneal (i.p.) injection of 10
5
TCID
50
of SHRV/ml. Mortalities exceeded 40% in infected fish, and clinical presentation of infection included petechial hemorrhaging, redness of the abdomen, and erratic swim behavior. Virus reisolation and reverse transcription-PCR analysis of the viral nucleocapsid gene confirmed the presence of SHRV. Histological sections of moribund embryonic and juvenile fish revealed necrosis of the pharyngeal epithelium and liver, in addition to congestion of the swim bladder by cell debris. Histopathology in adult fish injected i.p. was confined to the site of injection. The antiviral response in zebrafish was monitored by quantitative real-time PCR analysis of zebrafish interferon (IFN) and Mx expression. IFN and Mx levels were elevated in zebrafish exposed to SHRV, although expression and intensity differed with age and route of infection. This study is the first to examine the pathogenesis of SHRV infection in zebrafish. Furthermore, this study is the first to describe experimental infection of zebrafish embryos with a viral pathogen, which will be important for future experiments involving targeted gene disruption and forward genetic screens.
Nitric Oxide Inhibits the Replication Cycle of Severe Acute Respiratory Syndrome Coronavirus
Authors: Åkerström Sara , Mousavi-Jazi Mehrdad , Klingström Jonas , Leijon Mikael , Lundkvist Åke , Mirazimi Ali
Published: January 2005

Nitric oxide (NO) is an important signaling molecule between cells which has been shown to have an inhibitory effect on some virus infections. The purpose of this study was to examine whether NO inhibits the replication cycle of the severe acute respiratory syndrome coronavirus (SARS CoV) in vitro. We found that an organic NO donor,
S
-nitroso-
N
-acetylpenicillamine, significantly inhibited the replication cycle of SARS CoV in a concentration-dependent manner. We also show here that NO inhibits viral protein and RNA synthesis. Furthermore, we demonstrate that NO generated by inducible nitric oxide synthase, an enzyme that produces NO, inhibits the SARS CoV replication cycle.
G→A Hypermutation in Protease and Reverse Transcriptase Regions of Human Immunodeficiency Virus Type 1 Residing in Resting CD4
+
T Cells In Vivo
Authors: Kieffer Tara L. , Kwon Patty , Nettles Richard E. , Han Yefei , Ray Stuart C. , Siliciano Robert F.
Published: January 2005

In vitro studies have shown that the host cytidine deaminase APOBEC3G causes lethal hypermutation in human immunodeficiency virus type 1 reverse transcripts unless its incorporation into virions is blocked by Vif. By examining stably archived sequences in resting CD4
+
T cells, we show that hypermutation occurs in most if not all infected individuals. Hypermutated sequences comprised >9% of archived species in resting CD4
+
T cells but were not found in plasma virus. Mutations occurred in predicted contexts, with notable hotspots. Thus, defects in Vif function in vivo give rise to hypermutated viral genomes that can be integrated but do not produce progeny viruses.
New and interesting ascomycetes from Everglades National Park, Florida
Authors: Ahn Young-mee , Crane J L
Published: January 2005

A new parasitic fungus and a new hyperbiotrophic fungus were found on the leaves of the subtropical plant, Tetrazygia bicolor (Mill.) Cogn., collected from Florida, USA. The parasitic fungus is placed in the genus Asterina as a new species, Asterina tetrazygiicola Ahn & Crane, sp. nov. The hyperbiotrophic fungus on A. tetrazygiicola is assigned to the genus Phaeodimeriella as Phaeodimeriella asterinae Ahn & Crane sp. nov. Both fungi are described, illustrated, and typified. A previously described species, Asterina tetrazygiae Ryan, living on Tetrazygia elaeagnoides (Sw.) DC., is redescribed, illustrated, and lectotypified from the original Puerto Rican material. A lectotype is chosen for Asterina melastomatacearum Ryan.Key words: Asterina, epiphytic fungi, hyperbiotrophic fungi, Phaeodimeriella, systematics.
Taxonomic variation among North and South American subspecies of Fragaria virginiana Miller and Fragaria chiloensis (L.) Miller
Authors: Hancock J F , Serçe S , Portman C M , Callow P W , Luby J J
Published: January 2005

