bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting Proteins for Degradation by Arabidopsis COP1: Teamwork Is What Matters
Authors: Lin Rongcheng , Wang Haiyang
Published: January 2007

Arabidopsis COP1 (Constitutive Photomorphogenic 1) defines a key repressor of photomorphogenesis in darkness by acting as an E3 ubiquitin ligase in the nucleus, and is responsible for the targeted degradation of a number of photomorphogenesis‐promoting factors, including phyA, HY5, LAF1, and HFR1. Light activation of multiple classes of photoreceptors (including both phytochromes and cryptochromes) inactivates COP1 and reduces its nuclear abundance, allowing the accumulation of these positively acting light signaling intermediates to promote photomorphogenic development. Recent studies suggest that Arabidopsis COP1 teams up with a family of SPA proteins (SPA1‐SPA4) to form the physiologically active COP1‐SPA E3 ubiquitin ligase complexes. These COP1‐SPA complexes play overlapping and distinct functions in regulating seedling photomorphogenesis under different light conditions and adult plant growth. Further, the COP1‐SPA complexes act in concert at a biochemical level with the CDD (COP10, DET1, and DDB1) complex and COP9 signalosome (CSN) to orchestrate the repression of photomorphogenesis.
Polycomb‐group (Pc‐G) Proteins Control Seed Development in Arabidopsis thaliana L.
Authors: Wang Xiao‐Xue , Ma Li‐Geng
Published: January 2007

Polycomb‐group (Pc‐G) proteins repress their target gene expression by assemble complexes in Drosophila and mammals. Three groups of Pc‐G genes, controlling seed development, flower development and vernalization response, have been identified in Arabidopsis (Arabidopsis thaliana L.). MEDEA (MEA), FERTILIZATION INDEPENDENT SEED2 (FIS2), and FERTILIZATION INDEPENDENT ENDOSPERM (FIE) are Pc‐G genes in Arabidopsis. Their functions in seed development have been extensively explored. The advanced findings of molecular mechanism on how MEA, FIS2 and FIE control seed development in Arabidopsis are reviewed in this paper.
Molecular Biological and Biochemical Studies Reveal New Pathways Important for Cotton Fiber Development
Authors: Xu Yu , Li Hong‐Bin , Zhu Yu‐Xian
Published: January 2007

As one of the longest single‐celled seed trichomes, fibers provide an excellent model for studying fundamental biological processes such as cell differentiation, cell expansion, and cell wall biosynthesis. In this review, we summarize recent progress in cotton functional genomic studies that characterize the dynamic changes in the transcriptomes of fiber cells. Extensive expression profilings of cotton fiber transcriptomes have provided comprehensive information, as quite a number of transcription factors and enzyme‐coding genes have been shown to express preferentially during the fiber elongation period. Biosynthesis of the plant hormone ethylene is found significantly upregulated during the fiber growth period as revealed by both microarray analysis and by biochemical and physiological studies. It is suggested that genetic engineering of the ethylene pathway may improve the quality and the productivity of cotton lint. Many metabolic pathways, such as biosynthesis of cellulose and matrix polysaccharides are preferentially expressed in actively growing fiber cells. Five gene families, including proline‐rich proteins (PRP), arabinogalactan proteins (AGP), expansins, tubulins and lipid transfer proteins (LTP) are activated during early fiber development, indicating that they may also be needed for cell elongation. In conclusion, we identify a few areas of future research for cotton functional genomic studies.
Phytochrome‐regulated Gene Expression
Authors: Quail Peter H.
Published: January 2007

Identification of all genes involved in the phytochrome (phy)‐mediated responses of plants to their light environment is an important goal in providing an overall understanding of light‐regulated growth and development. This article highlights and integrates the central findings of two recent comprehensive studies in Arabidopsis that have identified the genome‐wide set of phy‐regulated genes that respond rapidly to red‐light signals upon first exposure of dark‐grown seedlings, and have tested the functional relevance to normal seedling photomorphogenesis of an initial subset of these genes. The data: (a) reveal considerable complexity in the channeling of the light signals through the different phy‐family members (phyA to phyE) to responsive genes; (b) identify a diversity of transcription‐factor‐encoding genes as major early, if not primary, targets of phy signaling, and, therefore, as potentially important regulators in the transcriptional‐network hierarchy; and (c) identify auxin‐related genes as the dominant class among rapidly‐regulated, hormone‐related genes. However, reverse‐genetic functional profiling of a selected subset of these genes reveals that only a limited fraction are necessary for optimal phy‐induced seedling deetiolation.
Preceptor rewards: How to say thank you for mentoring the next generation of nurse practitioners
Authors: Campbell Suzanne Hetzel , Hawkins Joellen W.
Published: January 2007

Purpose: To answer the question how do faculty nurture and reward clinical preceptors and what supports do preceptors require?

Data sources: Data came from the literature and from surveying a purposive sample of 26 faculty members teaching clinical courses and arranging precepted experiences for nurse practitioner (NP) students at 26 public and private institutions across the United States. The vehicles for the survey were personal contact and e‐mail.

