bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of
Rhodococcus
sp. Strain RHA1
Authors: Gonçalves Edmilson R. , Hara Hirofumi , Miyazawa Daisuke , Davies Julian E. , Eltis Lindsay D. , Mohn William W.
Published: September 2006

Rhodococcus
sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes.
Detection of Microcystin-Producing Cyanobacteria in FinnishLakes with Genus-Specific Microcystin Synthetase Gene E (mcyE) PCR and Associations withEnvironmental Factors
Authors: Rantala Anne , Rajaniemi-Wacklin Pirjo , Lyra Christina , Lepistö Liisa , Rintala Jukka , Mankiewicz-Boczek Joanna , Sivonen Kaarina
Published: September 2006

We studied the frequency and composition of potential microcystin (MC) producers in 70 Finnish lakes with general and genus-specific microcystin synthetase gene E (mcyE) PCR. Potential MC-producingMicrocystis,PlanktothrixandAnabaenaspp. existed in 70%, 63%, and 37% of the lake samples, respectively. Approximately two-thirds of the lake samples contained one or two potential MC producers, while all three genera existed in 24% of the samples. In oligotrophic lakes, the occurrence of only one MC producer was most common. The combination ofMicrocystisandPlanktothrixwas slightly more prevalent than others in mesotrophic lakes, and the cooccurrence of all three MC producers was most widespread in both eutrophic and hypertrophic lakes. The proportion of the three-producer lakes increased with the trophic status of the lakes. In correlation analysis, the presence of multiple MC-producing genera was associated with higher cyanobacterial and phytoplankton biomass, pH, chlorophylla, total nitrogen, and MC concentrations. Total nitrogen, pH, and the surface area of the lake predicted the occurrence probability ofmcyEgenes, whereas total phosphorus alone accounted for MC concentrations in the samples by logistic and linear regression analyses. In conclusion, the results suggested that eutrophication increased the cooccurrence of potentially MC-producing cyanobacterial genera, raising the risk of toxic-bloom formation.
Reductive Dehalogenase Gene Expression as a Biomarker for Physiological Activity of
Dehalococcoides
spp
Authors: Lee Patrick K. H. , Johnson David R. , Holmes Victor F. , He Jianzhong , Alvarez-Cohen Lisa
Published: September 2006

This study characterizes the transcriptional expression of the reductive dehalogenase (RDase)-encoding
tceA
and
vcrA
genes and evaluates their applicability as potential biological markers of
Dehalococcoides
activity. When
Dehalococcoides ethenogenes
195 was provided with trichloroethene (TCE) as the electron acceptor, the expression of the
tceA
gene increased by 90-fold relative to that in cells starved of chlorinated ethenes, demonstrating that
tceA
gene expression is indicative of the active physiological state of this strain. In a
Dehalococcoides
-containing enrichment culture that contains both the
tceA
and
vcrA
genes, the
tceA
gene was up-regulated in response to TCE and
cis
-1,2-dichloroethene (cDCE) exposure, while the
vcrA
gene was up-regulated in response to TCE, cDCE, and vinyl chloride (VC). When chlorinated ethenes were depleted, the RDase-encoding gene transcripts decayed exponentially, with a half-life between 4.8 and 6.1 h, until they reached a stable background level after 2 days. We found that while gene expression correlated generally to the presence of chlorinated ethenes, there was no apparent direct relationship between RDase-encoding transcript numbers and respective rates of TCE, cDCE, and VC dechlorination activities. However, elevated
tceA
and
vcrA
expression did correlate with chlorinated-ethene reduction beyond cDCE, suggesting that elevated RDase-encoding transcript numbers could serve as a biomarker for the physiological ability of
Dehalococcoides
spp. to dechlorinate beyond cDCE.
Molecular-Beacon Multiplex Real-Time PCR Assay for Detection of
Vibrio cholerae
Authors: Gubala Aneta J. , Proll David F.
Published: September 2006

A multiplex real-time PCR assay was developed using molecular beacons for the detection of
Vibrio cholerae
by targeting four important virulence and regulatory genes. The specificity and sensitivity of this assay, when tested with pure culture and spiked environmental water samples, were high, surpassing those of currently published PCR assays for the detection of this organism.
Stability and Change in Estuarine Biofilm Bacterial Community Diversity
Authors: Moss Joseph A. , Nocker Andreas , Lepo Joe E. , Snyder Richard A.
Published: September 2006

Biofouling communities contribute significantly to aquatic ecosystem productivity and biogeochemical cycling. Our knowledge of the distribution, composition, and activities of these microbially dominated communities is limited compared to other components of estuarine ecosystems. This study investigated the temporal stability and change of the dominant phylogenetic groups of the domain
Bacteria
in estuarine biofilm communities. Glass slides were deployed monthly over 1 year for 7-day incubations during peak tidal periods in East Sabine Bay, Fla. Community profiling was achieved by using 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes in combination with ribotyping, cloning, and sequencing to evaluate diversity and to identify dominant microorganisms. Bacterial community profiles from biofilms grown near the benthos showed distinct periods of constancy within winter and summer sampling periods. Similar periods of stability were also seen in T-RFLP patterns from floating biofilms. Alternating dominance of phylogenetic groups between seasons appeared to be associated with seasonal changes in temperature, nutrient availability, and light. The community structure appeared to be stable during these periods despite changes in salinity and in dissolved oxygen.
Rapid Quantitative Detection of
Lactobacillus sakei
in Meat and Fermented Sausages by Real-Time PCR
Authors: Martín Belén , Jofré Anna , Garriga Margarita , Pla Maria , Aymerich Teresa
Published: September 2006

