bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of the Functionalization of the Axial Phthalocyanine Ligands on the Energy Transfer in QD‐based Donor–Acceptor Pairs
Authors: Dayal Smita , Li Jun , Li Ying‐Syi , Wu Hongqiao , Samia Anna C. S. , Kenney Malcolm E. , Burda Clemens
Published: November 2007

This study examines the electronic coupling between quantum dots (QDs) and molecules on their surfaces as a function of the modality of their interaction. As a probe, the energy transfer (ET) between CdSe QDs and phthalocyanines (Pcs) was monitored and evaluated with regard to the functionalization of the axial phthalocyanine ligand, bulkiness of the functional group bridging the QD donor and Pc acceptor, and the number of the functionalized axial ligands. New silicon PCs and their conjugates with CdSe QDs were synthesized. The ET efficiency and kinetics were studied by steady state and femtosecond time‐resolved absorption spectroscopy. We observed a decrease in ET efficiency with the increase in functional group bulkiness, which could be explained by increasing steric hindrance between the ET pair. In addition, a higher ET efficiency was observed for amino and thiol functionalized Pcs compared to Pcs without functional group on the axial alkyl chain.
Methodology for Evaluation of Melanin Content and Production of Pigment Cells in Vitro†
Authors: Hu Dan‐Ning
Published: November 2007

Melanin has a photo‐screening, a biophysical/biochemical and a cosmetic effect. Melanin content of cultured pigmented cells can be measured by spectrophotometry and expressed either as melanin content per cell or melanin content per culture (area). Melanin production can be calculated from melanin content and cell number at the beginning and at the end of a culture using various formulas and expressed as melanin production per cell per day or melanin production per culture per day. Melanin content or production per cell have been used widely to compare melanin content in various cell lines or to compare the melanin content during different stages in the culture (e.g. growing stage and senescent stage). For the evaluation of changes in melanin content and production in a given pigment cell line after treatment with a special chemical, physical or biological stimulator or inhibitor, different parameters used for the evaluation of experimental data can lead to conflicting results. Melanin content per area is determined by melanin content per cell and the number of cells in this area. The biological and cosmetic effects of melanin in vivo are determined mainly by melanin content per area, not melanin content per cell. For example, if melanin content per cell is the same, but the number of cells in a given area is increased after the treatment, then the melanin content per area is also increased. Under this circumstance, the color of skin turns darker and the total antioxidant activity provided by melanin in this area is increased even though the melanin content per cell measured remains the same; therefore, melanin content or production per culture is more important than melanin content or production per cell under this circumstance.
An Automated Iridium‐Strip Heater for LA‐ICP‐MS Bulk Analysis of Geological Samples
Authors: Stoll Brigitte , Jochum Klaus Peter , Herwig Kirstin , Amini Marghaleray , Flanz Michael , Kreuzburg Berthold , Kuzmin Dmitry , Willbold Matthias , Enzweiler Jacinta
Published: November 2007

In this paper we describe a flux‐free fusion technique for the highly precise LA‐ICP‐MS bulk analysis of geological samples. For this purpose we have developed an automated iridium‐strip heater with temperature and melt time control. To optimise the homogeneity of the fused glasses and to reduce possible depletion of volatile elements during melting, we undertook experiments with basaltic rock and glass powders using different melting temperatures (1300–1700 °C) and melting times (5‐80 s). Major and trace element microanalysis was performed using EPMA and LA‐ICP‐MS. Homogeneous glasses were obtained for temperatures ≥ 1500 °C and melting times ≥ 10 s. High loss (20‐90%) of highly volatile elements (e.g., Cs, Ge, Sn, Pb) was observed for high melting temperatures (≥ 1600 °C) and long melting times (80 s). Standard melting conditions (1600 °C, 10 s) represent a compromise, as the glasses were homogeneous with respect to major and trace elements and, at the same time, were not depleted in elements with condensation temperatures (at a pressure of 10−4 bar) higher than about 900 K (e.g., Zr, Hf, Ba, Sr, REE, U, Mo, Ni, Rb, Ga). Several international geological reference materials with SiO2 ranging between 47% m/m and 59% m/m were prepared using our standard melting conditions (1600 °C, 10 s) and subsequently analysed by LA‐ICP‐MS. These samples also include the new Brazilian basaltic reference material BRP‐1. Matrix‐matched calibration of the LA‐ICP‐MS data was performed using the basaltic reference glasses KL2‐G, ML3B‐G, BCR‐2G and BHVO‐2G. Most analytical data agreed within uncertainty at the 95% confidence level with the GeoReM preferred values published in the GeoReM database for reference materials of geological and environmental interest. To demonstrate routine bulk LA‐ICP‐MS analyses of geochemical and cosmochemical samples using the whole rock fusion technique, we also present trace element data for ocean island basalts from Lanai (Hawaii) and of Martian meteorites.
Melanocyte‐lineage expression of Cre recombinase using Mitf regulatory elements
Authors: Alizadeh Azita , Fitch Karen R. , Niswender Colleen M. , McKnight G. Stanley , Barsh Gregory S.
Published: November 2007

