bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single intersubunit salt bridge affects oligomerization and catalytic activity in a bacterial quinone reductase
Authors: Binter Alexandra , Staunig Nicole , Jelesarov Ilian , Lohner Karl , Palfey Bruce A. , Deller Sigrid , Gruber Karl , Macheroux Peter 
Published: August 2009

YhdA, a thermostable NADPH:FMN oxidoreductase from Bacillus subtilis, reduces quinones via a ping‐pong bi‐bi mechanism with a pronounced preference for NADPH. The enzyme occurs as a stable tetramer in solution. The two extended dimer surfaces are packed against each other by a 90° rotation of one dimer with respect to the other. This assembly is stabilized by the formation of four salt bridges between K109 and D137 of the neighbouring protomers. To investigate the importance of the ion pair contacts, the K109L and D137L single replacement variants, as well as the K109L/D137L and K109D/D137K double replacement variants, were generated, expressed, purified, crystallized and biochemically characterized. The K109L and D137L variants form dimers instead of tetramers, whereas the K109L/D137L and K109D/D137K variants appear to exist in a dimer–tetramer equilibrium in solution. The crystal structures of the K109L and D137L variants confirm the dimeric state, with the K109L/D137L and K109D/D137K variants adopting a tetrameric assembly. Interestingly, all protein variants show a drastically reduced quinone reductase activity in steady‐state kinetics. Detailed analysis of the two half reactions revealed that the oxidative half reaction is not affected, whereas reduction of the bound FMN cofactor by NADPH is virtually abolished. Inspection of the crystal structures indicates that the side chain of K109 plays a dual role by forming a salt bridge to D137, as well as stabilizing a glycine‐rich loop in the vicinity of the FMN cofactor. In all protein variants, this glycine‐rich loop exhibits a much higher mobility, compared to the wild‐type. This appears to be incompatible with NADPH binding and thus leads to abrogation of flavin reduction.Structured digital abstract
MINT‐7229866, MINT‐7229874, MINT‐7229885, MINT‐7229894, MINT‐7229905: YhdA (uniprotkb:O07529) and YhdA (uniprotkb:O07529) bind (MI:0407) by blue native page (MI:0276)
MINT‐7229854: YhdA (uniprotkb:O07529) and YhdA (uniprotkb:O07529) bind (MI:0407) by x‐ray crystallography (MI:0114)
Acute exercise reverses TRB3 expression in the skeletal muscle and ameliorates whole body insulin sensitivity in diabetic mice
Authors: Matos A. , Ropelle E. R. , Pauli J. R. , Frederico M. J. S. , De Pinho R. A. , Velloso L. A. , De Souza C. T. 
Published: August 2009

AbstractAim:  TRB3 became of major interest in diabetes research when it was shown to interact with and inhibit the activity of Akt. Conversely, physical exercise has been linked to improved glucose homeostasis. Thus, the current study was designed to investigate the effects of acute exercise on TRB3 expression and whole body insulin sensitivity in obese diabetic mice.Methods:  Male leptin‐deficient (ob/ob) mice swam for two 3‐h‐long bouts, separated by a 45‐min rest period. After the second bout of exercise, food was withdrawn 6 h before antibody analysis. Eight hours after the exercise protocol, the mice were submitted to an insulin tolerance test (ITT). Gastrocnemius muscle samples were evaluated for insulin receptor (IR) and IRS‐1 tyrosine phosphorylation, Akt serine phosphorylation, TRB3/Akt association and membrane GLUT4 expression.Results:  Western blot analysis showed that TRB3 expression was reduced in the gastrocnemius of leptin‐deficient (ob/ob) mice submitted to exercise when compared with respective ob/ob mice at rest. In parallel, there was an increase in the insulin‐signalling pathway in skeletal muscle from leptin‐deficient mice after exercise. Furthermore, the GLUT4 membrane expression was increased in the muscle after the exercise protocol. Finally, a single session of exercise improved the glucose disappearance (KITT) rate in ob/ob mice.Conclusion:  Our results demonstrate that acute exercise reverses TRB3 expression and insulin signalling restoration in muscle. Thus, these results provide new insights into the mechanism by which physical activity ameliorates whole body insulin sensitivity in type 2 diabetes.
Growth of a non‐methanotroph on natural gas: ignoring the obvious to focus on the obscure
Authors: Cooley Richard B. , Bottomley Peter J. , Arp Daniel J. 
Published: August 2009