A quick and simple method for quantitative detection of
Lactobacillus sakei
in fermented sausages was successfully developed. It is based on Chelex-100-based DNA purification and real-time PCR enumeration using a
Taq
Man fluorescence probe. Primers and probes were designed in the
L. sakei
16S-23S rRNA intergenic transcribed spacer region, and the assay was evaluated using
L. sakei
genomic DNA and an artificially inoculated sausage model. The detection limit of this technique was approximately 3 cells per reaction mixture using both purified DNA and the inoculated sausage model. The quantification limit was established at 30 cells per reaction mixture in both models. The assay was then applied to enumerate
L. sakei
in real samples, and the results were compared to the MRS agar count method followed by confirmation of the percentage of
L. sakei
colonies. The results obtained by real-time PCR were not statistically significantly different than those obtained by plate count on MRS agar (
P
> 0.05), showing a satisfactory agreement between both methods. Therefore, the real-time PCR assay developed can be considered a promising rapid alternative method for the quantification of
L. sakei
and evaluation of the implantation of starter strains of
L. sakei
in fermented sausages.
Biological Filtration Limits Carbon Availability and Affects Downstream Biofilm Formation and Community Structure
Authors: Pang Chee Meng , Liu Wen-Tso
Published: September 2006

Carbon removal strategies have gained popularity in the mitigation of biofouling in water reuse processes, but current biofilm-monitoring practices based on organic-carbon concentrations may not provide an accurate representation of the in situ biofilm problem. This study evaluated a submerged microtiter plate assay for direct and rapid monitoring of biofilm formation by subjecting the plates to a continuous flow of either secondary effluent (SE) or biofilter-treated secondary effluent (BF). This method was very robust, based on a high correlation (
R
2
= 0.92) between the biomass (given by the
A
600
in the microtiter plate assay) and the biovolume (determined from independent biofilms developed on glass slides under identical conditions) measurements, and revealed that the biomasses in BF biofilms were consistently lower than those in SE biofilms. The influence of the organic-carbon content on the biofilm community composition and succession was further evaluated using molecular tools. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed a group of pioneer colonizers, possibly represented by
Sphingomonadaceae
and
Caulobacter
organisms, to be common in both SE and BF biofilms. However, differences in organic-carbon availabilities in the two water samples eventually led to the selection of distinct biofilm communities. Alphaproteobacterial populations were confirmed by fluorescence in situ hybridization to be enriched in SE biofilms, while
Betaproteobacteria
were dominant in BF biofilms. Cloning analyses further demonstrated that microorganisms adapted for survival under low-substrate conditions (e.g.,
Aquabacterium
,
Caulobacter
, and
Legionella
) were preferentially selected in the BF biofilm, suggesting that carbon limitation strategies may not achieve adequate biofouling control in the long run.
Multicopy Integration of Heterologous Genes, Using the Lactococcal Group II Intron Targeted to Bacterial Insertion Sequences
Authors: Rawsthorne Helen , Turner Kevin N. , Mills David A.
Published: September 2006

Group II introns are mobile genetic elements that can be redirected to invade specific genes. Here we describe the use of the lactococcal group II intron, Ll.ltrB, to achieve multicopy delivery of heterologous genes into the genome ofLactococcus lactisIL1403-UCD without the need for selectable markers. Ll.ltrB was retargeted to invade three transposase genes, thetragene found in IS904(tra904),tra981, andtra983, of which 9, 10, and 14 copies, respectively, were present in IL1403-UCD. Intron invasion oftra904,tra981, andtra983 allele groups occurred at high frequencies, and individual segregants possessed anywhere from one to nine copies of intron in the respectivetraalleles. To achieve multicopy delivery of a heterologous gene, a green fluorescent protein (GFP) marker was cloned into thetra904-targeted Ll.ltrB, and the resultant intron (Ll.ltrB::GFP) was induced to invade theL. lactis tra904 alleles. Segregants possessing Ll.ltrB::GFP in three, four, five, six, seven, and eight copies in differenttra904 alleles were obtained. In general, increasing the chromosomal copy number of Ll.ltrB::GFP resulted in strains expressing successively higher levels of GFP. However, strains possessing the same number of Ll.ltrB::GFP copies within different sets oftra904 alleles exhibited differential GFP expression, and segregants possessing seven or eight copies of Ll.ltrB::GFP grew poorly upon induction, suggesting that GFP expression from certain combinations of alleles was detrimental. The highest level of GFP expression was observed from a specific six-copy variant that produced GFP at a level analogous to that obtained with a multicopy plasmid. In addition, the high level of GFP expression was stable for over 120 generations. This work demonstrates that stable multicopy integration of heterologous genes can be readily achieved in bacterial genomes with group II intron delivery by targeting repeated elements.
Transformation of the Antibacterial Agent Norfloxacin by Environmental Mycobacteria
Authors: Adjei Michael D. , Heinze Thomas M. , Deck Joanna , Freeman James P. , Williams Anna J. , Sutherland John B.
Published: September 2006