Manipulation of gene expression in melanocytes is an important tool for studying pigment cell biology. We constructed transgenic mice in which Cre recombinase was placed under the control of regulatory elements from the Microphthalmia‐associated transcriptional factor (Mitf) gene using bacterial artificial chromosome (BAC). Bacterial artificial chromosome that contained either 50 or 108 kb DNA 5′ to the melanocyte‐specific (1M) transcriptional start site gave rise to transgenic lines in which Cre is expressed specifically in cells of the melanocyte lineage, as judged by activation of the Gt(Rosa)26tm1Sor(R26R) reporter locus. Activation of R26R is first detectable in melanoblasts of midgestation embryos, and completely marks all melanocyte components of the skin in postnatal animals. To test the utility of the MitfCre transgene, we used a loxP‐targeted allele of the protein kinase A alpha catalytic subunit (Prkaca), modified such that Cre‐mediated recombination activates PKA signaling. On an agouti background, animals carrying both the MitfCre transgene and the targeted Prkaca allele (CαR) exhibited a darker coat color than control littermates, due to a shift from pheomelanin to eumelanin synthesis. Our results confirm that PKA signaling is a key component of pigment type‐switching, and provide a new tool for studying pigment cell biology.
Measurement of serum branched‐chain amino acids to tyrosine ratio level is useful in a prediction of a change of serum albumin level in chronic liver disease
Authors: Suzuki Kazutomo , Suzuki Kazuyoshi , Koizumi Kazuhito , Ichimura Hiroki , Oka Shigeki , Takada Hiroshi , Kuwayama Hajime
Published: November 2007

Aim:  In patients with hepatitis C virus (HCV)‐associated chronic liver diseases, especially in those with liver cirrhosis, accurate evaluation of their protein nutrition status is very important to improve their quality of life. Whereas the serum albumin level is commonly used to evaluate patients' protein nutrition status, in the present study, the serum amino acid levels were measured, as they also provide valuable information.

Methods:  Serum albumin levels and branched‐chain amino acids (BCAA) to tyrosine ratio (BTR) were determined in 447 patients with HCV‐associated chronic liver diseases (313 with chronic hepatitis and 134 with liver cirrhosis).

Results:  Chronic hepatitis progressed to liver cirrhosis, serum albumin and serum BTR levels decreased significantlyas chronic hepatitis progressed to liver cirrhosis. Hypoalbuminemia was significantly more common in patients with liver cirrhosis than in those with chronic hepatitis; however, the incidence of an amino acid imbalance was significantly higher than that of hypoalbuminemia in patients with liver cirrhosis. The presence of an amino acid imbalance was associated with a reduction in the serum albumin level 1 year later.

Conclusions:  It is important to evaluate serum albumin levels and the BTR in patients with HCV‐associated chronic liver diseases.
Effect of symptomatic gastroesophageal reflux disease on quality of life of patients with chronic liver disease
Authors: Suzuki Kazutomo , Suzuki Kazuyoshi , Koizumi Kazuhito , Takada Hiroshi , Nishiki Ryoichi , Ichimura Hiroki , Oka Shigeki , Kuwayama Hajime
Published: November 2007

Aim:  Reflux esophagitis is becoming increasingly more prevalent in Japan. It has been noted that symptomatic gastroesophageal reflux disease (GERD) and chronic liver disease may adversely affect patients' quality of life.

Methods:  In the present study, 238 chronic liver disease patients (151 patients with chronic hepatitis and 87 patients with liver cirrhosis) were enrolled. The diagnosis of GERD was made based on the Quality‐of‐Life and Utility Evaluation Survey Technology questionnaire. Health‐related quality of life was evaluated using the Short Forum 36 questionnaire.

Results:  Symptomatic GERD was present in 31.8% (48/151) of patients with chronic hepatitis and 36.8% (32/87) of patients with liver cirrhosis. Among the chronic hepatitis group, compared to the GERD‐negative group, the GERD‐positive group had significantly lower scores in six domains, including “rolelimitation due to physical problem”, “bodily pain”, “general health perception”, “vitality”, “role limitation due to emotional problem”, and “mental health”. Among the cirrhotic group, compared to the GERD‐negative group, the GERD‐positive group had significantly lower scores in the “role limitation due to emotional problem” domain. Significant improvement in the “physical functioning”, ”bodily pain”, and “general health perception” domain scores was noted in chronic hepatitis patients treated with rabeprazole.

Conclusion:  The QOL of chronic liver disease patients with symptomatic GERD was impaired.
Pelioid‐type hepatocellular carcinoma with numerous eosinophilic infiltrations in a patient with primary biliary cirrhosis
Authors: Watanabe Takuya , Aikawa Keiko , Kanefuji Tsutomu , Yamazaki Kazuhide , Hirono Haruka , Hasegawa Katsuhiko , Soga Kenji , Shibasaki Koichi , Umezu Hajime , Nomoto Minoru
Published: November 2007