Conclusions: Schools offer preceptor rewards varying widely in their monetary value, from tuition and continuing education vouchers, verification of hours toward recertification, access to services and events on campus, reduced price or free admission to museums, cultural and sports events, and lectures. Faculty nurture preceptors by nominating them for awards, providing letters of reference, editing manuscripts, and collaborating on research projects. Supports for preceptors from the literature reflected National Organization of Nurse Practitioner Faculties guidelines (2000), and the policies of schools and clinical agencies, such as providing copies of program objectives and student credentials.

Implications for practice and education: As NP programs have proliferated, there is increased pressure on faculty to find, nurture, reward, and retain good preceptors. Faculty must continue to work with program and agency administrators to comply with policies and create preceptor rewards to recognize their gifts to us, to our schools, and to the profession.
Job satisfaction among Arizona adult nurse practitioners
Authors: Schiestel Charlotte
Published: January 2007

Purpose: A literature review for studies of job satisfaction among nurse practitioners (NPs) suggests that the true determinants of job satisfaction have not been discovered. The purpose of this study was to determine job satisfaction among adult health NPs (ANPs) practicing in Arizona.

Data sources: The Misener nurse practitioner job satisfaction scale was mailed to 329 Arizona ANPs who were certified by the Arizona State Board of Nursing (47% response rate).

Conclusions: The mean overall satisfaction score was 4.69 out of a possible score of 6.0 for very satisfied. Differences in employer type, gender, annual income, membership in professional nursing organization, or full‐time versus part‐time employment status did not result in significantly different scores on the job satisfaction scale in this group.

Implications for practice: A deep and sustained nursing shortage, the exodus of experienced nurses from the profession, and a projected shortage of primary care providers have generated interest among professional groups, private and government healthcare commissions, and the healthcare industry in determining what factors may influence an individual to choose and remain active in nursing practice. Researchers, educators, employers, and the healthcare industry must look beyond well‐worn assumptions about job satisfaction to explore what the individual NP finds satisfying about his or her role.
A case study of an older adult with severe anemia refusing blood transfusion
Authors: Thomas C. Michelle , Coleman Harriet R. , Morritt Taub Leslie‐Faith
Published: January 2007

Purpose: To discuss the diagnosis and treatment of severe anemia in an older adult who presents the challenge of declining blood transfusion in a real‐world scenario where critical thinking, evidence‐based care, and collaboration with other providers must come together to serve this patient’s unique needs.

Data sources: Extensive review of the scientific literature on anemia and the situation in which a patient refuses blood transfusion presented in a case study format.

Conclusions: A thorough physical assessment, complete health history, and appropriate diagnostic workup should be used to distinguish the normal effects of senescence from the signs and symptoms of anemia. Common conditions that cause anemia in the elderly include chronic disease, iron deficiency, and gastrointestinal bleeding. These conditions may result in profound anemia. The challenge can be compounded when, because of religious tenets, a patient does not accept a blood transfusion. This case study challenges nurse practitioners to apply knowledge, seek guidance, and make appropriate referrals to care for a patient in order to render care within the parameters of the patient’s belief system.

Implications for practice: The astute primary care provider recognizes that anemia is not an expected physiological change associated with aging but a manifestation of an underlying disease process. Fatigue, weakness, and dyspnea are all symptoms of anemia that may be overlooked and attributed to the aging process. Further, in keeping with the principles of autonomy and self‐determination, it is the clinician’s duty to work with all patients to restore them to a state of optimal health while respecting deeply held spiritual beliefs.
The transtheoretical model and primary care: “The Times They Are A Changin’”
Authors: Singer Ethan A.
Published: January 2007

Purpose: To identify the transtheoretical model and the five stages of change that assist to bring about behavioral change. A case study is presented to illustrate how the model can be applied by primary care nurse practitioners (NPs) to assist patients toward a healthier lifestyle.

Data sources: Scientific literature, theoretical framework, and case study.

Conclusions: The transtheoretical model has implications in primary care to assist NPs in assessing what stage a patient may be in, offering encouragement to promote a healthier lifestyle change, and reassessing the patient to maintain the desired healthy behavior.

Implications for practice: Primary care NPs can use the transtheoretical model to better advance patients into a healthy behavioral change. Documentation of the current stage a patient is in can promote continuity of care among providers, outline specific health promotion initiatives to enhance patient care, and provide documentation during regulatory inspections.
How well are nurse practitioners prepared for practice: Results of a 2004 questionnaire study
Authors: Hart Ann Marie , Macnee Carol L.
Published: January 2007

Purpose: The purpose of this study was to evaluate the perceived preparedness of nurse practitioners (NPs) for practice after completing their basic NP educational programs and to evaluate NPs’ perceived preparedness in and their perceived importance of select clinical content areas basic to NP education.

Data sources: This cross‐sectional descriptive study used a written questionnaire consisting of 32 items, two of which contained 25 subitems. Subjects were asked to rate their overall level of preparedness when they completed their NP program and both their level of preparation in and the importance of 25 clinical content areas. The questionnaires were administered to attendees at two large national NP conferences in 2004; a total of 562 questionnaires were completed and used in the analysis.

