bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of Nitrogen Reductase and Nitrite Reductase Genes in Soil of Thinned and Clear-Cut Douglas-Fir Stands by Using Real-Time PCR
Authors: Levy-Booth David J. , Winder Richard S. 
Published: August 2010

ABSTRACT

The abundance of
nifH
,
nirS
, and
nirK
gene fragments involved in nitrogen (N) fixation and denitrification in thinned second-growth Douglas-fir (
Pseudotsuga menziesii
subsp.
menziesii
[Mirb.] Franco) forest soil was investigated by using quantitative real-time PCR. Prokaryotic N cycling is an important aspect of N availability in forest soil. The abundance of universal
nifH
,
Azotobacter
sp.-specific
nifH
(
nifH-
g1),
nirS
, and
nirK
gene fragments in unthinned control and 30, 90, and 100% thinning treatments were compared at two long-term research sites on Vancouver Island, Canada. The soil was analyzed for organic matter (OM), total carbon (C), total N, NH
4
-N, NO
3
-N, and phosphorus (P). The soil horizon accounted for the greatest variation in nutrient status, followed by the site location. The 30% thinning treatment was associated with significantly greater
nifH
-g1 abundance than the control treatment in one site; at the same site,
nirS
in the mineral soil horizon was significantly reduced by thinning. The abundance of
nirS
genes significantly correlated with the abundance of
nirK
genes. In addition, significant correlations were observed between
nifH
-g1 abundance and C and N in the organic horizon and between
nirS
and
nirK
and N in the mineral horizon. Overall, no clear influence of tree thinning on
nifH
,
nirS
, and
nirK
was observed. However, soil OM, C, and N were found to significantly influence N-cycling gene abundance.
Comparative Genomic Characterization of
Actinobacillus pleuropneumoniae
Authors: Xu Zhuofei , Chen Xiabing , Li Lu , Li Tingting , Wang Shengyue , Chen Huanchun , Zhou Rui 
Published: August 2010

ABSTRACT

The Gram-negative bacterium
Actinobacillus pleuropneumoniae
is the etiologic agent of porcine contagious pleuropneumoniae, a lethal respiratory infectious disease causing great economic losses in the swine industry worldwide. In order to better interpret the genetic background of serotypic diversity, nine genomes of
A. pleuropneumoniae
reference strains of serovars 1, 2, 4, 6, 9, 10, 11, 12, and 13 were sequenced by using rapid high-throughput approach. Based on 12 genomes of corresponding serovar reference strains including three publicly available complete genomes (serovars 3, 5b, and 7) of this bacterium, we performed a comprehensive analysis of comparative genomics and first reported a global genomic characterization for this pathogen. Clustering of 26,012 predicted protein-coding genes showed that the pan genome of
A. pleuropneumoniae
consists of 3,303 gene clusters, which contain 1,709 core genome genes, 822 distributed genes, and 772 strain-specific genes. The genome components involved in the biogenesis of capsular polysaccharide and lipopolysaccharide O antigen relative to serovar diversity were compared, and their genetic diversity was depicted. Our findings shed more light on genomic features associated with serovar diversity of
A. pleuropneumoniae
and provide broader insight into both pathogenesis research and clinical/epidemiological application against the severe disease caused by this swine pathogen.
Loss of Compartmentalization of σ
E
Activity Need Not Prevent Formation of Spores by
Bacillus subtilis
Authors: Chary Vasant K. , Xenopoulos Panagiotis , Eldar Avigdor , Piggot Patrick J. 
Published: August 2010