SummaryMethanotrophs are well known for their ability to grow on methane in natural gas environments; however, these environments also contain low concentrations of longer‐chain‐length gaseous alkanes. This mixture of alkanes poses a problem for organisms that might otherwise grow on alkanes ≥ C2 because methane could inhibit oxidation of growth substrates and lead to an accumulation of toxic C1 metabolites. Here, we have characterized the growth of a C2–C9 alkane‐utilizing bacterium, Thauera butanivorans, in conditions containing high concentrations of methane and small amounts (< 3% of total alkane) of C2–C4. During such growth, methanol accumulates transiently before being consumed in an O2‐dependent process that leads to the formation of a proton gradient and subsequent ATP generation. In contrast, formaldehyde‐dependent O2 consumption is insensitive to uncouplers and does not lead to significant ATP production. This efficient C1 oxidation process that regains much of the energy loss inflicted by oxidizing methane, coupled with an alkane monooxygenase effective at limiting methane oxidation, allows T. butanivorans to grow uninhibited in natural gas environments. Although longer‐chain‐length gaseous alkane‐utilizing organisms have been previously identified to grow in natural gas seepages, the data presented here represent the first detailed characterization of the physiological effects associated with inadvertent methane oxidation by a non‐methanotroph, and suggest the presence of a well‐evolved series of biochemical processes that allow them to grow in natural gas deposits without the need for developing the unique metabolic machinery characteristic of methanotrophs.
Whole‐community genome amplification (WCGA) leads to compositional bias in methane‐oxidizing communities as assessed by pmoA‐based microarray analyses and QPCR
Authors: Bodelier Paul L. E. , Kamst Miranda , Meima‐Franke Marion , Stralis‐Pavese Nancy , Bodrossy Levente 
Published: August 2009

SummaryWhole‐genome amplification (WGA) using multiple displacement amplification (MDA) has recently been introduced to the field of environmental microbiology. The amplification of single‐cell genomes or whole‐community metagenomes decreases the minimum amount of DNA needed for subsequent molecular community analyses. The resolution of profiling methods of environmental microbial communities will increase substantially by the use of the whole‐community genome amplification (WCGA) procedure, assuming that the original community composition is not affected qualitatively as well as quantitatively. The present study aims to test if WCGA introduces a bias when applied to aerobic proteobacterial methanotrophic communities. For this, first, we subjected samples from freshwater lake sediment to WCGA, and amplified using primers targeting the pmoA gene coding for the α‐subunit of the methane monooxygenase enzyme. Second, we analysed community composition using a diagnostic microarray and quantitative PCR (QPCR) assays. These methods clearly demonstrated that the WCGA amplification introduced a bias. Thus, numbers of γ‐proteobacterial methanotrophs (‘type Ia’) increased significantly while the α‐proteobacterial methanotrophs (‘type II’) were not amplified by the WCGA procedure. It is hypothesized that this bias is caused by the differences in GC content, which may compromise the efficiency of the MDA reaction.
Tensile Strength of Superior Labral Repairs in the Throwing Position
Authors: Alexander Susan , Southgate Dominic F. L , Hill Adam M. , Bull Anthony M. J. , Wallace Andrew L. 
Published: August 2009

Background Type II superior labral (SLAP) tears commonly occur in athletes in the abducted and externally rotated position in the late cocking phase of throwing. This study investigates arthroscopic repairs of SLAP lesions using a knotless polymeric (KINSA) anchor. Methods Superficial tissues were dissected from 10 cadaveric shoulders. The glenohumeral capsule was preserved. Type II SLAP tears were created through arthroscopic portals and repaired with two anchors anterior and posterior to the biceps tendon. Glenohumeral joints were then fixed in 60° gleno-humeral abduction in the scapular plane with 1 Nm torque in external rotation to recreate the late cocking phase of the throwing cycle. Specimens were mounted onto an Instron machine and the biceps tendon was loaded until failure. Results The mean ultimate peak load was 239 N (SD 101 N). The primary mode of failure was in the tendon substance and 19 out of 20 anchors remained intact in bone. Conclusion To our knowledge this is the first study to investigate arthroscopic SLAP repairs in an intact joint in this susceptible position. We conclude that the KINSA anchor can withstand high tensile loads and may be used to treat SLAP tears in high-demand overhead throwing athletes.
Immune Responses of Human Immature Dendritic Cells Can Be Modulated by the Recombinant
Aspergillus fumigatus
Antigen Aspf1
Authors: Ok Michael , Latgé Jean Paul , Baeuerlein Carina , Ebel Frank , Mezger Markus , Topp Max , Kurzai Oliver , Killian Doreen , Kapp Markus , Grigoleit Goetz-Ulrich , Sennefelder Helga , Arroyo Javier , Einsele Hermann , Loeffler Juergen 
Published: August 2009

