bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Microautoradiography Combined with Fluorescence In Situ Hybridization To Determine Dimethylsulfoniopropionate Incorporation by Marine Bacterioplankton Taxa
Authors: Vila Maria , Simó Rafel , Kiene Ronald P. , Pinhassi Jarone , González José M. , Moran Mary Ann , Pedrós-Alió Carlos
Published: August 2004

The fraction of planktonic heterotrophic bacteria capable of incorporating dissolved dimethylsulfoniopropionate (DMSP) and leucine was determined at two coastal sites by microautoradioagraphy (AU). In Gulf of Mexico seawater microcosm experiments, the proportion of prokaryotes that incorporated sulfur from [
35
S]DMSP ranged between 27 and 51% of 4′,6-diamidino-2-phenylindole (DAPI)-positive cells, similar to or slightly lower than the proportion incorporating [
3
H]leucine. In the northwest Mediterranean coast, the proportion of cells incorporating sulfur from [
35
S]DMSP increased from 5 to 42% from January to March, coinciding with the development of a phytoplankton bloom. At the same time, the proportion of cells incorporating [
3
H]leucine increased from 21 to 40%. The combination of AU and fluorescence in situ hybridization (FISH) revealed that the
Roseobacter
clade (α-proteobacteria) accounted for 13 to 43% of the microorganisms incorporating [
35
S]DMSP at both sampling sites. Significant uptake of sulfur from DMSP was also found among members of the γ-proteobacteria and
Cytophaga-Flavobacterium
groups.
Roseobacter
and γ-proteobacteria exhibited the highest percentage of DAPI-positive cells incorporating
35
S from DMSP (around 50%). Altogether, the application of AU with [
35
S]DMSP combined with FISH indicated that utilization of S from DMSP is a widespread feature among active marine bacteria, comparable to leucine utilization. These results point toward DMSP as an important substrate for a broad and diverse fraction of marine bacterioplankton.
Chemotaxis of
Silicibacter
sp. Strain TM1040 toward Dinoflagellate Products
Authors: Miller Todd R. , Hnilicka Kristin , Dziedzic Amanda , Desplats Paula , Belas Robert
Published: August 2004

The α-proteobacteria phylogenetically related to the
Roseobacter
clade are predominantly responsible for the degradation of organosulfur compounds, including the algal osmolyte dimethylsulfoniopropionate (DMSP).
Silicibacter
sp. strain TM1040, isolated from a DMSP-producing
Pfiesteria piscicida
dinoflagellate culture, degrades DMSP, producing 3-methylmercaptopropionate. TM1040 possesses three lophotrichous flagella and is highly motile, leading to a hypothesis that TM1040 interacts with
P. piscicida
through a chemotactic response to compounds produced by its dinoflagellate host. A combination of a rapid chemotaxis screening assay and a quantitative capillary assay were used to measure chemotaxis of TM1040. These bacteria are highly attracted to dinoflagellate homogenates; however, the response decreases when homogenates are preheated to 80°C. To help identify the essential attractant molecules within the homogenates, a series of pure compounds were tested for their ability to serve as attractants. The results show that TM1040 is strongly attracted to amino acids and DMSP metabolites, while being only mildly responsive to sugars and the tricarboxylic acid cycle intermediates. Adding pure DMSP, methionine, or valine to the chemotaxis buffer resulted in a decreased response to the homogenates, indicating that exogenous addition of these chemicals blocks chemotaxis and suggesting that DMSP and amino acids are essential attractant molecules in the dinoflagellate homogenates. The implication of
Silicibacter
sp. strain TM1040 chemotaxis in establishing and maintaining its interaction with
P. piscicida
is discussed.
Identification of an Na+-Dependent Transporter Associated with Saxitoxin-Producing Strains of the CyanobacteriumAnabaena circinalis
Authors: Pomati Francesco , Burns Brendan P. , Neilan Brett A.
Published: August 2004

Blooms of the freshwater cyanobacteriumAnabaena circinalisare recognized as an important health risk worldwide due to the production of a range of toxins such as saxitoxin (STX) and its derivatives. In this study we used HIP1 octameric-palindrome repeated-sequence PCR to compare the genomic structure of phylogenetically similar Australian isolates ofA. circinalis. STX-producing and nontoxic cyanobacterial strains showed different HIP1 (highly iterated octameric palindrome 1) DNA patterns, and characteristic interrepeat amplicons for each group were identified. Suppression subtractive hybridization (SSH) was performed using HIP1 PCR-generated libraries to further identify toxic-strain-specific genes. An STX-producing strain and a nontoxic strain ofA. circinaliswere chosen as testers in two distinct experiments. The two categories of SSH putative tester-specific sequences were characterized by different families of encoded proteins that may be representative of the differences in metabolism between STX-producing and nontoxicA. circinalisstrains. DNA-microarray hybridization and genomic screening revealed a toxic-strain-specific HIP1 fragment coding for a putative Na+-dependent transporter. Analysis of this gene demonstrated analogy to themrpFgene ofBacillus subtilis, whose encoded protein is involved in Na+-specific pH homeostasis. The application of this gene as a molecular probe in laboratory and environmental screening for STX-producingA. circinalisstrains was demonstrated. The possible role of this putative Na+-dependent transporter in the toxic cyanobacterial phenotype is also discussed, in light of recent physiological studies of STX-producing cyanobacteria.
Detection and Quantification of the Red Tide Dinoflagellate
Karenia brevis
by Real-Time Nucleic Acid Sequence-Based Amplification
Authors: Casper Erica T. , Paul John H. , Smith Matthew C. , Gray Michael
Published: August 2004