ABSTRACT

Compartmentalization of the activities of RNA polymerase sigma factors is a hallmark of formation of spores by
Bacillus subtilis
. It is initiated soon after the asymmetrically located sporulation division takes place with the activation of σ
F
in the smaller cell, the prespore. σ
F
then directs a signal via the membrane protease SpoIIGA to activate σ
E
in the larger mother cell by processing of pro-σ
E
. Here, we show that σ
E
can be activated in the prespore with little effect on sporulation efficiency, implying that complete compartmentalization of σ
E
activity is not essential for spore formation. σ
E
activity in the prespore can be obtained by inducing transcription in the prespore of
spoIIGA
or of
sigE
*, which encodes a constitutively active form of σ
E
, but not of
spoIIGB
, which encodes pro-σ
E
. We infer that σ
E
compartmentalization is partially attributed to a competition between the compartments for the activation signaling protein SpoIIR. Normally, SpoIIGA is predominantly located in the mother cell and as a consequence confines σ
E
activation to it. In addition, we find that CsfB, previously shown to inhibit σ
G
, is independently inhibiting σ
E
activity in the prespore. CsfB thus appears to serve a gatekeeper function in blocking the action of two sigma factors in the prespore: it prevents σ
G
from becoming active before completion of engulfment and helps prevent σ
E
from becoming active at all.
Molecular and Catalytic Properties of the Aldehyde Dehydrogenase of
Gluconacetobacter diazotrophicus
, a Quinoheme Protein Containing Pyrroloquinoline Quinone, Cytochrome
b
, and Cytochrome
c
Authors: Gómez-Manzo S. , Chavez-Pacheco J. L. , Contreras-Zentella M. , Sosa-Torres M. E. , Arreguín-Espinosa R. , Pérez de la Mora M. , Membrillo-Hernández J. , Escamilla J. E. 
Published: August 2010

ABSTRACT

Several aldehyde dehydrogenase (ALDH) complexes have been purified from the membranes of acetic acid bacteria. The enzyme structures and the chemical nature of the prosthetic groups associated with these enzymes remain a matter of debate. We report here on the molecular and catalytic properties of the membrane-bound ALDH complex of the diazotrophic bacterium
Gluconacetobacter diazotrophicus
. The purified ALDH complex is a heterodimer comprising two subunits of 79.7 and 50 kDa, respectively. Reversed-phase high-pressure liquid chromatography (HPLC) and electron paramagnetic resonance spectroscopy led us to demonstrate, for the first time, the unequivocal presence of a pyrroloquinoline quinone prosthetic group associated with an ALDH complex from acetic acid bacteria. In addition, heme
b
was detected by UV-visible light (UV-Vis) spectroscopy and confirmed by reversed-phase HPLC. The smaller subunit bears three cytochromes
c
. Aliphatic aldehydes, but not formaldehyde, were suitable substrates. Using ferricyanide as an electron acceptor, the enzyme showed an optimum pH of 3.5 that shifted to pH 7.0 when phenazine methosulfate plus 2,6-dichlorophenolindophenol were the electron acceptors. Acetaldehyde did not reduce measurable levels of the cytochrome
b
and
c
centers; however, the dithionite-reduced hemes were conveniently oxidized by ubiquinone-1; this finding suggests that cytochrome
b
and the cytochromes
c
constitute an intramolecular redox sequence that delivers electrons to the membrane ubiquinone.
A Periplasmic LolA Derivative with a Lethal Disulfide Bond Activates the Cpx Stress Response System
Authors: Tao Kazuyuki , Watanabe Shoji , Narita Shin-ichiro , Tokuda Hajime 
Published: August 2010

ABSTRACT
LolA accommodates the acyl chains of lipoproteins in its hydrophobic cavity and shuttles between the inner and outer membranes through the hydrophilic periplasm to place lipoproteins in the outer membrane. The LolA(I93C/F140C) derivative, in which Cys replaces Ile at position 93 and Phe at position 140, strongly inhibited growth in the absence of a reducing agent because of the lethal intramolecular disulfide bond between the two Cys residues. Expression of I93C/F140C was found to activate the Cpx two-component system, which responds to cell envelope stress. The inhibition of growth by I93C/F140C was partly suppressed by overproduction of LolCDE, which is an ATP-binding cassette transporter and mediates the transfer of lipoproteins from the inner membrane to LolA. A substantial portion of the oxidized form, but not the reduced one, of I93C/F140C expressed on LolCDE overproduction was recovered in the membrane fraction, whereas wild-type LolA was localized in the periplasm even when LolCDE was overproduced. Moreover, LolCDE overproduction stabilized I93C/F140C and therefore caused an increase in its level. Taken together, these results indicate that oxidized I93C/F140C stably binds to LolCDE, which causes strong envelope stress.
Complete Genome Sequence of
Methanothermobacter marburgensis
, a Methanoarchaeon Model Organism
Authors: Liesegang Heiko , Kaster Anne-Kristin , Wiezer Arnim , Goenrich Meike , Wollherr Antje , Seedorf Henning , Gottschalk Gerhard , Thauer Rudolf K. 
Published: August 2010

