bluuebunny/crossref_metadata_2025 huggingface dataset:
Duplex Real-Time PCR Assay for Detection of
Streptococcus pneumoniae
in Clinical Samples and Determination of Penicillin Susceptibility
Authors: Harris Kathryn A. , Turner Paul , Green Elaine A. , Hartley John C.
Published: June 2008

We have developed a duplex real-time PCR for the rapid diagnosis of
Streptococcus pneumoniae
infection from culture-negative clinical samples with the simultaneous determination of penicillin susceptibility. The assay amplifies a
lytA
gene target and a penicillin binding protein 2b (
pbp2b
) gene target in penicillin-susceptible organisms. The assay was shown to be sensitive (detects 0.5 CFU per PCR) and specific for the detection of
S
.
pneumoniae
DNA. The assay was validated by comparing
pbp2b
PCR results with MIC data for 27
S
.
pneumoniae
isolates. All 5 isolates with penicillin MICs of >1.0 mg/liter were
pbp2b
real-time PCR negative, as were 9 of the 10 isolates with penicillin MICs of 0.12 to 1.0 mg/liter. One isolate with a penicillin MIC of 0.12 to 1.0 mg/liter gave an equivocal
pbp2b
real-time PCR result. Twelve isolates were penicillin susceptible (MICs of ≤0.06 mg/liter) and
pbp2b
real-time PCR positive. These data were used to establish an algorithm for the interpretation of penicillin susceptibility from the duplex PCR result.
pbp2b
real-time PCR results were also compared to an established PCR-restriction fragment length polymorphism (RFLP) method previously applied to these 27 isolates and 46 culture-negative clinical samples (containing
S
.
pneumoniae
DNA by broad-range 16S rRNA gene PCR). Discordant results were seen for four isolates and six culture-negative clinical samples, as PCR-RFLP could not reliably detect penicillin MICs of 0.12 to 1.0 mg/liter. We report prospective application of the duplex PCR assay to the diagnosis of
S
.
pneumoniae
infection from 200 culture-negative clinical specimens sent to the laboratory for diagnostic broad-range 16S rRNA gene PCR. One hundred six were negative in the duplex PCR. Ninety-four were
lytA
PCR positive, and 70 of these were also
pbp2b
PCR positive and interpreted as penicillin susceptible. Fourteen were
pbp2b
PCR negative and interpreted as having reduced susceptibility to penicillin. For the remaining 10 samples, susceptibility to penicillin was not determined.
West Nile Virus Nonstructural Protein 1 Inhibits TLR3 Signal Transduction
Authors: Wilson Jason R. , de Sessions Paola Florez , Leon Megan A. , Scholle Frank
Published: June 2008

The innate immune response is the first line of defense against foreign pathogens. The recognition of virus-associated molecular patterns, including double- and single-stranded RNA, by pattern recognition receptors initiates a cascade of signaling reactions. These result in the transcriptional upregulation and secretion of proinflammatory cytokines that induce an antiviral state. Many viruses have evolved mechanisms to antagonize these responses in order to help them establish a productive infection. We have previously shown that West Nile virus (WNV) is able to inhibit Toll-like receptor 3 (TLR3)-mediated activation of interferon (IFN) regulatory factor 3 (IRF3) (F. Scholle and P. W. Mason, Virology 342:77-87, 2005). In the present study, the WNV nonstructural (NS) proteins were analyzed individually for their ability to antagonize signal transduction mediated by TLR3. We report that expression of WNV NS1 inhibits TLR3-induced transcriptional activation of the IFN-β promoter and of an NF-κB-responsive promoter. This inhibition was due to a failure of the TLR3 ligand poly(I:C) to induce nuclear translocation of IRF3 and NF-κB. Furthermore, NS1 expression also inhibited TLR3-dependent production of interleukin-6 and the establishment of an antiviral state. The function of NS1 in flavivirus infection is not well understood. NS1 is required for viral RNA replication and is also secreted from mammalian cells but not from insect cells. Here, we identify a previously unrecognized role for NS1 in the modulation of signaling pathways of the innate immune response to WNV infection.
The Effects of Alternate Polypurine Tracts (PPTs) and Mutations of Sequences Adjacent to the PPT on Viral Replication and Cleavage Specificity of the Rous Sarcoma Virus Reverse Transcriptase
Authors: Chang Kevin W. , Oh Jangsuk , Alvord W. Gregory , Hughes Stephen H.
Published: June 2008

We previously reported that a mutant Rous sarcoma virus (RSV) with an alternate polypurine tract (PPT), DuckHepBFlipPPT, had unexpectedly high titers and that the PPT was miscleaved primarily at one position following a GA dinucleotide by the RNase H of reverse transcriptase (RT). This miscleavage resulted in a portion of the 3′ end of the PPT (5′-ATGTA) being added to the end of U3 of the linear viral DNA. To better understand the RNase H cleavage by RSV RT, we made a number of mutations within the DuckHepBFlipPPT and in the sequences adjacent to the PPT. Deleting the entire ATGTA sequence from the DuckHepBFlipPPT increased the relative titer to wild-type levels, while point mutations within the ATGTA sequence reduced the relative titer but had minimal effects on the cleavage specificity. However, mutating a sequence 5′ of ATGTA affected the relative titer of the virus and caused the RNase H of RSV RT to lose the ability to cleave the PPT specifically. In addition, although mutations in the conserved stretch of thymidine residues upstream of the PPT did not affect the relative titer or cleavage specificity, the mutation of some of the nucleotides immediately upstream of the PPT did affect the titer and cleavage specificity. Taken together, our studies show that the structure of the PPT in the context of the cognate RT, rather than a specific sequence, is important for the proper cleavage by RSV RT.
A Replication-Competent, Neuronal Spread-Defective, Live Attenuated Herpes Simplex Virus Type 1 Vaccine
Authors: Brittle Elizabeth E. , Wang Fushan , Lubinski John M. , Bunte Ralph M. , Friedman Harvey M.
Published: June 2008