A 65‐year‐old woman with liver injury was referred to our hospital in 1992. She was diagnosed with primary biliary cirrhosis (PBC) of Scheuer's histological classification stage IV. She was treated with 600 mg/day of ursodeoxycholic acid. A 1‐cm mass in S7 was detected in August 1995. The serum α‐fetoprotein (AFP) level increased to 1288 ng/mL in January 1996. Angiography showed a cotton wool‐like appearance in the delayed phase. Because the size of the tumor appeared to be increasing and the serum AFP levels increased with high levels of L3 fraction, a pelioid‐type hepatocellular carcinoma (HCC) was strongly suspected. Hepatic artery infusion with SMANCS and partial resection of S7 and S8 of the liver were performed in March 1996. The pathological diagnosis for theresected liver tumor was pelioid‐type HCC. The serum AFP level decreased to 50 ng/mL after the operation, but relapsed HCC was detected in S6 and S7. Angiography in September 1996 revealed multiple hypervascular lesions, and hepatic artery infusion with SMANCS was again performed; however, we were unable to suppress the progression of the relapsed HCC. The patient died due to an intra‐abdominal rupture of relapsed HCC and subsequent liver failure in December 1996. We report a rare case of pelioid‐type HCC with numerous eosinophilic infiltrations arising from PBC.
Identification of de novo STAT3 target gene in liver regeneration
Authors: Zhang Hui‐qi , Haga Sanae , Fukai Moto , Oikawa Yuko , Inoue Hiroshi , Ogawa Wataru , Kano Arihiko , Maruyama Atsushi , Fu Xin‐Yuan , Todo Satoru , Enosawa Shin , Ozaki Michitaka
Published: November 2007

The process of liver regeneration is regulated by complex mechanisms. Although signal transducer and activator of transcription‐3 (STAT3), a transcription factor which targets mainly mitotic genes, definitely plays an important role in liver regeneration, the exact roles of STAT3 are not completely understood.

Aim:  In this report, we tried to search for a new target of STAT3 involved in liver regeneration in mice.

Methods:  We generated liver‐specific STAT3 knockout (L‐S3KO) mice and a STAT3 knockout cell line of mouse origin. Using chromatin immunoprecipitation, we screened 12 genes to which STAT3 binds after partial hepatectomy (PH). Of these genes, we analyzed the S3‐IE3 clone that is located on chromosome‐3 and possesses STAT3 binding sites in it.

Results:  We showed that STAT3 binds to a specific site on S3‐IE3, and that interleukin‐6 (IL‐6) stimulates its transcriptional activity. The mRNA and protein levels of the net gene, which is located downstream of S3‐IE3, were negatively regulated in the control cells, but not in the STAT3 knockout cells after IL‐6 stimulation. Similarly in in vivo mouse PH, the mRNA and protein levels of net were also negatively regulated after PH, but not in L‐S3KO mice.

Conclusion:  The net gene is located downstream of a newly‐recognized STAT3 binding site (S3‐IE3) and negatively regulated after IL‐6 stimulation and PH, although its role is still unclear.
Human plasmacytoid dendritic cells from patients with chronic hepatitis B virus infection induce the generation of a higher proportion of CD4+ and CD25+ regulatory T cells compared with healthy patients
Authors: Hong Jun , Gong Zuo Jiong
Published: November 2007

This study was undertaken to investigate whether plasmacytoid dendritic cells (PDC) are involved in the generation of a higher proportion of CD4+ and CD25+ regulatory T (Treg) cells in chronic hepatitis B virus (HBV) infection compared with healthy patients. The amount, phenotype, and function of Treg cells in CD4+ T cells primed by PDC from 46 chronic HBV patients, 25 healthy controls, and 10 individuals with resolved HBV infection were studied by flow cytometry, reverse transcription polymerase chain reaction, enzyme‐linked immunosorbent assay, and proliferation assay. CD4+ T cells primed by PDC from chronic HBV patients were more effective than CD4+ T cells primed by PDC from the healthy controls and the resolved HBV patients in suppressing the hepatitis B core antigen‐specific proliferation and the interferon production. The interleukin‐10 and transforming growth factor‐β1 could also be detected in the supernatants of the PDC‐primed CD4+ T cells. A higher percentage of Treg cells, defined as CD4,CD25, CD45RO, and cytotoxic T‐lymphocyte‐associated antigen 4‐positive cells, was detected within the population of CD4+ T cells primed by PDC from chronic HBV patients compared with the healthy controls and individuals with resolved HBV infection. Accordingly, CD25+ Treg cells from PDC‐primed CD4+ T cells displayed a high Fox P3 messenger RNA level. Depleting CD4+ and CD25+ Treg cells from CD4+ T cells primed by PDC from the chronic HBV patients, the healthy volunteers, and the resolved HBV patients made PDC‐primed CD4+ T lose the capability in suppressing HBV‐specific T cells. PDC from the patients with chronic HBV infection induced the generation of a higher proportion of CD4+ and CD25+ Treg cells compared with the healthy patients.
A case of severe recurrent hepatitis with common variable immunodeficiency
Authors: Fukushima Koji , Ueno Yoshiyuki , Kanegane Hirokazu , Yamagiwa Yoko , Inoue Jun , Kido Osamu , Nagasaki Futoshi , Kogure Takayuki , Kakazu Eiji , Nakagome Yu , Matsuda Yasunori , Obara Noriyuki , Kimura Osamu , Shimosegawa Tooru
Published: November 2007