A morphometric comparison was done in the greenhouse of 220 genotypes representing all the American taxa of octoploid strawberries. Only two groups of Fragaria virginiana Miller (Staudt) and Fragaria chiloensis (L.) Miller were well separated in both principle component and cluster analyses: a group composed primarily of F. chiloensis subspecies plus some F. virginiana ssp. glauca (Wats.) Staudt and F. virginiana ssp. platypetala (Rydberg) Staudt and another group composed primarily of F. virginiana ssp. virginiana Duchesne; and F. virginiana ssp. grayana (E. Vilmorin ex Gay) with some F. virginiana ssp. glauca and F. virginiana ssp. platypetala. Among the individual traits examined, only hair orientation reliably distinguished F. chiloensis ssp. lucida (E. Vilmorin ex Gay) from F. chiloensis ssp. pacifica Staudt, and F. virginiana ssp. grayana from F. virginiana ssp. virginiana. Little separation was observed between North and South American F. chiloensis in our principle component and cluster analyses, although these groups did show significant individual discontinuities for a number of traits. Individuals representing the cultivated race of F. chiloensis were in a relatively tight cluster within the scatter of native F. chiloensis. Taken together, these data indicate that F. virginiana and F. chiloensis may be extreme forms of the same biological species and that many of the subspecies designations currently employed in F. virginiana and F. chiloensis should not be recognized. We suggest, however, that there is sufficient morphological and geographical separation to warrant the species designations F. chiloensis and F. virginiana. Fragaria chiloensis ssp. pacifica and Fragaria chiloensis ssp. lucida do not appear to deserve distinct subspecies rank, nor do F. virginiana ssp. virginiana and F. virginiana ssp. grayana. North and South American F. chiloensis are morphologically quite similar, but probably deserve subspecies rank, based on their isolation from each other and the fact that they are evolving separately. Fragaria virginiana ssp. glauca and F. virginiana ssp. platypetala should probably be joined as a single subspecies and retained within F. virginiana until further investigations more definitively determine affinity to other F. virginiana and F. chiloensis subspecies.Key words: Rosaceae, interspecies hybridization, polyploidy.
Thermogenic flowering of taro (Colocasia esculenta, Araceae)
Authors: Ivancic Anton , Lebot Vincent , Roupsard Olivier , Garcia José Quero , Okpul Tom
Published: January 2005

Thermogenesis and its association with taro (Colocasia esculenta (L.) Schott) flowering was studied during the warmest period of the year (December 2002 – February 2003) within a large collection of heterogeneous plant material on Espiritu Santo, Vanuatu. On each studied inflorescence, temperatures of the three main parts of the spadix and the ambient air were recorded during a period of 38 h. The investigation indicates that significant thermogenic activity of taro inflorescences takes place during two successive nights: (1) during the night when an inflorescence becomes odorous (the female phase) and (2) a night later, when microsporogenesis approaches its final phase (the male phase). The highest average difference between mean temperatures of the ambient air and inflorescences were documented during the female phase, at 0500 hours (the mean temperature of the sterile appendix was 29.1 ± 0.9 °C (P = 0.05) and this was 6.8 °C above the temperature of the ambient air). Thermogenic activity is synchronized with the protogynous nature of the species and insect pollination in the early morning hours. Its main putative functions are (1) to reduce the deviations of ambient air temperatures during the most critical periods of flowering, and (2) to promote cross-pollination. It stops 1–1.5 h after pollen has been released.Key words: taro, Colocasia esculenta, thermogenesis, inflorescence development, pollination.
Incidence of geitonogamy differs between two populations in the hawkmoth-pollinated Platanthera bifolia (Orchidaceae)
Authors: Maad Johanne , Reinhammar Lars Gunnar
Published: January 2005

