bluuebunny/crossref_metadata_2025_split huggingface dataset:
A flexible protein linker improves the function of epitope‐tagged proteins in Saccharomyces cerevisiae
Authors: Sabourin Michelle , Tuzon Creighton T. , Fisher Timothy S. , Zakian Virginia A. 
Published: December 2006

AbstractEpitope tagging permits the detection of proteins when protein‐specific antibodies are not available. However, the epitope tag can reduce the function of the tagged protein. Here we describe a cassette that can be used to introduce an eight amino acid flexible linker between multiple Myc epitopes and the open reading frame of a given gene. We show that inserting the linker improves the in vivo ability of the telomerase subunits Est2p and Est1p to maintain telomere length. The methods used here are generally applicable to improve the function of tagged proteins in both Saccharomyces cerevisiae and Schizosaccharomyces pombe. Copyright © 2007 John Wiley & Sons, Ltd.
Revised procedures for yeast metabolites extraction: application to a glucose pulse to carbon‐limited yeast cultures, which reveals a transient activation of the purine salvage pathway
Authors: Loret Marie Odile , Pedersen Lene , François Jean 
Published: December 2006

AbstractIn this study we have revised our original procedure of yeast metabolites extraction. We showed that: (a) less than 5% of intracellular metabolites leaks out during the step of rapid arrest of cellular metabolism by quenching yeast cells into a 60% methanol solution kept at −40 °C; and (b) with a few exception, the stability of metabolites were not altered during the 3 min boiling procedure in a buffered ethanol solution. However, there was a loss of external added metabolites of 5–30%, depending on the type of metabolites. This was mainly attributable to their retention on cellular debris after ethanol treatment, which prevented centrifugation of the cellular extracts before evaporation of ethanol. We further simplified our previous high‐performance ionic chromatography (HPIC) techniques for easier, more reliable and robust quantitative measurements of organic acids, sugar phosphates and sugar nucleotides, and extended these techniques to purine and pyrimidine bases, using a variable wavelength detector set at 220 and 260 nm in tandem with a pulsed electrochemical or suppressed conductivity detector. These protocols were successfully applied to a glucose pulse to carbon‐limited yeast cultures on purines metabolism. This study showed that glucose induced a fast activation of the purine salvage pathway, as indicated by a transient drop of ATP and ADP with a concomitant rise of IMP and inosine. This metabolic perturbation was accompanied by a rapid increase in the activity of the ISN1‐encoded specific IMP‐5′‐nucleotidase. The mechanism of this activation remains to be determined. Copyright © 2007 John Wiley & Sons, Ltd.
Attachment of MAL32‐encoded maltase on the outside of yeast cells improves maltotriose utilization
Authors: Dietvorst J. , Blieck L. , Brandt R. , Van Dijck P. , Steensma H. Y. 
Published: December 2006

AbstractThe fermentation of maltotriose, the second most abundant fermentable sugar in wort, is often incomplete during high‐gravity brewing. Poor maltotriose consumption is due to environmental stress conditions during high‐gravity fermentation and especially to a low uptake of this sugar by some industrial strains. In this study we investigated whether the use of strains with an α‐glucosidase attached to the outside of the cell might be a possible way to reduce residual maltotriose. To this end, the N‐terminal leader sequence of Kre1 and the carboxy‐terminal anchoring domain of either Cwp2 or Flo1 were used to target maltase encoded by MAL32 to the cell surface. We showed that Mal32 displayed on the cell surface of Saccharomyces cerevisiae laboratory strains was capable of hydrolysis of α‐1,4‐linkages, and that it increased the ability of a strain lacking a functional maltose permease to grow on maltotriose. Moreover, the enzyme was also expressed and found to be active in an industrial strain. These data show that expressing a suitable maltase on the cell surface might provide a means of modifying yeast for more complete maltotriose utilization in brewing and other fermentation applications. Copyright © 2007 John Wiley & Sons, Ltd.
AGU Plan
Authors: Anonymous  
Published: December 2006