Severe hepatitis with an indistinct etiology manifested in a 16‐year‐old boy who had no particular history. The histological features of the liver and clinical course of the patient were similar to those of patients with autoimmune hepatitis characterized by interface hepatitis and severe lobular inflammation of the liver and recurrent exacerbations of hepatitis. We administered intravenous glycyrrhizin preparation daily or three times a week combined with the oral administration of ursodeoxycholic acid daily throughout the term after the initial onset of disease for the control of disease activity. The normalization of the concentration of alanine aminotransferase in serum was achieved in response to the therapy during the course. The serum concentration of immunoglobulins of the patient gradually decreased from the onset of the disease to an unacceptable level without globulin preparation during the following period of 17 months. Immunological tests revealed impairment of immunoglobulin production bythe B cell population of the patient, which led to the diagnosis of the patient as common variable immunodeficiency (CVID). The patient, with improved liver histology after 27 months from the onset of disease, benefited from the current combination therapy without severe infection through the avoidance of overimmunosuppression. CVID is defined as a heterogeneous syndrome characterized by various degrees of hypogammaglobulinemia without any specific predisposing causes, frequently associated with autoimmunity. Diagnostic criteria and therapeutic options of persistent hepatitis with CVID are to be established, as discussed in the current report.
Long‐term follow up of esophageal varices after balloon‐occluded retrograde transvenous obliteration for gastric varices
Authors: Nakamura Shinichi , Torii Nobuyuki , Yatsuji Satoru , Konishi Hiroyuki , Kishino Maiko , Taniai Makiko , Tokushige Katsutoshi , Hashimoto Etsuko , Shiratori Keiko
Published: November 2007

Aim:  Because the procedure of balloon‐occluded retrograde transvenous obliteration (B‐RTO) causes extensive thrombosis of the major shunt that connects the spleen and gastric/renal venous systems, an increase in portal pressure is unavoidable. The aim of the present study was to assess the long‐term outcome of B‐RTO, including changes in esophageal varices.

Methods:  B‐RTO was conducted in 22 patients with gastric varices, who were divided according to the severity of esophageal varices at baseline; there were no esophageal varices (n = 7), F1 varices (n = 11), and F2 varices (n = 4). The outcome measures included the development/worsening of esophageal varices after B‐RTO and survival rates.

Results:  The cumulative bleeding‐free probability for all 22 patients at 3 years after B‐RTO was 100%. The overall 3‐year survival was 94.4%. Seven patients who had no esophageal varices prior to B‐RTO did not develop any after the procedure. Seven (63.6%) of the 11 patients with stage F1 esophageal varices prior to B‐RTO showed no changes in the varices after B‐RTO, while two patients progressed to F2 varices and two developed F3 varices. The cumulative treatment‐free probability of the esophageal varices at 24 months after B‐RTO was 100% for patients without esophageal varices at baseline, 80.8% for patients with pre‐existing F1 varices, and 75% for those with pre‐existing F2 varices.

Conclusion:  Although the B‐RTO procedure is considered useful for the treatment of gastric varices, changes in hemodynamics due to obliteration of this major shunt must be taken into account and observed closely.
Direct binding of ligandin to uridine 5'‐diphosphate glucuronosyltransferase 1A1
Authors: Akizawa Emi , Koiwai Kotaro , Hayano Takahide , Maezawa So , Matsushita Toyofumi , Koiwai Osamu
Published: November 2007

Aim:  Bilirubin, a final degradation product of heme produced mainly in the spleen, is carried to the liver through its binding to albumin in the blood circulation. After its transport to hepatocytes, ligandin (glutathione S‐transferase; GST) carries bilirubin to the endoplasmic reticulum (ER). uridine 5'‐diphosphate‐glucuronosyltransferase 1A1 (UGT1A1) glucuronidates bilirubin for solubilization in the ER.

Methods:  By GST pull‐down and co‐immunoprecipitation assays, GSTA2, a member of the α‐class of GST, was observed to directly bind to UGT1A1 through the region present inside the ER.

Results:  GSTA2 was detected in the microsomal fraction together with the cytosolic fraction after hepatocyte fractionation.

Conclusion:  These results strongly suggest that bilirubin is directly delivered to UGT1A1 from ligandin for glucuronidation.
Heat (Mass) Transfer Distribution in a Two-Pass Trapezoidal Channel With a 180deg Turn
Authors: Lee S. W. , Ahn H. S. , Lau S. C.
Published: November 2007

The heat transfer characteristics of airflows in serpentine cooling channels in stator vanes of gas turbines were studied. The cooling channels were modeled as a two-pass trapezoidal channel with a 180deg turn. Naphthalene sublimation experiments were conducted and the heat and mass transfer analogy was applied to study the local heat (mass) transfer distributions on one of the two primary walls of the channel. Results were obtained for turbulent airflow through the channel with smooth walls, and with transverse ribs on one wall and on two opposite walls, over a range of Reynolds numbers between about 10,000 and 60,000. The results showed that there was a very large variation of the local heat (mass) transfer distribution in the turn and downstream of the turn. In all of the cases studied, the regional average heat (mass) transfer was higher on the downstream half of the turn than on the upstream half of the turn and was higher in the turn with the flow entering the channel through the smaller straight section than when the flow was reversed. The shape of the local heat (mass) transfer distribution at the turn was not significantly affected by varying the air mass flow rate. In the smooth wall case, the local heat (mass) transfer was high near the end wall and the downstream outer wall in the turn and was relatively low in two regions near the upstream outer wall and the downstream edge at the tip of the divider wall in the turn. With ribs on two opposite walls, the variation of the local heat (mass) transfer was larger, especially in the turn and downstream of the turn, than in the smooth wall case. The pressure drop across the turn was higher in the case of the flow entering the channel through the larger straight section than when the flow was reversed. As expected, the ribs increased the pressure drop across the turn.
Reflectionless eigenstates of the sech2 potential
Authors: Lekner John
Published: November 2007