Herpes simplex virus type 1 (HSV-1) produces oral lesions, encephalitis, keratitis, and severe infections in the immunocompromised host. HSV-1 is almost as common as HSV-2 in causing first episodes of genital herpes, a disease that is associated with an increased risk of human immunodeficiency virus acquisition and transmission. No approved vaccines are currently available to protect against HSV-1 or HSV-2 infection. We developed a novel HSV vaccine strategy that uses a replication-competent strain of HSV-1, NS-gEnull, which has a defect in anterograde and retrograde directional spread and cell-to-cell spread. Following scratch inoculation on the mouse flank, NS-gEnull replicated at the site of inoculation without causing disease. Importantly, the vaccine strain was not isolated from dorsal root ganglia (DRG). We used the flank model to challenge vaccinated mice and demonstrated that NS-gEnull was highly protective against wild-type HSV-1. The challenge virus replicated to low titers at the site of inoculation; therefore, the vaccine strain did not provide sterilizing immunity. Nevertheless, challenge by HSV-1 or HSV-2 resulted in less-severe disease at the inoculation site, and vaccinated mice were totally protected against zosteriform disease and death. After HSV-1 challenge, latent virus was recovered by DRG explant cocultures from <10% of vaccinated mice compared with 100% of mock-vaccinated mice. The vaccine provided protection against disease and death after intravaginal challenge and markedly lowered the titers of the challenge virus in the vagina. Therefore, the HSV-1 gEnull strain is an excellent candidate for further vaccine development.
Human Respiratory Syncytial Virus Glycoproteins Are Not Required for Apical Targeting and Release from Polarized Epithelial Cells
Authors: Batonick Melissa , Oomens Antonius G. P. , Wertz Gail W.
Published: June 2008

Human respiratory syncytial virus (HRSV) is released from the apical membrane of polarized epithelial cells. However, little is known about the processes of assembly and release of HRSV and which viral gene products are involved in the directional maturation of the virus. Based on previous studies showing that the fusion (F) glycoprotein contained an intrinsic apical sorting signal and that N- and O-linked glycans can act as apical targeting signals, we investigated whether the glycoproteins of HRSV were involved in its directional targeting and release. We generated recombinant viruses with each of the three glycoprotein genes deleted individually or in groups. Each deleted gene was replaced with a reporter gene to maintain wild-type levels of gene expression. The effects of deleting the glycoprotein genes on apical maturation and on targeting of individual proteins in polarized epithelial cells were examined by using biological, biochemical, and microscopic assays. The results of these studies showed that the HRSV glycoproteins are not required for apical maturation or release of the virus. Further, deletion of one or more of the glycoprotein genes did not affect the intracellular targeting of the remaining viral glycoproteins or the nucleocapsid protein to the apical membrane.
Basidiocarp development in Gloeophyllum (Lenzites) saepiarium in the natural environment
Authors: States Jack
Published: June 2008

Basidiocarp development in Gloeophyllum saepiarium begins with the emergence of vegetative hyphae from the wood, their exposure to the relatively severe, fluctuating conditions of light and moisture, and their loss of direct contact with the substratum. In response to these changes the hyphae become organized into hyphal strands composed of generative hyphae and skeletal hyphae. Hyphal strands direct the growth of the advancing margin and are involved in the development of tomentum, context, and hymenophore. Their marked sensitivity to light and humidity accounts for the presence of growth zones in the basidiocarp. Atmospheric humidity is considered to be the factor of primary importance in influencing the growth, differentiation, and orientation of the hyphae in the perennial basidiocarp during the growing season. The close association of skeletal and generative hyphae allows the fruit body to withstand the extended dry periods characteristic of its xeric habitat, and to develop over a long period of time.
Comparative needle anatomy and relative ozone sensitivity of four pine species
Authors: Evans Lance S. , Miller Paul R.
Published: June 2008

Relative ozone sensitivity was evaluated according to morphological and histological characteristics in four Pinus species grown in containers under greenhouse conditions in California's San Bernardino National Forest. The secondary leaves of the more ozone-sensitive species exhibited a larger number of stomata per cross-sectional area of mesophyll cells while the number of mesophyll cells per stoma was lower. The number of hypodermal layers and thickness of epidermal and hypodermal layers were negatively correlated with ozone sensitivity. In more ozone-tolerant pine species, initial injury was more closely associated with substomatal mesophyll cells. Ozone injury affected a greater proportion of the entire needle of the sensitive species as evidenced by histological symptoms closer to the needle base.
The isolation of nucleic acids from woody tissue using dimethyl sulfoxide
Authors: Gusta L. V. , Runeckles V. C.
Published: June 2008

