bluuebunny/crossref_metadata_2025 huggingface dataset:
Idiosyncratic Consumption Risk and the Cross Section of Asset Returns
Authors: JACOBS KRIS , WANG KEVIN Q.
Published: September 2004

This paper investigates the importance of idiosyncratic consumption risk for the cross‐sectional variation in asset returns. We find that besides the rate of aggregate consumption growth, the cross‐sectional variance of consumption growth is also a priced factor. This suggests that consumers are not fully insured against idiosyncratic consumption risk, and that asset returns reflect their attempts to reduce their exposure to this risk. The resulting two‐factor consumption‐based asset pricing model significantly outperforms the CAPM, and its performance compares favorably with that of the Fama–French three‐factor model.
Remuneration, Retention, and Reputation Incentives for Outside Directors
Authors: YERMACK DAVID
Published: September 2004

I study incentives received by outside directors in Fortune 500 firms from compensation, replacement, and the opportunity to obtain other directorships. Previous research has only shown these relations to apply under limited circumstances such as financial distress. Together these incentive mechanisms provide directors with wealth increases of approximately 11 cents per $1,000 rise in firm value. Although smaller than the performance sensitivities of CEOs, outside directors' incentives imply a change in wealth of about $285,000 for a 1 standard deviation (SD) change in typical firm performance. Cross‐sectional patterns of director equity awards conform to agency and financial theories.
Bids and Allocations in European IPO Bookbuilding
Authors: JENKINSON TIM , JONES HOWARD
Published: September 2004

This paper uses evidence from a data set of 27 European IPOs to analyze how investors bid and the factors that influence their allocations. We also make use of a unique ranking of investor quality, associated with the likelihood of flipping the IPO. We find that investors perceived to be long‐term holders of the stock are consistently favored in allocation and in out‐turn profits. In contrast to Cornelli and Goldreich (2001), we find little evidence that more informative bids receive larger allocations or higher profits. Our results cast doubt upon the extent of information production during the bookbuilding period.
The Development of Secondary Market Liquidity for NYSE‐Listed IPOs
Authors: CORWIN SHANE A. , HARRIS JEFFREY H. , LIPSON MARC L.
Published: September 2004

For NYSE‐listed IPOs, limit order submissions and depth relative to volume are unusually low on the first trading day. Initial buy‐side liquidity is higher for IPOs with high‐quality underwriters, large syndicates, low insider sales, and high premarket demand, while sell‐side liquidity is higher for IPOs that represent a large fraction of outstanding shares and have low premarket demand. Our results suggest that uncertainty and offer design affect initial liquidity, though order flow stabilizes quickly. We also find that submission strategies are influenced by expected underwriter stabilization and preopening order flow contains information about both initial prices and subsequent returns.
Quality of Life in Women With Breast Cancer in Turkey
Authors: Uzun Özge , Aslan Fatma Eti , Selimen Deniz , Koç Mehmet
Published: September 2004

Purpose

: To determine quality of life (QoL) of Turkish women with breast cancer, and to examine whether QoL was related to sociodemographic or clinical variables.

Design

: This descriptive study was conducted with a convenience sample of 72 Turkish women with breast cancer recruited from two hospitals in Turkey.

Methods

: The data were collected using a questionnaire, the Quality of Life Scale (QoLS), and the Visual Analogue Scale (VAS), and were analyzed using descriptive statistics.

Findings

: Two sociodemographic variables (educational background and employment status) were related to QoL of women with breast cancer. No statistically significant difference was found between patients with and without pain on scores obtained from the overall QoLS.

Conclusions

: The mean scores of total scale and subscales related to QoL perceived by women were considered to be moderately high. However, findings showed that educational level, employment status, and level of pain affected the level of QoL in Turkish women with breast cancer in varying degrees. Further studies are needed to determine specific effects of sociodemographic and clinical variables on QoL.
Role Strain and Ease in Decision‐Making to Withdraw or Withhold Life Support for Elderly Relatives
Authors: Hansen Lissi , Archbold Patricia G. , Stewart Barbara J.
Published: September 2004

Purpose

: To describe the concepts of role strain and role satisfaction (renamed ease in decision‐making following analysis) experienced by family caregivers when making decisions to withdraw or withhold life support for elderly relatives in a variety of settings.

Methods

: Semi‐structured interviews were conducted with 17 family caregivers to obtain descriptions of their experiences when making decisions about life support for elderly relatives. Content analysis was used to analyze the data.

Findings

: Role strain was complex, dynamic, and multidimensional, and it evolved over time before, during, and after decision making about life support. Role satisfaction, the concept name used at the beginning of the study, did not match descriptions or the experience of family caregivers, and a revised name, ease in decision‐making, was selected.

Conclusions

: The concepts of role strain and ease in decision‐making have not previously been used in studies of decisions about life support. Both role strain and ease in decision‐making augment the existing literature on role strain in family care by providing a more complete picture of caregivers' responses during their experience of making life‐support decisions. Research focused on the measurement of strain and ease in decision‐making is needed to understand their interrelationship as well as their association with such variables as caregiver grief and health.
Cross‐Cultural Relationships Between Nurses and Filipino Canadian Patients
Authors: Pasco Alberta Catherine Y. , Morse Janice M. , Olson Joanne K.
Published: September 2004

Purpose

: To describe culturally embedded values that implicitly guide Filipino Canadian patients' interactions with Canadian nurses and are integral to nurse‐patient relationships.