The one-dimensional potential well V(x)=−(ℏ2ν(ν+1)∕2ma2)sech2(x∕a) does not reflect waves of any energy when ν is a positive integer. We show that in this reflectionless case the solutions of Schrödinger’s equation can be expressed in terms of elementary functions. Wave packets can be constructed from these energy eigenstates, and the propagation of such wave packets through the potential region can be studied analytically. We find that the group velocity of a particular packet can substantially exceed the group velocity of a free-space Gaussian packet. The bound states of the potential can also be expressed in terms of elementary functions when ν is an integer. The special properties of the integer ν potentials are associated with critical binding.
Interrupted Time Series Analysis of Vancomycin Compared to Cefuroxime for Surgical Prophylaxis in Patients Undergoing Cardiac Surgery
Authors: Garey K. W. , Lai D. , Dao-Tran T. K. , Gentry L. O. , Hwang L. Y. , Davis B. R.
Published: November 2007

The increased incidence of methicillin-resistant
Staphylococcus aureus
(MRSA), the emergence of community-acquired MRSA, and the continued high incidence of methicillin-resistant
Staphylococcus epidermidis
have required that certain institutions choose vancomycin for surgical prophylaxis. However, the data supporting the use of vancomycin for surgical prophylaxis are controversial. The purpose of this project was to assess the effect of the change from cefuroxime to vancomycin for surgical site infection (SSI) rates in patients undergoing coronary artery bypass graft (CABG) surgery. The monthly rates of SSIs from 2001 to 2005 were analyzed before and after a change from cefuroxime to vancomycin antibiotic prophylaxis in patients undergoing CABG by using an interrupted time series analysis. Patients who underwent cardiac valve replacement surgery and who had received vancomycin during the entire study period were used as a comparator group. A total of 6,465 patients underwent CABG surgery (
n
= 4,239) or valve replacement surgery (
n
= 2,226) during the study period. On average, the monthly SSI incidence rate in patients undergoing CABG surgery decreased by 2.1 cases per 100 surgeries after the switch from cefuroxime to vancomycin (
P
= 0.042) when patients undergoing valve replacement were used as a comparator group. The change in SSI rates was associated with a decrease in the incidence of infections caused by coagulase-negative
Staphylococcus
and MRSA isolates, with little change in the incidence of SSIs due to other gram-positive organisms or gram-negative organisms. In institutions with a high incidence of methicillin-resistant
Staphylococcus
species, this study provides evidence for the clinical efficacy of vancomycin prophylaxis for the prevention of postoperative SSIs in patients undergoing CABG surgery.
Comparative Analysis of the σB-Dependent Stress Responses inListeria monocytogenesandListeria innocuaStrains Exposed to Selected Stress Conditions
Authors: Raengpradub Sarita , Wiedmann Martin , Boor Kathryn J.
Published: November 2007

The alternative sigma factor σBcontributes to transcription of stress response and virulence genes in diverse gram-positive bacterial species. The composition and functions of theListeria monocytogenesandListeria innocuaσBregulons were hypothesized to differ due to virulence differences between these closely related species. Transcript levels in stationary-phase cells and in cells exposed to salt stress were characterized by microarray analyses for both species. InL. monocytogenes, 168 genes were positively regulated by σB; 145 of these genes were preceded by a putative σBconsensus promoter. InL. innocua, 64 genes were positively regulated by σB. σBcontributed to acid stress survival in log-phase cells for both species but to survival in stationary-phase cells only forL. monocytogenes. In summary, (i) theL. monocytogenesσBregulon includes >140 genes that are both directly and positively regulated by σB, including genes encoding proteins with importance in stress response, virulence, transcriptional regulation, carbohydrate metabolism, and transport; (ii) a number ofL. monocytogenesgenes encoding flagellar proteins show higher transcript levels in the ΔsigBmutant, and bothL. monocytogenesandL. innocuaΔsigBnull mutants have increased motility compared to the respective isogenic parent strains, suggesting that σBaffects motility and chemotaxis; and (iii) althoughL. monocytogenesandL. innocuadiffer in σB-dependent acid stress resistance and have species-specific σB-dependent genes, theL. monocytogenesandL. innocuaσBregulons show considerable conservation, with a common set of at least 49 genes that are σBdependent in both species.
Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities
Authors: Smith Nancy R. , Kishchuk Barbara E. , Mohn William W.
Published: November 2007

Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH
4
+
and NO
3
−
due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments.
Gamma
- and
Alphaproteobacteria
were highly characteristic of the unburned treatments, while
Betaproteobacteria
and members of
Bacillus
were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.
Production and Characterization of
Bacillus thuringiensis
Cry1Ac-Resistant Cotton Bollworm
Helicoverpa zea
(Boddie)
Authors: Anilkumar Konasale J. , Rodrigo-Simón Ana , Ferré Juan , Pusztai-Carey Marianne , Sivasupramaniam Sakuntala , Moar William J.
Published: November 2007