A procedure is described for the isolation of nucleic acids from apple bark tissue using dimethyl sulfoxide. Nucleic acids isolated by this method are high in yield, and exhibit a high degree of purity as evidenced by their spectra. Experimental evidence is given to show that extraction of the tissue with dimethyl sulfoxide before the extraction of nucleic acids removes protein and pigments. Little or no ribonuclease activity could be detected in apple bark tissue after extraction with dimethyl sulfoxide. Ribonuclease activity was shown to be strongly inhibited by high concentrations of dimethyl sulfoxide.
Spore germination, penetration, and root colonization of six species of vesicular–arbuscular mycorrhizal fungi on soybean
Authors: Nuffelen Marjan Van , Schenck N. C.
Published: June 2008

Six species of vesicular–arbuscular (VA) mycorrhizal fungi, each at 500 spores per kilogram of pasteurized soil, were compared for spore germination, hyphal root penetration, and root colonization on soybean in a repeated greenhouse experiment. Generally, the six species were categorized into two groups. Those species in group I (Glomus mosseae, Gl. intraradices, and Gigaspora heterogama) had higher spore germination, root penetration, percentage root colonization values, and fungal growth rates in the roots than those species in group II (Gl. etunicatum, Gi. margarita, and Entrophospora sp.). However, when we calculated the fungal growth rate (centimetres per day) per penetration point or used Smith and Walker's equation, the highest values were assigned to group II. Fungal growth rate per penetration point was inversely proportional to the number of penetration points, indicating growth "interference" among hyphae originating from different penetration points in the root. The number of penetration points was correlated significantly with root length but not with percentage of root colonization. Dry root weight was significantly correlated with length of colonized roots in both experiments, while shoot weight was correlated with colonized root length in only one of the two experiments. Glomus mosseae was the only species which induced a significant increase both in dry shoot weight and numbers of Rhizobium nodules as compared with those for nonmycorrhizal plants.
Nitrogen uptake and growth in vitro by Hebeloma crustuliniforme and other Pacific Northwest mycorrhizal fungi
Authors: Littke Willis R. , Bledsoe Caroline S. , Edmonds Robert L.
Published: June 2008

Since little is known about the nitrogen (N) physiology of ectomycorrhizal fungi, this study was initiated to study both radial and biomass growth and N uptake of Hebeloma crustuliniforme and other Pacific Northwest ectomycorrhizal fungi. Hebeloma crustuliniforme utilized either nitrate or ammonium as the N source in buffered liquid media, but biomass growth was greatest with ammonium. Without buffers, biomass growth on ammonium-based media was reduced, apparently owing to low pH. These results emphasize the strong interrelationship between N source and pH of the media. A pronounced pH optimum for biomass growth of H. crustuliniforme occurred at pH 5.0. Ammonium uptake rates were five to nine times greater than nitrate uptake rates over a range of N concentrations (40–600 μM). Radial growth rates of a range of mycorrhizal fungi were greater on high-N than on low-N media. For those few species that grew faster on low-N medium, their growth habit was more diffuse and dry weight production was decreased, indicating that radial growth had occurred at the expense of biomass production.
Karyotypes of Leptarrhena and Tanakaea (Saxifragaceae)
Authors: Soltis Douglas E.
Published: June 2008

In an attempt to clarify subtribal relationships in tribe Saxifrageae, chromosome numbers and karyotypes were determined for the two species comprising subtribe Leptarrheninae: Leptarrhena pyrolifolia and Tanakaea radicans. In both species 2n = 14, a common chromosome number throughout Saxifrageae. The two species have distinctive karyotypes that appear to differ in the centromeric positions of three pairs of chromosomes. These findings, in conjunction with earlier studies, demonstrate that genera of Saxifrageae often differ karyotypically. Leptarrhena exhibits considerable karyotypic similarity to genera of subtribe Saxifraginae characterized by a base chromosome number of x = 7. Chromosomal data, therefore, do not clearly differentiate subtribes Saxifraginae and Leptarrheninae. This observation is in agreement with evidence from paly-nology and flavonoid chemistry. Karyotypic studies continue to demonstrate the conservative nature of chromosomal evolution in tribe Saxifrageae.
The effect of light on development of the rosette growth habit of winter wheat
Authors: Roberts D. W. A.
Published: June 2008

Young plants of the cold-hardy winter wheat (Triticum aestivum L. emend. Thell.) Kharkov 22 MC did not develop atypical prostrate or rosette growth habit unless light supply exceeded 350 klux∙h∙day−1. Prostrate habit developed under both short (10-h) and long (16-h or 24-h) photoperiods. Under a given photoperiod, expression of this trait intensified as light intensities increased. This finding was demonstrated in both field and growth-cabinet experiments. The degree of development of the rosette growth habit may be assessed by plotting plant height against plant age. Plants that develop typical rosettes decline in height when the rosettes develop whereas plants that remain erect show a continuous increase in height.
The movement of water from peatland into surrounding groundwater
Authors: Keough Janet R. , Pippen Richard W.
Published: June 2008