ABSTRACT

The circular genome sequence of the chemolithoautotrophic euryarchaeon
Methanothermobacter marburgensis
, with 1,639,135 bp, was determined and compared with that of
Methanothermobacter thermautotrophicus
. The genomes of the two model methanogens differ substantially in protein coding sequences, in insertion sequence (IS)-like elements, and in clustered regularly interspaced short palindromic repeats (CRISPR) loci.
Complete Genome Sequence of
Mycoplasma hyorhinis
Strain HUB-1
Authors: Liu Wei , Fang Liurong , Li Sha , Li Qiang , Zhou Zhemin , Feng Zhixin , Luo Rui , Shao Guoqing , Wang Lei , Chen Huanchun , Xiao Shaobo 
Published: August 2010

ABSTRACT

Mycoplasma hyorhinis
is generally considered a swine pathogen yet is most commonly found infecting laboratory cell lines. An increasing body of evidence suggests that chronic infections with
M. hyorhinis
may cause oncogenic transformation. Here, we announce the complete genome sequence of
M. hyorhinis
strain HUB-1.
Using the Transcription Factor Inhibitor of DNA Binding 1 to Selectively Target Endothelial Progenitor Cells Offers Novel Strategies to Inhibit Tumor Angiogenesis and Growth
Authors: Mellick Albert S. , Plummer Prue N. , Nolan Daniel J. , Gao Dingcheng , Bambino Kathryn , Hahn Mary , Catena Raul , Turner Vivian , McDonnell Kevin , Benezra Robert , Brink Robert , Swarbrick Alexander , Mittal Vivek 
Published: September 2010

Abstract
Tumor angiogenesis is essential for malignant growth and metastasis. Bone marrow (BM)–derived endothelial progenitor cells (EPC) contribute to angiogenesis-mediated tumor growth. EPC ablation can reduce tumor growth; however, the lack of a marker that can track EPCs from the BM to tumor neovasculature has impeded progress in understanding the molecular mechanisms underlying EPC biology. Here, we report the use of transgenic mouse and lentiviral models to monitor the BM-derived compartment of the tumor stroma; this approach exploits the selectivity of the transcription factor inhibitor of DNA binding 1 (Id1) for EPCs to track EPCs in the BM, blood, and tumor stroma, as well as mature EPCs. Acute ablation of BM-derived EPCs using Id1-directed delivery of a suicide gene reduced circulating EPCs and yielded significant defects in angiogenesis-mediated tumor growth. Additionally, use of the Id1 proximal promoter to express microRNA-30–based short hairpin RNA inhibited the expression of critical EPC-intrinsic factors, confirming that signaling through vascular endothelial growth factor receptor 2 is required for EPC-mediated tumor biology. By exploiting the selectivity of Id1 gene expression in EPCs, our results establish a strategy to track and target EPCs in vivo, clarifying the significant role that EPCs play in BM-mediated tumor angiogenesis. Cancer Res; 70(18); 7273–82. ©2010 AACR.
The Promise of MicroRNA Replacement Therapy
Authors: Bader Andreas G. , Brown David , Winkler Matthew 
Published: September 2010

Abstract
MicroRNAs (miRNA), a class of natural RNA-interfering agents, have recently been identified as attractive targets for therapeutic intervention. The rationale for developing miRNA therapeutics is based on the premise that aberrantly expressed miRNAs play key roles in the development of human disease, and that correcting these miRNA deficiencies by either antagonizing or restoring miRNA function may provide a therapeutic benefit. Although miRNA antagonists are conceptually similar to other inhibitory therapies, restoring the function of a miRNA by miRNA replacement is a less well characterized approach. Here, we discuss the specific properties of miRNA replacement and review recent examples that explored the therapeutic delivery of miRNA mimics in animal models of cancer. Cancer Res; 70(18); 7027–30. ©2010 AACR.
Visual field expansion after visual restoration therapy
Authors: Marshall Randolph S , Chmayssani Mohamad , O'Brien Katherine A , Handy Catherine , Greenstein Vivienne C 
Published: August 2010

