bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urea Unfolding of Opsin in Phospholipid Bicelles†
Authors: McKibbin Craig , Farmer Nicola A. , Edwards Patricia C. , Villa Claudio , Booth Paula J. 
Published: January 2009

AbstractOpsin is the unstable apo‐protein of the light‐activated G protein‐coupled receptor rhodopsin. We investigated the stability of bovine opsin, solubilized in 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC)/detergent bicelles, against urea‐induced unfolding. A single irreversible protein unfolding transition was observed from changes in intrinsic tryptophan fluorescence and far‐UV circular dichroism. This unfolding transition correlated with loss of protein activity. Changes in tertiary structure, as indicated by fluorescence measurements, were concomitant with an approximate 50% reduction in α‐helical content of opsin, indicating that global unfolding had been induced by urea. The urea concentration at the midpoint of unfolding was dependent on the lipid/detergent environment, occurring at approximately 1.2 m urea in DMPC/1,2‐dihexanoyl‐sn‐glycero‐3‐phosphocholine bicelles, while being significantly stabilized to approximately 3.5 m urea in DMPC/3‐[(cholamidopropyl)dimethylammonio]‐1‐propanesulfonate bicelles. These findings demonstrate that interactions with the surrounding lipids and detergent are highly influential in the unfolding of membrane protein structure. The urea/bicelle system offers the possibility for a more detailed understanding of the structural changes that take place upon irreversible unfolding of opsin.
Studies on the Stability of the Human Cone Visual Pigments†
Authors: Ramon Eva , Mao Xiang , Ridge Kevin D. 
Published: January 2009

AbstractThe retina of vertebrates contains two kinds of photoreceptor cells, rods and cones, which contain their specific visual pigments that are responsible for scotopic and photopic vision, respectively. In cone photoreceptor cells, there are three types of color pigments: blue, green and red, each with a distinctive absorption maximum. The goal of this investigation was to identify optimal conditions under which these pigments could be obtained and isolated in a stable form, thereby facilitating structural studies using high‐resolution approaches. For this purpose, all three human cone opsins were initially expressed in mammalian cells, reconstituted with 11‐cis retinal, detergent solubilized, purified and their stability compared with rod rhodopsin. As all three pigments showed dramatically reduced stability relative to rhodopsin, site‐directed mutagenesis was used in an attempt to engineer stability into the green cone pigment. The mutations introduced some structural motifs and sites of posttranslational modification present in rhodopsin, as well as amino acid substitutions that have been found to stabilize the rod opsin apo‐protein. We also modified the hydrophobic environment of the green cone pigment by varying the detergent and detergent/lipid composition used during solubilization and purification, and compared them with the retinal reconstituted pigment in membranes. Our results show that these changes do not significantly improve the inherent instability of the human cone pigments, and in some cases, lead to a decrease in stability and protein aggregation. We conclude that further efforts are required to stabilize the human cone pigments in a form suitable for high‐resolution structural studies.
The Heterotrimeric G‐protein Complex Modulates Light Sensitivity in Arabidopsis thaliana Seed Germination
Authors: Botto Javier F. , Ibarra Silvia , Jones Alan M. 
Published: January 2009

AbstractRelease of dormancy and induction of seed germination are complex traits finely regulated by hormonal signals and environmental cues such as temperature and light. The Red (R):Far‐Red (FR) phytochrome photoreceptors mediate light regulation of seed germination. We investigated the possible involvement of heterotrimeric G‐protein complex in the phytochrome signaling pathways of Arabidopsis thaliana seed germination. Germination rates of null mutants of the alpha (Gα) and beta (Gβ) subunits of the G‐protein (Atgpa1‐4 and agb1‐2, respectively) and the double mutant (agb1‐2/gpa1‐4) are lower than the wildtype (WT) under continuous or pulsed light. The Gα and Gβ subunits play a role in seed germination under hourly pulses of R lower than 0.1 μmol m−2 s−1 whereas the Gβ subunit plays a role in higher R fluences. The germination of double mutants of G‐protein subunits with phyA‐211 and phyB‐9 suggests that AtGPA1 seems to act as a positive regulator of phyA and probably phyB signaling pathways, while the role of AGB1 is ambiguous. The imbibition of seeds at 4°C and 35°C alters the R and FR light responsiveness of WT and G‐protein mutants to a similar magnitude. Thus, Gα and Gβ subunits of the heterotrimeric G‐protein complex modulate light induction of seed germination by phytochromes and are dispensable for the control of dormancy by low and high temperatures prior to irradiation. We discuss the possible indirect role of the G‐protein complex on the phytochrome‐regulated germination through hormonal signaling pathways.
A novel third generation bisphosphonate, minodronate (YM529), prevented proliferation and migration of hepatocellular carcinoma cells through inhibition of mevalonate pathway
Authors: Kogure Takayuki , Ueno Yoshiyuki , Kimura Osamu , Kondo Yasuteru , Inoue Jun , Fukushima Koji , Iwasaki Takao , Shimosegawa Tooru 
Published: January 2009