The flow of groundwater between and out of two adjacent bogs in southwest Michigan was investigated. Both wetlands are kettlelike depressions located in a complex upland covered by glacial outwash and till. Neither bog has an inlet or outlet stream. Their vegetation is typical of bogs, dominated by Sphagnum spp., Chamaedaphne calyculata, and Vaccinium corymbosum; however, only the south bog is forested with Larix lancina. The water table within the study area slopes through the north bog to the south bog. Both wetland surfaces are somewhat elevated above the surrounding groundwater and surrounded by "lagg" zones. The groundwater table around the bogs is only slightly affected by heavy precipitation, and water table fluctuations are least on the downslope side of each bog. Alkalinity, pH, and Ca2+ generally decrease from north of the north bog to the south end of the south bog. This is evidence that groundwater is moving down gradient through both bogs and that waters seeping out of the wetlands locally change the chemical nature of surrounding groundwater.
Deposition of Casparian bands and suberin lamellae in the exodermis and endodermis of young corn and onion roots
Authors: Perumalla C. J. , Peterson Carol A.
Published: June 2008

The Casparian band of the exodermis of corn and onion roots matures further from the root tip than its counterpart in the endodermis. A complete suberin lamella in the exodermal cells usually develops about 10 mm proximal to the exodermal Casparian band. The distance between the exodermal Casparian band and suberin lamella in the endodermis was usually much greater than in the exodermis. Both the exodermal Casparian band and suberin lamella matured closer to the tip in onion than in corn roots. The distance from the root tip at which the exodermal Casparian band matured increased with root age during the 5-day period studied in corn grown in hydroponics and vermiculite, and onion grown in hydroponics. This difference was most pronounced in corn, in which the Casparian band matured 20 mm from the root tip when the root was 20 mm long but matured 120 mm from the tip 4 days later when the root was 170 mm long. When the growth rate of corn roots was drastically inhibited by adding polyethylene glycol to the hydroponic medium, the exodermal Casparian band and suberin lamellae were present within 10 mm of the root tip. The position in the root at which the exodermis matures is thus highly variable and can depend on the plant species, and the age and growth rate of the individual root.
Polyribosome fractions and protein synthesis in stem rust infected wheat
Authors: Greenland Andrew , Shaw Michael
Published: June 2008

The effects of infection by stem-rust fungus on polyribosomal RNA fractions and protein synthesis in vitro and in vivo in near-isogenic resistant (Sr6) and susceptible (sr6) lines of wheat were determined. In infected resistant leaves the proportion of ribosomes present as polyribosomes was greater than that in healthy (uninfected) leaves at 1, 3, and 6 days and that in susceptible leaves at 1 and 3 days after inoculation. In the latter there were large increases in the pelletable RNA content (ribosomes, ribosomal subunits, and polyribosomes) and proportion of ribosomes present as polyribosomes from day 6. In vitro translation failed to detect any marked differences in polyribosomal translation products in resistant and susceptible leaves in response to infection. Labelling of polypeptides in vivo and separation by one- and two-dimensional electrophoresis showed that at 1 day after inoculation, two groups of high molecular mass polypeptides (80–96 and 100–110 kDa) were more heavily labelled and two novel polypeptides were present in resistant and susceptible leaves in response to infection. Synthesis of the high molecular weight and two novel polypeptides was maintained in infected resistant leaves up to 6 days after inoculation. In susceptible leaves the amount of radiolabel incorporated into these polypeptides and several proteins prominently labelled in uninfected controls declined rapidly from 3 days after inoculation.
History of late- and post-glacial vegetation and disturbance around Upper South Branch Pond, northern Maine
Authors: Anderson R. Scott , Davis Ronald B. , Miller Norton G. , Stuckenrath Robert
Published: June 2008

The changing character of vegetation and the effects of disturbance on vegetation are inferred from pollen, plant macrofossils, charcoal, and microlepidopteran larvel head capsules in sediment cores from Upper South Branch Pond, Maine. Following deglaciation 12 500 – 12 000 years ago, a herb–shrub tundra developed which included moss species characteristic of calcareous, mineral soils. Fire and infestation by microlepidopterans were unimportant initially but became important upon arrival of spruce, paper birch, balsam fir, white pine, and tamarack trees (ca. 10 200 – 9500 years BP). Fires were infrequent in the watershed between 7500 and 5000 years BP. The relatively stable forests of this period, dominated by hemlock and yellow birch, grew in what may have been the moistest part of the Holocene. The maximum postglacial abundance of microlepidopteran larvae is centered around the hemlock decline (ca. 4800 years BP). Subsequently, the forest was composed largely of deciduous trees and white pine. Fire incidence was greater, and fewer fossils of microlepidoptera were deposited. Lack of major disturbances between ca. 3300 and 2600 years BP coincided with increases in hemlock, tamarack, yellow birch, and arbor vitae. Increases in boreal conifers began by about 1700 years ago, suggesting cooler, and perhaps wetter, climate. An increase in microlepidoptera accompanied the recent expansion of boreal conifers.
Excretion of nitrogen assimilated from N2 fixed by nodulated roots of alfalfa (Medicago sativa)
Authors: Ta T. C. , Macdowall F. D. H. , Faris M. A.
Published: June 2008