Conclusions: Ten percent of the sample perceived that they were very well prepared for practice as an NP after completing their basic NP education. Fifty‐one percent perceived that they were only somewhat or minimally prepared. Current age, years since graduation from an NP program, and age when attending the NP program did not differ significantly for those who felt prepared versus those who did not. For a number of content areas, subjects did not perceive that they were well prepared in the same areas that they perceived were very important.

Implications for practice: Our results indicate that formal NP education is not preparing new NPs to feel ready for practice and suggests several areas where NP educational programs need to be strengthened. Practicing NPs are the basis of the NP profession, and their views need to be sought, listened to, and reflected upon as we advance toward expanded preparation at the doctoral level.
Village Elections, Accountability and Income Distribution in Rural China
Authors: Yao Yang
Published: January 2007

China has experimented with village elections for nearly 20 years. Using village and household survey data collected from 48 villages of 8 Chinese provinces for the period 1986–2002, this paper studies how the introduction of elections affects village governance and income distribution in Chinese villages. The econometric analysis finds the following outcomes. First, village elections have increased the share of public expenditure and reduced the share of administrative expenditure in the village budget, so the accountability of the elected village committee has been enhanced. Second, elections have not led to more income redistribution; instead, they have reduced the progressiveness of income redistribution. Third, elections have reduced income inequality measured by the Gini coefficient in villages. The reduction is equivalent to 5.7 percent of the sample average, or 32 percent of the growth of the Gini coefficient in the period of 1987‐2002. Because village elections have not led to more income redistribution, this positive effect must have come from more public investment, which benefits the poor more than wealthier people. The general conclusion that we draw from our results is that, despite institutional constraints, village elections have improved village governance and the life of villagers.

(Edited by Xinyu Fan)
Sustaining Economic Growth in China under Energy and Climate Security Constraints
Authors: Lu Xuedu , Pan Jiahua , Chen Ying
Published: January 2007

After over a quarter of a century of high economic growth, there is no sign that China will slow its pace of economic development. In the meantime, domestic energy security and international climate security have become of increasing concern given China's growth patterns. In this paper, the authors look at the future prospects of growth of the economy, energy demand and greenhouse gas emissions. For China as a developing country, energy security constitutes a more immediate and challenging constraint for China in meeting its development target than the problem of emission reduction. Energy efficiency and diversification have been actively pursued for addressing energy security issue but with positive co‐benefit of climate security. International cooperation can promote both securities for a health growth of the economy.

(Edited by Xinyu Fan)
FDI Flows between China and ASEAN: Emerging Factors and Prospect
Authors: Shu Yuan , Zeng Kaisheng
Published: January 2007

Economic relations between China and ASEAN have further intensified since the 1990s. Foreign direct investment (FDI) flows between the two economic giants have reached a new high, attracting the attention of policy‐makers and economists. The present paper investigates recent contextual changes and identifies some significant emerging factors that exert influence on the flows of FDI between China and ASEAN. This paper also analyzes the development trend of FDI between the two economies, and it is found that the FDI flows are at a historical turning point.

(Edited by Xiaoming Feng)
What Do Employers Want? Views of Chinese and Canadian Job Seekers
Authors: Sun Ying , Luke Chan M. W. , Tiessen James H.
Published: January 2007

Rapid globalization has led to many studies of cross‐cultural issues and their implications for management. As China's importance in the international economy rises, the level of international business cooperation continues to increase. This paper first identifies differences in the cultural orientations of Chinese and Canadians entering the job market and then examines how these orientations are related to their perceptions of the criteria employers use when hiring. The analyses show that the cultural differences are not consistent with Hofstede's previous work. Further, there are significant differences in the qualities that are considered important when seeking a job. The results of this study increase mutual understanding and improve business relationships between the two countries.

(Edited by Zhinan Zhang)
Experimental Investigation of the Effects of a Moving Shock Wave on Compressor Stator Flow
Authors: Langford Matthew D. , Breeze-Stringfellow Andrew , Guillot Stephen A. , Solomon William , Ng Wing F. , Estevadeordal Jordi
Published: January 2007

Linear cascade testing was performed to simulate the flow conditions experienced by stator blades in an axial compressor with supersonic relative Mach numbers at the inlet to the downstream embedded rotors. Experiments were conducted in a transonic blow-down wind tunnel with a nominal inlet Mach number of 0.65. A single moving normal shock introduced at the exit of the stator cascade simulated the bow shock from a downstream rotor. The shock was generated using a shock tube external to the wind tunnel. Pressure measurements indicated that the stator matched its design intent loading, turning, and loss under steady flow conditions. Effects of the passing shock on the stator flowfield were investigated using shadowgraph photography and digital particle image velocimetry (DPIV). Measurements were taken with three different shock strengths. In each case, the passing shock induced a vortex around the trailing edge of the stator. The size and strength of these vortices were directly related to the shock strength. A suction side separation on the trailing edge of the stator was observed and found to correlate with the vortex blockage.
Online Water Wash Tests of GE J85-13
Authors: Syverud Elisabet , Bakken Lars E.
Published: January 2007