We estimated geitonogamy in individuals with different inflorescence sizes in a small (100–200 flowering individuals) and a large population (>700 flowering individuals) of the self-compatible, moth-pollinated orchid Platanthera bifolia (L.) L. C. Rich. (Orchidaceae). Geitonogamy was estimated as the percent reduction in pollen receipt by emasculated compared with control plants over seven nights. Geitonogamy in the small population was 23% and 38% during 2 years, respectively. In contrast, no geitonogamy was detected during a single flowering season in the large population. Geitonogamy did not vary with inflorescence size and emasculation had no impact on fruit set. The difference in geitonogamy between the populations in the present study may be related to pollinator abundance and behaviour. We suggest that incidence of geitonogamy will be higher if the pollinator carries smaller pollen loads when arriving at a plant because there will be a smaller fraction of cross-pollen carried after visiting one flower. Geitonogamy may be influenced by available number of mates, pollen load size, pollinator behaviour, and pollen carryover.Key words: geitonogamy, population size, inflorescence size, pollen-limitation, pollen carryover, self-pollination.
Characterization of thesleepy spermmutant in the fernCeratopteris richardii: A new model for the study of axonemal function
Authors: Renzaglia Karen S , Wood Kelly Davidson , Rupp Gerald , Hickok Leslie G
Published: January 2005

Structural and motility characteristics of the zzz1 "sleepy sperm" mutant of Ceratopteris richardii Brongn. are described using scanning electron, transmission electron, light, and fluorescence microscopy. Although the zzz1 phenotype segregates as the product of a single gene mutation, the expression of the mutation varies within a single haploid gametophyte. The majority of mutant sperm cells are slow to initiate motility and typically swim in a slow, spiraling pattern. However, motility phenotypes range from immotile to wild-type (normal). This variable phenotypic expression is associated with a wide range of defects in the microtubule systems, especially the flagellar axonemes and the spline, a structure that provides a structural backbone for the cell. Defects in the spline microtubule array are associated with atypical cell shape and organellar positioning. Axonemal aberrations include an absence of the central pair complex and clumped flagella. We hypothesize that the gene product encoded by the zzz1 locus is not required for the establishment of the cytoskeletal elements necessary for sperm motility but rather is needed for stability and (or) repair (recycling) of these structures. This interpretation is consistent with the variable expression of zzz1 sperm, which appears to be age dependent.Key words: axoneme, microtubule, motility mutant, sperm cell, ultrastructure.
Changes in polyamine contents and arginine decarboxylase activity associated with elongation growth of hypocotyls inRhizophora apiculataBl.
Authors: Swamy P M , Usha R , Kiranmayee P , Ramamurthy N
Published: January 2005

Changes in polyamine (putrescine, spermidine, spermine) contents and arginine decarboxylase activity in three different regions of developing hypocotyls of Rhizophora apiculata Bl. were analyzed. Among the three polyamines, spermidine was present in higher quantities than either putrescine or spermine. Spermine occurred in the lowest quantities. Spermidine declined rapidly with the age of the hypocotyl. In contrast, a marked increase in putrescine was observed with the age of the hypocotyl. Arginine decarboxylase activity increased during the various developmental stages of hypocotyl growth, particularly in the final stage. The results suggest that putrescine plays a major role in the growth of the hypocotyl as evidenced by simultaneous increase in the content of putrescine and arginine decarboxylase activity.Key words: arginine decarboxylase, elongation, hypocotyls, polyamines, Rhizophora apiculata.
Planktonic diatom communities in High Arctic lakes (Store Koldewey, Northeast Greenland)
Authors: Cremer Holger , Wagner Bernd
Published: January 2005

This contribution documents with light micrographs the planktonic diatom flora in seven high arctic lakes on Store Koldewey, an island off Northeast Greenland. The lakes have maximum water depths between 6.1 and 72.0 m. Basic limnological analyses indicate that all lakes are cold, monomictic, clear, oligotrophic, and alkaline. Planktonic diatoms and chrysophyte statospores were present in all but one lake. Eight planktonic diatom taxa were identified in the phytoplankton samples: Aulacoseira islandica (O. Müller) Simonsen, Aulacoseira tethera Haworth, Aulacoseira sp. 1, Cyclotella antiqua W. Smith, Cyclotella pseudostelligera Hustedt, Cyclotella rossii Håkansson, Fragilaria tenera (W. Smith) Lange-Bertalot, and Stephanodiscus minutulus (Kützing) Cleve et Möller. Fragilaria tenera was present in two morphotypes; the "normally shaped" type and a type with abnormally shaped valves, which has mostly been recorded in metal-polluted lakes. The diatom communities were generally dominated by only one or two species. The water columns of the lakes with a water depth greater than 10 m accomodate a moderate to high proportion of primarily benthic diatoms.Key words: Greenland, High Arctic, limnology, diatoms, valve morphology.
Germination characteristics of Agriophyllum squarrosum
Authors: Zheng Yuanrun , Gao Yong , An Ping , Shimizu Hideyuki , Rimmington Glyn M
Published: January 2005