Nucleic acid sequence-based amplification (NASBA) is an isothermal method of RNA amplification that has been previously used in clinical diagnostic testing. A real-time NASBA assay has been developed for the detection of
rbcL
mRNA from the red tide dinoflagellate
Karenia brevis
. This assay is sensitive to one
K. brevis
cell and 1.0 fg of in vitro transcript, with occasional detection of lower concentrations of transcript. The assay did not detect
rbcL
mRNA from a wide range of nontarget organisms and environmental clones, while 10 strains (all tested) of
K. brevis
were detected. By the use of standard curves based on time to positivity, concentrations of
K. brevis
in environmental samples were predicted by NASBA and classified into different levels of blooms per the Florida Fish and Wildlife Conservation Commission (FWC) system. NASBA classification matched FWC classification (based on cell counts) 72% of the time. Those samples that did not match were off by only one class. NASBA is sensitive, rapid, and effective and may be used as an additional or alternative method to detect and quantify
K. brevis
in the marine environment.
veA
Is Required for Toxin and Sclerotial Production in
Aspergillus parasiticus
Authors: Calvo Ana M. , Bok Jinwoo , Brooks Wilhelmina , Keller Nancy P.
Published: August 2004

It was long been noted that secondary metabolism is associated with fungal development. In
Aspergillus nidulans
, conidiation and mycotoxin production are linked by a G protein signaling pathway. Also in
A. nidulans
, cleistothecial development and mycotoxin production are controlled by a gene called
veA
. Here we report the characterization of a
veA
ortholog in the aflatoxin-producing fungus
A. parasiticus
. Cleistothecia are not produced by
Aspergillus parasiticus
; instead, this fungus produces spherical structures called sclerotia that allow for survival under adverse conditions. Deletion of
veA
from
A. parasiticus
resulted in the blockage of sclerotial formation as well as a blockage in the production of aflatoxin intermediates. Our results indicate that
A. parasiticus veA
is required for the expression of
aflR
and
aflJ
, which regulate the activation of the aflatoxin gene cluster. In addition to these findings, we observed that deletion of
veA
reduced conidiation both on the culture medium and on peanut seed. The fact that
veA
is necessary for conidiation, production of resistant structures, and aflatoxin biosynthesis makes
veA
a good candidate gene to control aflatoxin biosynthesis or fungal development and in this way to greatly decrease its devastating impact on health and the economy.
Comparisons of Different Hypervariable Regions ofrrsGenes for Use in Fingerprinting of Microbial Communities by PCR-Denaturing Gradient Gel Electrophoresis
Authors: Yu Zhongtang , Morrison Mark
Published: August 2004

Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial diversity and community structure, but no systematic comparison has been made of the DGGE profiles obtained when different hypervariable (V) regions are amplified from the same community DNA samples. We report here a study to make such comparisons and establish a preferred choice of V region(s) to examine by DGGE, when community DNA extracted from samples of digesta is used. When the members of the phylogenetically representative set of 218rrsgenes archived in the RDP II database were compared, the V1 region was found to be the most variable, followed by the V9 and V3 regions. The temperature of the lowest-melting-temperature (Tm(L)) domain for each V region was also calculated for theserrsgenes, and the V1 to V4 region was found to be most heterogeneous with respect toTm(L). The averageTm(L)values and their standard deviations for each V region were then used to devise the denaturing gradients suitable for separating 95% of all the sequences, and the PCR-DGGE profiles produced from the same community DNA samples with these conditions were compared. The resulting DGGE profiles were substantially different in terms of the number, resolution, and relative intensity of the amplification products. The DGGE profiles of the V3 region were best, and the V3 to V5 and V6 to V8 regions produced better DGGE profiles than did other multiple V-region amplicons. Introduction of degenerate bases in the primers used to amplify the V1 or V3 region alone did not improve DGGE banding profiles. Our results show that DGGE analysis of gastrointestinal microbiomes is best accomplished by the amplification of either the V3 or V1 region ofrrsgenes, but if a longer amplification product is desired, then the V3 to V5 or V6 to V8 region should be targeted.
Protein Folding Failure Sets High-Temperature Limit on Growth of Phage P22 in
Salmonella enterica
Serovar Typhimurium
Authors: Pope Welkin H. , Haase-Pettingell Cameron , King Jonathan
Published: August 2004

The high-temperature limit for growth of microorganisms differs greatly depending on their species and habitat. The importance of an organism's ability to manage thermal stress is reflected in the ubiquitous distribution of the heat shock chaperones. Although many chaperones function to reduce protein folding defects, it has been difficult to identify the specific protein folding pathways that set the high-temperature limit of growth for a given microorganism. We have investigated this for a simple system, phage P22 infection of
Salmonella enterica
serovar Typhimurium. Production of infectious particles exhibited a broad maximum of 150 phage per cell when host cells were grown at between 30 and 39°C in minimal medium. Production of infectious phage declined sharply in the range of 40 to 41°C, and at 42°C, production had fallen to less than 1% of the maximum rate. The host cells maintained optimal division rates at these temperatures. The decrease in phage infectivity was steeper than the loss of physical particles, suggesting that noninfectious particles were formed at higher temperatures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a decrease in the tailspike adhesins assembled on phage particles purified from cultures incubated at higher temperatures. The infectivity of these particles was restored by in vitro incubation with soluble tailspike trimers. Examination of tailspike folding and assembly in lysates of phage-infected cells confirmed that the fraction of polypeptide chains able to reach the native state in vivo decreased with increasing temperature, indicating a thermal folding defect rather than a particle assembly defect. Thus, we believe that the folding pathway of the tailspike adhesin sets the high-temperature limit for P22 formation in
Salmonella
serovar Typhimurium.
Characterization of Coliphage PR772 and Evaluation of Its Use for Virus Filter Performance Testing
Authors: Lute Scott , Aranha Hazel , Tremblay Denise , Liang Dehai , Ackermann Hans-W. , Chu Benjamin , Moineau Sylvain , Brorson Kurt
Published: August 2004