This paper reports the results of a series of online water wash tests of a GE J85-13 jet engine at the test facilities of the Royal Norwegian Air Force. The engine performance was deteriorated by injecting atomized saltwater at the engine inlet. The engine was then online washed with water injected at three different droplet sizes (25, 75, and 200μm) and at water-to-air ratios ranging from 0.4% to 3% by mass. Engine performance was measured using standard on-engine instrumentation. Extra temperature and pressure sensors in the compressor section provided additional information of the propagation of deposits in the aft stages. The measurements were supported by visual observations. The overall engine performance improved rapidly with online wash. The buildup of deposits in the aft stages was influenced both by the droplet size and the water-to-air ratio. The water-to-air ratio was the most important parameter to achieve effective online washing.
Effects of Glutathione and Ascorbic Acid on Streptomycin Sensitivity of
Escherichia coli
Authors: Goswami Manish , Mangoli Suhas H. , Jawali Narendra
Published: January 2007

We examined the effects of antioxidants and the role of reactive oxygen species (ROS) on the antibacterial action of aminoglycosides in
Escherichia coli
. We concluded that reduced streptomycin sensitivity in the presence of glutathione and ascorbic acid is not due to the antioxidant-mediated scavenging of ROS.
High-Level Telithromycin Resistance in a Clinical Isolate of
Streptococcus pneumoniae
Authors: Wolter Nicole , Smith Anthony M. , Low Donald E. , Klugman Keith P.
Published: January 2007

A rare clinical isolate of
Streptococcus pneumoniae
, highly resistant to telithromycin, contained
erm
(B) with a truncated leader peptide and a mutant ribosomal protein L4. By transformation of susceptible strains, this study shows that high-level telithromycin resistance is conferred by
erm
(B), wild type or mutant, in combination with a
69
GTG
71
-to-TPS mutation in ribosomal protein L4.
Validation of Mixed-Genome Microarrays as a Method for Genetic Discrimination
Authors: Wan Yan , Broschat Shira L. , Call Douglas R.
Published: January 2007

Comparative genomic hybridizations have been used to examine genetic relationships among bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains (whole-genome microarrays), or they may be composed of random DNA fragments from a large number of strains (mixed-genome microarrays [MGMs]). In this work both experimental and virtual arrays are analyzed to assess the validity of genetic inferences from these experiments with a focus on MGMs. Empirical data are analyzed from an
Enterococcus
MGM, while a virtual MGM is constructed in silico using sequenced genomes (
Streptococcus
). On average, a small MGM is capable of correctly deriving phylogenetic relationships between seven species of
Enterococcus
with accuracies of 100% (
n
= 100 probes) and 95% (
n
= 46 probes); more probes are required for intraspecific differentiation. Compared to multilocus sequence methods and whole-genome microarrays, MGMs provide additional discrimination between closely related strains and offer the possibility of identifying unique strain or lineage markers. Representational bias can have mixed effects. Microarrays composed of probes from a single genome can be used to derive phylogenetic relationships, although branch length can be exaggerated for the reference strain. We describe a case where disproportional representation of different strains used to construct an MGM can result in inaccurate phylogenetic inferences, and we illustrate an algorithm that is capable of correcting this type of bias. The bias correction algorithm automatically provides bootstrap confidence values and can provide multiple bias-corrected trees with high confidence values.
Localization of Ruminal Cellulolytic Bacteria on Plant Fibrous Materials as Determined by Fluorescence In Situ Hybridization and Real-Time PCR
Authors: Shinkai Takumi , Kobayashi Yasuo
Published: January 2007

To visualize and localize specific bacteria associated with plant materials, a new fluorescence in situ hybridization (FISH) protocol was established. By using this protocol, we successfully minimized the autofluorescence of orchard grass hay and detected rumen bacteria attached to the hay under a fluorescence microscope. Real-time PCR assays were also employed to quantitatively monitor the representative fibrolytic species
Fibrobacter succinogenes
and
Ruminococcus flavefaciens
and also total bacteria attached to the hay.
F. succinogenes
was found firmly attached to not only the cut edges but also undamaged inner surfaces of the hay. Cells of phylogenetic group 1 of
F. succinogenes
were detected on many stem and leaf sheath fragments of the hay, even on fragments on which few other bacteria were seen. Cells of phylogenetic group 2 of
F. succinogenes
were often detected on hay fragments coexisting with many other bacteria. On the basis of 16S rRNA gene copy number analysis, the numbers of bacteria attached to the leaf sheaths were higher than those attached to the stems (
P
< 0.05). In addition,
R. flavefaciens
had a greater tendency than
F. succinogenes
to be found on the leaf sheath (
P
< 0.01) with formation of many pits.
F. succinogenes
, particularly phylogenetic group 1, is suggested to possibly play an important role in fiber digestion, because it is clearly detectable by FISH and is the bacterium with the largest population size in the less easily degradable hay stem.
Characterization of Airborne Molds, Endotoxins, and Glucans in Homes in New Orleans after Hurricanes Katrina and Rita
Authors: Rao Carol Y. , Riggs Margaret A. , Chew Ginger L. , Muilenberg Michael L. , Thorne Peter S. , Van Sickle David , Dunn Kevin H. , Brown Clive
Published: January 2007