Because fluoroquinolone antimicrobial agents may be released into the environment, the potential for environmental bacteria to biotransform these drugs was investigated. Eight
Mycobacterium
sp. cultures in a sorbitol-yeast extract medium were dosed with 100 μg ml
−1
of norfloxacin and incubated for 7 days. The MICs of norfloxacin for these strains, tested by an agar dilution method, were 1.6 to 25 μg ml
−1
. Cultures were extracted with ethyl acetate, and potential metabolites in the extracts were purified by high-performance liquid chromatography. The metabolites were identified using mass spectrometry and nuclear magnetic resonance spectroscopy.
N
-Acetylnorfloxacin (5 to 50% of the total absorbance at 280 nm) was produced by the eight
Mycobacterium
strains.
N
-Nitrosonorfloxacin (5 to 30% of the total absorbance) was also produced by
Mycobacterium
sp. strain PYR100 and
Mycobacterium gilvum
PYR-GCK. The MICs of
N
-nitrosonorfloxacin and
N
-acetylnorfloxacin were 2- to 38- and 4- to 1,000-fold higher, respectively, than those of norfloxacin for several different bacteria, including the two strains that produced both metabolites. Although
N
-nitrosonorfloxacin had less antibacterial activity, nitrosamines are potentially carcinogenic. The biotransformation of fluoroquinolones by mycobacteria may serve as a resistance mechanism.
Detection of
Enterobacter sakazakii
in Dried Infant Milk Formula by Cationic-Magnetic-Bead Capture
Authors: Mullane N. R. , Murray J. , Drudy D. , Prentice N. , Whyte P. , Wall P. G. , Parton A. , Fanning S.
Published: September 2006

Enterobacter sakazakii
has been associated with life-threatening infections in premature low-birth-weight infants. Contaminated infant milk formula (IMF) has been implicated in cases of
E. sakazakii
meningitis. Quick and sensitive methods to detect low-level contamination sporadically present in IMF preparations would positively contribute towards risk reduction across the infant formula food chain. Here we report on the development of a simple method, combining charged separation and growth on selective agar, to detect
E. sakazakii
in IMF. This protocol can reliably detect 1 to 5 CFU of
E. sakazakii
in 500 g of IMF in less than 24 h.
Evaluation of Freeze-Dried Kefir Coculture as Starter in Feta-Type Cheese Production
Authors: Kourkoutas Y. , Kandylis P. , Panas P. , Dooley J. S. G. , Nigam P. , Koutinas A. A.
Published: September 2006

The use of freeze-dried kefir coculture as a starter in the production of feta-type cheese was investigated. Maturation of the produced cheese at 4°C was monitored for up to 70 days, and the effects of the starter culture, the salting method, and the ripening process on quality characteristics were studied. The use of kefir coculture as a starter led to increased lactic acid concentrations and decreased pH values in the final product associated with significantly higher conversion rates compared to salted rennet cheese. Determination of bacterial diversity at the end of the ripening process in salted kefir and rennet cheeses by denaturing gradient gel electrophoresis technology, based on both DNA and RNA analyses, suggested a potential species-specific inhibition of members of the genera
Staphylococcus
and
Psychrobacter
by kefir coculture. The main active microbial associations in salted kefir cheese appeared to be members of the genera
Pseudomonas
and
Lactococcus
, while in salted rennet cheese,
Oxalobacteraceae
,
Janthinobacterium
,
Psychrobacter
, and
Pseudomonas
species were noted. The effect of the starter culture on the production of aroma-related compounds responsible for cheese flavor was also studied by the solid-phase microextraction-gas chromatography-mass spectrometry technique. Kefir coculture also appeared to extend the shelf life of unsalted cheese. Spoilage of kefir cheese was observed on the 9th and 20th days of preservation at 10 and 5°C, respectively, while spoilage in the corresponding rennet cheese was detected on the 7th and 16th days. Microbial counts during preservation of both types of unsalted cheese increased steadily and reached similar levels, with the exception of staphylococci, which were significantly lower in unsalted kefir cheese. All types of cheese produced with kefir as a starter were approved and accepted by the panel during the preliminary sensory evaluation compared to commercial feta-type cheese.
ON THE POSSIBILITY OF AN INTERSUBBAND LASER IN SILICON-ON-INSULATOR
Authors: LURYI SERGE , ZASLAVSKY ALEX
Published: September 2006

As thin Si quantum wells with oxide barriers have become an experimental reality in silicon-on-insulator technology, we discuss the feasibility of a terahertz laser based on an intersubband transition in such a Si quantum well. Electrons tunnel into an upper two-dimensional subband from a thin polysilicon gate through an ultrathin tunneling oxide and are extracted laterally from the Si well by diffusion. Population inversion arises because lateral diffusion to the contacts can be a faster process than intersubband relaxation and also because the in-plane diffusivity in the upper subband is suppressed by the interaction with a nearby subband characterized by a heavy in-plane mass. Thick oxide layers provide optical confinement and the main optical loss mechanism is the weak free-carrier absorption in thin doped regions in the polysilicon gate and substrate. A voltage on the substrate may provide some tunability of the gain peak.
HIGH-POWER SWITCHING USING III-NITRIDE METAL-OXIDE-SEMICONDUCTOR HETEROSTRUCTURES
Authors: SIMIN G. , KHAN M. ASIF , SHUR M. S. , GASKA R.
Published: September 2006