AGU programs and activities are guided by a plan adopted by Council.The plan is a living document created from input provided by the policy and operating committees, Sections, and Focus Groups. The chart below is an overview of the major sectors of the plan: Goals, Objectives, and Strategies.Goals are giant steps on the way to the Union's vision of the future. They do not change significantly in content from one planning horizon to the next. Achievement is expected to occur on a time horizon of a decade or more.
Mars and mine dumps
Authors: Burt Donald M. , Wohletz Kenneth H. , Knauth L. Paul 
Published: December 2006

Abundant sulfates appear to exist on the surface of Mars and have commonly been attributed to a planet‐wide volcanogenic ‘acid fog’—where clouds of acid mist react directly with surface rocks or acidify surface waters—from which the sulfates precipitated [e.g., Clark and Baird, 1979]. In particular, Meridiani Planum, a plain located just south of the Martian equator, hosts many sulfate minerals.Squyres et al. [2004, 2006] and Squyres and Knoll [2005] hypothesized that the sulfate minerals there, particularly acid sulfates such as jarosite, precipitated from high concentrations of sulfuric acid in flowing and standing water and groundwater. However, such explanations are problematic, because magnesia and alkali‐bearing minerals in the basaltic regolith should have been able to neutralize sulfuric acid rapidly, making precipitation of acid sulfates such as jarosite impossible.
Coordination of U.S. river science
Authors: Zielinski Sarah 
Published: December 2006

The U.S. Geological Survey is well‐poised to lead a national river science initiative but will need to expand its monitoring efforts and determine how to coordinate interdisciplinary research across USGS and other government agencies, according to a recent report from a committee of the U.S. National Academies.Committee Chair Don Siegel,a hydrogeologist in the Department of Earth Sciences at Syracuse University, N.Y., said that the USGS has unique strengths—including a reputation for providing high‐quality, unbiased data and expertise in many areas of river science—that would allow the agency to look at whole river systems at multiple scales and across state boundaries.
Fifty years of ocean observations in the Pacific Northeast
Authors: Whitney Frank , Tortell Philippe 
Published: December 2006

Ocean Station Papa, at 50°N, 145°W in the Alaska Gyre (Figure 1), started as a weather station in the 1940s. In 1956, oceanographers began collecting a suite of standard measurements from the cool subarctic waters at Ocean Station Papa (OSP), including temperature, salinity, oxygen, and plankton.Three years later, a series of sampling stations was added along the 1400‐kilometer ‘Line P’ from the Canadian coast to OSRto aid in understanding ocean variability.From 1956 to 1981, weather ships made the transit to and from OSP every six weeks, resulting in high temporal resolution sampling. The weather ship era ended in 1981 when satellites began providing better data for forecasting ocean weather. Since then, Canadian research vessels have continued to sample along Line P two to five times each year. In this recent era, transport of carbon within the ocean has become a major research focus.
Funding a Capitol cause
Authors: O'Riordan Catherine 
Published: December 2006

Contributions to AGU's Capitol Cause Fund have been instrumental in efforts to inform members of the U.S. Congress and their staffs about a range of Earth and space science issues. Since its inception in 2004, these funds have provided support for AGU to conduct a number of educational briefings on Capitol Hill. These have included briefings about background levels of ozone in the atmosphere; the Intergovernmental Panel on Climate Change (IPCC) process; two AGU position statements: Human Impacts on Climate, and Renewing Investment in Ocean Research; and the AGU white paper Hurricanes and the Gulf Coast: Science and Sustainable Rebuilding.More than 3,000 AGU members contribute annually to the Capitol Cause fund. Their support helps sustain efforts to deliver sound science to Capitol Hill and to communicate directly with policy makers. Additional funds are needed to expand activities and member involvement.
LECTINS*
Authors: Boyd William C. 
Published: December 2006