Aim:  Skeletal metastases and bone metasitasis are a common occurrence in patients with advanced hepatocellular carcinoma (HCC). Bisphosphonates (BPs), which are used for the treatment of osteoporosis and tumor‐associated hypercalcemia, have recently been reported to decrease skeletal morbidity in patients with metastatic bone disease. Several studies revealed that nitrogen‐containing BPs (N‐BPs) could inhibit tumor growth and migration, indicating the possibility that N‐BPs have direct inhibitory effects. We aimed to determine the effects of novel a N‐BP (YM529) on human HCC cells in vitro.Methods:  HCC cells were treated with various concentrations of YM529 and the growth inhibition rate was determined. Apoptosis was evaluated by caspase‐3/7 assay and caspase‐9 cleavage detection. The effects of YM529 on the migration of HCC cells induced by hepatocyte growth factor (HGF) were determined by cell migration assay. To evaluate the involvement of the mevalonate pathway, farnesol (FOH) and geranylgeraniol (GGOH) were added.Results:  YM529 inhibited the proliferation of HCC cells in a dose‐dependent manner. The activation of caspase‐3/7 and cleavage of caspase‐9 demonstrated the involvement of apoptosis in cytotoxicity. GGOH reduced the growth inhibitory effect of YM529 and suppressed the induction of caspase‐3/7 activities by YM529 on HCC cells. YM529 inhibited tumor cell migration induced by HGF and this effect was reduced by co‐treatment with GGOH.Conclusion:  YM529 inhibited the cell proliferation and migration of HCC cells, implicating the involvement of the mevalonate pathway. These results suggest that N‐BPs are potential agents for the treatment of HCC skeletal metastases.
UGT1A1 gene polymorphism as a potential factor inducing iron overload in the pathogenesis of type 1 hereditary hemochromatosis
Authors: Romanowski Tomasz , Sikorska Katarzyna , Bielawski Krzysztof Piotr 
Published: January 2009

Aim  Hereditary hemochromatosis is a common genetic disorder characterized by iron overload and subsequent organ damage. It is caused in most cases by HFE gene mutations which penetrance can be affected by many factors. The aim of this study was to establish the role of UGT1A1 gene polymorphism and serum bilirubin concentration in the pathogenesis of hereditary hemochromatosis.Methods  Biochemical, histopathological and genetic data indicating iron excess and serum total bilirubin concentration were determined in 32 patients with the type 1 hereditary hemochromatosis. Fluorescent molecular probes assays were used for genotyping of UGT1A1*28 and UGT1A1*60 mutations in these individuals.Results  High incidence and a significant correlation of UGT1A1 gene mutations with increased serum bilirubin level and lower grades of liver tissue inflammatory activity were observed in study participants. UGT1A1*28 and UGT1A1*60 mutations were strongly linked together. Two of the subjects presented very rare genotypes of UGT1A1 gene: (TA)5/7 and c.‐64G>C heterozygotes.Conclusions  UGT1A1 gene polymorphism and as its consequence of high serum bilirubin level may promote iron accumulation in hemochromatosis patients by reducing the activity of inflammation. We proposed a possible mechanism of this interaction.
In Vitro Comparison of the Efficacies of Natamycin and Silver Nitrate against Ocular Fungi
Authors: Xu Yan , Pang Guangren , Gao Chuanwen , Zhao Dongqing , Zhou Lutan , Sun Shengtao , Wang Bingliang 
Published: January 2009