Agriophyllum squarrosum (L.) Moq. (Chenopodiaceae), a pioneer species of natural succession in semi-arid regions of China, is widely used for vegetation rehabilitation by air seeding. Experiments were conducted to determine the effects of light intensity and photoperiod, as well as constant and alternating temperatures, on germination to improve the technology of air seeding. Seed of A. squarrosum rarely (<18.5%) germinated at 5/15, 10/20, 15/25, and 20/30 °C (night/day); 39.5% of seeds germinated at 25/35 °C in a 14-h (215 µmol·m2·s1) photoperiod. Under dark conditions there was a high final percent seed germination (>90%), except for 71.8% final percent seed germination at 5/15 °C. Constant temperature conditions were associated with lower seed germination (<50%). Less than 13% of seeds germinated at different light intensities (25400 µmol·m2·s1) at 10/20 °C. There was no significant difference in final percent germination when seeds were exposed to 400, 100, or 25 µmol m2 s1 for 2 h daily. Final percent germination and germination rate deceased rapidly when the photoperiod was increased under 400 µmol·m2·s1. Only 49.2% of seeds germinated after 3 d. Because of the deleterious effect of light on germination, air seeding in late May is recommended.Key words: Agriophyllum squarrosum, air seeding, alternating temperature, constant temperature, light, semi-arid regions.
Genetic variation, population structure, and mating system in bigleaf maple (AcermacrophyllumPursh)
Authors: Iddrisu Mohammed N , Ritland Kermit
Published: January 2005

Genetic diversity, population genetic structure, and mating system of bigleaf maple (Acer macrophyllum Pursh) was estimated with isozymes and compared with other North American angiosperms. On average, populations were polymorphic at 61% of the loci, with 1.71 alleles per locus. The mean expected heterozygosity (HE= 0.152) was similar to other North American angiosperms. The level of population differentiation was moderately low (FST= 0.054), indicating extensive gene flow among populations (Nm= 4.39), and there was no isolation by distance. Genetic distances averaged 0.011 and ranged from 0.001 to 0.042, but no relationship between geographic distances was apparent. Outcrossing rates in two populations were high (95%) but significantly less than one, with no biparental inbreeding evident. A relatively high level of correlated matings, consistent with two to five effective pollen donors per tree, was found, indicating that low density and limited pollinator dispersal are prevalent.Key words: isozymes, bigleaf maple, outcrossing rates, population genetics, gene flow, angiosperms.
Landscape patterns of phenotypic variation and population structuring in a selfing grass,Elymus glaucus(blue wildrye)
Authors: Erickson Vicky J , Mandel Nancy L , Sorensen Frank C
Published: January 2005

Source-related phenotypic variance was investigated in a common garden study of populations of Elymus glaucus Buckley (blue wildrye) from the Blue Mountain Ecological Province of northeastern Oregon and adjoining Washington. The primary objective of this study was to assess geographic patterns of potentially adaptive differentiation in this self-fertile allotetraploid grass, and use this information to develop a framework for guiding seed movement and preserving adaptive patterns of genetic variation in ongoing restoration work. Progeny of 188 families were grown for 3 years under two moisture treatments and measured for a wide range of traits involving growth, morphology, fecundity, and phenology. Variation among seed sources was analyzed in relation to physiographic and climatic trends, and to various spatial stratifications such as ecoregions, watersheds, edaphic classifications, etc. Principal component (PC) analysis extracted four primary PCs that together accounted for 67% of the variance in measured traits. Regression and cluster analyses revealed predominantly ecotypic or stepped-clinal distribution of genetic variation. Three distinct geographic groups of locations accounted for over 84% of the variation in PC-1 and PC-2 scores; group differences were best described by longitude and ecoregion. Clinal variation in PC-3 and PC-4 scores was present in the largest geographic group. Four geographic subdivisions were proposed for delimiting E. glaucus seed transfer in the Blue Mountains.Key words: Elymus glaucus, morphological variation, local adaptation, seed transfer, seed zones, polyploid.
A late Pleistocene Steller sea lion (Eumetopias jubatus) from Courtenay, British Columbia: its death, associated biota, and paleoenvironment
Authors: Harington C R , Ross R LM , Mathewes R W , Stewart K M , Beattie O
Published: January 2005