ABSTRACT

Invasive aspergillosis is a significant cause of morbidity and mortality in patients after stem cell transplantation, in solid organ transplant recipients, and in patients with hematological malignancies. The interactions between human immature dendritic cells (iDCs) and
Aspergillus fumigatus
antigens are widely uncharacterized. We analyzed the immune response of iDCs to different recombinant
A. fumigatus
antigens (Aspf1 and Crf1). One of these antigens, the 18-kDa RNase Aspf1, triggered the increased level of expression of genes encoding proinflammatory cytokines and chemokines, and augmented the activation of NFκB and the apoptosis of iDCs. Furthermore, by fluorescence microscopy, we could demonstrate that in the first 3 h a major portion of Aspf1 accumulates on the cell surface. Finally, we could show an increased segregation of cytokines and chemokines after the stimulation of iDCs by an Aspf1 deletion mutant strain of
A. fumigatus
.
Detection of
Coccidioides
Antigenemia following Dissociation of Immune Complexes
Authors: Durkin Michelle , Estok Lois , Hospenthal Duane , Crum-Cianflone Nancy , Swartzentruber Samantha , Hackett Emily , Wheat L. Joseph 
Published: August 2009

ABSTRACT

Having reported that pretreatment of serum samples with EDTA at 100°C improved the sensitivity for the detection of
Histoplasma
antigenemia, we have evaluated this method for the detection of
Coccidioides
antigenemia. Urine and serum samples from patients with coccidioidomycosis were tested using the MVista
Coccidioides
enzyme immunoassay, and serum samples with and without EDTA-heat treatment were tested. Antigenemia was detected in 28.6% of patients whose samples were not EDTA-heat treated and in 73.1% of those whose samples were treated. Antigenuria was detected in 50% of patients. Specificity of 100% was obtained in healthy subjects, but cross-reactions were seen in 22.2% of patients with histoplasmosis or blastomycosis. EDTA-heat treatment improves the sensitivity for the detection of
Coccidioides
antigenemia.
Genomic Analyses of Recombinant Adenovirus Type 11a in China
Authors: Yang Zhaohui , Zhu Zhen , Tang Liuying , Wang Li , Tan Xiaojuan , Yu Pengbo , Zhang Yong , Tian Xiaoping , Wang Jingjun , Zhang Yan , Li Dexin , Xu Wenbo 
Published: August 2009

ABSTRACT
Whole-genome sequencing of human adenovirus type 11 (HAdV-11) strain QS, isolated in China, was conducted, and its sequence was compared with the sequences of strains within the species of HAdVs. The HAdV-11 QS genome contains 34,755 nucleotides. Similar to the other HAdV subgenus B sequences, the HAdV-11 QS genome coded 37 functional proteins and could be divided into four early, two intermediate, and five late transcription regions. The amino acid sequences of the fiber and the hypervariable regions (HVRs) within the hexon gene of HAdV-11 QS were identical to the corresponding sequences of the HAdV-11a strain; further analyses that compared those amino acid sequences with the amino acid sequences of the HAdV species subgenus B:2 strains revealed that the highest degree of homology (>99.2%) existed between HAdV-11 QS and the prototypical HAdV-14 strain, except for a few coding sequences of HVRs within the hexon gene, DNA polymerase, pVI, and pre-terminal protein. This indicate that HAdV-11 strain QS, isolated in China, is a recombinant adenovirus of HAdV-14, and the recombination analyses also confirmed this finding. It is difficult to clarify the time and manner of the recombination, and further investigations are required to determine whether the emergence of recombination between HAdV-11a and HAdV-14 might increase virulence, thereby posing a new global challenge with regard to acute respiratory diseases in the near future.
Porphyromonas gingivalis
Strain Diversity
Authors: Igboin Christina O. , Griffen Ann L. , Leys Eugene J. 
Published: August 2009