Laboratory-selected
Bacillus thuringiensis
-resistant colonies are important tools for elucidating
B. thuringiensis
resistance mechanisms. However, cotton bollworm,
Helicoverpa zea
, a target pest of transgenic corn and cotton expressing
B. thuringiensis
Cry1Ac (Bt corn and cotton), has proven difficult to select for stable resistance. Two populations of
H. zea
(AR and MR), resistant to the
B. thuringiensis
protein found in all commercial Bt cotton varieties (Cry1Ac), were established by selection with Cry1Ac activated toxin (AR) or MVP II (MR). Cry1Ac toxin reflects the form ingested by
H. zea
when feeding on Bt cotton, whereas MVP II is a Cry1Ac formulation used for resistance selection and monitoring. The resistance ratio (RR) for AR exceeded 100-fold after 11 generations and has been maintained at this level for nine generations. This is the first report of stable Cry1Ac resistance in
H. zea
. MR crashed after 11 generations, reaching only an RR of 12. AR was only partially cross-resistant to MVP II, suggesting that MVP II does not have the same Cry1Ac selection pressure as Cry1Ac toxin against
H. zea
and that proteases may be involved with resistance. AR was highly cross-resistant to Cry1Ab toxin but only slightly cross-resistant to Cry1Ab expressing corn leaf powder. AR was not cross-resistant to Cry2Aa2, Cry2Ab2-expressing corn leaf powder, Vip3A, and cypermethrin. Toxin-binding assays showed no significant differences, indicating that resistance was not linked to a reduction in binding. These results aid in understanding why this pest has not evolved
B. thuringiensis
resistance, and highlight the need to choose carefully the form of
B. thuringiensis
protein used in experiments.
Degradation of Bis(4-Hydroxyphenyl)Methane (Bisphenol F) by
Sphingobium yanoikuyae
Strain FM-2 Isolated from River Water
Authors: Inoue Daisuke , Hara Shoji , Kashihara Mari , Murai Yusaku , Danzl Erica , Sei Kazunari , Tsunoi Shinji , Fujita Masanori , Ike Michihiko
Published: November 2007

Three bacteria capable of utilizing bis(4-hydroxyphenyl)methane (bisphenol F [BPF]) as the sole carbon source were isolated from river water, and they all belonged to the family
Sphingomonadaceae
. One of the isolates, designated
Sphingobium yanoikuyae
strain FM-2, at an initial cell density of 0.01 (optical density at 600 nm) completely degraded 0.5 mM BPF within 9 h without any lag period under inductive conditions. Degradation assays of various bisphenols revealed that the BPF-metabolizing system of strain FM-2 was effective only on the limited range of bisphenols consisting of two phenolic rings joined together through a bridging carbon without any methyl substitution on the rings or on the bridging structure. A BPF biodegradation pathway was proposed on the basis of metabolite production patterns and identification of the metabolites. The initial step of BPF biodegradation involves hydroxylation of the bridging carbon to form bis(4-hydroxyphenyl)methanol, followed by oxidation to 4,4′-dihydroxybenzophenone. The 4,4′-dihydroxybenzophenone appears to be further oxidized by the Baeyer-Villiger reaction to 4-hydroxyphenyl 4-hydroxybenzoate, which is then cleaved by oxidation to form 4-hydroxybenzoate and 1,4-hydroquinone. Both of the resultant simple aromatic compounds are mineralized.
Evaluation of
Escherichia coli
Host Strain CB390 for Simultaneous Detection of Somatic and F-Specific Coliphages
Authors: Guzmán Carolina , Mocé-Llivina Laura , Lucena Francisco , Jofre Juan
Published: November 2007

Escherichia coli
WG5, the strain recommended by the International Organization for Standardization (ISO) to detect somatic coliphages, was transformed to F
+
by introducing the plasmid Famp, which rendered it capable of simultaneously detecting both somatic and F-specific coliphages. Indeed, this strain, CB390, proved as effective in detecting similar numbers of phages as the sum of somatic and F-specific bacteriophages detected by the host strains recommended by both the ISO and the U.S. Environmental Protection Agency standardized methods.
Methyl Sulfide Production by a Novel Carbon Monoxide Metabolism inMethanosarcina acetivorans
Authors: Moran James J. , House Christopher H. , Vrentas Jennifer M. , Freeman Katherine H.
Published: November 2007

We observed dimethyl sulfide and methanthiol production in pure incubations of the methanogenMethanosarcina acetivoranswhen carbon monoxide (CO) served as the only electron donor. Energy conservation likely uses sodium ion gradients for ATP synthesis. This novel metabolism permits utilization of CO by the methanogen, resulting in quantitative sulfide methylation.
The Cytochrome P450 Lanosterol 14α-Demethylase Gene Is a Demethylation Inhibitor Fungicide Resistance Determinant in
Monilinia fructicola
Field Isolates from Georgia
Authors: Luo Chao-Xi , Schnabel Guido
Published: November 2007