Root excretions into the medium of hydroponically grown N2-fixing alfalfa were studied by quantitative and qualitative measurement of nitrogenous compounds in frequently collected aliquots of the culture solutions. Considerable amounts of several nitrogenous compounds were excreted from the nodulated roots. Ammonia, glutamate, serine, alanine, and aspartate were the main compounds excreted and were similar in proportion to the soluble nitrogenous compounds in nodule and root tissues, with the exception of asparagine. Asparagine was present in very high concentrations in the plant tissues and also in the root xylem exudates destined for the shoots, but it was not detected in the solution bathing the roots. 15N2 was also supplied to the nodulated roots of alfalfa and the flow of the label was followed both in the plant tissues and in the culture solution. Results showed that the amounts of nitrogenous compounds excreted to the medium were related to their formation following N2 fixation and also indicated that the recently fixed nitrogen was the main source of the excreted N compounds.
The anther cuticle of Zea mays
Authors: Cheng P. C. , Greyson R. I. , Walden D. B.
Published: June 2008

The cuticular membrane of the anther of Zea mays is ridged or rugose over most of its surface. The ridges arise during anther development and are confined to the cuticular membrane itself with no coincident folding of the cell wall, although some fibrous wall-like material becomes incorporated within the ridges. The height of a ridge, on mature anthers, is about 0.5 μm and although ridges are aligned, for the most part, in the long axis of the organ, ridges are continuous across cell boundaries in all directions. From transmission electron microscope views we conclude that the cuticle is homogeneous with a thickness of approximately 100 nm. The cuticular layer can be removed from the underlying wall by ZnCl2–HCl hydrolysis. Older anthers yield intact cuticles with persistent ridges. The ridges are not retained by cuticles from young anthers. Chloroform or hexane extraction removes about 30% of the dry weight from isolated cuticles. Characterization of the extract by gas–liquid chromatography – mass spectrometry reveals it is mainly composed of a mixture of odd- and even-numbered straight-chain, saturated hydrocarbons (C25 to C34).
A new species of Hirsutella with an unusual synanamorph
Authors: Evans Harry C. , Samson Robert A.
Published: June 2008

A new species of Hirsutella, H.pichilinguensis, on lepidopteran larvae collected in rain forest in Ecuador, is described. The new taxon is characterized by synnemata bearing phialides with a verruculose neck and by 0- to 1-septate conidia. In addition, a dominant synanamorph is present, which produces large, narrowly clavate, distoseptate, hyaline, thick-walled phragmos-pores. The taxonomic position of this distinctive synanamorph is obscure, although similarities in form and function can be drawn with the entomogenous hyphomycete genera Desmidiospora Thaxter and Tetracrium Hennings.
Esterase specificity of patatin from two potato cultivars
Authors: Racusen David
Published: June 2008

'Désirée' potato tubers contained about one-half the patatin of 'Kennebec', a typical commercial cultivar. The 'Désirée' patatin, like that of 'Kennebec', copurified with esterase activity, but it consisted of only two major ionic forms and its ability to hydrolyse p-nitrophenyl esters was relatively low. Despite these differences, the esterase of 'Désirée' patatin was quite active toward other substrates. Patatin isoforms, separated by isoelectric focusing, had the same esterase substrate preference as the cultivar-specific patatin from which they were derived.
Seasonal deposition of ferric hydroxide plaque on roots of wetland plants
Authors: Crowder A. A. , Macfie S. M.
Published: June 2008

In three wetlands in southeastern Ontario, ferric hydroxide was deposited on the roots of Typha latifolia (maximum, 67 × 103 ppm); in four other wetlands, deposition was negligible (< 103 ppm). Iron deposition was seasonal, with the peak period in July–August corresponding to peak biomass production of shoots. In one wetland where Carex rostrata and Phragmites australis occurred, seasonal plaque formation was similar. Plaque formation was not obviously related to Eh and pH regimes.
Response of a Typha marsh community to draining, flooding, and seasonal burning
Authors: Mallik A. U. , Wein Ross W.
Published: June 2008

A Typha marsh community was subjected to draining and seasonal burning treatments to control the growth of emergent aquatics. Treatments resulted in an increase in total number of species after 3 years. Cover and frequency of Aster novi-belgii, Lycopus uniflorus, Epilobium watsonii, Brachythecium salebrosum, Pleurozium schreberi, and Cladonia cristatella increased appreciably on the drained side whereas those of Carex spp., Lysimachia terrestris, Epilobium palustre, Pellia epiphylla, Sphagnum squarrosum, Drepanocladus exannulatus, and Helodium blandowii increased on the flooded side. Draining plus summer burning produced the lowest cover, stem density, plant height, and stem base diameter of Typha. An attempt was made to interpret the effects of disturbance on the natural paludification process that leads to the development of patches of fen within the marsh.
Population biology of Ammophila breviligulata and Calamovilfa longifolia on Lake Huron sand dunes. II. Ultrastructure of organelles and photosynthetic properties
Authors: Elfman Beverly , Maun M. A. , Hopkins W. G.
Published: June 2008