III-Nitride Metal-Oxide-Semiconductor Heterojunction (MOSH) structure consists of a thin dielectric layer deposited on top of a semiconductor heterostructure with a 2D electron gas at the heterojunction interface. MOSH structures are the key components for high-power low-loss, fast RF switches. The paper discusses two types of high-power switches using III-Nitride MOSH structures. The first type uses the MOSH structure as the gate region of an AlGaN/GaN HFET. The second type uses MOSH structure as a switching capacitor. In the 2GHz - 10 GHz frequency range, switching powers from 20 to 60 W/mm have been achieved with the insertion loss below 1 dB.
RECENT DEVELOPMENT OF SB-BASED PHOTOTRANSISTORS IN THE 0.9- TO 2.2-μM WAVELENGTH RANGE FOR APPLICATIONS TO LASER REMOTE SENSING
Authors: ABEDIN M. NURUL , REFAAT TAMER F. , SULIMA OLEG V. , SINGH UPENDRA N.
Published: September 2006

We have investigated commercially available photodiodes and also recent developed Sb -based phototransistors in order to compare their performances for applications to laser remote sensing. A custom-designed phototransistor in the 0.9- to 2.2-μm wavelength range has been developed at AstroPower and characterized at NASA Langley's Detector Characterization Laboratory. The phototransistor's performance greatly exceeds the previously reported results at this wavelength range in the literature. The detector testing included spectral response, dark current and noise measurements. Spectral response measurements were carried out to determine the responsivity at 2-μm wavelength at different bias voltages with fixed temperature; and different temperatures with fixed bias voltage. Current versus voltage characteristics were also recorded at different temperatures. Results show high responsivity of 2650 AIW corresponding to an internal gain of three orders of magnitude, and high detectivity (D*) of 3.9×1011 cm.Hz 1/2/ W that is equivalent to a noise-equivalent-power of 4.6×10-14 W/Hz 1/2 (-4.0 V @ -20°C) with a light collecting area diameter of 200-μm. It appears that this recently developed 2-μm phototransistor's performances such as responsivity, detectivity, and gain are improved significantly as compared to the previously published APD and SAM APD using similar materials. These detectors are considered as phototransistors based-on their structures and performance characteristics and may have great potential for high sensitivity differential absorption lidar (DIAL) measurements of carbon dioxide and water vapor at 2.05-μm and 1.9-μm, respectively.
HIGH POWER TYPE-I GASB-BASED LASERS
Authors: BELENKY G. , SHTERENGAS L. , KIM J. G. , MARTINELLI R. U. , SUCHALKIN S.
Published: September 2006

Challenges and limitations in development of the mid-infrared room temperature CW operated diode lasers with wavelength longer than 2 μm are discussed. The major breakthrough in terms of high power performance in this spectral range was achieved with type-I true quaternary InGaAsSb heavily compressively strained QW GaSb -based lasers. We have demonstrated 1 W CW at 2.5 μm, 500 mW and 160 mW CW at 2.7 and 2.8 μm, respectively. High power 2.3 μm linear laser arrays output 10W CW at room temperature. Experimental results show that there is no fundamental limitation to extend CW RT operating wavelength of these devices to over 3 μm spectral region. It is carrier leakage and material quality issues that limit device performance at wavelength longer than 2.5 μm. The role of Auger recombination is not decisive in type-I MQW GaSb -based lasers. We speculate that it is high differential gain and, as a result, low threshold carrier concentration that can account for muted effect of Auger on type-I GaSb -based laser performance. Dilute-nitride GaSb -based type-I QWs are proposed for development of CW room temperature operated lasers in spectral range 3 - 4 μm.
BIO-MOLECULAR INSPIRED ELECTRONIC ARCHITECTURES FOR ENHANCED SENSING OF THz-FREQUENCY BIO-SIGNATURES
Authors: WOOLARD DWIGHT L. , LUO YING , GELMONT BORIS L. , GLOBUS TATIANA , JENSEN JAMES O.
Published: September 2006

A new bio-molecular electronic architectural concept is presented that has potential for defining nanoscale sensor platforms with enhanced capabilities for sensing terahertz (THz) frequency bio-signatures. This architecture makes strategic use of integrated biological elements to enable communication and high-level function within densely-packed nanoelectronic systems. Specifically, a completely new paradigm for establishing hybrid Electro-THz-Optical (ETO) communication channels is introduced. Here, the THz-frequency spectral characteristics that are uniquely associated with the embedded bio-molecules are utilized directly in the architecture design and this immediately allows for defining new methods for enhanced sensing of THz bio-signatures. This integrated sensor concept greatly facilitates the collection of THz bio-signatures associated with embedded bio-molecules via interactions with the time-dependent signals propagating through the nanoelectronic circuit. In addition, it leads to a new Multi-State Spectral Sensing (MS3) approach where bio-signature information can be collected from multiple metastable state conformations. This paper presents new simulation results for a class of bio-molecular components that exhibit the prescribed type of ETO characteristics. Most noteworthy, this research derives THz spectral bio-signatures for organic molecules that are amenable to photo-induced metastable-state conformations and establishes an initial scientific foundation and design blueprint for an enhanced THz bio-signature sensing capability.
SPIN DEPENDENT TRANSPORT IN QUANTUM AND CLASSICALLY CONFIGURED DEVICES
Authors: GRUBIN H. L. , CUI H. L.
Published: September 2006