Virus filtration is a key clearance unit operation in the manufacture of recombinant protein, monoclonal antibody, and plasma-derived biopharmaceuticals. Recently, a consensus has developed among filter manufacturers and end users about the desirability of a common nomenclature and a standardized test for classifying and identifying virus-retentive filters. The Parenteral Drug Association virus filter task force has chosen PR772 as the model bacteriophage to standardize nomenclature for large-pore-size virus-retentive filters (filters designed to retain viruses larger than 50 to 60 nm in size). Previously, the coliphage PR772 (
Tectiviridae
family) has been used in some filtration studies as a surrogate for mammalian viruses of around 50 to 60 nm. In this report, we describe specific properties of PR772 critical to the support of its use for the standardization of virus filters. The complete genomic sequence of virulent phage PR772 was determined. Its genome contains 14,946 bp with an overall G+C content of 48.3 mol%, and 32 open reading frames of at least 40 codons. Comparison of the PR772 nucleotide sequence with the genome of
Tectiviridae
family prototype phage PRD1 revealed 97.2% identity at the DNA level. By dynamic light-scattering analysis, its hydrodynamic diameter was measured as 82 ± 6 nm, consistent with use in testing large-virus-retentive filters. Finally, dynamic light-scattering analysis of PR772 preparations purified on CsCl gradients showed that the phage preparations are largely monodispersed. In summary, PR772 appears to be an appropriate model bacteriophage for standardization of nomenclature for larger-pore-size virus-retentive filters.
Dominant Microbial Composition and Its Vertical Distribution in Saline Meromictic Lake Kaiike (Japan) as Revealed by Quantitative Oligonucleotide Probe Membrane Hybridization
Authors: Koizumi Yoshikazu , Kojima Hisaya , Fukui Manabu
Published: August 2004

Vertical distributions of dominant bacterial populations in saline meromictic Lake Kaiike were investigated throughout the water column and sediment by quantitative oligonucleotide probe membrane hybridization. Three oligonucleotide probes specific for the small-subunit (SSU) rRNA of three groups of
Chlorobiaceae
were newly designed. In addition, three general domain (
Bacteria
,
Archaea
, and
Eukarya
)-specific probes, two δ-
Proteobacteria
-specific probes, a
Chlorobiaceae
-specific probe, and a
Chloroflexi
-specific probe were used after optimization of their washing conditions. The abundance of the sum of SSU rRNAs hybridizing with probes specific for three groups of
Chlorobiaceae
relative to total SSU rRNA peaked in the chemocline, accounting for up to 68%. The abundance of the δ-proteobacterial SSU rRNA relative to total SSU rRNA rapidly increased just below the chemocline up to 29% in anoxic water and peaked at the 2- to 3-cm sediment depth at ca. 34%. The abundance of SSU rRNAs hybridizing with the probe specific for the phylum
Chloroflexi
relative to total SSU rRNA was highest (31 to 54%) in the top of the sediment but then steeply declined with depth and became stable at 11 to 19%, indicating the robust coexistence of sulfate-reducing bacteria and
Chloroflexi
in the top of the sediment. Any SSU rRNA of
Chloroflexi
in the water column was under the detection limit. The summation of the signals of group-specific probes used in this study accounted for up to 89% of total SSU rRNA, suggesting that the DGGE-oligonucleotide probe hybridization approach, in contrast to conventional culture-dependent approaches, was very effective in covering dominant populations.
Differential Gene Expression To Investigate the Effect of (
5Z
)-4-Bromo- 5-(Bromomethylene)-3-Butyl-2(
5H
)-Furanone on
Bacillus subtilis
Authors: Ren Dacheng , Bedzyk Laura A. , Setlow Peter , England Dacre F. , Kjelleberg Staffan , Thomas Stuart M. , Ye Rick W. , Wood Thomas K.
Published: August 2004

(
5Z
)-4-Bromo-5-(bromomethylene)-3-butyl-2(
5H
)-furanone (furanone) from the red marine alga
Delisea pulchra
was found previously to inhibit the growth, swarming, and biofilm formation of gram-positive bacteria. Using the gram-positive bacterium
Bacillus subtilis
as a test organism, we observed cell killing by 20 μg of furanone per ml, while 5 μg of furanone per ml inhibited growth approximately twofold without killing the cells. To discover the mechanism of this inhibition on a genetic level and to investigate furanone as a novel antibiotic, full-genome DNA microarrays were used to analyze the gene expression profiles of
B. subtilis
grown with and without 5 μg of furanone per ml. This agent induced 92 genes more than fivefold (
P
< 0.05) and repressed 15 genes more than fivefold (
P
< 0.05). The induced genes include genes involved in stress responses (such as the class III heat shock genes
clpC
,
clpE
, and
ctsR
and the class I heat shock genes
groES
, but no class II or IV heat shock genes), fatty acid biosynthesis, lichenan degradation, transport, and metabolism, as well as 59 genes with unknown functions. The microarray results for four genes were confirmed by RNA dot blotting. Mutation of a stress response gene,
clpC
, caused
B. subtilis
to be much more sensitive to 5 μg of furanone per ml (there was no growth in 8 h, while the wild-type strain grew to the stationary phase in 8 h) and confirmed the importance of the induction of this gene as identified by the microarray analysis.
Model System for Growing and Quantifying
Streptococcus pneumoniae
Biofilms In Situ and in Real Time
Authors: Donlan R. M. , Piede J. A. , Heyes C. D. , Sanii L. , Murga R. , Edmonds P. , El-Sayed I. , El-Sayed M. A.
Published: August 2004