Organellar ultrastructure and photosynthetic properties of two grasses, Calamovilfa longifolia (Hook) Scribn. and Ammophila breviligulata Fern., growing on Lake Huron sand dunes were compared. Thylakoids of C. longifolia contained a relatively greater complement of the photosystem I (PSI) – chlorophyll a – protein complex, whereas thylakoids from A. breviligulata had a relatively greater complement of light-harvesting chlorophyll a + b complex. The chlorophyll a/b ratios of the mesophyll chloroplast thykaloids reflected the content of chlorophyll–protein complexes present in the membranes. Digitonin fractionation of mesophyll thylakoids from C. longifolia revealed that the PSI-enriched fraction contained more chlorophyll than the photosystem II (PSII) enriched fraction. Conversely, the PSII-enriched fraction accounted for the larger proportion of total chlorophyll in thylakoids from A. breviligulata. Whole chain electron transport (PSII + PSI) activity was greater in C. longifolia mesophyll thylakoids, at all light intensities. Chloroplast and mitochondrial ultrastructure were compared. The bundle sheath chloroplasts of C. longifolia contain extensive grana stacking and are distributed throughout the cell. The mitochondria of the bundle sheath and mesophyll cells are strikingly dimorphic. A suberin lamella is apparently absent from the bundle sheath cell walls. These results support the designation of C. longifolia as a C4 species of the nicotinamide adenine dinucleotide – malic enzyme type.
Stem pitting and annual ring discoloration in yellow birch
Authors: Thomas K. I. , Wall R. E.
Published: June 2008

The stem tissues of yellow birch (Betula alleghaniensis Britton) saplings, with wavy bands of stained xylem parallel to the annual rings and depressions in the xylem at the xylem–phloem interface (stem pitting), were studied microscopically. The bands of stained xylem consisted of abnormally formed parenchyma (parenchymatous wood) interspersed with collapsed cells. Rays in the affected areas showed increases in both cell numbers and cell size, often being indistinguishable from adjacent parenchymatous wood. Aggregate rays were associated with stained bands as well as with stem pitting in the xylem and corresponding protrusions of the phloem.
Seed burial effect on species presence along a mid-Atlantic beach
Authors: Tyndall R. Wayne , Teramura Alan H. , Mulchi Charles L. , Douglass Larry W.
Published: June 2008

The importance of seed burial to species presence on mid-Atlantic beaches was studied on Currituck Bank, North Carolina. Sand accretion and seed depth were measured and compared with potential shoot length and buried shoot length of dominant beach, foredune, and sand-flat species. Excessive seed burial plays an important role in the rarity of Uniola paniculata L. and Spartina patens (Aiton) Muhl. on the beach.
On PP and SS reflection point anomalies
Authors: Buchbinder G. G. R.
Published: June 2008

Reflection point residuals of PP and SS waves obtained from the residuals of PP-P and SS-S with respect to the J–B tables are shown to be in need of corrections. Recent velocity models of the Earth's mantle predict residuals that differ considerably amongst themselves and from the J–B tables. Before useful reflection point residuals can be determined by this method a reference model has to approximate closely the actual velocity distribution of the Earth between the source and receiver. Lateral variations, layering in velocity, and scattering in the vicinity of the reflection point of short-period PP also contribute large uncertainties in defining the reflection points of PP and its precursors. All of the foregoing problems suggest that interpretations of PP and SS wave residuals in terms of structure near the symmetric reflections points, as far as they have been determined up to now, are subject to serious errors.
A brief description of calcite spheres from Pliocene strata in the Dome Gulf et al. C-50 well, Beaufort Sea, arctic Canada
Authors: Dixon J. , McNeil D. H. , Michael G. P.
Published: June 2008

Calcite spheres and ellipsoids, up to 0.4 mm in diameter, occur abundantly in Pliocene and possible Upper Miocene shelf sediments in the Dome Gulf et al. Ukalerk C-50 well, drilled in the Beaufort Sea. Similar structures were recovered from coeval strata in the Imperial IOE et al. Isserk E-27 well and from slightly younger strata in the Dome Hunt Nektoralik K-59 and Hunt Dome Kopanoar M-13 wells. They consist of fibrous and platy calcite enclosing grains of barite, quartz, feldspar, clay minerals, and, very rarely, ferro-manganese minerals. The quartz, feldspar, and clay minerals are predominantly detrital with some authigenic overgrowths on the quartz and feldspar. The spheres and ellipsoids are interpreted to have formed during early diagenesis as micronodules, probably at, or near to, the sediment–water interface. However, a faecal pelletoidal origin cannot be totally ruled out.
Late Quaternary volcanic ash in the peatlands of central Alberta
Authors: Zoltai S. C.
Published: June 2008

Three distinct volcanic-ash layers were identified in peat deposits through visual, microscopic, and chemical means. These layers were related to known volcanic events through the 14C dating of 34 peat samples. The upper layer was probably Bridge River ash, deposited about 2350 years BP. The middle layer was possibly St. Helens Y tephra, deposited around 3400 years BP. The lower ash was related to Mazama tephra, deposited about 6600 years BP. Ash-enriched layers were formed in the accumulating peat as aerial deposition of tephra occurred, often for several hundred years before and after the presumed main eruption, as shown by 14C dates and peat accumulation rates. This implies periodic eruptions by the volcanoes, not all of which produced distinct ash layers in areas distant from the source. Redeposition from wind-eroded beds of Mazama ash during the dry postglacial climatic maximum is a possibility.
Diapiric trondhjemites of the western Dharwar craton, southern India
Authors: Rogers John J. W. , Callahan Elaine J.
Published: June 2008