Design

and

Methods

: A focused ethnography was conducted, with a purposive sample of 23 Filipino Canadians who received care in Canadian hospitals. Data consisted of interviews, field notes, and diary.

Findings

: When receiving care, patients delineated hindi ibang tao (one of us) and ibang tao (not one of us) and this determined their preference for who performed personal and private tasks or received information. The urgency of the patients' conditions, the intimacy required for most nursing procedures, and short hospitalizations meant that patients often interacted without progressing through the cultural levels of pakikitungo (formality), pakikibagay (adjustability), and pakikisama (acceptance). Rather, the crisis of being hospitalized forced patients to immediately move toward the cultural levels of pakikipagpalagayang‐loob (mutual comfort) or pakikiisa (oneness). Patients' willingness to trust and to share their kapwa‐oriented worldview in relating with fellow human beings, and their use of their languages of words, gaze, touch, and food, allowed nurses to become hindi ibang tao (one of us). Caregiving roles and establishing relationships also distinguished that hindi ibang tao (one of us) was to bantay (watch over) the patient, whereas ibang tao (not one of us) was expected to alaga (care for) them (i.e., provide professional care).

Conclusions

: Communicating and caring effectively requires understanding of Filipino Canadians' languages of words, gaze, touch, and food and their levels of interaction. Culturally safe nurse‐patient relationships can then develop.
A Comparison of Three Measures of Elder Abuse
Authors: Meeks‐Sjostrom Diana
Published: September 2004

Purpose

: To present a comparison of three measures for assessing elder abuse.

Design and Methods

: Three measures for assessing elder abuse were identified through a literature review. The characteristics and uses of each measure were reviewed and evaluated.

Findings

: The Indicators of Abuse (IOA) is a 22‐item tool for discriminating abuse and nonabuse cases; it is completed by a health care professional after a home assessment is conducted. The Elder Abuse and Neglect Assessment (EAI) is a 44‐item scale comprised of seven sections to review signs, symptoms, and subjective complaints of elder abuse, neglect, exploitation, and abandonment; it can be used by health care providers in all clinical settings. The Elder Abuse Screening Test (EAST) is a 15‐item tool to be completed by a health care provider based on the patient's responses. This screening tool is limited because of the small unrepresentative samples used to test it, the low internal consistency, and a relatively high false‐negative rate.

Conclusions

: An instrument to accurately assess elder abuse in long‐term care is needed. Proper identification of elder abuse is the first step in assisting victims in dealing with abusive situations.
MR Perfusion Imaging for the Detection of Myocardial Ischemia
Authors: Janssen C. H. C. , Kuijpers D. , Oudkerk M.
Published: September 2004

A wide variety of imaging modalities is available for the diagnosis of ischemic coronary artery disease (CAD). Myocardial hypo‐perfusion is one of the first steps in the ischemic cascade and can be detected before clinical symptoms, ECG alterations or wall motion abnormalities occur. Currently, nuclear medicine techniques (scintigraphy) such as single‐photon emission computed tomography using Thalium‐201 or TC‐99 m sestamibi are most frequently used for the imaging of myocardial perfusion. Positron emission tomography (PET) is the reference standard for myocardial perfusion imaging. These techniques attain a sensitivity and specificity for the detection of myocardial ischemia of, respectively, 83–95 and 53–95%. However, PET is not widely available, which makes it relatively inaccessible. Other disadvantages of myocardial perfusion imaging scintigraphy are: high costs, long‐time commitment, radiation exposure, specificity depending on quality control of laboratory and trained readers and low specificity in presence of left bundle branch block. As a result of the fast hardware and software development magnetic resonance imaging (MRI) has become a promising new technique for perfusion imaging. This paper will give an introduction to myocardial perfusion MRI for the detection of ischemic heart disease followed by an overview of the post‐processing procedures.
System for Segmentation and Selective Visualization of the Coronary Artery Tree for Evaluation of Stenosis, Soft Plaque and Calcification in Cardiac CTA
Authors: Krishnamoorthy P. , Brejl M. , van Ooijen P. M. A.
Published: September 2004

Recent advances in multidetector computed tomography (MDCT) technology provide opportunities for non‐invasive high‐resolution diagnostic imaging of the coronary arteries. The amount of image data generated in a coronary computed tomography angiography (CTA) study typically requires that the analysis be done using a 3D workstation. Manual interpretation of the data is normally feasible; however, semi‐automated and automated tools for coronary artery analysis can significantly shorten the analysis time. In this article, we discuss the coronary artery analysis package available on the Vitrea 2 (Vital Images, Inc.) workstation. The software is intended to expedite the review workflow by providing semi‐automated interactive tools for tracking vessels, automated curved and oblique reformations, and advanced 3D visualization. Early results from clinical evaluation indicate that using the automated tools can decrease the reading time by approximately a factor of 2.
Bmp4
and Morphological Variation of Beaks in Darwin's Finches
Authors: Abzhanov Arhat , Protas Meredith , Grant B. Rosemary , Grant Peter R. , Tabin Clifford J.
Published: September 2004

Darwin's finches are a classic example of species diversification by natural selection. Their impressive variation in beak morphology is associated with the exploitation of a variety of ecological niches, but its developmental basis is unknown. We performed a comparative analysis of expression patterns of various growth factors in species comprising the genus
Geospiza.
We found that expression of
Bmp4
in the mesenchyme of the upper beaks strongly correlated with deep and broad beak morphology. When misexpressed in chicken embryos,
Bmp4
caused morphological transformations paralleling the beak morphology of the large ground finch
G. magnirostris
.
The First Lord from Science
Authors: Rigden John S.
Published: September 2004

Degrees Kelvin:
A Tale of Genius, Invention, and Tragedy. by David Lindley. Joseph Henry Press, Washington, DC, 2004. 374 pp. $27.95, C$37.95. ISBN 0-309-09073-3.