A partial juvenile Steller sea lion (Eumetopias jubatus) skeleton from nearshore marine sands at Courtenay, Vancouver Island, British Columbia has been radiocarbon dated to 12 570 ± 70 BP. This date is supported by both stratigraphic and regional sea-level emergence data and is similar to radiocarbon dates on a Steller sea lion humerus from Bowen Island, just north of Vancouver. The juvenile apparently died from a blow to the braincase, most likely caused by a Steller sea lion bull. The Courtenay specimen is significant since very few Pleistocene otariid fossils are complete enough to be assigned to modern taxa. Associated mollusk remains indicate that the marine paleoclimate of the fossil locality was considerably colder than now — close to that along the northern reaches of Cook Inlet and Prince William Sound, Alaska. Pollen and plant macrofossils collected from the Courtenay site clearly demonstrate the presence of lodgepole pine (Pinus contorta) forests nearby during this early late-glacial interval. Fish remains (mainly Pacific cod and walleye pollock, with some salmon) from this site probably reflect selection by adult sea lions at a rookery.
Timing and duration of melting in the mid orogenic crust: Constraints from UPb (SHRIMP) data, Muskoka and Shawanaga domains, Grenville Province, Ontario
Authors: Slagstad Trond , Hamilton Michael A , Jamieson Rebecca A , Culshaw Nicholas G
Published: January 2005

The Central Gneiss Belt in the Grenville Province, Ontario, exposes metaplutonic rocks, orthogneisses, and minor paragneisses that were deformed and metamorphosed at crustal depths of 2035 km during the Mesoproterozoic Grenvillian orogeny. We present sensitive high-resolution ion microprobe (SHRIMP) UPb zircon data from eight samples of migmatitic orthogneiss, granite, and pegmatite from the Muskoka and Shawanaga domains that constrain the age and duration of partial melting in the mid orogenic crust. Our results support earlier interpretations that the protoliths to these migmatitic orthogneisses formed at ca. 1450 Ma. Emplacement and crystallization of granite and pegmatite in the Shawanaga domain took place at ca. 1089 Ma, apparently coevally with deformation and high-grade metamorphism. Leucosomes in the Muskoka and Shawanaga domains yield ages of 1067 and 1047 Ma, respectively, interpreted as the ages of melt crystallization. The geochronological data and field observations suggest that melt was present at the mid-crustal level of the Grenville orogen during a significant part of its deformational history, probably at least 2030 million years. By analogy with modern orogens, the amount and duration of melting observed in the Muskoka and Shawanaga domains may have had an impact on the orogenic evolution of the area.
Biodegradation of monoethanolamine in soil monitored by electrical conductivity measurement: an observational approach
Authors: Wong R CK , Bentley L R , Ndegwa A W , Chu A , Gharibi M , Lunn S RD
Published: January 2005

Monoethanolamine (MEA) is commonly used by the natural gas industry to remove acid gases from the natural gas stream. A series of pan test studies was conducted to examine the biodegradability of MEA in soil recovered from a decommissioned sour gas processing plant site. Test results indicate that MEA was successfully biodegraded or transformed into simple compounds under aerobic and anaerobic conditions. The electrical conductivity (EC) of the soil evolved with changing chemical conditions of its by-products during degradation of MEA. Based on experimental observations, five ranges of EC were correlated with five geochemical zones consisting of various concentrations of MEA and its by-products. The five ranges of EC were translated into equivalent in situ EC ranges. Using these in situ EC ranges, an electrical resistivity tomography image was used to create a geochemical interpretation of the subsurface beneath the plant site. The geochemical interpretation can provide useful information for detailed site assessment and remediation design.Key words: electrical conductivity, biodegradation, monoethanolamine, ammonia, acetate, electrical resistivity tomography, site characterization, observational approach.
A digital face mapping case study in an underground hard rock mine
Authors: Lemy Frank , Hadjigeorgiou John
Published: January 2005