ABSTRACT

The in vitro activity of the silver nitrat
e
was assessed in comparison with that of natamycin against 128 corneal
Fusarium
isolates and 90 corneal
Aspergillus
isolates. MIC
90
s of silver nitrat
e
were 2 μg/ml for
Fusarium
spp. and 1 μg/ml for
Aspergillus
spp. MIC
90
s of natamycin were 8 μg/ml for
Fusarium
spp. and 32 μg/ml for
Aspergillus
spp. Silver nitrat
e
exhibited potent antifungal activity against ocular fungi in vitro.
Radioimmunotherapy Is Effective against High-Inoculum
Cryptococcus neoformans
Infection in Mice and Does Not Select for Radiation-Resistant Cryptococcal Cells
Authors: Bryan Ruth A. , Jiang Zewei , Huang Xianchun , Morgenstern Alfred , Bruchertseifer Frank , Sellers Rani , Casadevall Arturo , Dadachova Ekaterina 
Published: January 2009

ABSTRACT
We investigated the utility of radioimmunotherapy (RIT) in the treatment of experimental cryptococcal infection with high-inoculum and the possibility of RIT treatment selecting for fungal cells with radiation-resistant phenotypes. RIT reduced mortality in high-burden infections, and we found no evidence for the development of radiation-resistant cells.
Dry Powder Nitroimidazopyran Antibiotic PA-824 Aerosol for Inhalation
Authors: Sung Jean C. , Garcia-Contreras Lucila , VerBerkmoes Jarod L. , Peloquin Charles A. , Elbert Katharina J. , Hickey Anthony J. , Edwards David A. 
Published: January 2009

ABSTRACT
We formulated PA-824, a nitroimidazopyran with promise for the treatment of tuberculosis, for efficient aerosol delivery to the lungs in a dry powder porous particle form. The objectives of this study were to prepare and characterize a particulate form of PA-824, assess the stability of this aerosol formulation under different environmental conditions, and determine the pharmacokinetic parameters for the powder after pulmonary administration. The drug was spray dried into porous particles containing a high drug load and possessing desirable aerosol properties for efficient deposition in the lungs. The physical, aerodynamic, and chemical properties of the dry powder were stable at room temperature for 6 months and under refrigerated conditions for at least 1 year. Pharmacokinetic parameters were determined in guinea pigs after the pulmonary administration of the PA-824 powder formulation at three doses (20, 40, and 60 mg/kg of body weight) and compared to those after the intravenous (20 mg/kg) and oral (40 mg/kg) delivery of the drug. Oral and inhaled delivery of PA-824 achieved equivalent systemic delivery at the same body dose within the first 12 h of dosing. However, animals dosed by the pulmonary route showed drug loads that remained locally in the lungs for 32 h postexposure, whereas those given the drug orally cleared the drug more rapidly. Therefore, we expect from these pharmacokinetic data that pulmonary delivery may achieve the same efficacy as oral delivery at the same body dose, with a potential improvement in efficacy related to pulmonary infection. This may translate into the ability to deliver lower body doses of this drug for the treatment of tuberculosis by aerosol.
Escherichia coli
Populations in Great Lakes Waterfowl Exhibit Spatial Stability and Temporal Shifting
Authors: Hansen Dennis L. , Ishii Satoshi , Sadowsky Michael J. , Hicks Randall E. 
Published: January 2009

ABSTRACT

Populations of
Escherichia coli
from juvenile and adult ring-billed gulls, juvenile common terns, and adult Canada geese were sampled over 6 years at five locations on Lake Superior (Duluth, MN, and Wisconsin) and Lake Michigan (Wisconsin, Illinois, and Indiana) to determine the extent of spatial and temporal variability in
E. coli
strains. Strain identity was determined using horizontal fluorophore-enhanced repetitive element palindromic DNA fingerprinting. Multivariate statistics were used to determine if spatial or temporal changes in
E. coli
populations occurred in waterfowl species. Pairwise multivariate analyses of variance revealed that
E. coli
populations of adult gulls from three regions of Lake Michigan and the Wisconsin shore of Lake Superior were similar to one another but different from an
E. coli
population of gulls from the Duluth region of Lake Superior. Juvenile and adult gulls from the Duluth area harbored different
E. coli
populations. The
E. coli
strains from juvenile gulls, however, were similar to those found in juvenile terns obtained from the same island rookery. Temporal changes in
E. coli
populations from several waterfowl species were also demonstrated for this site. Although portions of source tracking databases might be successfully used in other geographic regions, it is clear that juvenile birds should not be the sole source of
E. coli
strains used for source tracking databases, and multiple-year libraries should be constructed in order to identify the potential sources of
E. coli
in the environment.
Tailoring the P450 Monooxygenase Gene for FR-008/Candicidin Biosynthesis
Authors: Chen Shi , Mao Xiangzhao , Shen Yaling , Zhou Yongjun , Li Jialiang , Wang Lianrong , Tao Xinyi , Yang Liang , Wang Yuxiao , Zhou Xiufen , Deng Zixin , Wei Dongzhi 
Published: January 2009