The author offers a popular biography that explores William Thomson's career in science, interactions with contemporaries, and personal life.
Characterization and Heterologous Expression of the Oxalyl Coenzyme A Decarboxylase Gene from
Bifidobacterium lactis
Authors: Federici Federica , Vitali Beatrice , Gotti Roberto , Pasca Maria Rosalia , Gobbi Silvia , Peck Ammon B. , Brigidi Patrizia
Published: September 2004

Oxalyl coenzyme A (CoA) decarboxylase (Oxc) is a key enzyme in the catabolism of the highly toxic compound oxalate, catalyzing the decarboxylation of oxalyl-CoA to formyl-CoA. The gene encoding a novel oxalyl-CoA decarboxylase from
Bifidobacterium lactis
DSM 10140 (
oxc
) was identified and characterized. This strain, isolated from yogurt, showed the highest oxalate-degrading activity in a preliminary screening with 12 strains belonging to
Bifidobacterium
, an anaerobic intestinal bacterial group largely used in probiotic products. The
oxc
gene was isolated by probing a
B. lactis
genomic library with a probe obtained by amplification of the oxalyl-CoA decarboxylase gene from
Oxalobacter formigenes
, an anaerobic bacterium of the human intestinal microflora. The
oxc
DNA sequence analysis revealed an open reading frame of 1,773 bp encoding a deduced 590-amino-acid protein with a molecular mass of about 63 kDa. Analysis of amino acid sequence showed a significant homology (47%) with oxalyl-CoA decarboxylase of
O. formigenes
and a typical thiamine pyrophosphate-binding site that has been reported for several decarboxylase enzymes. Primer extension experiments with
oxc
performed by using RNA isolated from
B. lactis
identified the transcriptional start site 28 bp upstream of the ATG start codon, immediately adjacent to a presumed promoter region. The protein overexpressed in
Escherichia coli
cross-reacted with an anti-
O. formigenes
oxalyl-CoA decarboxylase antibody. Enzymatic activity, when evaluated by capillary electrophoresis analysis, demonstrated that the consumption substrate oxalyl-CoA was regulated by a product inhibition of the enzyme. These findings suggest a potential role for
Bifidobacterium
in the intestinal degradation of oxalate.
Display of Bacterial Lipase on the
Escherichia coli
Cell Surface by Using FadL as an Anchoring Motif and Use of the Enzyme in Enantioselective Biocatalysis
Authors: Lee Seung Hwan , Choi Jong-Il , Park Si Jae , Lee Sang Yup , Park Byoung Chul
Published: September 2004

We have developed a novel cell surface display system by employing FadL as an anchoring motif, which is an outer membrane protein involved in long-chain fatty acid transport in
Escherichia coli
. A thermostable
Bacillus
sp. strain TG43 lipase (44.5 kDa) could be successfully displayed on the cell surface of
E. coli
in an active form by C-terminal deletion-fusion of lipase at the ninth external loop of FadL. The localization of the truncated FadL-lipase fusion protein on the cell surface was confirmed by confocal microscopy and Western blot analysis. Lipase activity was mainly detected with whole cells, but not with the culture supernatant, suggesting that cell lysis was not a problem. The activity of cell surface-displayed lipase was examined at different temperatures and pHs and was found to be the highest at 50°C and pH 9 to 10. Cell surface-displayed lipase was quite stable, even at 60 and 70°C, and retained over 90% of the full activity after incubation at 50°C for a week. As a potential application, cell surface-displayed lipase was used as a whole-cell catalyst for kinetic resolution of racemic methyl mandelate. In 36 h of reaction, (
S
)-mandelic acid could be produced with the enantiomeric excess of 99% and the enantiomeric ratio of 292, which are remarkably higher than values obtained with crude lipase or cross-linked lipase crystal. These results suggest that FadL may be a useful anchoring motif for displaying enzymes on the cell surface of
E. coli
for whole-cell biocatalysis.
Effect of Length of Time before Incorporation on Survival of Pathogenic Bacteria Present in Livestock Wastes Applied to Agricultural Soil
Authors: Hutchison M. L. , Walters L. D. , Moore A. , Crookes K. M. , Avery S. M.
Published: September 2004