This paper presents a case study of a digital discontinuity mapping system used as a rock mass characterization tool in an underground hard rock mine. This mapping system allows for a fast acquisition of information that can best characterize the geological structural regime without exposing workers to potentially unsafe conditions. This method can be used to overcome some of the shortcomings of traditional mapping methods, such as limited access to rock exposures. Photographic images of the exposed rock mass are introduced into a software package that has been developed to extract potential discontinuity traces using detection algorithms. Detected features that do not describe discontinuity traces are removed from the images using artificial neural networks. Operator intervention can improve the reliability of the system by linking incomplete discontinuity segments. This developed process results in the construction of a discontinuity trace map that can be used for rock mass characterization purposes. The system was employed to construct discontinuity trace maps of twenty 1.8 m by 1.8 m mapping windows from two locations in an underground hard rock mine. The ability of the system to quantify the geomechanical characteristics of the rock mass was evaluated by comparing the results with those of manually drawn discontinuity trace maps. The results of this study have helped to evaluate the digital face mapping system and identify its limitations.Key words: rock mass characterization, image processing, discontinuity networks, neural networks.
Uncoupled axial, flexural, and circumferential pipesoil interaction analyses of partially supported jointed water mains
Authors: Rajani Balvant , Tesfamariam Solomon
Published: January 2005

Pipelines used in the distribution of potable water are a vital part of everyday life. The pipelines buried in soilbackfill are exposed to different deleterious reactions; as a result, the design factor of safety may be significantly degraded and, consequently, pipelines may fail prematurely. Proactive pipeline management, which entails optimal maintenance, repair, or replacement strategies, helps increase the longevity of pipelines. The effect of different deterioration mechanisms and operating conditions needs to be understood to develop good proactive management practices. In this paper, a Winkler-type analytical model is developed to quantify the contributions of different stress drivers, e.g., pipe material type and size, bedding conditions, and temperature. Sensitivity analyses indicate that the extent of the unsupported length developed as a result of scour has a significant influence on the flexural pipesoil response. As well, plastic pipes tolerate less loss of support than metallic pipes.Key words: jointed water mains, Winkler model, pipesoil interaction, elastoplastic soil.
Soil-particle and pore orientations during drained and undrained shear of a cohesive sandy siltclay soil
Authors: Cetin Hasan , Söylemez Mehmet
Published: January 2005

The orientations of particles, pores, and other constituents of an artificially made cohesive sandy siltclay soil were studied to investigate how they change during drained and undrained shear. The results show that the orientation pattern before shearing is nearly random, although there may be some degree of preferred orientation caused by the overburden pressure. The degree of preferred orientation increases as the shearing increases until failure in both the drained and undrained tests and increases towards the failure plane. After failure, the degree of preferred orientation does not change considerably near the failure plane but does continue to increase away from it. The number of oriented particles, pores, and other constituents increases, but their averages stay about the same as the shearing continues after failure in the drained tests. The differences between the degrees of preferred orientations 5 and 10 mm away from the failure planes at different shear (horizontal) displacements are much less in the drained tests than in the undrained tests, indicating formation of a wider deformation zone in the drained tests. This is probably because particles in the drained tests have enough time to respond to the applied shear stresses and change their orientation. This may explain why deformations occur in wide zones along tectonically active creeping (aseismic) faults, whose mechanisms are analogous to those of drained shear tests, and in narrow zones along seismic faults, whose mechanisms are analogous to those of undrained shear tests.Key words: shear test, soil structure, soil fabric, preferred orientation, seismic, aseismic.
Compression and consolidation characteristics of structured natural clay
Authors: Chai J -C , Miura N , Zhu H -H , Yudhbir
Published: January 2005