In August and September 2005, Hurricanes Katrina and Rita caused breeches in the New Orleans, LA, levee system, resulting in catastrophic flooding. The city remained flooded for several weeks, leading to extraordinary mold growth in homes. To characterize the potential risks of mold exposures, we measured airborne molds and markers of molds and bacteria in New Orleans area homes. In October 2005, we collected air samples from 5 mildly water-damaged houses, 15 moderately to heavily water-damaged houses, and 11 outdoor locations. The air filters were analyzed for culturable fungi, spores, (1→3,1→6)-β-
d
-glucans, and endotoxins. Culturable fungi were significantly higher in the moderately/heavily water-damaged houses (geometric mean = 67,000 CFU/m
3
) than in the mildly water-damaged houses (geometric mean = 3,700 CFU/m
3
) (
P
= 0.02). The predominant molds found were
Aspergillus niger
,
Penicillium
spp.,
Trichoderma
, and
Paecilomyces
. The indoor and outdoor geometric means for endotoxins were 22.3 endotoxin units (EU)/m
3
and 10.5 EU/m
3
, respectively, and for (1→3,1→6)-β-
d
-glucans were 1.7 μg/m
3
and 0.9 μg/m
3
, respectively. In the moderately/heavily water-damaged houses, the geometric means were 31.3 EU/m
3
for endotoxins and 1.8 μg/m
3
for (1→3,1→6)-β-
d
-glucans. Molds, endotoxins, and fungal glucans were detected in the environment after Hurricanes Katrina and Rita in New Orleans at concentrations that have been associated with health effects. The species and concentrations were different from those previously reported for non-water-damaged buildings in the southeastern United States.
Quantitative Assessment of the Tetracycline Resistance Gene Pool in Cheese Samples by Real-Time TaqMan PCR
Authors: Manuzon Michele Y. , Hanna Scott E. , Luo Hongliang , Yu Zhongtang , Harper W. James , Wang Hua H.
Published: January 2007

A TaqMan real-time PCR assay was developed to quantify the
tetS
gene pool present in retail cheeses. This protocol offers a rapid, specific, sensitive, and culture-independent method for assessing antibiotic resistance genes in food samples rich in fats and proteins.
Characterization of IS
Xax1
, a Novel Insertion Sequence Restricted to
Xanthomonas axonopodis
pv. phaseoli (Variants fuscans and non-fuscans) and
Xanthomonas axonopodis
pv. vesicatoria
Authors: Alavi Seyed Mehdi , Poussier Stéphane , Manceau Charles
Published: January 2007

IS
Xax1
is a novel insertion sequence belonging to the IS
256
and
Mutator
families. Dot blot, Southern blot, and PCR analyses revealed that IS
Xax1
is restricted to
Xanthomonas axonopodis
pv. phaseoli (variants fuscans and non-fuscans) and
X. axonopodis
pv. vesicatoria strains. Directed AFLP also showed that a high degree of polymorphism is associated with IS
Xax1
insertion in these strains.
Photoreactivation and Dark Repair in UV-Treated Microorganisms: Effect of Temperature
Authors: Salcedo I. , Andrade J. A. , Quiroga J. M. , Nebot E.
Published: January 2007

Because of the lack of readily available information about the influence of temperature on microorganism reactivation processes subsequent to inactivation with UV radiation, a series of batch reactivation studies were performed at 5, 10, 15, 20, 25, and 30°C. A special effort was made to model the reactivation process to enable the effect of the temperature variable to be quantified. Because an earlier-proposed kinetic model (K. Kashimada, N. Kamiko, K. Yamamoto, and S. Ohgaki, Water Sci. Technol. 33:261-269, 1996), a first-order saturation type, does not adequately fit the data obtained in experiments of reactivation in conditions of light and darkness, a modification of that model is proposed. The new model, which actually coincides with the classical logistic equation, incorporates two kinetic parameters: the maximum survival ratio (

S
m

) and the second-order reactivation rate constant (
k
2
). In order to interpret correctly the reactivation occurring in conditions of darkness, a new term for the decay is added to the logistic equation. The new model accurately fits the data obtained in reactivation experiments, permitting the interpretation of the kinetic parameters

S
m

,
k
2
, and
M
(for only repair in darkness), where
M
is mortality, a zero-order decay rate constant, and their relationship with various environmental conditions, such as microbial type, light, and temperature. The parameters

S
m

and
k
2
(and
M
for reactivation in conditions of darkness) show exponential dependence on the reactivating temperature, and it is possible to predict their values and hence the reactivation curve from the equations proposed in this work.
Individual and Combined Effects of pH and Lactic Acid Concentration on
Listeria innocua
Inactivation: Development of a Predictive Model and Assessment of Experimental Variability
Authors: Janssen M. , Geeraerd A. H. , Cappuyns A. , Garcia-Gonzalez L. , Schockaert G. , Van Houteghem N. , Vereecken K. M. , Debevere J. , Devlieghere F. , Van Impe J. F.
Published: January 2007