In response to reports that the contamination of food can occur during the on-farm primary phase of food production, we report data that describes a possible cost-effective intervention measure. The effect of time before soil incorporation of livestock wastes spread to land on the rate of decline of zoonotic agents present in the waste was investigated. Fresh livestock wastes were inoculated with laboratory-culturedSalmonella,Listeria, andCampylobacterspp. andEscherichia coliO157 before they were spead onto soil. Incorporation of the spread wastes was either immediate, delayed for 1 week, or did not occur at all. Bacterial decline was monitored over time and found to be significantly more rapid for all waste types when they were left on the soil surface. There were no significant differences in initial bacterial decline rates when wastes were spread in summer or winter. Our results indicate that not incorporating contaminated livestock wastes into soil is a potential intervention measure that may help to limit the spread of zoonotic agents further up the food chain. The implications of these findings are discussed in relation to current advice for livestock waste disposal.
Copper Ions Stimulate Polyphosphate Degradation and Phosphate Efflux in
Acidithiobacillus ferrooxidans
Authors: Alvarez Sergio , Jerez Carlos A.
Published: September 2004

For some bacteria and algae, it has been proposed that inorganic polyphosphates and transport of metal-phosphate complexes could participate in heavy metal tolerance. To test for this possibility in
Acidithiobacillus ferrooxidans
, a microorganism with a high level of resistance to heavy metals, the polyphosphate levels were determined when the bacterium was grown in or shifted to the presence of a high copper concentration (100 mM). Under these conditions, cells showed a rapid decrease in polyphosphate levels with a concomitant increase in exopolyphosphatase activity and a stimulation of phosphate efflux. Copper in the range of 1 to 2 μM greatly stimulated exopolyphosphatase activity in cell extracts from
A. ferrooxidans
. The same was seen to a lesser extent with cadmium and zinc. Bioinformatic analysis of the available
A. ferrooxidans
ATCC 23270 genomic sequence did not show a putative
pit
gene for phosphate efflux but rather an open reading frame similar in primary and secondary structure to that of the
Saccharomyces cerevisiae
phosphate transporter that is functional at acidic pH (Pho84). Our results support a model for metal detoxification in which heavy metals stimulate polyphosphate hydrolysis and the metal-phosphate complexes formed are transported out of the cell as part of a possibly functional heavy metal tolerance mechanism in
A. ferrooxidans
.
Direct Correlation between Rates of Anaerobic Respiration and Levels of mRNA for Key Respiratory Genes in
Geobacter sulfurreducens
Authors: Chin Kuk-Jeong , Esteve-Núñez Abraham , Leang Ching , Lovley Derek R.
Published: September 2004

The predominance of
Geobacter
species in environments in which Fe(III) reduction is important has suggested that Fe(III) reduction rates might be estimated in
Geobacter
-dominated environments by assessing in situ activity with molecular techniques. To determine whether mRNA levels of key respiratory genes might be correlated with respiration rates in
Geobacter sulfurreducens
, studies were conducted with fumarate as the electron acceptor and acetate as the limiting electron donor in anaerobic continuous cultures. Levels of mRNA for a fumarate reductase gene,
frdA
, quantified by real-time reverse transcription-PCR were directly correlated with fumarate reduction rates. In similar studies with Fe(III) as the electron acceptor, mRNA levels for
omcB
, a gene for an outer membrane
c
-type cytochrome involved in Fe(III) reduction, were positively correlated with Fe(III) reduction rates. Levels of mRNA for
frdA
and
omcB
were also positively correlated with fumarate and Fe(III) reduction rates, respectively, when growth was limited by the availability of fumarate or Fe(III), but mRNA levels were higher than in acetate-limited cultures. Levels of mRNA for
omcC
, which encodes a
c
-type cytochrome highly similar to OmcB but not necessary for Fe(III) reduction, followed patterns different than those of
omcB
. This agrees with the previous finding that OmcC is not involved in Fe(III) reduction and suggests that changes in mRNA levels of
omcB
are related to its role in Fe(III) reduction. These results demonstrate that mRNA levels for respiratory genes might be used to estimate in situ Fe(III) reduction rates in
Geobacter
-dominated environments but suggest that information on environmental conditions and/or the metabolic state of
Geobacter
species is also required for accurate rate estimates.
Cell Density-Dependent Gene Contributes to Efficient Seed Colonization by
Pseudomonas putida
KT2440
Authors: Espinosa-Urgel Manuel , Ramos Juan-Luis
Published: September 2004

We have characterized the expression pattern of a gene,
ddcA
, involved in initial colonization of corn seeds by
Pseudomonas putida
KT2440. The
ddcA
gene codes for a putative membrane polypeptide belonging to a family of conserved proteins of unknown function. Members of this family are widespread among prokaryotes and include the products of a
Salmonella enterica
serovar Typhimurium gene expressed during invasion of macrophages and
psiE
, an
Escherichia coli
phosphate starvation-inducible gene. Although its specific role is undetermined, the presence of
ddcA
in multicopy restored the seed adhesion capacity of a KT2440
ddcA
mutant. Expression of
ddcA
is growth phase regulated, being maximal at the beginning of stationary phase. It is independent of RpoS, nutrient depletion, or phosphate starvation, and it is not the result of changes in the medium pH during growth. Expression of
ddcA
is directly dependent on cell density, being also stimulated by the addition of conditioned medium and of seed exudates. This is the first evidence suggesting the existence of a quorum-sensing system in
P. putida
KT2440. The potential implication of such a signaling process in seed adhesion and colonization by the bacterium is discussed.
Acidified Litter Benefits the Intestinal Flora Balance of Broiler Chickens
Authors: Garrido Margarita Novoa , Skjervheim Magne , Oppegaard Hanne , Sørum Henning
Published: September 2004