This paper presents of development of quantum transport equations for barrier devices with both electron and hole transport in dilute magnetic semiconductor (DMS) structures. The equations are developed from the time dependent equation of motion of the density matrix equation in the coordinate representation, from which both the spin drift and diffusion and transient Wigner equations are obtained, for a system in which high 'g' factor materials result in significant spin-splitting of the valence and conduction bands. Then for a structure in which the DMS layer is confined to the first barrier solutions to the coupled Poisson's and spin dependent Wigner equations yield the IV and carrier distributions. Negative differential conductance as well as the significant unequal spinup and spin down charge distributions are obtained.
DESIGN, MODELING, TESTING, AND SPICE PARAMETER EXTRACTION OF DIMOS TRANSISTOR IN 4H-SILICON CARBIDE
Authors: HASANUZZAMAN MD , ISLAM SYED K. , TOLBERT LEON M. , OZPINECI BURAK
Published: September 2006

In this paper, an analytical model for a vertical double implanted metal-oxide semiconductor (DIMOS) transistor structure in 4H-Silicon Carbide ( SiC ) is presented. Simulation for transport characteristics of the SiC MOSFET with the exact device geometry is carried out using the commercial device simulator MEDICI. A rigorous experimental testing and characterization is done on a 4H- SiC DIMOS transistor test device. SPICE parameters are extracted from the measurements, and a SPICE model for the DIMOS transistor has been developed. The presented work is a part of team efforts of material, device, and power electronics researchers at the University of Tennessee and Oak Ridge National Laboratory.
DESIGN QUALITY OF PUBLIC TOILET FACILITIES
Authors: SIU KIN WAI MICHAEL
Published: September 2006

More people have been considering the quality of design of public toilets and the issue of how closely this relates to the quality of the daily lives. However, the fact is that many so-called modern cities are still not equipped with public toilets of quality that matches their technological and economical development. Since the late 1990s, studies of public toilet environments and facilities have been conducted in Hong Kong — a densely populated metropolitan city and well-known tourist spot. Taking Hong Kong as a case, this paper argues that, when people in general put their focus and expectation on technological advancement, another significant way of ensuring and improving the design quality of facilities (that is, facilities with a high degree of userfitness) is to conduct serious, on-going, and in-depth studies on human-product interactions.
Tissue-specific regulation of ubiquitin (UbC) transcription by glucocorticoids: in vivo and in vitro analyses
Authors: Marinovic Anne C. , Zheng Bin , Mitch William E. , Price S. Russ
Published: September 2006

In uremia, muscle wasting involves increased glucocorticoid production and activation of the ubiquitin-proteasome proteolytic pathway, including increased expression of ubiquitin. Previously, we reported that glucocorticoids stimulate ubiquitin transcription by a mechanism involving Sp1 in L6 muscle cells (Marinovic AC, Zheng B, Mitch WE, Price SR. J Biol Chem 277: 16673–16681, 2002). This finding was surprising because Sp1 is a general transcriptional activator. To better understand the mechanism of glucocorticoid-induced ubiquitin ( UbC) gene transcription, we examined whether this response occurs in many organs or uniquely in skeletal muscle. Glucocorticoid-responsive cells of different organs were transfected with a human UbC promoter-luciferase reporter plasmid; dexamethasone stimulated UbC reporter activity 220% ( P < 0.05) in L6 skeletal muscle cells but not in HepG2 hepatocytes, NRK kidney cells, CaCo-2 colon cells, or H9c2 cardiomyocytes. Transactivation of the Sp1-responsive SV40 viral promoter was also increased in muscle but not in other nonmuscle cells. The muscle-specific nature of the UbC response was confirmed in vivo in rats with insulin deficiency, a condition associated with high glucocorticoid production: UbC mRNA was elevated in skeletal muscle but not in liver, kidney, intestine, or heart. Electrophoretic mobility shift assays and in vivo genomic footprinting demonstrated that insulin deficiency increased Sp1 binding to GC-rich elements in the UbC promoter. Thus glucocorticoids increase UbC transcription by a mechanism involving Sp1 that is unique to muscle.
Excitatory and Inhibitory Actions of Isoflurane in Bovine Chromaffin Cells
Authors: Xie Z. , Herring B. E. , Fox A. P.
Published: September 2006