SUMMARYBlood group specific plant agglutinins (named lectins by the present author) were discovered in 1945, first mentioned in 1947, and described in detail by Renkonen in 1948 and by Boyd in 1949. Similar agglutinins have since been found in some invertebrates. Thousands of species have now been screened for such activity. The commonest activities are anti‐A, anti‐H, anti‐N, and someimes anti‐B and anti‐M. A specificity apparently new was found in Arachis hypogaea, and a report of a specificity pertaining to the Rh‐system has appeared. Lectins have been used in routine blood grouping, in the determination of the subgroups of A and AB, in the diagnosis of secretors, and in various theoretical investigations. They have been used to estimate the minimum number of moleules per red cell required for agglutination and in attempts to determine the number of molecules that can combine with a red cell. Lectins have been purified and characterized. Their quantitative precipitin behavior with blood‐group subtances has been studied. It has been possible to alter the specificity of lectins by selective inhibition and by chemical modification.
THE EFFECT OF ISOANTIBODIES ON RED‐CELL SURVIVAL
Authors: Mollison P. L. 
Published: December 2006

SummaryThis paper reviews the progress in relating in vitro characteristics of isoanti‐bodies, such as Ig class, ability to bind complement, and serum concentration, to the rate of destruction of incompatible red cells that they bring about in vivo.In man, those IgG antibodies that do not bind complement, e.g. anti‐Rh, bring about clearance predominantly in the spleen; in the absence of the spleen, the cells are cleared 100 times more slowly. In the rabbit, with a relatively smaller and evidently less efficient spleen, the minimum concentration of IgG, noncomplement‐binding antibody (anti‐HgA) required for clearance of a dose of 0.02 ml red cells/kg is about 100 times greater than in man.In detecting the presence of low concentrations of anti‐Rh, estimation of the rate of clearance of a small dose (0.02 ml/kg of red cells) is about ten times more sensitive than the indirect antiglobulin test, even after modifying this test to increase its sensitivity.Those IgG antibodies that bind complement bring about far more rapid clearance than those that do not, and IgM antibodies are more efficient still. If noncomplement‐binding antibodies are compared, the ratio of IgM:IgG molecules required for a given rate of clearance is less than 1:100.When small amounts of incompatible red cells are injected into recipients whose serum contains a low concentration of IgM antibody, two‐component curves of destruction are observed. There is evidence that this is due partly to heterogeneity of antigen within the red‐cell population, but that probably the major factor is the limited amount of antibody available.In man, when relatively small volumes (1‐10 ml) of red cells are transfused to previously untransfused subjects, evidence of primary immunization in the form of accelerated destruction of red cells, beginning at 10‐20 days after transfusion and leading to virtually complete clearance of the cells within 30 days, is observed in approximately 30% of recipients. Although it is postulated that this kind of red‐cell‐survival curve (collapse curve) is due to the production of small amounts of isoantibody, no antibody can, as a rule, be detected serologically, and its specificity is a matter for speculation. Experiments in rabbits show that, as in man, collapse curves are less frequently observed when relatively large volumes of red cells are transfused.
A Note on Distal Functions
Authors: FILALI M. 
Published: December 2006

ABSTRACT: The function f(n)= exp(ip(n)) is known to be distal on the group of the integers whenever p is a real polynomial. We establish a simple criterion from which we deduce the following generalization:Let R be a discrete ring, X a character of the additive group of R, and p a polynomial function on R and with coefficients in R. Then the function f(s) =X(p(s)) is distal on the additive group of R.
α-Proteobacterial Symbionts of Marine Bryozoans in the GenusWatersipora
Authors: Anderson Christine M. , Haygood Margo G. 
Published: December 2006

ABSTRACTBacterial symbionts that resembled mollicutes were discovered in the marine bryozoanWatersipora arcuatain the 1980s. In this study, we used PCR and sequencing of 16S rRNA genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of “W. subtorquata” and “W. arcuata” from several locations along the California coast are actually closely related α-Proteobacteria, not mollicutes. We propose the names“CandidatusEndowatersipora palomitas” and “CandidatusEndowatersipora rubus” for the symbionts of “W. subtorquata” and “W. arcuata,” respectively.
Mutation of
Candida tropicalis
by Irradiation with a He-Ne Laser To Increase Its Ability To Degrade Phenol
Authors: Jiang Yan , Wen Jianping , Jia Xiaoqiang , Caiyin Qinggele , Hu Zongding 
Published: December 2006