ABSTRACT

Porphyromonas gingivalis
is implicated in the etiology of chronic periodontitis. Genotyping studies suggest that genetic variability exists among
P. gingivalis
strains; however, the extent of variability remains unclear and regions of variability remain largely unidentified. To assess
P. gingivalis
strain diversity, we previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type strains in clinical samples and identified 22 heteroduplex types. Additionally, we used ISR sequence analysis to determine the relatedness of
P. gingivalis
strains to one another and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of the strains. In the current study, heteroduplex analysis of the ISR was used to determine the worldwide genetic variability and distribution of
P. gingivalis
, and microarray-based comparative genomic hybridization (CGH) analysis was used to more comprehensively examine the variability of major heteroduplex type strains by using the entire genome. Heteroduplex analysis of clinical samples from geographically diverse populations identified 6 predominant geographically widespread heteroduplex types (prevalence, ≥5%) and 14 rare heterodpulex types (prevalence, <2%) which are found in one or a few locations. CGH analysis of the genomes of seven clinically prevalent heteroduplex type strains identified 133 genes from strain W83 that were divergent in at least one of the other strains. The relatedness of the strains to one another determined on the basis of genome content (microarray) analysis was highly similar to their relatedness determined on the basis of ISR sequence analysis, and a striking correlation between the genome contents and disease-associated phenotypes of the strains was observed.
First Case of Disseminated
Mycobacterium bolletii
Infection in a Young Adult Patient
Authors: Koh Won-Jung , Kwon O. Jung , Lee Nam Young , Kook Yoon-Hoh , Lee Hyung-Ki , Kim Bum-Joon 
Published: August 2009

ABSTRACT

Mycobacterium bolletii
is a rapidly growing nontuberculous mycobacterium first characterized in 2006. Here, we report a case of disseminated infection caused by
M. bolletii
in a young adult patient. To our knowledge, this is the first case of disseminated
M. bolletii
infection in an otherwise healthy young adult.
Fatal
Actinomucor elegans
var.
kuwaitiensis
Infection following Combat Trauma
Authors: Tully Charla C. , Romanelli Anna M. , Sutton Deanna A. , Wickes Brian L. , Hospenthal Duane R. 
Published: August 2009

ABSTRACT

We report the first case of invasive mucormycosis secondary to
Actinomucor elegan
s
infection. A severely injured soldier with a fatal
A. elegans
var.
kuwaitiensis
infection is described. The identification of this fungus was performed by classical and molecular methods, and this report documents the pathogenicity of the recently described variety
Actinomucor elegans
var.
kuwaitiensis.
Baleno: Expanding Retail Operations in China
Authors: Luk Sherriff T. K. , Chen Ivy S. N. 
Published: August 2009

Fuelled by impressive economic growth in recent years, consumers' demand for clothing in China had been increasing. Expenditure on clothing of urban households rose from 374.19 billion yuan in 2004 to 509.29 billion yuan in 2006 (an increase of 36.1%), and for rural households, this increased from 91.66 billion yuan to 118.36 billion yuan (an increase of 29.1%). Baleno, a casual wear retailer, had used mainly franchising to expand its retail network. This method allowed for rapid expansion but controlling franchisees in China could be problematic. Opening directly managed stores, on the other hand, required more capital. Baleno needed to decide how it should keep up with the growth in demand and with the expansion of its competitors.
Some Aspects of Complexities for Quantum Processes
Authors: Watanabe Noboru 
Published: August 2009

In quantum information theory, Emch, Conne, and Stormer were the first who studied the complexity of quantum dynamical processes. After that, Ohya introduced the [Formula: see text]-mixing entropy for general quantum systems and he defined the mean entropy and the mean mutual entropy for quantum dynamical systems based on the [Formula: see text]-mixing entropy. Conne, Narnhoffer and Thirring introduced the dynamical entropy (CNT entropy) and several researchers discussed this concept. Alicki and Fannes defined a different dynamical entropy — AF entropy. In 1995, Voiculescu proposed the dynamical approximation entropy. Accardi, Ohya and Watanabe defined yet another dynamical entropy (AOW entropy) through a quantum Markov process in 1997. In 1999, Kossakowski, Ohya and Watanabe introduced the dynamical entropy (KOW entropy) with respect to completely positive maps. In this paper, we discuss the complexity of quantum dynamical processes to calculate the dynamical entropy for noisy optical channels.In order to discuss the efficiency of information communication processes, a measure of complexity of initial state itself and a measure of transmitted complexity through communication channels are necessary. Quantum entropies were formulated on the basis of the quantum probability theory. In quantum communication systems, von Neumann entropy and Ohya mutual entropy relate to these measures of complexities, respectively. Recently, several mutual entropy type measures (Lindblad-Nielsen entropy and coherent entropy) were defined making use of entropy exchange with respect to a channel and initial state. In this paper, we show which of the measures is the most suitable one for discussing the efficiency of information transmission for quantum processes.
Cell Type–Specific Targeted Mutations of Kras and Pten Document Proliferation Arrest in Granulosa Cells versus Oncogenic Insult to Ovarian Surface Epithelial Cells
Authors: Fan Heng-Yu , Liu Zhilin , Paquet Marilene , Wang Jinrong , Lydon John P. , DeMayo Francesco J. , Richards JoAnne S. 
Published: August 2009