Resistance in
Monilinia fructicola
to demethylation inhibitor (DMI) fungicides is beginning to emerge in North America, but its molecular basis is unknown. Two potential genetic determinants of DMI fungicide resistance including the 14α-demethylase gene (Mf
CYP51
) and the ATP-binding cassette transporter gene Mf
ABC1
, were investigated in six resistant (DMI-R) and six sensitive (DMI-S) field isolates. No point mutations leading to an amino acid change were found in the Mf
CYP51
gene. The constitutive expression of the Mf
CYP51
gene in DMI-R isolates was significantly higher compared to DMI-S isolates. Gene expression was not induced in mycelium of DMI-R or DMI-S isolates treated with 0.3 μg of propiconazole/ml. A slightly higher average Mf
CYP51
copy number value was detected in DMI-R isolates (1.35) compared to DMI-S isolates (1.13); however, this difference could not be verified in Southern hybridization experiments or explain the up to 11-fold-increased Mf
CYP51
mRNA levels in DMI-R isolates. Analysis of the upstream nucleotide sequence of the Mf
CYP51
gene revealed a unique 65-bp repetitive element at base pair position −117 from the translational start site in DMI-R isolates but not in DMI-S isolates. This repetitive element contained a putative promoter and was named Mona. The link between Mona and the DMI resistance phenotype became even more apparent after studying the genetic diversity between the isolates. In contrast to DMI-S isolates, DMI-R isolates contained an Mf
CYP51
gene of identical nucleotide sequence associated with Mona. Still, DMI-R isolates were not genetically identical as revealed by Microsatellite-PCR analysis. Also, real-time PCR analysis of genomic DNA indicated that the relative copy number of Mona among DMI-S and DMI-R isolates varied, suggesting its potential for mobility. Interestingly, constitutive expression of the Mf
ABC1
gene in DMI-R isolates was slightly lower than that of DMI-S isolates, but expression of the Mf
ABC1
gene in DMI-R isolates was induced in mycelium after propiconazole treatment. Therefore, the Mf
ABC1
gene may play a minor role in DMI fungicide resistance in
M. fructicola
. Our results strongly suggest that overexpression of the Mf
CYP51
gene is an important mechanism in conferring DMI fungicide resistance in
M. fructicola
field isolates from Georgia and that this overexpression is correlated with Mona located upstream of the Mf
CYP51
gene.
Protein Kinases Involved in Mating and Osmotic Stress in the Yeast
Kluyveromyces lactis
Authors: Kawasaki Laura , Castañeda-Bueno María , Sánchez-Paredes Edith , Velázquez-Zavala Nancy , Torres-Quiroz Francisco , Ongay-Larios Laura , Coria Roberto
Published: November 2007

Systematic disruption of genes encoding kinases and mitogen-activated protein kinases (MAPKs) was performed in
Kluyveromyces lactis
haploid cells. The mutated strains were assayed by their capacity to mate and to respond to hyperosmotic stress. The
K. lactis
Ste11p (KlSte11p) MAPK kinase kinase (MAPKKK) was found to act in both mating and osmoresponse pathways while the scaffold KlSte5p and the MAPK KlFus3p appeared to be specific for mating. The p21-activated kinase KlSte20p and the kinase KlSte50p participated in both pathways. Protein association experiments showed interaction of KlSte50p and KlSte20p with Gα and Gβ, respectively, the G protein subunits involved in the mating pathway. Both KlSte50p and KlSte20p also showed interaction with KlSte11p. Disruption mutants of the
K. lactis PBS2
(Kl
PBS2
) and Kl
HOG1
genes of the canonical osmotic response pathway resulted in mutations sensitive to high salt and high sorbitol but dispensable for mating. Mutations that eliminate the MAPKK KlSte7p activity had a strong effect on mating and also showed sensitivity to osmotic stress. Finally, we found evidence of physical interaction between KlSte7p and KlHog1p, in addition to diminished Hog1p phosphorylation after a hyperosmotic shock in cells lacking KlSte7p. This study reveals novel roles for components of transduction systems in yeast.
Fitting Periplasmic Membrane Fusion Proteins to Inner Membrane Transporters: Mutations That Enable
Escherichia coli
AcrA To Function with
Pseudomonas aeruginosa
MexB
Authors: Krishnamoorthy Ganesh , Tikhonova Elena B. , Zgurskaya Helen I.
Published: November 2007

AcrAB-TolC from
Escherichia coli
is a multidrug efflux complex capable of transenvelope transport. In this complex, AcrA is a periplasmic membrane fusion protein that establishes a functional connection between the inner membrane transporter AcrB of the RND superfamily and the outer membrane channel TolC. To gain insight into the mechanism of the functional association between components of this complex, we replaced AcrB with its close homolog MexB from
Pseudomonas aeruginosa
. Surprisingly, we found that AcrA is promiscuous and can form a partially functional complex with MexB and TolC. The chimeric AcrA-MexB-TolC complex protected cells from sodium dodecyl sulfate, novobiocin, and ethidium bromide but failed with other known substrates of MexB. We next identified single and double mutations in AcrA and MexB that enabled the complete functional fit between AcrA, MexB, and TolC. Mutations in either the α-helical hairpin of AcrA making contact with TolC or the β-barrel domain lying on MexB improved the functional alignment between components of the complex. Our results suggest that three components of multidrug efflux pumps do not associate in an “all-or-nothing” fashion but accommodate a certain degree of flexibility. This flexibility in the association between components affects the transport efficiency of RND pumps.
Effects of Glycosylation on Swimming Ability and Flagellar Polymorphic Transformation in
Pseudomonas syringae
pv. tabaci 6605
Authors: Taguchi Fumiko , Shibata Satoshi , Suzuki Tomoko , Ogawa Yujiro , Aizawa Shin-Ichi , Takeuchi Kasumi , Ichinose Yuki
Published: November 2007

The role of flagellin glycosylation on motility was investigated in
Pseudomonas syringae
pv. tabaci. The swimming activity of glycosylation-defective mutants was prominently decreased in a highly viscous medium. The mutants showed differences in polymorphic transitions and in the bundle formation of flagella, indicating that glycosylation stabilizes the filament structure and lubricates the rotation of the bundle.
Identification and Characterization of Two Novel Methyltransferase Genes That Determine the Serotype 12-Specific Structure of Glycopeptidolipids of
Mycobacterium intracellulare
Authors: Nakata Noboru , Fujiwara Nagatoshi , Naka Takashi , Yano Ikuya , Kobayashi Kazuo , Maeda Shinji
Published: November 2007