Isoflurane, a halogenated volatile anesthetic, is thought to produce anesthesia by depressing CNS function. Many anesthetics, including isoflurane, are thought to modulate and/or directly activate GABAA receptors. Chromaffin cells are known to express functional GABAA receptors. We previously showed that activation of the GABAA receptors, with specific agonists, leads to cellular excitation resulting from the depolarized anion equilibrium potential. In this study, our goal was to determine whether isoflurane mimicked this response and to explore the functional consequences of this activation. Furthermore, we sought to study the actions of isoflurane on nicotinic acetylcholine receptors (nAChRs) as they mediate the “sympathetic drive” in these cells. For these studies the Ca2+-indicator dye fura-2 was used to assay [Ca2+]i. Amperometric measurements were used to assay catecholamine release. We show that bovine adrenal chromaffin cells were excited by isoflurane at clinically relevant concentrations. Isoflurane directly activated GABAA receptors found in chromaffin cells, which depolarized the cells and elevated [Ca2+]i. Application of isoflurane directly to the chromaffin cells elicited catecholamine secretion from these cells. At the same time, isoflurane suppressed activation of nAChRs, which presumably blocks “sympathetic drive” to the chromaffin cells. These latter results may help explain why isoflurane produces the hypotension observed clinically.
Inositol-1,4,5-Trisphosphate and Ryanodine-Dependent Ca2+ Signaling in a Chronic Dog Model of Atrial Fibrillation
Authors: Zhao Zhi-Hong , Zhang Hai-Cheng , Xu Yuan , Zhang Ping , Li Xue-Bing , Liu Yuan-Sheng , Guo Ji-Hong
Published: September 2006

Ca2+ signaling regulation plays an important role in triggering and/or maintaining atrial fibrillation (AF). Little is known about the relationship of the inositol-1,4,5-triphosphate receptors (InsP3Rs) and ryanodine receptors (RyRs) in left atrium to chronic AF. In this study, we investigated the expression and function of InsP3R1, InsP3R2 and RyR2 in a chronic dog model of AF. AF was induced in 6 dogs by rapid right atrial pacing for 24 weeks, and a sham procedure was performed in 5 dogs (control group). The intact left atrial myocytes were used to examine the expression and function of InsP3Rs, RyRs by BODIPYO,R TR-X ryanodine, heparin-fluorescein conjugate, and were stimulated by caffeine, ATP to release Ca2+ through RyRs, InsP3Rs separately. We also assessed the molecular components of left atrial tissue underlying the amount of RyR2, InsP3R1 and InsP3R2 determined by RT-PCR, immunohistochemistry and Western blot analysis. In the chronic AF group, the Ca2+ released through RyRs is not altered, but the Ca2+ released through InsP3Rs increased significantly. RyR2 distributed in cytosol of myocytes, cellular membrane; its expression significantly decreased in AF group compared to controls. InsP3R1 distributed in cytosol, InsP3R2 distributed not only in cytosol, cellular membrane, but also in nuclear envelope and intercalated discs. The InsP3R1 and InsP3R2 expression significantly increased in chronic AF group compared to controls. These results indicated that in a chronic dog model of AF, the expression and function of RyR2 down-regulated; on the contrary, the expression and function of InsP3R1, InsP3R2 up-regulated, and InsP3R2 may be the major InsP3Rs, which regulate intracellular or even intercellular Ca2+ signal transmission.
Multiple Episodes of a Transient Global Left Ventricular Dysfunction Reminiscent to Apical Ballooning
Authors: Nef Holger M. , Möllmann Helge , Vogt Achim , Weber Michael , Deetjen Anja , Dill Thorsten , Brandt Roland , Hamm Christian W. , Elsässer Albrecht
Published: September 2006

A new cardiac syndrome with transient left ventricular dysfunction has been recently reported and is referred to as Tako-Tsubo cardiomyopathy, which is characterized by a transient akinesia of the apex and compensatory basal hyperkinesis. Today, the etiology remains unknown. We report for the first time of a patient with multiple episodes of a transient global left ventricular dysfunction which is reminiscent to apical ballooning.These episodes were always preceded by severe emotional stress proposing a potential common pathomechanism.
Comparison of Experimental Lung Injury from Acute Renal Failure with Injury due to Sepsis
Authors: Kim Do Jin , Park Soo Hyun , Sheen Mee Rie , Jeon Un Sil , Kim Seung Whan , Koh Eun Suk , Woo Seung Kyoon
Published: September 2006

Background: Acute renal failure (ARF) and acute respiratory distress syndrome (ARDS) coexist frequently, and the mortality rate of this combination is very high. It is well established that cytokines and chemokines play a major role in the pathogenesis of ARDS. In addition, heat shock proteins (HSPs) have been shown to be protective against ARDS. Objectives: The purpose of this study was to investigate the pathophysiology of ARDS in two different conditions, sepsis and ARF. Methods: We examined five different rat animal models including sham-operated control, sepsis and three ARF models induced by renal ischemia/reperfusion injury, bilateral nephrectomy or bilateral ligation of renal pedicles. We analyzed pulmonary histology, pulmonary vascular permeability, cellular infiltration, and expression of cytokines, chemokines and HSPs. Results: Like sepsis, the three forms of ARF led to ARDS, as manifested by increased pulmonary vascular permeability and histological changes consistent with ARDS. On the other hand, ARF and sepsis differed in that ARF was associated with markedly lower levels of pulmonary cellular infiltration. Furthermore, while pulmonary expression of tumor necrosis factor-α increased in sepsis, cytokine-induced neutrophil chemoattractant 2 increased in nephrectomized rats indicating that different inflammatory mediators were involved in the injury mechanism. Finally, pulmonary expression of multiple HSPs including HSP27-1, HSP70, HSP70-4, HSP70-8 and HSP90 was significantly different between the two conditions. Conclusions: We conclude that the pathophysiology of ARDS following ARF is distinct from that in sepsis. ARF-induced ARDS is characterized by a low level of cellular infiltration, induction of cytokine-induced neutrophil chemoattractant 2, and a discrete expression profile of HSPs.
Nonparametric Trend Statistic Incorporating Dispersion Differences in Sib Pair Linkage for Quantitative Traits
Authors: Kim Man-Ki , Hong You-Jin , Song Hae-Hiang
Published: September 2006