Streptococcus pneumoniae
forms biofilms, but little is known about its extracellular polymeric substances (EPS) or the kinetics of biofilm formation. A system was developed to enable the simultaneous measurement of cells and the EPS of biofilm-associated
S. pneumoniae
in situ over time. A biofilm reactor containing germanium coupons was interfaced to an attenuated total reflectance (ATR) germanium cell of a Fourier transform infrared (FTIR) laser spectrometer. Biofilm-associated cells were recovered from the coupons and quantified by total and viable cell count methods. ATR-FTIR spectroscopy of biofilms formed on the germanium internal reflection element (IRE) of the ATR cell provided a continuous spectrum of biofilm protein and polysaccharide (a measure of the EPS). Staining of the biofilms on the IRE surface with specific fluorescent probes provided confirmatory evidence for the biofilm structure and the presence of biofilm polysaccharides. Biofilm protein and polysaccharides were detected within hours after inoculation and continued to increase for the next 141 h. The polysaccharide band increased at a substantially higher rate than did the protein band, demonstrating increasing coverage of the IRE surface with biofilm polysaccharides. The biofilm total cell counts on germanium coupons stabilized after 21 h, at approximately 10
5
cells per cm
2
, while viable counts decreased as the biofilm aged. This system is unique in its ability to detect and quantify biofilm-associated cells and EPS of
S. pneumoniae
over time by using multiple, corroborative techniques. This approach could prove useful for the study of biofilm processes of this or other microorganisms of clinical or industrial relevance.
VdNEP, an Elicitor from
Verticillium dahliae
, Induces Cotton Plant Wilting
Authors: Wang Jian-Ying , Cai Yu , Gou Jin-Ying , Mao Ying-Bo , Xu Yan-Hua , Jiang Wei-Hong , Chen Xiao-Ya
Published: August 2004

Verticillium wilt is a vascular disease of cotton. The causal fungus,
Verticillium dahliae
, secretes elicitors in culture. We have generated ∼1,000 5′-terminal expressed sequence tags (ESTs) from a cultured mycelium of
V. dahliae
. A number of ESTs were found to encode proteins harboring putative signal peptides for secretion, and their cDNAs were isolated. Heterologous expression led to the identification of a protein with elicitor activities. This protein, named
V. dahliae
necrosis- and ethylene-inducing protein (VdNEP), is composed of 233 amino acids and has high sequence identities with fungal necrosis- and ethylene-inducing proteins. Infiltration of the bacterially expressed His-VdNEP into
Nicotiana benthamiana
leaves resulted in necrotic lesion formation. In
Arabidopsis thaliana
, the fusion protein also triggered production of reactive oxygen species and induced the expression of
PR
genes. When added into suspension cultured cells of cotton (
Gossypium arboreum
), the fusion protein elicited the biosynthesis of gossypol and related sesquiterpene phytoalexins at low concentrations, and it induced cell death at higher concentrations. On cotton cotyledons and leaves, His-VdNEP induced dehydration and wilting, similar to symptoms caused by a crude preparation of
V. dahliae
elicitors. Northern blotting showed a low level of
VdNEP
expression in the mycelium during culture. These data suggest that VdNEP is a wilt-inducing factor and that it participates in cotton-
V. dahliae
interactions.
Direct Production of Ethanol from Raw Corn Starch via Fermentation by Use of a Novel Surface-Engineered Yeast Strain Codisplaying Glucoamylase and α-Amylase
Authors: Shigechi Hisayori , Koh Jun , Fujita Yasuya , Matsumoto Takeshi , Bito Yohei , Ueda Mitsuyoshi , Satoh Eiichi , Fukuda Hideki , Kondo Akihiko
Published: August 2004

Direct and efficient production of ethanol by fermentation from raw corn starch was achieved by using the yeast
Saccharomyces cerevisiae
codisplaying
Rhizopus oryzae
glucoamylase and
Streptococcus bovis
α-amylase by using the C-terminal-half region of α-agglutinin and the flocculation functional domain of Flo1p as the respective anchor proteins. In 72-h fermentation, this strain produced 61.8 g of ethanol/liter, with 86.5% of theoretical yield from raw corn starch.
Temporal Transcription Map of the Virulent
Streptococcus thermophilus
Bacteriophage Sfi19
Authors: Ventura Marco , Brüssow Harald
Published: August 2004

A transcription map was developed for the virulent
Streptococcus thermophilus
phage Sfi19 on the basis of systematic Northern blot hybridizations. All deduced 5′ ends were confirmed by primer extension experiments. Three classes of transcripts were detected based on the different times of appearance. Early transcripts were identified in three genome regions; middle transcripts covered
cro
-like, DNA replication, and transcriptional regulation genes; and late genes consisted of structural and lysis genes. Chloramphenicol treatment suppressed the translation of a putative transcriptional factor necessary for the production of late transcripts and shifted middle transcripts to early transcription times.
Slow post-orogenic cooling in a deeply eroded orogen: Reindeer Zone, Trans-Hudson Orogen, Saskatchewan
Authors: Chakungal Joyia , Reynolds Peter H , Jamieson Rebecca A , Corrigan David
Published: July 2004