The alterations in the balance of the normal intestinal bacterial flora of chickens exposed to acidified wood-derived litter were analyzed and compared to those of a control group exposed to nonacidified litter. A total of 1,728 broilers were divided into two groups, with six replicates in each. One group was exposed to dry wood-derived litter, and the other was exposed to dry wood-derived litter sprayed with a mixture of sodium lignosulfonate, formic acid, and propionic acid. At five different times, five chickens from each pen were killed and the intestinal contents from ileum and caeca were collected. The samples were diluted and plated onto selective media to identify coliforms,
Lactobacillus
spp.,
Clostridium perfringens
, and
Enterococcus
spp. Covariance analysis of bacterial counts showed significantly lower counts for
C. perfringens
in the caeca and the ileum and for
Enterococcus
spp. and
Lactobacillus
spp. in the ileum in chickens exposed to the acidified litter.
Lactobacillus
spp. showed significantly higher counts in the caeca in chickens exposed to acidified litter. There was no difference between the two litters with regard to coliforms in the ileum and the caeca or to
Enterococcus
spp. in the caeca. The study shows that exposing the chickens to acidified litter lowers the intestinal bacterial number, especially in the ileum, without negative consequences for the chicken's health or performance. Of special interest are the lower counts of
C. perfringens
and
Enterococcus
spp. that might reduce the risk of developing clinical or subclinical necrotic enteritis and growth depression.
Nonmarine Crenarchaeol in Nevada Hot Springs
Authors: Pearson A. , Huang Z. , Ingalls A. E. , Romanek C. S. , Wiegel J. , Freeman K. H. , Smittenberg R. H. , Zhang C. L.
Published: September 2004

Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids of the
Crenarchaeota
. The structurally unusual GDGT crenarchaeol has been proposed as a taxonomically specific biomarker for the marine planktonic group I archaea. It is found ubiquitously in the marine water column and in sediments. In this work, samples of microbial community biomass were obtained from several alkaline and neutral-pH hot springs in Nevada, United States. Lipid extracts of these samples were analyzed by high-performance liquid chromatography-mass spectrometry and by gas chromatography-mass spectrometry. Each sample contained GDGTs, and among these compounds was crenarchaeol. The distribution of archaeal lipids in Nevada hot springs did not appear to correlate with temperature, as has been observed in the marine environment. Instead, a significant correlation with the concentration of bicarbonate was observed. Archaeal DNA was analyzed by denaturing gradient gel electrophoresis. All samples contained 16S rRNA gene sequences which were more strongly related to thermophilic crenarchaeota than to
Cenarchaeum symbiosum
, a marine nonthermophilic crenarchaeon. The occurrence of crenarchaeol in environments containing sequences affiliated with thermophilic crenarchaeota suggests a wide phenotypic distribution of this compound. The results also indicate that crenarchaeol can no longer be considered an exclusive biomarker for marine species.
Molecular Characterization of CcpA and Involvement of This Protein in Transcriptional Regulation of Lactate Dehydrogenase and Pyruvate Formate-Lyase in the Ruminal Bacterium
Streptococcus bovis
Authors: Asanuma Narito , Yoshii Takahiro , Hino Tsuneo
Published: September 2004

A
ccpA
gene that encodes global catabolite control protein A (CcpA) in
Streptococcus bovis
was identified and characterized, and the involvement of CcpA in transcriptional control of a gene (
ldh
) encoding lactate dehydrogenase (LDH) and a gene (
pfl
) encoding pyruvate formate-lyase (PFL) was examined. The
ccpA
gene was shown to be transcribed as a monocistronic operon. A catabolite-responsive element (
cre
) was found in the promoter region of
ccpA
, suggesting that
ccpA
transcription in
S. bovis
is autogenously regulated. CcpA required HPr that was phosphorylated at the serine residue at position 46 (HPr-[Ser-P]) for binding to the
cre
site, but glucose 6-phosphate, fructose 1,6-bisphosphate, and NADP had no effect on binding. Diauxic growth was observed when
S. bovis
was grown in a medium containing glucose and lactose, but it disappeared when
ccpA
was disrupted, which indicates that CcpA is involved in catabolite repression in
S. bovis
. The level of
ccpA
mRNA was higher when cells were grown on glucose than when they were grown on lactose, which was in line with the level of
ldh
mRNA. When cells were grown on glucose, the
ldh
mRNA level was lower but the
pfl
mRNA level was higher in a
ccpA
-disrupted mutant than in the parent strain, which suggests that
ldh
transcription is enhanced and
pfl
transcription is suppressed by CcpA. The
ccpA
-disrupted mutant produced less lactate and more formate than the parent, probably because the mutant had reduced LDH activity and elevated PFL activity. In the upper region of both
ldh
and
pfl
, a
cre
-like sequence was found, suggesting that the complex consisting of CcpA and HPr-[Ser-P] binds to the possible
cre
sites. Thus, CcpA appears to be involved in the global regulation of sugar utilization in
S. bovis
.
Combined Use of Cultivation-Dependent and Cultivation-Independent Methods Indicates that Members of Most Haloarchaeal Groups in an Australian Crystallizer Pond Are Cultivable
Authors: Burns D. G. , Camakaris H. M. , Janssen P. H. , Dyall-Smith M. L.
Published: September 2004