The Haseman-Elston (HE) regression method and its extensions are widely used in genetic studies for detecting linkage to quantitative trait loci (QTL) using sib pairs. The principle underlying the simple HE regression method is that the similarity in phenotypes between two siblings increases as they share an increasing number of alleles identical by descent (IBD) from their parents at a particular marker locus. In such a procedure, similarity was identified with the locations, that is, means of groups of sib pairs sharing 0, 1, and 2 alleles IBD. A more powerful, rank-based nonparametric test to detect increasing similarity in sib pairs is presented by combining univariate trend statistics not only of locations, but also of dispersions of the squared phenotypic differences of two siblings for three groups. This trend test does not rely on distributional assumptions, and is applicable to the skewed or leptokurtic phenotypic distributions, in addition to normal or near normal phenotypic distributions. The performances of nonparametric trend statistics, including nonparametric regression slope, are compared with the HE regression methods as genetic linkage strategies.
Haplotype Reconstruction and Estimation of Haplotype Frequencies from Nuclear Families with Only One Parent Available
Authors: Ding Xiangdong , Zhang Qin , Flury Christine , Simianer Henner
Published: September 2006

Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families can be an alternative strategy in determining the linkage phase. In this paper, haplotype reconstruction and estimation of haplotype frequencies via expectation maximization (EM) algorithm including nuclear families with only one parent available is proposed. Parent and his (her) child are treated as parent-child pair with one shared haplotype. This reduces the number of potential haplotype pairs for both parent and child separately, resulting in a higher accuracy of the estimation. In a series of simulations, the comparisons of PHASE, GENEHUNTER, EM-based approach for complete nuclear families and our approach are carried out. In all situations, EM-based approach for trio data is comparable but slightly worse error rate than PHASE, our approach is slightly better and much faster than PHASE for incomplete trios, the performance of GENEHUNTER is very bad in simple nuclear family settings and dramatically decreased with the number of markers being increased. On the other hand, the comparison result of different sampling designs demonstrates that sampling trios is the most efficient design to estimate haplotype frequencies in populations under same genotyping cost.
Plasma Homocysteine, Cobalamin/Folate Status, and Vascular Disease in a Large Population of Psychogeriatric Patients
Authors: Nilsson Karin , Gustafson Lars , Hultberg Björn
Published: September 2006

Background: Cobalamin/folate deficiency and vascular disease are prevalent in elderly subjects and may lead to mental symptoms, but may even more often influence the severity of other organic and non-organic mental diseases. In the present study, we have evaluated cobalamin–folate status and the presence of vascular disease in 1,982 psychogeriatric patients investigated and diagnosed in a psychogeriatric clinic. The objective of the present study is to obtain information on the role of cobalamin/folate status and vascular disease in different diagnoses of psychogeriatric patients and their association with plasma homocysteine (tHcy). Methods: We have measured serum cobalamin, blood/serum folate, serum creatinine, plasma tHcy and evaluated the presence of vascular disease in 1,982 well-defined psychogeriatric patients. Results and Conclusions: The present study indicates that cobalamin/folate deficiencies do not play an important role in cognitive dysfunction in psychogeriatric patients, since only about 7% of the study population had metabolic cobalamin/folate deficiencies. Furthermore, cobalamin/folate deficiencies were rare in younger patients (below 70 years of age). We were also able to confirm our previous finding that there was no association between dementia of Alzheimer type (AD) and plasma tHcy level or metabolic cobalamin/folate deficiencies. Furthermore, we observed a low proportion of vascular disease in patients with AD, which does not give support for an association between well-defined AD and the presence of vascular disease. The presence of vascular disease was higher and of similar degree in patients with mild cognitive impairment and depression, which indicates an association between these diagnoses and the presence of vascular disease. The present study also shows that at plasma tHcy levels below 14 µmol/l, the likelihood of cobalamin/folate deficiency is small and further investigation of cobalamin/folate status could be omitted.
The ethnonarrative approach
Authors: Hansen Hans
Published: September 2006

While much research within narrative theory has focused on discourse in organizations, context should be a central focus because it is material in the production of meaning. In this article, I suggest an ethnonarrative approach that seeks to combine ethnographic methods and narrative methods in conducting hermeneutic analyses of narratives and stories, shifting not only between texts and contexts, but texts within a context of construction. Narrative research relies on analysis of various texts and often ignores context, while ethnographic methods are especially attuned to making observations and interpretations regarding the context in which texts are produced. The ethnonarrative approach highlights the multiple materials at play in narrative construction and attempts to demonstrate contextual influence on meaning making. The ethnonarrative approach is distinguished by a focus on the context of construction, the endosymbiotic relationship between text/context, and the social act as the level of analysis.
When good overcomes bad: The impact of volunteers on those they help
Authors: Ronel Natti
Published: September 2006