We present 40Ar/39Ar hornblende and muscovite data from a 200 km transect across the northern flank of the Paleoproterozoic Trans-Hudson Orogen (THO) exposed along Reindeer Lake in Saskatchewan, Canada. The transect crosses a series of distinct lithotectonic domains that experienced pressuretemperature (PT) conditions of 600730 °C at 4.56.0 kbar (1 kbar = 100 MPa) during D2 peak metamorphism at 18201790 Ma. The distribution of 40Ar/39Ar hornblende ages shows that most of the transect cooled through approximately 500 °C by ca. 1765 Ma, with two significant exceptions. At the north end of the transect, older ages in the Peter Lake Domain (up to 2200 Ma) suggest that this region did not experience high-grade metamorphism that affected the rest of the transect and may indicate a structural break between these Archean rocks and the Cree Lake Zone to the north. In the south-central part of the transect, UPb (monazite, titanite) and 40Ar/39Ar (hornblende, muscovite) ages indicate that rocks in the vicinity of the Duck Lake Shear Zone, a ductile thrust zone separating the Kisseynew and La Ronge domains, cooled at a rate of 6 °C/Ma and that cooling was delayed by ca. 2025 million years relative to that of adjacent regions. Based on generic thermaltectonic models for large hot orogens, we suggest that delayed cooling in the vicinity of the shear zone reflects post-orogenic thermal relaxation of lower crustal isotherms that were perturbed by the effects of convergence.
A geothermally influenced wetland containing unconsolidated geochemical sediments
Authors: Channing A , Edwards D , Sturtevant S
Published: July 2004

Hot spring waters flowing from Porkchop Geyser, Norris Geyser Basin, Yellowstone National Park, USA. enter a shallow wetland basin and precipitate opal-A silica particulate. Particulate formation by chemical (rather than biochemical) and colloidal mechanisms is suggested by floc- and shard-like particle morphologies comprising opal-A silica nanospheres and microspheres of colloidal dimensions and precipitation from waters with opaque milky-blue colouration, indicative of aqueous silica-sol conditions. Sediment accumulates in the wetland at a rate of ca. 2025 mm/year, is unconsolidated, and massive to diffusely bedded to laminated. Post depositional features include soft sediment deformation and scouring, and in drying conditions, relatively deep desiccation. Establishment of geochemically dominated wetland sedimentation is favoured where alkali-chloride hot spring fluids of circum neutral to basic pH and high silica concentration discharge to and cool (to < ca. 35 °C) within topographic depressions that receive only small volumes of non-hot spring water. Local wetland vegetation, which is composed of hydrophytes, halophytes, and alkali-tolerant species more typical of coastal wetlands, colonizes the soft wetland substrate and may be relatively quickly buried by rapid sediment accumulation. Prior to the evolution of the diatom silica-sink, geothermal wetlands containing geochemically precipitated silica sediments may have been much more common and widespread. Rhizoliths, chert nodules with organic cores, scour fabrics, soft sediment deformation, desiccation cracks, and massive to diffuse bedding preserved in Palaeozoic geothermal environments may all be evidence of ancient unconsolidated geochemical sediments and geothermal wetland conditions.
Geochemistry of North Shore Hypabyssal dikes and sills in the Midcontinent Rift of Minnesota: an example  the 47th Avenue sill
Authors: Seifert Karl E , Olmsted James F
Published: July 2004

This study presents geochemical data for several of the numerous small to large dikes and sills, including the 47th Avenue sill, exposed along the shore of Lake Superior in and north of Duluth, Minnesota. These intrusions are late magmatic features of the Proterozoic Midcontinent Rift System and together form the North Shore Hypabyssal Group. The dikes are geochemically distinct from the sills, and, when the two are exposed together, the younger dike intrudes the older sill. Dikes are primitive with Mg# up to 68, have positive εNd values, and are oriented approximately northsouth with steep westerly or near vertical dips. The older sills are more evolved, usually have εNd values near or below 0, and have the same gentle easterly dip as the thick sequence of North Shore Volcanic Group flows they intrude. Dike compositions correlate best with a mixture of widespread basalt compositions types 4 and 5, with primitive geochemistry and positive εNd values, whereas sill compositions are similar to widespread basalt composition type 4 typical of most North Shore Volcanic Group flows. The 47th Avenue sill in Duluth is an evolved single intrusion North Shore Hypabyssal Group diabase sill with trough banding, sharp lower and upper contacts, and a spectacular fractured and undulating roof zone containing blocks of the overlying ferroandesite flow.
Application of comparative genomics to narrow-leafed lupin (Lupinus angustifoliusL.) using sequence information from soybean andArabidopsis
Authors: Francki Michael G , Mullan Daniel J
Published: August 2004

The completion of genome-sequencing initiatives for model plants and EST databases for major crop species provides a large resource for gaining fundamental knowledge of complex gene interactions and the functional significance of proteins. There are increasingly numerous opportunities to transfer this information to other plant species with uncharacterized genomes and make advances in genome analysis, gene expression, and predicted protein function. In this study, we have used DNA sequences from soybean and Arabidopsis to determine the feasibility of applying comparative genomics to narrow-leafed lupin. We have used transcribed sequences from soybean and showed that a high proportion cross hybridize to lupin DNA, identifying similar genes and providing landmarks for estimating the degree of chromosomal synteny between species. To further investigate comparative relationships in this study, a detailed analysis of three lupin genes and comparison of orthologs from soybean and Arabidopsis shows that, in some cases, gene structure and expression are highly conserved and their proteins may have similar function. In other cases, genes show variation in expression profiles indicating alternative functions across species. The advantages and limitation of using soybean and Arabidopsis sequences for comparative genomics in lupins are discussed.Key words: comparative genomics, narrow-leafed lupins, soybean, Arabidopsis.
Regeneration of somatic hybrids in relation to the nuclear and cytoplasmic genomes of wheat andSetaria italica
Authors: Xiang Fengning , Xia Guangmin , Zhi Daying , Wang Jing , Nie Hui , Chen Huimin
Published: August 2004