In food technology, organic acids (e.g., lactic acid, acetic acid, and citric acid) are popular preservatives. The purpose of this study was to separate the individual effects of the influencing factors pH and undissociated lactic acid on
Listeria innocua
inactivation. Therefore, the inactivation process was investigated under controlled, initial conditions of pH (pH
0
) and undissociated lactic acid ([LaH]
0
). The resulting inactivation curves consisted of a (sometimes negligible) shoulder period followed by a descent phase. In a few cases, a tailing phase was observed. Depending on the conditions, the descent phase contained one or two log-linear parts or had a convex or concave shape. In addition, the inactivation process was characterized by a certain variability, dependent on the severity of the conditions. Furthermore, in the neighborhood of the growth/no growth interface sometimes contradictory observations occurred. Overall, the individual effects of the influencing factors pH and undissociated lactic acid could clearly be distinguished and were also apparent based on fluorescence microscopy. Appropriate model types were developed and enabled prediction of which conditions of pH
0
and [LaH]
0
are necessary to obtain a predetermined inactivation (number of decimal reductions) within a predetermined time range.
Strong Impact on the Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Community of a PAH-Polluted Soil but Marginal Effect on PAH Degradation when Priming with Bioremediated Soil Dominated by Mycobacteria
Authors: Johnsen Anders R. , Schmidt Stine , Hybholt Trine K. , Henriksen Sidsel , Jacobsen Carsten S. , Andersen Ole
Published: January 2007

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by
Mycobacterium
spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene
pdo1
. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no
pdo1
genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.
Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water
Authors: Shanks Orin C. , Domingo Jorge W. Santo , Lu Jingrang , Kelty Catherine A. , Graham James E.
Published: January 2007

We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human and pig fecal samples, 351 plasmid clones were sequenced and were determined to define 289 different genomic DNA regions. These putative human-specific fecal bacterial DNA sequences were then analyzed by dot blot hybridization, which confirmed that 98% were present in the source human fecal microbial community and absent from the original pig fecal DNA extract. Comparative sequence analyses of these sequences suggested that a large number (43.5%) were predicted to encode bacterial secreted or surface-associated proteins. Deoxyoligonucleotide primers capable of annealing to a subset of 26 of the candidate sequences predicted to encode factors involved in interactions with host cells were then used in the PCR and did not amplify markers in DNA from any additional pig fecal specimens. These 26 PCR assays exhibited a range of specificity in tests with 11 other animal sources, with more than half amplifying markers only in specimens from dogs or cats. Four assays were more specific, detecting markers only in specimens from humans, including those from 18 different human populations examined. We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds.
Growth Yields in Bacterial Denitrification and Nitrate Ammonification
Authors: Strohm Tobin O. , Griffin Ben , Zumft Walter G. , Schink Bernhard
Published: January 2007

Denitrification and nitrate ammonification are considered the highest-energy-yielding respiration systems in anoxic environments after oxygen has been consumed. The corresponding free energy changes are 7 and 35% lower than that of aerobic respiration, respectively. Growth yield determinations with pure cultures of
Paracoccus denitrificans
and
Pseudomonas stutzeri
revealed that far less energy is converted via ATP into cell mass than expected from the above calculations. Denitrification with formate or hydrogen as electron donor yielded about 2.4 to 3.0 g dry matter per mol formate or hydrogen and 15 to 18 g dry matter per mol acetate. Similar yields with acetate were obtained with
Pseudomonas stutzeri. Wolinella succinogenes
and
Sulfurospirillum deleyianum
, which reduce nitrate to ammonia, both exhibited similar yield values with formate or H
2
plus nitrate. The results indicate that ATP synthesis in denitrification is far lower than expected from the free energy changes and even lower than in nitrate ammonification. The results are discussed against the background of our present understanding of electron flow in denitrification and with respect to the importance of denitrification and nitrate ammonification in the environment.
Structure and Function Analysis of CaMdr1p, a Major Facilitator Superfamily Antifungal Efflux Transporter Protein of
Candida albicans
: Identification of Amino Acid Residues Critical for Drug/H
+
Transport
Authors: Pasrija Ritu , Banerjee Dibyendu , Prasad Rajendra
Published: January 2007