ABSTRACT

Candida tropicalis
isolated from acclimated activated sludge was used in this study. Cell suspensions with 5 × 10
7
cells ml
−1
were irradiated by using a He-Ne laser. After mutagenesis, the irradiated cell suspension was diluted and plated on yeast extract-peptone-dextrose (YEPD) medium. Plates with approximately 20 individual colonies were selected, and all individual colonies were harvested for phenol biodegradation. The phenol biodegradation stabilities for 70 phenol biodegradation-positive mutants, mutant strains CTM 1 to 70, ranked according to their original phenol biodegradation potentials, were tested continuously during transfers. Finally, mutant strain CTM 2, which degraded 2,600 mg liter
−1
phenol within 70.5 h, was obtained on the basis of its capacity and hereditary stability for phenol biodegradation. The phenol hydroxylase gene sequences were cloned in wild and mutant strains. The results showed that four amino acids were mutated by irradiation with a laser. In order to compare the activity of phenol hydroxylase in wild and mutant strains, their genes were expressed in
Escherichia coli
BL21(DE3) and enzyme activities were spectrophotometrically determined. It was clear that the activity of phenol hydroxylase was promoted after irradiation with a He-Ne laser. In addition, the cell growth and intrinsic phenol biodegradation kinetics of mutant strain CTM 2 in batch cultures were also described by Haldane's kinetic equation with a wide range of initial phenol concentrations from 0 to 2,600 mg liter
−1
. The specific growth and degradation rates further demonstrated that the CTM 2 mutant strain possessed a higher capacity to resist phenol toxicity than wild
C. tropicalis
did.
Identification of
Escherichia coli
O157:H7 Genomic Regions Conserved in Strains with a Genotype Associated with Human Infection
Authors: Steele Marina , Ziebell Kim , Zhang Yongxiang , Benson Andrew , Konczy Paulina , Johnson Roger , Gannon Victor 
Published: December 2006

ABSTRACT

Beta-glucuronidase-negative, sorbitol-nonfermenting isolates of Shiga toxin-producing
Escherichia coli
O157 comprise part of a clone complex of related enterohemorrhagic
E. coli
isolates. High-resolution genotyping shows that the O157 populations have diverged into two different lineages that appear to have different ecologies. To identify genomic regions unique to the most common human-associated genotype, suppression subtractive hybridization was used to identify DNA sequences present in two clinical strains representing the human lineage I O157:H7 strains but absent from two bovine-derived lineage II strains. PCR assays were then used to test for the presence of these regions in 10 lineage I strains and 20 lineage II strains. Twelve conserved regions of genomic difference for lineage I (CRD
I
) were identified that were each present in at least seven of the lineage I strains but absent in most of the lineage II strains tested. The boundaries of the lineage I conserved regions were further delimited by PCR. Eleven of these CRD
I
were associated with
E. coli
Sakai S-loops 14, 16, 69, 72, 78, 82, 83, 91 to 93, 153, and 286, and the final CRD
I
was located on the pO157 virulence plasmid. Several potential virulence factors were identified within these regions, including a putative hemolysin-activating protein, an iron transport system, and several possible regulatory genes. Cluster analysis based on lineage I conserved regions showed that the presence/absence of these regions was congruent with the inferred phylogeny of the strains.
Comparative Analysis of Virulence Genes, Genetic Diversity, and Phylogeny of Commensal and Enterotoxigenic
Escherichia coli
Isolates from Weaned Pigs
Authors: Wu Xi-Yang , Chapman Toni , Trott Darren J. , Bettelheim Karl , Do Thuy N. , Driesen Steve , Walker Mark J. , Chin James 
Published: December 2006