Haloarchaea are the dominant microbial flora in hypersaline waters with near-saturating salt levels. The haloarchaeal diversity of an Australian saltern crystallizer pond was examined by use of a library of PCR-amplified 16S rRNA genes and by cultivation. High viable counts (10
6
CFU/ml) were obtained on solid media. Long incubation times (≥8 weeks) appeared to be more important than the medium composition for maximizing viable counts and diversity. Of 66 isolates examined, all belonged to the family
Halobacteriaceae
, including members related to species of the genera
Haloferax
,
Halorubrum
, and
Natronomonas
. In addition, isolates belonging to a novel group (the ADL group), previously detected only as 16S rRNA genes in an Antarctic hypersaline lake (Deep Lake), were cultivated for the first time. The 16S rRNA gene library identified the following five main groups:
Halorubrum
groups 1 and 2 (49%), the SHOW (square haloarchaea of Walsby) group (33%), the ADL group (16%), and the
Natronomonas
group (2%). There were two significant differences between the organisms detected in cultivation and 16S rRNA sequence results. Firstly,
Haloferax
spp. were frequently isolated on plates (15% of all isolates) but were not detected in the 16S rRNA sequences. Control experiments indicated that a bias against
Haloferax
sequences in the generation of the 16S rRNA gene library was unlikely, suggesting that
Haloferax
spp. readily form colonies, even though they were not a dominant group. Secondly, while the 16S rRNA gene library identified the SHOW group as a major component of the microbial community, no isolates of this group were obtained. This inability to culture members of the SHOW group remains an outstanding problem in studying the ecology of hypersaline environments.
Role of Hexose Transport in Control of Glycolytic Flux in
Saccharomyces cerevisiae
Authors: Elbing Karin , Larsson Christer , Bill Roslyn M. , Albers Eva , Snoep Jacky L. , Boles Eckhard , Hohmann Stefan , Gustafsson Lena
Published: September 2004

The yeast
Saccharomyces cerevisiae
predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type
S. cerevisiae
does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in
S. cerevisiae
and will provide new tools for the control of industrial fermentations.
Comparison of Fluorescence Microscopy and Solid-Phase Cytometry Methods for Counting Bacteria in Water
Authors: Lisle John T. , Hamilton Martin A. , Willse Alan R. , McFeters Gordon A.
Published: September 2004

Total direct counts of bacterial abundance are central in assessing the biomass and bacteriological quality of water in ecological and industrial applications. Several factors have been identified that contribute to the variability in bacterial abundance counts when using fluorescent microscopy, the most significant of which is retaining an adequate number of cells per filter to ensure an acceptable level of statistical confidence in the resulting data. Previous studies that have assessed the components of total-direct-count methods that contribute to this variance have attempted to maintain a bacterial cell abundance value per filter of approximately 10
6
cells filter
−1
. In this study we have established the lower limit for the number of bacterial cells per filter at which the statistical reliability of the abundance estimate is no longer acceptable. Our results indicate that when the numbers of bacterial cells per filter were progressively reduced below 10
5
, the microscopic methods increasingly overestimated the true bacterial abundance (range, 15.0 to 99.3%). The solid-phase cytometer only slightly overestimated the true bacterial abundances and was more consistent over the same range of bacterial abundances per filter (range, 8.9 to 12.5%). The solid-phase cytometer method for conducting total direct counts of bacteria was less biased and performed significantly better than any of the microscope methods. It was also found that microscopic count data from counting 5 fields on three separate filters were statistically equivalent to data from counting 20 fields on a single filter.
Heads or Tails: Host-Parasite Interactions in the
Drosophila-Wolbachia
System
Authors: Veneti Zoe , Clark Michael E. , Karr Timothy L. , Savakis Charalambos , Bourtzis Kostas
Published: September 2004

Wolbachia
strains are endosymbiotic bacteria typically found in the reproductive tracts of arthropods. These bacteria manipulate host reproduction to ensure maternal transmission. They are usually transmitted vertically, so it has been predicted that they have evolved a mechanism to target the host's germ cells during development. Through cytological analysis we found that
Wolbachia
strains display various affinities for the germ line of
Drosophila
. Different
Wolbachia
strains show posterior, anterior, or cortical localization in
Drosophila
embryos, and this localization is congruent with the classification of the organisms based on the
wsp
(
Wolbachia
surface protein) gene sequence. This embryonic distribution pattern is established during early oogenesis and does not change until late stages of embryogenesis. The posterior and anterior localization of
Wolbachia
resembles that of
oskar
and
bicoid
mRNAs, respectively, which define the anterior-posterior axis in the
Drosophila
oocyte. By comparing the properties of a single
Wolbachia
strain in different host backgrounds and the properties of different
Wolbachia
strains in the same host background, we concluded that bacterial factors determine distribution, while bacterial density seems to be limited by the host. Possible implications concerning cytoplasmic incompatibility and evolution of strains are discussed.
Microautoradiographic Study of
Rhodocyclus
-Related Polyphosphate-Accumulating Bacteria in Full-Scale Enhanced Biological Phosphorus Removal Plants
Authors: Kong Yunhong , Nielsen Jeppe Lund , Nielsen Per Halkjær
Published: September 2004