Objective: To determine whether visual field expansion occurs with visual restoration therapy (VRT), using fundus-controlled microperimetry to assess visual fields. Design: This longitudinal cohort analysis assesses patients’ visual fields before and after visual restoration therapy using microperimetry and standard high-resolution perimetry. Subjects: Seven patients with stroke-induced homonymous field cuts were studied. Intervention: Visual restoration therapy is a computerized, home-based treatment aimed at reducing the size of the visual field defect of stroke patients with hemianopia through repetitive stimulation of the visual borderzone adjacent to the blind field. During twice-daily therapy for three months patients maintain central fixation while responding to eccentrically placed stimuli in the visual borderzone. The programme is adjusted monthly to changes in the patient’s visual field. Controversy exists as to whether expansion of visual fields measured at home with high-resolution perimetry is due to inadvertent eye movements and therefore would overrepresent the treatment’s effect. Main measures: Microperimentry uses an infrared camera to track retinal vessels so that any shift or movement between the reference image and the real-time fundus image corrects the stimulus position, thus delivering stimuli to known retinal locations, and allowing accurate assessment of visual fields independent of eye movements. Results: There was an average improvement in stimulus detection rate by microperimetry of 12.5% (range —1.4% to 38.9%, P =0.033). Six of 7 patients had ≥ 3% improvement in stimulus detection by home-based perimetry. Conclusion: Our results demonstrate modest but real expansion in visual fields following visual restoration therapy which is not due to eye movements.
Acute Achilles Tendon Rupture
Authors: Nilsson-Helander Katarina , Grävare Silbernagel Karin , Thomeé Roland , Faxén Eva , Olsson Nicklas , Eriksson Bengt I. , Karlsson Jon 
Published: August 2010

Background There is no consensus regarding the optimal treatment for patients with acute Achilles tendon rupture. Few randomized controlled studies have compared outcomes after surgical or nonsurgical treatment with both groups receiving early mobilization. Purpose This study was undertaken to compare outcomes of patients with acute Achilles tendon rupture treated with or without surgery using early mobilization and identical rehabilitation protocols. Study Design Randomized, controlled trial; Level of evidence, 1. Methods Ninety-seven patients (79 men, 18 women; mean age, 41 years) with acute Achilles tendon rupture were treated and followed for 1 year. The primary end point was rerupturing. Patients were evaluated using the Achilles tendon Total Rupture Score (ATRS), functional tests, and clinical examination at 6 and 12 months after injury. Results There were 6 (12%) reruptures in the nonsurgical group and 2 (4%) in the surgical group (P = .377). The mean 6- and 12-month ATRS were 72 and 88 points in the surgical group and 71 and 86 points in the nonsurgical group, respectively. Improvements in ATRS between 6 and 12 months were significant for both groups, with no significant between-group differences. At the 6-month evaluation, the surgical group had better results compared with the nonsurgically treated group in some of the muscle function tests; however, at the 12-month evaluation there were no differences between the 2 groups except for the heel-rise work test in favor of the surgical group. At the 12-month follow-up, the level of function of the injured leg remained significantly lower than that of the uninjured leg in both groups. Conclusion The results of this study did not demonstrate any statistically significant difference between surgical and nonsurgical treatment. Furthermore, the study suggests that early mobilization is beneficial for patients with acute Achilles tendon rupture whether they are treated surgically or nonsurgically. The preferred treatment strategy for patients with acute Achilles tendon rupture remains a subject of debate. Although the study met the sample size dictated by the authors’ a priori power calculation, the difference in the rerupture rate might be considered clinically important by some.
Complex karyotype newly defined: the strongest prognostic factor in advanced childhood myelodysplastic syndrome
Authors: Göhring Gudrun , Michalova Kyra , Beverloo H. Berna , Betts David , Harbott Jochen , Haas Oskar A. , Kerndrup Gitte , Sainati Laura , Bergstraesser Eva , Hasle Henrik , Starý Jan , Trebo Monika , van den Heuvel-Eibrink Marry M. , Zecca Marco , van Wering Elisabeth R. , Fischer Alexandra , Noellke Peter , Strahm Brigitte , Locatelli Franco , Niemeyer Charlotte M. , Schlegelberger Brigitte 
Published: August 2010