ABSTRACT

If the acquisition of virulence genes (VGs) for pathogenicity were not solely acquired through horizontal gene transfers of pathogenicity islands, transposons, and phages, then clonal clusters of enterotoxigenic
Escherichia coli
(ETEC) would contain few or even none of the VGs found in strains responsible for extraintestinal infections. To evaluate this possibility, 47 postweaning diarrhea (PWD) ETEC strains from different geographical origins and 158 commensal
E. coli
isolates from the gastrointestinal tracts of eight group-housed healthy pigs were screened for 36 extraintestinal and 18 enteric VGs using multiplex PCR assays. Of 36 extraintestinal VGs, only 8 were detected (
fimH
,
traT
,
fyuA
,
hlyA
,
kpsMtII
,
k5
,
iha
, and
ompT
) in the ETEC collection. Among these,
hlyA
(α-hemolysin) and
iha
(nonhemagglutinating adhesin) occurred significantly more frequently among the ETEC isolates than in the commensal isolates. Clustering analysis based on the VG profiles separated commensal and ETEC isolates and even differentiated serogroup O141 from O149. On the other hand, pulsed-field gel electrophoresis (PFGE) successfully clustered ETEC isolates according to both serotype and geographical origin. In contrast, the commensal isolates were heterogeneous with respect to both serotype and DNA fingerprint. This study has validated the use of VG profiling to examine pathogenic relationships between porcine ETEC isolates. The clonal relationships of these isolates can be further clarified by PFGE fingerprinting. The presence of extraintestinal VGs in porcine ETEC confirmed the hypothesis that individual virulence gene acquisitions can occur concurrently against a background of horizontal gene transfers of pathogenicity islands. Over time, this could enable specific clonotypes to respond to host selection pressure and to evolve into new strains with increased virulence.
Use of 16S rRNA and
rpoB
Genes as Molecular Markers for Microbial Ecology Studies
Authors: Case Rebecca J. , Boucher Yan , Dahllöf Ingela , Holmström Carola , Doolittle W. Ford , Kjelleberg Staffan 
Published: December 2006

ABSTRACT

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene
rpoB
. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such “heterogeneity hot spots” occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below.
rpoB
provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as
rpoB
could complement the information provided by the 16S rRNA gene.
Sensitive Quantitative Detection of Commensal Bacteria by rRNA-Targeted Reverse Transcription-PCR
Authors: Matsuda Kazunori , Tsuji Hirokazu , Asahara Takashi , Kado Yukiko , Nomoto Koji 
Published: December 2006

ABSTRACT

A sensitive rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) method was developed for exact and sensitive enumeration of subdominant bacterial populations. Using group- or species-specific primers for 16S or 23S rRNA, analytical curves were constructed for
Escherichia coli
,
Enterococcus faecalis
,
Staphylococcus aureus
,
Clostridium perfringens
, and
Pseudomonas aeruginosa
, and the threshold cycle value was found to be linear up to an RNA amount of 10
−3
cell per RT-PCR. The number of bacteria in culture was determined by RT-qPCR, and the results correlated well with the CFU count over the range from 10
0
to 10
5
CFU. The bacterial counts obtained by RT-qPCR were the same as the CFU counts irrespective of the growth phase in vitro, except for
C. perfringens
during starvation periods; the viable cell counts obtained by using a combination of 4′,6-diamidino-2-phenylindole (DAPI) staining and SYTO9-propidium iodide double staining were in good agreement with the RT-qPCR counts rather than with the CFU counts. The RT-qPCR method could detect endogenous
Enterobacteriaceae
and
P. aeruginosa
in feces of hospitalized patients (
n
= 38) at a level of 10
3
cells per g of feces, and for enumeration of
S. aureus
or
P. aeruginosa
spiked into human peripheral blood, the lower detection limit for RT-qPCR quantification of the bacteria was 2 cells per ml of blood, suggesting that this method was equivalent to the conventional culture method. As only 5 h was needed for RT-qPCR quantification, we suggest that rRNA-targeted RT-qPCR assays provide a sensitive and convenient system for quantification of commensal bacteria and for examining their possible invasion of a host.