The ecophysiology of uncultured
Rhodocyclus
-related polyphosphate-accumulating organisms (PAO) present in three full-scale enhanced biological phosphorus removal (EBPR) activated sludge plants was studied by using microautoradiography combined with fluorescence in situ hybridization. The investigations showed that these organisms were present in all plants examined and constituted 5 to 10, 10 to 15, and 17 to 22% of the community biomass. The behavior of these bacteria generally was consistent with the biochemical models proposed for PAO, based on studies of lab-scale investigations of enriched and often unknown PAO cultures.
Rhodocyclus
-related PAO were able to accumulate short-chain substrates, including acetate, propionate, and pyruvate, under anaerobic conditions, but they could not assimilate many other low-molecular-weight compounds, such as ethanol and butyrate. They were able to assimilate two substrates (e.g., acetate and propionate) simultaneously. Leucine and thymidine could not be assimilated as sole substrates and could only be assimilated as cosubstrates with acetate, perhaps serving as N sources. Glucose could not be assimilated by the
Rhodocyclus
-related PAO, but it was easily fermented in the sludge to products that were subsequently consumed. Glycolysis, and not the tricarboxylic acid cycle, was the source that provided the reducing power needed by the
Rhodocyclus
-related PAO to form the intracellular polyhydroxyalkanoate storage compounds during anaerobic substrate assimilation. The
Rhodocyclus
-related PAO were able to take up orthophosphate and accumulate polyphosphate when oxygen, nitrate, or nitrite was present as an electron acceptor. Furthermore, in the presence of acetate growth was sustained by using oxygen, as well as nitrate or nitrite, as an electron acceptor. This strongly indicates that
Rhodocyclus
-related PAO were able to denitrify and thus played a role in the denitrification occurring in full-scale EBPR plants.
Construction of a Xylan-Fermenting Yeast Strain through Codisplay of Xylanolytic Enzymes on the Surface of Xylose-Utilizing
Saccharomyces cerevisiae
Cells
Authors: Katahira Satoshi , Fujita Yasuya , Mizuike Atsuko , Fukuda Hideki , Kondo Akihiko
Published: September 2004

Hemicellulose is one of the major forms of biomass in lignocellulose, and its essential component is xylan. We used a cell surface engineering system based on α-agglutinin to construct a
Saccharomyces cerevisiae
yeast strain codisplaying two types of xylan-degrading enzymes, namely, xylanase II (XYNII) from
Trichoderma reesei
QM9414 and β-xylosidase (XylA) from
Aspergillus oryzae
NiaD300, on the cell surface. In a high-performance liquid chromatography analysis, xylose was detected as the main product of the yeast strain codisplaying XYNII and XylA, while xylobiose and xylotriose were detected as the main products of a yeast strain displaying XYNII on the cell surface. These results indicate that xylan is sequentially hydrolyzed to xylose by the codisplayed XYNII and XylA. In a further step toward achieving the simultaneous saccharification and fermentation of xylan, a xylan-utilizing
S. cerevisiae
strain was constructed by codisplaying XYNII and XylA and introducing genes for xylose utilization, namely, those encoding xylose reductase and xylitol dehydrogenase from
Pichia stipitis
and xylulokinase from
S. cerevisiae
. After 62 h of fermentation, 7.1 g of ethanol per liter was directly produced from birchwood xylan, and the yield in terms of grams of ethanol per gram of carbohydrate consumed was 0.30 g/g. These results demonstrate that the direct conversion of xylan to ethanol is accomplished by the xylan-utilizing
S. cerevisiae
strain.
Shewanella oneidensis
MR-1 Restores Menaquinone Synthesis to a Menaquinone-Negative Mutant
Authors: Myers Charles R. , Myers Judith M.
Published: September 2004

The mechanisms underlying the use of insoluble electron acceptors by metal-reducing bacteria, such as
Shewanella oneidensis
MR-1, are currently under intensive study. Current models for shuttling electrons across the outer membrane (OM) of MR-1 include roles for OM cytochromes and the possible excretion of a redox shuttle. While MR-1 is able to release a substance that restores the ability of a menaquinone (MK)-negative mutant, CMA-1, to reduce the humic acid analog anthraquinone-2,6-disulfonate (AQDS), cross-feeding experiments conducted here showed that the substance released by MR-1 restores the growth of CMA-1 on several soluble electron acceptors. Various strains derived from MR-1 also release this substance; these include mutants lacking the OM cytochromes OmcA and OmcB and the OM protein MtrB. Even though strains lacking OmcB and MtrB cannot reduce Fe(III) or AQDS, they still release a substance that restores the ability of CMA-1 to use MK-dependent electron acceptors, including AQDS and Fe(III). Quinone analysis showed that this released substance restores MK synthesis in CMA-1. This ability to restore MK synthesis in CMA-1 explains the cross-feeding results and challenges the previous hypothesis that this substance represents a redox shuttle that facilitates metal respiration.
Comparison of Atomic Force Microscopy Interaction Forces between Bacteria and Silicon Nitride Substrata for Three Commonly Used Immobilization Methods
Authors: Vadillo-Rodríguez Virginia , Busscher Henk J. , Norde Willem , de Vries Joop , Dijkstra René J. B. , Stokroos Ietse , van der Mei Henny C.
Published: September 2004

Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanometer scale. For AFM, bacterial cells need to be firmly anchored to a substratum surface in order to withstand the friction forces from the silicon nitride tip. Different strategies for the immobilization of bacteria have been described in the literature. This paper compares AFM interaction forces obtained between
Klebsiella terrigena
and silicon nitride for three commonly used immobilization methods, i.e., mechanical trapping of bacteria in membrane filters, physical adsorption of negatively charged bacteria to a positively charged surface, and glutaraldehyde fixation of bacteria to the tip of the microscope. We have shown that different sample preparation techniques give rise to dissimilar interaction forces. Indeed, the physical adsorption of bacterial cells on modified substrata may promote structural rearrangements in bacterial cell surface structures, while glutaraldehyde treatment was shown to induce physicochemical and mechanical changes on bacterial cell surface properties. In general, mechanical trapping of single bacterial cells in filters appears to be the most reliable method for immobilization.
The Pool of ADP and ATP Regulates Anaerobic Product Formation in Resting Cells of
Lactococcus lactis
Authors: Palmfeldt Johan , Paese Marco , Hahn-Hägerdal Bärbel , van Niel Ed W. J.
Published: September 2004

Lactococcus lactis
grows homofermentatively on glucose, while its growth on maltose under anaerobic conditions results in mixed acid product formation in which formate, acetate, and ethanol are formed in addition to lactate. Maltose was used as a carbon source to study mixed acid product formation as a function of the growth rate. In batch and nitrogen-limited chemostat cultures mixed acid product formation was shown to be linked to the growth rate, and homolactic fermentation occurred only in resting cells. Two of the four lactococcal strains investigated with maltose,
L. lactis
65.1 and MG1363, showed more pronounced mixed acid product formation during growth than
L. lactis
ATCC 19435 or IL-1403. In resting cell experiments all four strains exhibited homolactic fermentation. In resting cells the intracellular concentrations of ADP, ATP, and fructose 1,6-bisphosphate were increased and the concentration of P
i
was decreased compared with the concentrations in growing cells. Addition of an ionophore (monensin or valinomycin) to resting cultures of
L. lactis
65.1 induced mixed acid product formation concomitant with decreases in the ADP, ATP, and fructose 1,6-bisphosphate concentrations. ADP and ATP were shown to inhibit glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase, and alcohol dehydrogenase in vitro. Alcohol dehydrogenase was the most sensitive enzyme and was totally inhibited at an adenine nucleotide concentration of 16 mM, which is close to the sum of the intracellular concentrations of ADP and ATP of resting cells. This inhibition of alcohol dehydrogenase might be partially responsible for the homolactic behavior of resting cells. A hypothesis regarding the level of the ATP-ADP pool as a regulating mechanism for the glycolytic flux and product formation in
L. lactis
is discussed.
Regulation of the
N
-Acyl Homoserine Lactone-Dependent Quorum-Sensing System in Rhizosphere
Pseudomonas putida
WCS358 and Cross-Talk with the Stationary-Phase RpoS Sigma Factor and the Global Regulator GacA
Authors: Bertani Iris , Venturi Vittorio
Published: September 2004

Quorum sensing is a cell population-density dependent regulatory system which in gram-negative bacteria often involves the production and detection of
N
-acyl homoserine lactones (AHLs). Some
Pseudomonas putida
strains have been reported to produce AHLs, and one quorum-sensing locus has been identified. However, it appears that the majority of strains do not produce AHLs. In this study we report the identification and regulation of the AHL-dependent system of rhizosphere
P. putida
WCS358. This system is identical to the recently identified system of
P. putida
strain IsoF and very similar to the
las
system of
Pseudomonas aeruginosa
. It is composed of three genes, the
luxI
family member
ppuI
, the putative repressor
rsaL
, and the
luxR
family member
ppuR
. A genomic
ppuR
::Tn
5
mutant of strain WCS358 was identified by its inability to produce AHLs when it was cross-streaked in close proximity to an AHL biosensor, whereas an
rsaL
::Tn
5
genomic mutant was identified by its ability to overproduce AHL molecules. Using transcriptional promoter fusions, we studied expression profiles of the
rsaL
,
ppuI
, and
ppuR
promoters in various genetic backgrounds. At the onset of the stationary phase, the autoinducer synthase
ppuI
gene expression is under positive regulation by PpuR-AHL and under negative regulation by RsaL, indicating that the molecules could be in competition for binding at the
ppuI
promoter. In genomic
rsaL
::Tn
5
mutants
ppuI
expression and production of AHL levels increased dramatically; however, both processes were still under growth phase regulation, indicating that RsaL is not involved in repressing AHL production at low cell densities. The roles of the global response regulator GacA and the stationary-phase sigma factor RpoS in the regulation of the AHL system at the onset of the stationary phase were also investigated. The
P. putida
WCS358
gacA
gene was cloned and inactivated in the genome. It was determined that the three global regulatory systems are closely linked, with quorum sensing and RpoS regulating each other and GacA positively regulating
ppuI
expression. Studies of the regulation of AHL quorum-sensing systems have lagged behind other studies and are important for understanding how these systems are integrated into the overall growth phase and metabolic status of the cells.