AbstractTo identify cytogenetic risk factors predicting outcome in children with advanced myelodysplastic syndrome, overall survival of 192 children prospectively enrolled in European Working Group of Myelodysplastic Syndrome in Childhood studies was evaluated with regard to karyotypic complexity. Structurally complex constitutes a new definition of complex karyotype characterized by more than or equal to 3 chromosomal aberrations, including at least one structural aberration. Five-year overall survival in patients with more than or equal to 3 clonal aberrations, which were not structurally complex, did not differ from that observed in patients with normal karyotype. Cox regression analysis revealed the presence of a monosomal and structurally complex karyotype to be strongly associated with poor prognosis (hazard ratio = 4.6, P < .01). Notably, a structurally complex karyotype without a monosomy was associated with a very short 2-year overall survival probability of only 14% (hazard ratio = 14.5; P < .01). The presence of a structurally complex karyotype was the strongest independent prognostic marker predicting poor outcome in children with advanced myelodysplastic syndrome.
Significance of Aurora B overexpression in hepatocellular carcinoma. Aurora B Overexpression in HCC
Authors: Lin Zhong-Zhe , Jeng Yung-Ming , Hu Fu-Chang , Pan Hung-Wei , Tsao Hsin-Wei , Lai Po-Lin , Lee Po-Huang , Cheng Ann-Lii , Hsu Hey-Chi 
Published: August 2010

Abstract

Background
To investigate the significance of Aurora B expression in hepatocellular carcinoma (HCC).

Methods
The Aurora B and Aurora A mRNA level was measured in 160 HCCs and the paired nontumorous liver tissues by reverse transcription-polymerase chain reaction. Mutations of the p53 and β-catenin genes were analyzed in 134 and 150 tumors, respectively, by direct sequencing of exon 2 to exon 11 of p53 and exon 3 of β-catenin. Anticancer effects of AZD1152-HQPA, an Aurora B kinase selective inhibitor, were examined in Huh-7 and Hep3B cell lines.

Results

Aurora B was overexpressed in 98 (61%) of 160 HCCs and in all 7 HCC cell lines examined. The overexpression of Aurora B was associated with Aurora A overexpression (P = 0.0003) and p53 mutation (P = 0.002) and was inversely associated with β-catenin mutation (P = 0.002). Aurora B overexpression correlated with worse clinicopathologic characteristics. Multivariate analysis confirmed that Aurora B overexpression was an independent poor prognostic factor, despite its interaction with Aurora A overexpression and mutations of p53 and β-catenin. In Huh-7 and Hep3B cells, AZD1152-HQPA induced proliferation blockade, histone H3 (Ser10) dephosphorylation, cell cycle disturbance, and apoptosis.

Conclusion

Aurora B overexpression is an independent molecular marker predicting tumor invasiveness and poor prognosis of HCC. Aurora B kinase selective inhibitors are potential therapeutic agents for HCC treatment.
Influence of loading conditions on the measurement of mode I critical stress intensity factor for wood and medium-density fiberboard by the single-edge-notched tension test
Authors: Yoshihara Hiroshi 
Published: September 2010

AbstractThe mode I critical stress intensity factorKIcfor wood and medium-density fiberboard (MDF) was obtained by conducting the single-edge-notched tension (SENT) test, designed for isotropic materials, under various loading conditions, and performing subsequent numerical analysis on the test data. The validity of the SENT test for this purpose was examined by conducting double cantilever beam (DCB) tests and comparing test data with those of the SENT tests. The best values ofKIcare obtained by conducting the SENT test under pin loading and introducing an additional crack length into the equations used for analyzing the test data.
Cost-Effectiveness of Image-Guided Spine Surgery
Authors: Watkins Robert Green , Gupta Akash , Watkins Robert Green 
Published: August 2010

Objective:
To determine if image-guided spine surgery is cost effective.

Methods:
A prospective case series of the first 100 patients undergoing thoracolumbar pedicle screw instrumentation under image-guidance was compared to a retrospective control group of the last 100 patients who underwent screw placement prior to the use of image-guidance. The image-guidance system was NaviVision (Vector Vision-BrainLAB) and Arcadis Orbic (Siemens).

Results:
The rate of revision surgery was reduced from 3% to 0% with the use of image guidance (p=0.08). The cost savings of image guidance for the placement of pedicle screws was $71,286 per 100 cases. Time required for pedicle screw placement with image guidance was 20 minutes for 2 screws, 29 minutes for 4 screws, 38 minutes for 6 screws, and 50 min for 8 screws. Cost savings for the time required for placement of pedicle screws with image guidance can be estimated by subtracting the time required with currently used techniques without image guidance from the above averages, then multiplying by $93 per minute. The approximate costs of the navigation system is $475,000 ( $225,000 for Vector Vision-BrainLAB and $250,000 for Arcadis Orbic-Siemens).

Conclusion:
Image guidance for the placement of pedicle screws may be cost effective in spine practices with heavy volume, that perform surgery in difficult cases, and that require long surgical times for the placement of pedicle screws.