The
Mycobacterium avium
complex is distributed ubiquitously in the environment. It is an important cause of pulmonary and extrapulmonary diseases in humans and animals. The species in this complex produce polar glycopeptidolipids (GPLs); of particular interest is their serotype-specific antigenicity. Several reports have described that GPL structure may play an important role in bacterial physiology and pathogenesis and in the host immune response. Recently, we determined the complete structure of the GPL derived from
Mycobacterium intracellulare
serotype 7 and characterized the serotype 7 GPL-specific gene cluster. The structure of serotype 7 GPL closely resembles that of serotype 12 GPL, except for O methylation. In the present study, we isolated and characterized the serotype 12-specific gene cluster involved in glycosylation of the GPL. Ten open reading frames (ORFs) and one pseudogene were observed in the cluster. The genetic organization of the serotype 12-specific gene cluster resembles that of the serotype 7-specific gene cluster, but two novel ORFs (
orfA
and
orfB
) encoding putative methyltransferases are present in the cluster. Functional analyses revealed that
orfA
and
orfB
encode methyltransferases that synthesize
O
-methyl groups at the C-4 position in the rhamnose residue next to the terminal hexose and at the C-3 position in the terminal hexose, respectively. Our results show that these two methyltransferase genes determine the structural difference of serotype 12-specific GPL from serotype 7-specific GPL.
PhyR Is Involved in the General Stress Response ofMethylobacterium extorquensAM1
Authors: Gourion Benjamin , Francez-Charlot Anne , Vorholt Julia A.
Published: November 2007

PhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described inMethylobacterium extorquensAM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, includingkatE,osmC,htrA,dnaK,gloA,dps, anduvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, inM. extorquensAM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.
The Wallowa Mountains, northeast Oregon
Authors: Taubeneck William H.
Published: November 2007

The Wallowa Mountains are mostly within the Eagle Cap Wilderness Area, which is accessible only on footor horseback. The only road that penetrates the mountains extends south from Lostine (Fig. 1) along the Lostine River and is continuously within 1,300 ft (400 m) of nearly all of the east contact of unit one (Fig. 1) of the Wallowa batholith; this road ends at location H in the east part of unit two.
Reproducibility of dynamically represented acoustic lung images from healthy individuals
Authors: Maher T M , Gat M , Allen D , Devaraj A , Wells A U , Geddes D M
Published: November 2007

Background and aim:

Acoustic lung imaging offers a unique method for visualising the lung. This study was designed to demonstrate reproducibility of acoustic lung images recorded from healthy individuals at different time points and to assess intra- and inter-rater agreement in the assessment of dynamically represented acoustic lung images.

Methods:

Recordings from 29 healthy volunteers were made on three separate occasions using vibration response imaging. Reproducibility was measured using quantitative, computerised assessment of vibration energy. Dynamically represented acoustic lung images were scored by six blinded raters.

Results:

Quantitative measurement of acoustic recordings was highly reproducible with an intraclass correlation score of 0.86 (very good agreement). Intraclass correlations for inter-rater agreement and reproducibility were 0.61 (good agreement) and 0.86 (very good agreement), respectively. There was no significant difference found between the six raters at any time point. Raters ranged from 88% to 95% in their ability to identically evaluate the different features of the same image presented to them blinded on two separate occasions.

Conclusion:

Acoustic lung imaging is reproducible in healthy individuals. Graphic representation of lung images can be interpreted with a high degree of accuracy by the same and by different reviewers.
Tectonic evolution of the North China Block: from orogen to craton to orogen
Authors: Kusky T. M. , Windley B. F. , Zhai M.-G.
Published: November 2007

The North China Craton contains one of the longest, most complex records of magmatism, sedimentation, and deformation on Earth, with deformation spanning the interval from the Early Archaean (3.8 Ga) to the present. The Early to Middle Archaean record preserves remnants of generally gneissic meta-igneous and metasedimentary rock terranes bounded by anastomosing shear zones. The Late Archaean record is marked by a collision between a passive margin sequence developed on an amalgamated Eastern Block, and an oceanic arc–ophiolitic assemblage preserved in the 1600 km long Central Orogenic Belt, an Archaean–Palaeoproterozoic orogen that preserves remnants of oceanic basin(s) that closed between the Eastern and Western Blocks. Foreland basin sediments related to this collision are overlain by 2.4 Ga flood basalts and shallow marine–continental sediments, all strongly deformed and metamorphosed in a 1.85 Ga Himalayan-style collision along the northern margin of the craton. The North China Craton saw relative quiescence until 700 Ma when subduction under the present southern margin formed the Qingling–Dabie Shan–Sulu orogen (700–250 Ma), the northern margin experienced orogenesis during closure of the Solonker Ocean (500–250 Ma), and subduction beneath the palaeo-Pacific margin affected easternmost China (200–100 Ma). Vast amounts of subduction beneath the North China Craton may have hydrated and weakened the subcontinental lithospheric mantle, which detached in the Mesozoic, probably triggered by collisions in the Dabie Shan and along the Solonker suture. This loss of the lithospheric mantle brought young asthenosphere close to the surface beneath the eastern half of the craton, which has been experiencing deformation and magmatism since, and is no longer a craton in the original sense of the word. Six of the 10 deadliest earthquakes in recorded history have occurred in the Eastern Block of the North China Craton, highlighting the importance of understanding decratonization and the orogen–craton–orogen cycle in Earth history.