Abstract
The small G-protein KRAS is crucial for mediating gonadotropin-induced events associated with ovulation. However, constitutive expression of KrasG12D in granulosa cells disrupted normal follicle development leading to the persistence of abnormal follicle-like structures containing nonmitotic cells. To determine what factors mediate this potent effect of KrasG12D, gene profiling analyses were done. We also analyzed KrasG12D;Cyp19-Cre and KrasG12;Pgr-Cre mutant mouse models that express Cre prior to or after the initiation of granulosa cell differentiation, respectively. KrasG12D induced cell cycle arrest in granulosa cells of the KrasG12D;Cyp19-Cre mice but not in the KrasG12D;Pgr-Cre mice, documenting the cell context–specific effect of KrasG12D. Expression of KrasG12D silenced the Kras gene, reduced cell cycle activator genes, and impaired the expression of granulosa cell and oocyte-specific genes. Conversely, levels of PTEN and phosphorylated p38 mitogen-activated protein kinase (MAPK) increased markedly in the mutant granulosa cells. Because disrupting Pten in granulosa cells leads to increased proliferation and survival, Pten was disrupted in the KrasG12D mutant mice. The Pten/Kras mutant mice were infertile but lacked granulosa cell tumors. By contrast, the Ptenfl/fl;KrasG12D;Amhr2-Cre mice developed aggressive ovarian surface epithelial cell tumors that did not occur in the Ptenfl/fl;KrasG12D;Cyp19-Cre or Ptenfl/fl;KrasG12D;Pgr-Cre mouse strains. These data document unequivocally that Amhr2-Cre is expressed in and mediates allelic recombination of oncogenic genes in ovarian surface epithelial cells. That KrasG12D/Pten mutant granulosa cells do not transform but rather undergo cell cycle arrest indicates that they resist the oncogenic insults of Kras/Pten by robust self-protecting mechanisms that silence the Kras gene and elevate PTEN and phosphorylated p38 MAPK. [Cancer Res 2009;69(16):6463–72]
The Dendritic Cell–like Functions of IFN-Producing Killer Dendritic Cells Reside in the CD11b+ Subset and Are Licensed by Tumor Cells
Authors: Terme Magali , Mignot Grégoire , Ullrich Evelyn , Bonmort Mathieu , Minard-Colin Véronique , Jacquet Alexandra , Schultze Joachim L. , Kroemer Guido , Leclerc Claude , Chaput Nathalie , Zitvogel Laurence 
Published: August 2009

AbstractIFN producing killer dendritic cells (IKDC) were originally defined as CD11cint B220+NK1.1+ (or CD49b+) cells that exert a potent tumoricidal activity in animals lacking B, T, and conventional natural killer effectors. MHC class II expression on tumor infiltrating IKDC prompted us to investigate their putative antigen presenting function. Here, we show that tumor cells license IKDC to acquire the properties of antigen presenting cells, i.e., expression of MHC class II and costimulatory CD86 molecules. We show that the CD11b+ subset of IKDC are able to prime naïve CD4+ T cells and cross-prime naïve CD8+ T lymphocytes. Licensing of IKDC by tumor cells was mandatory for the full differentiation of T cells into polarized effectors. IKDC could engulf and process soluble Ova protein in a CD206-dependent manner. Finally, we show that CD11b+IKDC is selectively endowed with CTLA4Ig-inhibitable antigen presenting capacities and that targeting this subset with the detoxified adenylate cyclase toxin of Bordetella pertussis fused to antigen resulted in efficient cross-presentation of antigen by IKDC to specific TCR transgenic CD8+T cells in vivo. Collectively, our data indicate that upon exposure to tumor cells, IKDC subserve DC-like functions. [Cancer Res 2009;69(16):6590–7]