ABSTRACT

Tailoring steps are often important for the activity of mature antibiotics. Here, we report that novel decarboxylated FR-008/candicidin derivatives were obtained from the P450 monooxygenase gene
fscP
mutant of
Streptomyces
sp. strain FR-008. The toxicity of decarboxylated FR-008/candicidin derivatives has been shown to be greatly reduced compared to that of wild-type FR-008/candicidin.
Isolation of a Human Intestinal Bacterium Capable of Daidzein and Genistein Conversion
Authors: Matthies Anastasia , Blaut Michael , Braune Annett 
Published: January 2009

ABSTRACT

A rod-shaped gram-positive anaerobic bacterium, strain HE8, was isolated from human feces. The isolate was able to convert the isoflavones daidzein and genistein to equol and 5-hydroxy-equol, respectively. Based on phenotypic and phylogenetic analyses, strain HE8 is described as a new species,
Slackia isoflavoniconvertens
.
Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California)
Authors: Harrison Benjamin K. , Zhang Husen , Berelson Will , Orphan Victoria J. 
Published: January 2009

ABSTRACT

The sulfate-methane transition zone (SMTZ) is a widespread feature of continental margins, representing a diffusion-controlled interface where there is enhanced microbial activity. SMTZ microbial activity is commonly associated with the anaerobic oxidation of methane (AOM), which is carried out by syntrophic associations between sulfate-reducing bacteria and methane-oxidizing archaea. While our understanding of the microorganisms catalyzing AOM has advanced, the diversity and ecological role of the greater microbial assemblage associated with the SMTZ have not been well characterized. In this study, the microbial diversity above, within, and beneath the Santa Barbara Basin SMTZ was described. ANME-1-related archaeal phylotypes appear to be the primary methane oxidizers in the Santa Barbara Basin SMTZ, which was independently supported by exclusive recovery of related methyl coenzyme M reductase genes (
mcrA
). Sulfate-reducing
Deltaproteobacteria
phylotypes affiliated with the
Desulfobacterales
and
Desulfosarcina-Desulfococcus
clades were also enriched in the SMTZ, as confirmed by analysis of dissimilatory sulfite reductase (
dsr
) gene diversity. Statistical methods demonstrated that there was a close relationship between the microbial assemblages recovered from the two horizons associated with the geochemically defined SMTZ, which could be distinguished from microbial diversity recovered from the sulfate-replete overlying horizons and methane-rich sediment beneath the transition zone. Comparison of the Santa Barbara Basin SMTZ microbial assemblage to microbial assemblages of methane seeps and other organic matter-rich sedimentary environments suggests that bacterial groups not typically associated with AOM, such as
Planctomycetes
and candidate division JS1, are additionally enriched within the SMTZ and may represent a common bacterial signature of many SMTZ environments worldwide.
Comparison of Loop-Mediated Isothermal Amplification Assay and Conventional Culture Methods for Detection of
Campylobacter jejuni
and
Campylobacter coli
in Naturally Contaminated Chicken Meat Samples
Authors: Yamazaki Wataru , Taguchi Masumi , Kawai Takao , Kawatsu Kentaro , Sakata Junko , Inoue Kiyoshi , Misawa Naoaki 
Published: January 2009