We have cloned and overexpressed multidrug transporter CaMdr1p as a green fluorescent protein-tagged protein to show its capability to extrude drug substrates. The drug extrusion was sensitive to pH and energy inhibitors and displayed selective substrate specificity. CaMdr1p has a unique and conserved antiporter motif, also called motif C [G(X
6
)G(X
3
)GP(X
2
)GP(X
2
)G], in its transmembrane segment 5 (TMS 5). Alanine scanning of all the amino acids of the TMS 5 by site-directed mutagenesis highlighted the importance of the motif, as well as that of other residues of TMS 5, in drug transport. The mutant variants of TMS 5 were placed in four different categories. The first category had four residues, G244, G251, G255, and G259, which are part of the conserved motif C, and their substitution with alanine resulted in increased sensitivity to drugs and displayed impaired efflux of drugs. Interestingly, first category mutants, when replaced with leucine, resulted in more dramatic loss of drug resistance and efflux. Notwithstanding the location in the core motif, the second category included residues which are part of the motif, such as P260, and those which were not part of the motif, such as L245, W248, P256, and F262, whose substitution with alanine resulted in a severe loss of drug resistance and efflux. The third category included G263, which is a part of motif C, but unlike other conserved glycines, its replacement with alanine or leucine showed no change in the phenotype. The replacement of the remaining 11 residues of the fourth category did not result in any change. The putative helical wheel projection showed clustering of functionally critical residues to one side and thus suggests an asymmetric nature of TMS 5.
Biosynthesis of the Thioquinolobactin Siderophore: an Interesting Variation on Sulfur Transfer
Authors: Godert Amy M. , Jin Mi , McLafferty Fred W. , Begley Tadhg P.
Published: January 2007

The thioquinolobactin siderophore from
Pseudomonas fluorescens
ATCC 17400 utilizes a variation of the sulfur transfer chemistry found in thiamine and molydobterin biosynthesis. A JAMM motif protein cleaves the C-terminal amino acid residues following a diglycine moiety on a small sulfur carrier protein, and the modified C terminus is activated and sulfurylated, forming a thiocarboxylate.
Role of an FtsK-Like Protein in Genetic Stability inStreptomyces coelicolorA3(2)
Authors: Wang Lei , Yu Yanfei , He Xinyi , Zhou Xiufen , Deng Zixin , Chater Keith F. , Tao Meifeng
Published: January 2007

Streptomyces coelicolorA3(2) does not have a canonical cell division cycle during most of its complex life cycle, yet it contains a gene (ftsKSC) encoding a protein similar to FtsK, which couples the completion of cell division and chromosome segregation in unicellular bacteria such asEscherichia coli. Here, we show that various constructedftsKSCmutants all grew apparently normally and sporulated but upon restreaking gave rise to many aberrant colonies and to high frequencies of chloramphenicol-sensitive mutants, a phenotype previously associated with large terminal deletions from the linear chromosome. Indeed, most of the aberrant colonies had lost large fragments near one or both chromosomal termini, as if chromosome ends had failed to reach their prespore destination before the closure of sporulation septa. A constructed FtsKSC-enhanced green fluorescent protein fusion protein was particularly abundant in aerial hyphae, forming distinctive complexes before localizing to each sporulation septum, suggesting a role for FtsKSCin chromosome segregation during sporulation. Use of a fluorescent reporter showed that whenftsKSCwas deleted, several spore compartments in most spore chains failed to express the late-sporulation-specific sigma factor genesigF, even though they contained chromosomal DNA. This suggested thatsigFexpression is autonomously activated in each spore compartment in response to completion of chromosome transfer, which would be a previously unknown checkpoint for late-sporulation-specific gene expression. These results provide new insight into the genetic instability prevalent among streptomycetes, including those used in the industrial production of antibiotics.
Reassessment of the Late Steps of Coenzyme B
12
Synthesis in
Salmonella enterica
: Evidence that Dephosphorylation of Adenosylcobalamin-5′-Phosphate by the CobC Phosphatase Is the Last Step of the Pathway
Authors: Zayas Carmen L. , Escalante-Semerena Jorge C.
Published: January 2007

We report that
cobC
strains of
Salmonella enterica
serovar Typhimurium are impaired in the ability to salvage cobyric acid (Cby), a de novo corrin ring biosynthetic intermediate, under aerobic growth conditions. In vivo and in vitro evidence support the conclusion that this new phenotype of
cobC
strains is due to the inability of serovar Typhimurium to dephosphorylate adenosylcobalamin-5′-phosphate (AdoCbl-5′-P), the product of the condensation of α-ribazole-5′-phosphate (α-RP) and adenosylcobinamide-GDP by the AdoCbl-5′-P synthase (CobS, EC 2.7.8.26) enzyme. Increased flux through the 5,6-dimethylbenzimidazole and cobinamide (Cbi) activation branches of the nucleotide loop assembly pathway in
cobC
strains restored AdoCbl-5′-P synthesis from Cby in a
cobC
strain. The rate of the CobS-catalyzed reaction was at least 2 orders of magnitude higher with α-RP than with α-ribazole as substrate. On the basis of the data reported herein, we conclude that removal of the phosphoryl group from AdoCbl-5′-P is the last step in AdoCbl biosynthesis in serovar Typhimurium and that the reaction is catalyzed by the AdoCbl-5′-P phosphatase (CobC) enzyme. Explanations for the correction of the Cby salvaging phenotype are discussed.
Evidence for Type III Restriction and Modification Systems in
Mycoplasma pulmonis
Authors: Dybvig Kevin , Cao Z. , French C. Todd , Yu Huilan
Published: January 2007

Mycoplasma pulmonis
possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.
Genes Required for Glycolipid Synthesis and Lipoteichoic Acid Anchoring in
Staphylococcus aureus
Authors: Gründling Angelika , Schneewind Olaf
Published: January 2007