Diapiric, comparatively massive trondhjemites were emplaced in the western part of the Dharwar craton of southern India about 3000 Ma ago. This age coincides with the age of (i) closure of Rb–Sr systems that now form the youngest isochrons in the predominantly gneissic terrane, and (ii) metasomatic enrichment of the gneisses in U. Younger events, principally about 2500 Ma ago, are recorded by sparse granites and by deformation of supracrustal sequences without major metamorphism. Thus, the trondhjemites appear to have formed during the last extensive thermochemical event in the craton. The trondhjemites are not associated with any mafic rocks and show very little fractionation within and among the various bodies.Presumably they formed as a single product of partial melting. Likely source materials for the magmas are rocks of basaltic composition (probably amphibolites) in the lower crust or along the crust–mantle boundary. Very low Zr and high Cr contents in the trondhjemites may indicate a slightly ultramafic (possibly basaltic komatiite) source. A lack of fractionation of Zr and Y and low light/heavy rare-earth element ratios in the trondhjemites may indicate an absence of equilibration of the magmas with major amounts of garnet. Lack of significant garnet equilibration could have resulted from production of hydrous magmas, either by partial melting of amphibolite or by introduction of water from an external source during the melting process.
Variability of Line Intercept Density Estimates (A Simulation Study of the Variance of Hydroacoustic Biomass Estimates)
Authors: Kimura Daniel K. , Lemberg Norman A.
Published: June 2008

"Line intercept density estimates" are defined as estimates of mean density arrived at by sampling density along randomly selected transects. For these estimates, the school (or patch) configuration being sampled strongly influences the variance of the mean density estimate. By simulating schools as circles (or ellipsoids) the variance component due to schooling was calculated by numerical integration, where the variance generating probability measure was a uniform distribution determined by the type of transect sampling employed. Results indicate that the component of variability due to schooling is large; that it can be effectively reduced (at practical sampling levels) by increasing sampling density; and that relative variance (as measured by a coefficient of variation) is extremely sensitive to the percentage of the sampling region covered by schools. Stratified methods of sampling (zig–zag and stratified parallel) were uniformly more efficient than random parallel sampling. Furthermore, zig–zag sampling was more efficient than stratified parallel sampling at low sampling intensities, while the opposite was true at high sampling intensities. No difference in efficiency was detected between sampling a rectangular as opposed to a square region. Although analyses were aimed principally at evaluating the variability of hydroacoustic biomass estimates, results are also applicable to line intercept estimates common in field ecology.Key words: transect sampling, hydroacoustic survey, simulation
Growth in Tropical Cephalopods: An Analysis Based on Statolith Microstructure
Authors: Jackson George D. , Choat J. Howard
Published: June 2008

Validated size-at-age data are presented for two tropical squid species (Loliolus noctiluca and Loligo chinensis) and a sepioid (Idiosepius pygmaeus). Estimates of age were obtained from daily increments in the statolith. All species reached adult size in less than 200 d. For each species, growth in mantle length was linear over the sizes sampled. In L. chinensis, growth was fastest during December–January (summer), with males showing faster growth rates than females. For I. pygmaeus, females generally had a higher growth rate than males. The slowest growth rates for both sexes occurred in the August–September (winter) period. The size-at-age data indicated rapid linear or exponential growth and a short life span of less than 1 yr. In contrast, growth curves generated from analysis of length frequency data (ELEFAN software package) suggested an asymptotic growth curve and ages in excess of 3 yr, and such analyses therefore appear inappropriate. The results of this study and a review of the literature revealed that rapid growth and short life span is the norm for pelagic cephalopods, with tropical species growing considerably faster than their temperate counterparts.
Mapping the Potential Spread of the Zebra Mussel (Dreissena polymorpha) in Ontario
Authors: Neary B. P. , Leach J. H.
Published: June 2008

The European zebra mussel (Dreissena polymorpha) is now firmly established in the lower Great Lakes and in isolated locations in the upper Great Lakes. Dispersal is aided by high fecundity, a planktonic larval stage, and ability of the mussel to be transported via shipping and recreational boating. Almost all waterbodies in Ontario which are downstream of established colonies or which can be reached through boating are vulnerable to invasion. However, there are ecological requirements (derived from European literature) which limit successful zebra mussel reproduction. Using data from over 6000 inland lakes in the province, we have prepared maps which show the distribution of pH, calcium, and major access routes and which indicate our estimated potential for success or failure of zebra mussel colonization. The utility of the maps is dependent on the validity of the ecological requirements for successful development of zebra mussel larvae, which were developed in Europe. There is a need to test the chemical requirements of the zebra mussel in North American waters.
A Bayesian Approach to Stock Assessment and Harvest Decisions Using the Sampling/Importance Resampling Algorithm
Authors: McAllister Murdoch K. , Pikitch Ellen K. , Punt Andre E. , Hilborn Ray
Published: June 2008