ABSTRACT

We investigated the efficacy of a loop-mediated isothermal amplification (LAMP) assay for detection of chicken meat samples naturally contaminated with
Campylobacter jejuni
and
Campylobacter coli
. A total of 144 Preston enrichment broth cultures from chicken meat samples were assessed by using the LAMP assay and conventional culture methods, which consist of a combination of Preston enrichment culturing and plating onto Butzler and modified charcoal cefoperazone deoxycholate agars. Compared with
C. jejuni
-
C. coli
isolation using the conventional culture test, the LAMP results showed 98.5% (67/68) and 97.4% (74/76) sensitivity and specificity, respectively, and the positive and negative predictive values were 97.1% (67/69) and 98.7% (74/75), respectively. The conventional culture test required more than 3 to 4 days to isolate and identify
C. jejuni
and
C. coli
in the Preston enrichment cultures. In contrast, the LAMP assay was markedly faster, requiring less than 90 min from the beginning of DNA extraction to final detection and differentiation of
C. jejuni
and
C. coli
. In total, the LAMP assay required 23.5 to 25.5 h from the beginning of the enrichment culture to final determination. These results suggest that our LAMP assay is a powerful tool for rapid, sensitive, and practical detection of
C. jejuni
and
C. coli
which may facilitate surveillance and control of
C. jejuni-C. coli
contamination in chicken, as well as investigations of food poisoning incidents caused by these organisms. This is the first report of a highly sensitive and specific LAMP assay to detect and differentiate
C. jejuni
and
C. coli
in chicken meat samples.
Prevalence and Impact of Bacteriophages on the Presence of
Escherichia coli
O157:H7 in Feedlot Cattle and Their Environment
Authors: Niu Y. D. , McAllister T. A. , Xu Y. , Johnson R. P. , Stephens T. P. , Stanford K. 
Published: January 2009

ABSTRACT

The relationship between endemic bacteriophages infecting
E. coli
O157:H7 (referred to as “phage”) and levels of shedding of
E. coli
O157:H7 by cattle was investigated in two commercial feedlots in southern Alberta, Canada. Between May and November 2007, 10 pens of cattle were monitored by collection of pooled fecal pats, water with sediment from troughs, manure slurry from the pen floor, and rectal fecal samples from individual animals (20 per pen) at two separate times. Bacteriophages infecting
E. coli
O157:H7 were detected more frequently (
P
< 0.001) after 18 to 20 h enrichment than by initial screening and were recovered in 239 of 855 samples (26.5% of 411 pooled fecal pats, 23.8% of 320 fecal grab samples, 21.8% of 87 water trough samples, and 94.6% of 37 pen floor slurry samples). Overall, prevalence of phage was highest (
P
< 0.001) in slurry. Recovery of phage from pooled fecal pats was highest (
P
< 0.05) in May. Overall recovery did not differ (
P
> 0.10) between fecal grab samples and pooled fecal pats. A higher prevalence of phage in fecal pats or water trough samples was associated (
P
< 0.01) with reduced prevalence of
E. coli
O157:H7 in rectal fecal samples. There was a weak but significant negative correlation between isolation of phage and
E. coli
O157:H7 in fecal grab samples (
r
= −0.11;
P
< 0.05). These data demonstrate that the prevalence of phage fluctuates in a manner similar to that described for
E. coli
O157:H7. Phage were more prevalent in manure slurry than other environmental sources. The likelihood of fecal shedding of
E. coli
O157:H7 was reduced if cattle in the pen harbored phage.
The Unique Branching Patterns of
Deinococcus
Glycogen Branching Enzymes Are Determined by Their N-Terminal Domains
Authors: Palomo M. , Kralj S. , van der Maarel M. J. E. C. , Dijkhuizen L. 
Published: January 2009

ABSTRACT

Glycogen branching enzymes (GBE) or 1,4-α-glucan branching enzymes (EC 2.4.1.18) introduce α-1,6 branching points in α-glucans, e.g., glycogen. To identify structural features in GBEs that determine their branching pattern specificity, the
Deinococcus geothermalis
and
Deinococcus radiodurans
GBE (GBE
Dg
and GBE
Dr
, respectively) were characterized. Compared to other GBEs described to date, these
Deinococcus
GBEs display unique branching patterns, both transferring relatively short side chains. In spite of their high amino acid sequence similarity (88%) the
D. geothermalis
enzyme had highest activity on amylose while the
D. radiodurans
enzyme preferred amylopectin. The side chain distributions of the products were clearly different: GBE
Dg
transferred a larger number of smaller side chains; specifically, DP5 chains corresponded to 10% of the total amount of transferred chains, versus 6.5% for GBE
Dr
. GH13-type GBEs are composed of a central (β/α) barrel catalytic domain and an N-terminal and a C-terminal domain. Characterization of hybrid
Deinococcus
GBEs revealed that the N2 modules of the N domains largely determined substrate specificity and the product branching pattern. The N2 module has recently been annotated as a carbohydrate binding module (CBM48). It appears likely that the distance between the sugar binding subsites in the active site and the CBM48 subdomain determines the average lengths of side chains transferred.