Staphylococcus aureus
lipoteichoic acid (LTA) is composed of a linear 1,3-linked polyglycerolphosphate chain and is tethered to the bacterial membrane by a glycolipid (diglucosyl-diacylglycerol [Glc
2
-DAG]). Glc
2
-DAG is synthesized in the bacterial cytoplasm by YpfP, a processive enzyme that transfers glucose to diacylglycerol (DAG), using UDP-glucose as its substrate. Here we present evidence that the
S. aureus
α-phosphoglucomutase (PgcA) and UTP:α-glucose 1-phosphate uridyltransferase (GtaB) homologs are required for the synthesis of Glc
2
-DAG. LtaA (
l
ipo
t
eichoic
a
cid protein
A
), a predicted membrane permease whose structural gene is located in an operon with
ypfP
, is not involved in Glc
2
-DAG synthesis but is required for synthesis of glycolipid-anchored LTA. Our data suggest a model in which LtaA facilitates the transport of Glc
2
-DAG from the inner (cytoplasmic) leaflet to the outer leaflet of the plasma membrane, delivering Glc
2
-DAG as a substrate for LTA synthesis, thereby generating glycolipid-anchored LTA. Glycolipid anchoring of LTA appears to play an important role during infection, as
S. aureus
variants lacking
ltaA
display defects in the pathogenesis of animal infections.
S-Layer Anchoring and Localization of an S-Layer-Associated Protease in
Caulobacter crescentus
Authors: Ford Matthew J. , Nomellini John F. , Smit John
Published: January 2007

The S-layer of the gram-negative bacterium
Caulobacter crescentus
is composed of a single protein, RsaA, that is secreted and assembled into a hexagonal crystalline array that covers the organism. Despite the widespread occurrence of comparable bacterial S-layers, little is known about S-layer attachment to cell surfaces, especially for gram-negative organisms. Having preliminary indications that the N terminus of RsaA anchors the monomer to the cell surface, we developed an assay to distinguish direct surface attachment from subunit-subunit interactions where small RsaA fragments are incubated with S-layer-negative cells to assess the ability of the fragments to reattach. In doing so, we found that the RsaA anchoring region lies in the first ∼225 amino acids and that this RsaA anchoring region requires a smooth lipopolysaccharide species found in the outer membrane. By making mutations at six semirandom sites, we learned that relatively minor perturbations within the first ∼225 amino acids of RsaA caused loss of anchoring. In other studies, we confirmed that only this N-terminal region has a direct role in S-layer anchoring. As a by-product of the anchoring studies, we discovered that Sap, the
C. crescentus
S-layer-associated protease, recognized a cleavage site in the truncated RsaA fragments that is not detected by Sap in full-length RsaA. This, in turn, led to the discovery that Sap was an extracellular membrane-bound protease, rather than intracellular, as previously proposed. Moreover, Sap was secreted to the cell surface primarily by the S-layer type I secretion apparatus.
The
cymA
Gene, Encoding a Tetraheme
c
-Type Cytochrome, Is Required for Arsenate Respiration in
Shewanella
Species
Authors: Murphy Julie N. , Saltikov Chad W.
Published: January 2007

In
Shewanella
sp. strain ANA-3, utilization of arsenate as a terminal electron acceptor is conferred by a two-gene operon,
arrAB
, which lacks a gene encoding a membrane-anchoring subunit for the soluble ArrAB protein complex. Analysis of the genome sequence of
Shewanella putrefaciens
strain CN-32 showed that it also contained the same
arrAB
operon with 100% nucleotide identity. Here, we report that CN-32 respires arsenate and that this metabolism is dependent on
arrA
and an additional gene encoding a membrane-associated tetraheme
c
-type cytochrome,
cymA
. Deletion of
cymA
in ANA-3 also eliminated growth on and reduction of arsenate. The Δ
cymA
strains of CN-32 and ANA-3 negatively affected the reduction of Fe(III) and Mn(IV) but not growth on nitrate. Unlike the CN-32 Δ
cymA
strain, growth on fumarate was absent in the Δ
cymA
strain of ANA-3. Both homologous and heterologous complementation of
cymA
in
trans
restored growth on arsenate in Δ
cymA
strains of both CN-32 and ANA-3. Transcription patterns of
cymA
showed that it was induced under anaerobic conditions in the presence of fumarate and arsenate. Nitrate-grown cells exhibited the greatest level of
cymA
expression in both wild-type strains. Lastly, site-directed mutagenesis of the first Cys to Ser in each of the four CXXCH
c
-heme binding motifs of the CN-32 CymA nearly eliminated growth on and reduction of arsenate. Together, these results indicate that the biochemical mechanism of arsenate respiration and reduction requires the interactions of ArrAB with a membrane-associated tetraheme cytochrome, which in the non-arsenate-respiring
Shewanella
species
Shewanella oneidensis
strain MR-1, has pleiotropic effects on Fe(III), Mn(IV), dimethyl sulfoxide, nitrate, nitrite, and fumarate respiration.