Scientific advice to fishery managers needs to be expressed in probabilistic terms to convey uncertainty about the consequences of alternative harvesting policies (policy performance indices). In most Bayesian approaches to such advice, relatively few of the model parameters used can be treated as uncertain, and deterministic assumptions about population dynamics are required; this can bias the degree of certainty and estimates of policy performance indices. We reformulate a Bayesian approach that uses the sampling/importance resampling algorithm to improve estimates of policy performance indices; it extends the number of parameters that can be treated as uncertain, does not require deterministic assumptions about population dynamics, and can use any of the types of fishery assessment models and data. Application of the approach to New Zealand's western stock of hoki (Macruronus novaezelandiae) shows that the use of Bayesian prior information for parameters such as the constant of proportionality for acoustic survey abundance indices can enhance management advice by reducing uncertainty in current stock size estimates; it also suggests that assuming historic recruitment is deterministic can create large negative biases (e.g., 26%) in estimates of biological and economic risks of alternative harvesting policies and that a stochastic recruitment assumption can be more appropriate.
Optimal allocation of sampling effort in lake sediment studies
Authors: Rowan David J. , Rasmussen Joseph B. , Kalff Jacob
Published: June 2008

A sampling algorithm requiring only bathymetric and catchment parameters has been derived from several recent empirical developments and should drastically reduce the number of sites and replicates necessary to characterize the distribution, trace element concentrations, and sediment accumulation rates of lake sediments. A test of this algorithm with sediments from 96 sites in three basins of morphometrically complex Jack Lake, Ontario, demonstrates the utility of this approach. A priori application of the algorithm would have reduced the number of sample sites on our sampling grid from 96 to 22 (a reduction of 77%), without losing precision. This reduction in sample sites (and in time and money expended) would allow for sampling additional lakes or sites of local significance (e.g., river or creek mouths, pollution point sources), or measuring additional parameters. The relationships between lake morphometry, sediment distribution, and sediment texture, along with the relationships between sediment texture and inter- and intra-site variability, can also be used to extrapolate sediment characteristics from a few samples to the whole lake or to predict the zone to which sediment is focused.
Influence of pH and hardness on toxicity of ammonia to the amphipod Hyalella azteca
Authors: Ankley G. T. , Schubauer-Berigan M. K. , Monson P. D.
Published: June 2008

The amphipod Hyalella azteca is frequently used for freshwater sediment tests throughout North America. A common potential toxicant in sediments is ammonia. Our objective was to characterize the influence of two key water quality variables, pH and hardness, on toxicity of ammonia to the amphipod. Ninety-six hour, water-only exposures of H. azteca to ammonia were conducted using three different water types with hardnesses of 42, 100, and 270 mg/L as CaCO3 and three levels of pH (ca. 6.5, 7.5, and 8.5). In the soft water, toxicity of total ammonia was constant across test pH. As water hardness increased, toxicity of ammonia (on a total basis) to the amphipod decreased and became more pH dependent. Our data suggest that in softer water the amphipod was quite sensitive to the ionized (NH4+) form of ammonia. This contrasts with most other species that have been tested, which typically are more sensitive to un-ionized (NH3) ammonia than to NH4+. These data provide baseline values for interpreting the possible contribution of ammonia to sediment toxicity in tests conducted with H. azteca and also indicate that in some situations NH4+ may be important in determining ammonia toxicity.
Influence of log additions on physical and biotic characteristics of a mountain stream
Authors: Wallace J. Bruce , Webster Jackson R. , Meyer Judith L.
Published: June 2008

Three pairs of cobble riffle study sites were established in a second-order stream in North Carolina and logs added to the downstream riffle at each site. At log addition transects, stream depth increased, current velocity decreased, cobble substratum was covered by sand and silt, and both coarse and fine particulate organic matter increased dramatically. Log additions had less dramatic effects on uptake lengths of ammonium, nitrate, and phosphate, but they had immediate and significant impacts on invertebrate community structure: abundances and biomass of scrapers and filterers decreased; collectors and predators increased; overall shredder biomass did not change, but biomass of trichopteran and dipteran shredders increased, while that of most plecopteran shredders decreased; and plecopteran predators also decreased despite greater abundances of potential prey. These observations suggest that physiological and morpho-behavioral constraints preclude many animals from tracking resources among patches when patches display very different abiotic conditions. Secondary production of scrapers and filterers decreased, whereas that of collectors and predators increased. The shifts in functional group abundances, biomass, and production between reference and debris-dam transects, which differed considerably from those previously reported for low-gradient, sandy-bottom streams, accentuate the importance of localized abiotic factors in structuring invertebrate communities within patches.
Corrélations entre des propriétés mécaniques dynamiques et statiques de sols argileux intacts et traités à la chaux
Authors: Locat Jacques , Beauséjour Normand
Published: June 2008

The use of an ultrasonic accelerometer has led to an empirical correlation between the wave velocity and the static mechanical strength deducted from destructive tests made on intact or lime-treated clays, and to an evaluation of the influence of certain physical soil parameters on wave velocity. The results give a good correlation between the dynamic elastic properties deducted from the shear wave velocity and the static mechanical properties of the intact and the lime-treated clays when measured without confining pressure. The results also confirm that the maximum dynamic shear modulus is proportional to undrained shear strength, independently of soil type. The structure of a lime-treated clay is more favorable to the transmission of shear waves than the same clay in an intact state having the same shear strength; the cause of this difference is associated with the compaction energy and the newly formed minerals resulting from the treatment. Finally, the study of these, treated soils has illustrated the effect of the cementation process on the mechanical behavior of clayey soils. Key words: ultrasonic accelerometer, shear wave velocity, clay, lime treated, cementation, elastic properties, static properties. [Journal translation]