Somatic hybridization via PEG (Polyethylene 6000)-mediated protoplast fusion was achieved between two different wheat culture lines (Triticum aestivum L., 'Jinan' 177, T1 and T2) and Setaria italica (L.) P. Beauv. The T1 recipient originated from non-regenerable long-term cell suspensions, while T2 was derived from embryogenic calli with a high regeneration capacity. Donor protoplasts were obtained from embryogenic calli of S. italica (S) (with low regeneration capacity) irradiated with different doses of ultraviolet light. Twenty-three putative hybrid cell lines were produced in fusion combinations with the donor protoplasts treated with UV light for 30 s (combination I) and 1 min (combination II), but only one (from combination II) differentiated into green plants. Three cell lines from combination I and five cell lines from combination II possessed the nuclear genomes of T1, T2, and S. italica as revealed by cytological, isozyme, RAPD, and 5S rDNA spacer sequence analyses. Genomic in situ hybridization (GISH) analysis showed that most hybrid cell lines had 2236 wheat chromosomes, 02 S. italica chromosomes, and 16 wheat  S. italica recombinant chromosomes, whereas the regenerable cell line had 4456 wheat chromosomes and 36 recombinant chromosomes, but no intact S. italica chromosomes. RFLP analysis of organellar DNA revealed that mitochondrial and chloroplast DNA of both parents coexisted in all hybrid cell lines and recombined in most hybrid cell lines. These results indicate that the regeneration of hybrid plants involves not only the integration of S. italica nuclear and organellar DNA, but also the genome complementation of T1 and T2.Key words: Triticum aestivum L., Setaria italica (L.) P. Beauv., asymmetric somatic hybridization, UV treatment, hybrid plant, nuclear and cytoplasmic genome.
Isolation of a family of resistance gene analogue sequences of the nucleotide binding site (NBS) type fromLensspecies
Authors: Yaish M W.F , Sáenz de Miera L E , Pérez de la Vega M
Published: August 2004

Most known plant disease-resistance genes (R genes) include in their encoded products domains such as a nucleotide-binding site (NBS) or leucine-rich repeats (LRRs). Sequences with unknown function, but encoding these conserved domains, have been defined as resistance gene analogues (RGAs). The conserved motifs within plant NBS domains make it possible to use degenerate primers and PCR to isolate RGAs. We used degenerate primers deduced from conserved motifs in the NBS domain of NBS-LRR resistance proteins to amplify genomic sequences from Lens species. Fragments from approximately 500-850 bp were obtained. The nucleotide sequence analysis of these fragments revealed 32 different RGA sequences in Lens species with a high similarity (up to 91%) to RGAs from other plants. The predicted amino acid sequences showed that lentil sequences contain all the conserved motifs (P-loop, kinase-2, kinase-3a, GLPL, and MHD) present in the majority of other known plant NBSLRR resistance genes. Phylogenetic analyses grouped the Lens NBS sequences with the Toll and interleukin-1 receptor (TIR) subclass of NBSLRR genes, as well as with RGA sequences isolated from other legume species. Using inverse PCR on one putative RGA of lentil, we were able to amplify the flanking regions of this sequence, which contained features found in R proteins.Key words: disease resistance genes, comparative analysis, lentils, TIR, LRR.
Gene expression profiling of the bovine gastrointestinal tract
Authors: Hansen Christiane , Fu Anna , Meng Yan , Okine Erasmus , Hawken Rachel , Barris Wes , Li Changxi , Moore Stephen S
Published: August 2004

Basal gene expression levels across the bovine gastrointestinal tract (GI) were examined in an attempt to formulate genetic explanations for the differences in function that are known or thought to exist between the various regions. Gene expression along the tract was studied through the random sequencing of a total of 16 412 clones from seven tissue-specific cDNA libraries spanning its length. The expressed sequence tags (ESTs) within each library were clustered to reduce clone redundancy and obtain longer consensus sequences. BLASTN and BLASTX searches against the NCBI human RefSeq databases were used to find putative matches for the bovine sequences and gene ontology assignments were made. Notable similarities and differences in gene expression were observed among the various compartments of the GI tract of the bovine. Many of the prominent transcripts have yet to be reliably identified and the prominence of others may be worthy of further examination. This collection of ESTs represents an important resource for the future construction of a GI tract specific microarray for further gene expression studies.Key words: gene expression, EST, gastrointestinal tract, cattle.
A direct repeat sequence associated with the centromeric retrotransposons in wheat
Authors: Ito Hidetaka , Nasuda Shuhei , Endo Takashi R
Published: August 2004