This qualitative study examines the impact of a personal encounter with perceived goodness, as represented by volunteers who are perceived as altruistic by those they help. It focuses on the encounter between at-risk street youths and lay volunteers in a mobile outreach service. The findings reveal that the street youths perceived the volunteers as representing pure altruism, and this stimulated several positive processes. Meeting the volunteers raised their awareness of giving without expecting a reward, which sharply contradicts their view of the world as a battlefield. Consequently, they understood and partially internalized the idea of non-material gratification. In some cases, the example set by the volunteers inspired the young people to consider volunteering themselves. Finally, they were able to generalize the altruistic image to the entire service and overcome their initial objections to a service run by the establishment. The proposed explanation, related to positive psychology, refers to the contrast between the example of the volunteers and the self centeredness of the street youths, which shifted slightly as a result.
Involvement, Development, and Retention
Authors: Chaves Christopher
Published: September 2006

The aim of this article is to orient those interested in adult community college student research to a wide array of discourses and theoretical tools that can help us understand the underlying complexity of the problems faced by this often-marginalized group. Reviewed are categories of theory about student involvement and engagement, student development, and adult learning that should inform how we educate adult community college students. This article concludes with a discussion of how all these theories, taken together, can improve adult education in community colleges.
Socio-Technical Agency in Financial Markets
Authors: Preda Alex
Published: September 2006

Recent discussions of calculative agency in financial markets (a variety of socio-technical agency) have stressed that technology constitutes markets through standardization. This raises the question of additional agential features of financial technologies, which may go beyond, supplement and embed standardization and calculability. I propose here the concept of ‘generator’ as a way of capturing such features of socio-technical agency in financial markets. I use this concept for examining the stock ticker, the first custom-tailored technology adopted by financial markets. I show that the ticker generated temporal structures and modes of visualizing these structures, together with representational languages, interpretive tools and boundaries associated with access to financial data.
Responding to Security Threats in the Post-9/11 Era
Authors: Taylor Brian D. , Fink Camille N. Y. , Liggett Robin
Published: September 2006

The 2001 terrorist attacks in the United States, and subsequent public transit system attacks in Madrid in 2004 and London in 2005, dramatically elevated concerns about the security of open, accessible transit systems. Accordingly, the authors report on a survey of 113 U.S. transit systems regarding their post-9/11 policies and practices. Sixteen of the 80 surveyed systems with rail service and/or enclosed bus or ferry terminals reported receiving a credible threat (e.g., bomb, chemical, biological, fire attacks) in the previous year, with most threats concentrated on just a few of the largest systems. Not surprisingly, attention to transit security increased significantly after 9/11, partly in response to federal mandates. Although attention to policing, security technologies, and public education all increased since 9/11, crime prevention through environmental design (CPTED) strategies increased the most. Despite measurable programmatic progress, however, many respondents believe that meaningfully securing urban transit systems remains a daunting, perhaps insurmountable, challenge.
Transitioning From a Pen-and-Paper Health Risk Appraisal to an Online Health Risk Appraisal at a Petroleum Company
Authors: Kashima Sara R.
Published: September 2006

Chevron Texaco’s Health and Medical Services Department made the decision to use existing technology and transition from a paper health risk appraisal (HRA) to an online questionnaire. A cross-functional team was formed and a year was spent researching online tools to find a vendor who could supply a product best suited to Chevron Texaco’s employee workforce. The purpose of this article is to describe the evolution of a paper-based HRA to an online tool as well as describe the project scope and strategy that a team of employees used in selecting the vendor. The article also describes implementation successes, challenges, and lessons learned in using the online tool with an industrial workforce. The strategy that was followed in deploying the Web site along with initial participation rates for this group of industrial employees are described.
Development and Implementation of a Food Store–Based Intervention to Improve Diet in the Republic of the Marshall Islands
Authors: Gittelsohn Joel , Dyckman William , Tan May Lynn , Boggs Malia K. , Frick Kevin D. , Alfred Julie , Winch Peter J. , Haberle Heather , Palafox Neal A.
Published: September 2006

Effective approaches for the prevention and reduction of obesity and obesity-related chronic diseases are urgently needed. Food store-centered programs represent one approach that may be both effective and sustainable. The authors developed a food store-based intervention in the Marshall Islands using qualitative and quantitative formative research methods, including a store usage survey (n = 184) and in-depth interviews with large-store managers (n = 13), small-store managers (n = 7), customers (n = 10), and community leaders (n = 4). This process was followed up by development and piloting of specific intervention components and workshops to finalize materials. The final intervention combined mass media (newspaper articles, video, radio announcements) and in-store components (shelf labels, cooking demonstrations, posters, recipe cards) and had high store-owner support and participation. High levels of exposure to the intervention were achieved during the 10-week period of implementation. This model for developing food store-based interventions is applicable to other settings.