The compression and consolidation behavior of some structured natural clays are discussed. It is shown that for some structured natural clays, the relation between void ratio (e) and mean effective stress (p′) is more linear in a ln(e + ec)  ln(p′) plot (where ec is a soil parameter) than in an e  ln(p′) plot. It is proposed that for structured natural clay with a sensitivity value greater than 4, a linear ln(e + ec)  ln(p′) relation can be used in settlement and consolidation calculation. The effect of introducing a linear ln(e + ec)  ln(p′) relation on the calculated loadsettlement curve and consolidation behavior of structured clays is discussed. The linear ln(e + ec)  ln(p′) relation was incorporated into the modified Camclay model by modifying the hardening law of the model. It is shown that using the linear ln(e + ec)  ln(p′) relation simulated the consolidation behavior of the structured natural clays better than using the linear e  ln(p′) relation.Key words: structured natural clay, compression, consolidation, constitutive model, numerical analysis.
Deformation characteristics of two cemented calcareous soils
Authors: Sharma Shambhu S , Fahey Martin
Published: January 2005

The effect of cementation on the deformation characteristics of two cemented calcareous soils was investigated through a series of undrained triaxial tests performed under both monotonic and cyclic loading conditions. Increasing the level of cementation significantly increased the initial stiffness, resulting in the stiffness being more independent of the confining pressure. The curves of stiffness degradation with strain obtained from both cemented and uncemented calcareous soils compared with those of other noncalcareous soils revealed that calcareous soil attains a faster rate of modulus reduction with a higher strain threshold. It was also observed that the pattern of stiffness degradation is very similar in both cemented and uncemented samples. The stiffness degradation curves obtained from cyclic tests were found to lie within the range defined by the corresponding monotonic tests. The effect of number of cycles on the stiffness during cyclic loading was also examined and is found to depend on whether the postyield behaviour is controlled by the cohesive or the frictional response. Examination of the variation of damping ratio with strain revealed that the observed difference in the stiffness degradation curves between calcareous and noncalcareous soils was also reflected in the damping ratio, with the damping ratio of calcareous soils being below the range defined for noncalcareous soils.Key words: calcareous soils, triaxial test, shear modulus, damping ratio, repeated loading.
Total synthesis of ()-xyloketal D and its enantiomer  Confirmation of absolute stereochemistry
Authors: Pettigrew Jeremy D , Freeman Rebecca P , Wilson Peter D
Published: January 2005

The total synthesis of ()-xyloketal D and its enantiomer have been achieved by the reaction of an ortho-quinone methide with (4R)- and (4S)-4,5-dihydro-2,4-dimethylfuran via a diastereoselective inverse electron demand DielsAlder reaction. This total synthesis confirmed the absolute stereochemistry of the natural product. The ortho-quinone methide was generated by reaction of an appropriately functionalized Mannich base with methyl iodide. The Mannich base was prepared in one step from 2,4-dihydroxyacetophenone, formaldehyde, and morpholine. The enantiomeric dihydrofurans were prepared from (2R)- and (2S)-2-methylpent-4-ynoic acid via a three-step reaction sequence. These chiral nonracemic synthetic precursors were prepared from the corresponding (R)-phenylglycinol-derived diastereomeric amides of the readily available racemic carboxylic acid. The absolute stereochemistry of these carboxylic acids was firmly established by conversion to a known compound that had been previously prepared from a chiral pool starting material.Key words: xyloketal D, inverse electron demand DielsAlder reaction, ortho-quinone methide, dihydrofuran.
CHARACTERIZATION OF □κ IN CORE MODELS
Authors: SCHIMMERLING ERNEST , ZEMAN MARTIN
Published: January 2005

We present a general construction of a □κ-sequence in Jensen's fine structural extender models. This construction yields a local definition of a canonical □κ-sequence as well as a characterization of those cardinals κ, for which the principle □κ fails. Such cardinals are called subcompact and can be described in terms of elementary embeddings. Our construction is carried out abstractly, making use only of a few fine structural properties of levels of the model, such as solidity and condensation.