A high-density BAC filter of Triticum monococcum was screened for the presence of a centromeric retrotransposon using the integrase region as a probe. Southern hybridization to the BAC digests using total genomic DNA probes of Triticum monococcum, Triticum aestivum, and Hordeum vulgare detected differentially hybridizing restriction fragments between wheat and barley. The fragments that hybridized to genomic DNA of wheat but not to that of barley were subcloned. Fluorescence in situ hybridization (FISH) analysis indicated that the clone pHind258 hybridized strongly to centromeric regions in wheat and rye and weakly to those in barley. The sequence of pHind258 was homologous to integrase and long terminal repeats of centromeric Ty3-gypsy retrotransposons of cereal species. Additionally, pHind258 has a pair of 192-bp direct repeats. FISH analysis indicated that the 192-bp repeat probe hybridized to centromeres of wheat and rye but not to those of barley. We found differential FISH signal intensities among wheat chromosomes using the 192-bp probe. In general, the A-genome chromosomes possess strong FISH signals, the B-genome chromosomes possess moderate signals, and the D-genome chromosomes possess weak signals. This was consistent with the estimated copy numbers of the 192-bp repeats in the ancestral species of hexaploid wheat.Key words: centromere, Ty3-gypsy retrotransposon, FISH, wheat, repetitive element.
Nucleoplasmin: a nuclear chaperone
Authors: Prado Adelina , Ramos Isbaal , Frehlick Lindsay J , Muga Arturo , Ausió Juan
Published: August 2004

In this article, we briefly review the structural and functional information currently available on nucleoplasmin. Special emphasis is placed on the discussion of the molecular mechanism involved in the sperm chromatin remodelling activity of this protein. A model is proposed based on current crystallographic data, recent biophysical and functional studies, as well as in the previously available information.Key words: nucleoplasmin, review, histone chaperone, sperm chromatin remodeling, nucleosome assembly.
Functional diversity of ISWI complexes
Authors: Dirscherl Sara S , Krebs Jocelyn E
Published: August 2004

The yeast SWI/SNF ATP-dependent chromatin remodeling complex was first identified and characterized over 10 years ago (F. Winston and M. Carlson. 1992. Trends Genet. 8: 387–391.) Since then, the number of distinct ATP-dependent chromatin remodeling complexes and the variety of roles they play in nuclear processes have become dizzying (J.A. Martens and F. Winston. 2003. Curr. Opin. Genet. Dev. 13: 136–142; A. Vacquero et al. 2003. Sci. Aging Knowledge Environ. 2003: RE4) — and that does not even include the companion suite of histone modifying enzymes, which exhibit a comparable diversity in both number of complexes and variety of functions (M.J. Carrozza et al. 2003. Trends Genet. 19: 321–329; W. Fischle et al. 2003. Curr. Opin. Cell Biol. 15: 172–183; M. Iizuka and M.M. Smith. 2003. Curr. Opin. Genet. Dev. 13: 1529–1539). This vast complexity is hardly surprising, given that all nuclear processes that involve DNA — transcription, replication, repair, recombination, sister chromatid cohesion, etc. — must all occur in the context of chromatin. The SWI/SNF-related ATP-dependent remodelers are divided into a number of subfamilies, all related by the SWI2/SNF2 ATPase at their catalytic core. In nearly every species where researchers have looked for them, one or more members of each subfamily have been identified. Even the budding yeast, with its comparatively small genome, contains eight different chromatin remodelers in five different subfamilies. This review will focus on just one subfamily, the Imitation Switch (ISWI) family, which is proving to be one of the most diverse groups of chromatin remodelers in both form and function.
Use of the surface proteins GapC and Mig ofStreptococcus dysgalactiaeas potential protective antigens against bovine mastitis
Authors: Bolton Alexandra , Song Xin-Ming , Willson Philip , Fontaine Michael C , Potter Andrew A , Perez-Casal Jose
Published: August 2004

Streptococcus dysgalactiae is a significant pathogen associated with bovine mastitis in lactating and nonlactating dairy cows, causing a severe inflammatory response of the mammary gland, which results in major economic losses to the dairy industry. Two proteins from S. dysgalactiae strain SDG8 were tested for their protective capacity against a homologous bacterial challenge in a dry cow model. The first was a bovine plasmin receptor protein (GapC), which shares 99.4% sequence identity to the plasmin-binding Plr protein of group A streptococci. The second protein product was Mig, a α2-M-, IgG-, and IgA-binding protein present on the cell surface of SDG8. We investigated the efficacy of immunization with purified recombinant forms of GapC and Mig by measuring the number of somatic cells and assessing the presence of the challenge strain in mammary secretions following challenge. In this model, we found that, although the number of quarters containing SDG8 was significantly reduced in the GapC- but not in the Mig-immunized animals, the somatic cell counts from teat secretions were significantly decreased in both the GapC and Mig vaccinates.Key words: Streptococcus dysgalactiae, bovine mastitis, Mig, GapC, GAPDH.
An indirect mutualism: ants deter seed predators from ovipositing in yucca fruit
Authors: Perry Jennifer C , Mondor Edward B , Addicott John F
Published: August 2004

An indirect mutualism arises when the beneficial effect of two species on each other depends upon the presence of a third species. Surveys, fruit dissections, and behavioural observations on yucca (Yucca glauca Nutt.) indicate that wood ants (species of Formica L., 1758) deter oviposition by non-pollinating, seed-predating moths (Tegeticula corruptrix Pellmyr, 1999) but not by pollinating moths (Tegeticula yuccasella (Riley, 1872)). Wood ants also have a direct negative effect on yuccas owing to flower bud feeding damage; however, damage is minor and variable. As wood ants decrease seed-predator oviposition by 38%, there is a net benefit of wood ants on yuccas. Thus, we suggest that an indirect mutualism can occur between wood ants and yuccas when non-pollinating yucca moths are present.
Germ-line versus somatic cells. I. Stereological study of differentiating embryonic tissues of Tetrodontophora bielanensis (Hexapoda, Collembola)
Authors: Świątek P , Vogelgesang M , Romek M , Klag J
Published: August 2004

We examined five different somatic tissues and compared them with germ-line cells to verify the "disposable soma" theory. Two embryonic stages and second-stage juveniles of Tetrodontophora bielanensis Waga, 1842 (Hexapoda, Collembola) were studied. Our results show that changes in relative volume of mitochondria during differentiation of cells correlate well with transformations of cell morphology. During morphological transformation of differentiating somatic cells, the relative volume of mitochondria in their cytoplasm is high, whereas in the differentiated tissues, this parameter is much lower. Surprisingly, the highest value of relative volume density of mitochondria is found in the cytoplasm of germ-line cells. If we accept that this parameter indicates the cell metabolism rate, then our results should be taken as supporting the "disposable soma" theory. It is also conceivable that the higher volume of mitochondria in the germ-line cells have nothing to do with energy production but, for instance, with the production or function of nuage material (germ-cell determinant) in the germ-line cells. These two possibilities are discussed.
Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes
Authors: Hogg Ian D , Hebert Paul D.N
Published: August 2004

We evaluated sequence diversity in the mitochondrial cytochrome-c oxidase I (COI; EC 1.9.3.1) gene as a tool for resolving differences among species of Arctic springtails. The Collembola examined in this analysis were collected from Igloolik, Cornwallis, and Somerset islands and included representatives from all major families found in the Arctic. Members of 13 genera and 19 species were examined, including 4 species of the genus Folsomia and 3 species of the genus Hypogastrura. In all cases, species were successfully discriminated. Sequence divergences within species were generally less than 1%, whereas divergences between species were greater than 8% in all cases. Divergences among individuals of one species of Folsomia were much higher (up to 13%), but this likely represents the presence of an undescribed sibling species. We conclude that DNA barcoding is a powerful tool for identifying species of Collembola and should regularly be useful as a complement to traditional, morphological taxonomy.
Plumage color as a dynamic trait: carotenoid pigmentation of male house finches (Carpodacus mexicanus) fades during the breeding season
Authors: McGraw Kevin J , Hill Geoffrey E
Published: August 2004

Evolutionary biologists studying sexually selected bird plumage generally consider this trait to be static throughout a breeding season and assign trait values to individuals on the basis of single measurements. We investigated the propensity for carotenoid-based color of feather patches in male house finches (Carpodacus mexicanus ( Muller, 1776)) to change during the breeding period. We recaptured and rescored 63 males and found that the hue of feathers faded significantly over the season. The degree of hue change was a direct function of the amount of time between plumage scores; feathers faded more as the interval between measurements increased. The magnitude of hue change was not, however, related to an individual's age or initial plumage redness, which suggests that certain birds are not more or less prone to fading. Collectively, these findings imply that researchers should more carefully track plumage color expression during the course of a year, as seasonal color shifts may have important consequences for late-season male–male competitive interactions and flexible female mating tactics (e.g., social mate switching, choice of extra-pair partners). Potential mechanisms for this seasonal plumage color shift are discussed.
STRONG-COUPLING ASYMPTOTIC EXPANSION FOR SCHRÖDINGER OPERATORS WITH A SINGULAR INTERACTION SUPPORTED BY A CURVE IN ℝ3
Authors: EXNER P. , KONDEJ S.
Published: August 2004

We investigate a class of generalized Schrödinger operators in L2(ℝ3) with a singular interaction supported by a smooth curve Γ. We find a strong-coupling asymptotic expansion of the discrete spectrum in the case when Γ is a loop or an infinite bent curve which is asymptotically straight. It is given in terms of an auxiliary one-dimensional Schrödinger operator with a potential determined by the curvature of Γ. In the same way, we obtain asymptotics of spectral bands for a periodic curve. In particular, the spectrum is shown to have open gaps in this case if Γ is not a straight line and the singular interaction is strong enough.
TWISTED ENTIRE CYCLIC COHOMOLOGY, J-L-O COCYCLES AND EQUIVARIANT SPECTRAL TRIPLES
Authors: GOSWAMI DEBASHISH
Published: August 2004

We study the "quantized calculus" corresponding to the algebraic ideas related to "twisted cyclic cohomology" introduced in [12]. With very similar definitions and techniques as those used in [9], we define and study "twisted entire cyclic cohomology" and the "twisted Chern character" associated with an appropriate operator theoretic data called "twisted spectral data", which consists of a spectral triple in the conventional sense of noncommutative geometry [1] and an additional positive operator having some specified properties. Furthermore, it is shown that given a spectral triple (in the conventional sense) which is equivariant under the (co-) action of a compact matrix pseudogroup, it is possible to obtain a canonical twisted spectral data and hence the corresponding (twisted) Chern character, which will be invariant (in the usual sense) under the (co-)action of the pseudogroup, in contrast to the fact that the Chern character coming from the conventional noncommutative geometry need not to be invariant. In the last section, we also try to detail out some remarks made in [3], in the context of a new definition of invariance satisfied by the conventional (untwisted) cyclic cocycles when lifted to an appropriate larger algebra.
ON THE CONSPICUOUS SEGREGATION BEHAVIOR ATPt–RhSURFACES
Authors: CREEMERS C. , HELFENSTEYN S. , LUYTEN J. , SCHURMANS M. , BRONGERSMA H. H.
Published: July 2004

Phase demixing is evaluated as a possible explanation for the anomalous temperature dependence of the Pt segregation at the Pt50Rh50(511), Pt25Rh75(110) and Pt25Rh75(100) surfaces. Calculations are performed in the quasichemical approximation and a broken bond scheme. Although the calculations based on systematic demixing tend to overestimate the surface enrichment, the qualitative agreement appears to be rather good.