bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational changes and loose packing promote E. coli Tryptophanase cold lability
Authors: Kogan Anna , Gdalevsky Garik Y , Cohen-Luria Rivka , Goldgur Yehuda , Phillips Robert S , Parola Abraham H , Almog Orna 
Published: October 2009

Abstract

Background
Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from Escherichia coli. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme with a Mw of 210 kD. PLP is covalently bound through an enamine bond to Lys270 at the active site. The incubation of holo E. coli Trpases at 2°C for 20 h results in breaking this enamine bond and PLP release, as well as a reversible loss of activity and dissociation into dimers. This sequence of events is termed cold lability and its understanding bears relevance to protein stability and shelf life.

Results
We studied the reversible cold lability of E. coli Trpase and its Y74F, C298S and W330F mutants. In contrast to the holo E. coli Trpase all apo forms of Trpase dissociated into dimers already at 25°C and even further upon cooling to 2°C. The crystal structures of the two mutants, Y74F and C298S in their apo form were determined at 1.9Å resolution. These apo mutants were found in an open conformation compared to the closed conformation found for P. vulgaris in its holo form. This conformational change is further supported by a high pressure study.

Conclusion
We suggest that cold lability of E. coli Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of E. coli Trpase to dimers and P. vulgaris Trpase to monomers.
Evaluating geographic imputation approaches for zip code level data: an application to a study of pediatric diabetes
Authors: Hibbert James D , Liese Angela D , Lawson Andrew , Porter Dwayne E , Puett Robin C , Standiford Debra , Liu Lenna , Dabelea Dana 
Published: October 2009

Abstract

Background
There is increasing interest in the study of place effects on health, facilitated in part by geographic information systems. Incomplete or missing address information reduces geocoding success. Several geographic imputation methods have been suggested to overcome this limitation. Accuracy evaluation of these methods can be focused at the level of individuals and at higher group-levels (e.g., spatial distribution).

Methods
We evaluated the accuracy of eight geo-imputation methods for address allocation from ZIP codes to census tracts at the individual and group level. The spatial apportioning approaches underlying the imputation methods included four fixed (deterministic) and four random (stochastic) allocation methods using land area, total population, population under age 20, and race/ethnicity as weighting factors. Data included more than 2,000 geocoded cases of diabetes mellitus among youth aged 0-19 in four U.S. regions. The imputed distribution of cases across tracts was compared to the true distribution using a chi-squared statistic.

Results
At the individual level, population-weighted (total or under age 20) fixed allocation showed the greatest level of accuracy, with correct census tract assignments averaging 30.01% across all regions, followed by the race/ethnicity-weighted random method (23.83%). The true distribution of cases across census tracts was that 58.2% of tracts exhibited no cases, 26.2% had one case, 9.5% had two cases, and less than 3% had three or more. This distribution was best captured by random allocation methods, with no significant differences (p-value > 0.90). However, significant differences in distributions based on fixed allocation methods were found (p-value < 0.0003).

Conclusion
Fixed imputation methods seemed to yield greatest accuracy at the individual level, suggesting use for studies on area-level environmental exposures. Fixed methods result in artificial clusters in single census tracts. For studies focusing on spatial distribution of disease, random methods seemed superior, as they most closely replicated the true spatial distribution. When selecting an imputation approach, researchers should consider carefully the study aims.
Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius
Authors: Wu Yongping , Zhou Jiyong , Zhang Xin , Zheng Xiaojuan , Jiang Xuetao , Shi Lixue , Yin Wei , Wang Junhua 
Published: October 2009

Abstract

Background
Two-dimensional gel electrophoresis (2-DE) is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF), a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

Results
An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v) 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS), 50 mM dithiothreitol (DTT), 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF), 20 U/ml Deoxyribonuclease I (DNase I), and 0.25 mg/ml Ribonuclease A (RNase A), combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG) strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF). When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found.

Conclusion
These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.
Immunological considerations of modern animal models of malignant primary brain tumors
Authors: Sughrue Michael E , Yang Isaac , Kane Ari J , Rutkowski Martin J , Fang Shanna , James C David , Parsa Andrew T 
Published: October 2009

AbstractRecent advances in animal models of glioma have facilitated a better understanding of biological mechanisms underlying gliomagenesis and glioma progression. The limitations of existing therapy, including surgery, chemotherapy, and radiotherapy, have prompted numerous investigators to search for new therapeutic approaches to improve quantity and quality of survival from these aggressive lesions. One of these approaches involves triggering a tumor specific immune response. However, a difficulty in this approach is the the scarcity of animal models of primary CNS neoplasms which faithfully recapitulate these tumors and their interaction with the host's immune system. In this article, we review the existing methods utilized to date for modeling gliomas in rodents, with a focus on the known as well as potential immunological aspects of these models. As this review demonstrates, many of these models have inherent immune system limitations, and the impact of these limitations on studies on the influence of pre-clinical therapeutics testing warrants further attention.
Retinoic acid enhances skeletal muscle progenitor formation and bypasses inhibition by bone morphogenetic protein 4 but not dominant negative β-catenin
Authors: Kennedy Karen AM , Porter Tammy , Mehta Virja , Ryan Scott D , Price Feodor , Peshdary Vian , Karamboulas Christina , Savage Josée , Drysdale Thomas A , Li Shun-Cheng , Bennett Steffany AL , Skerjanc Ilona S 
Published: October 2009

Abstract

Background

Understanding stem cell differentiation is essential for the future design of cell therapies. While retinoic acid (RA) is the most potent small molecule enhancer of skeletal myogenesis in stem cells, the stage and mechanism of its function has not yet been elucidated. Further, the intersection of RA with other signalling pathways that stimulate or inhibit myogenesis (such as Wnt and BMP4, respectively) is unknown. Thus, the purpose of this study is to examine the molecular mechanisms by which RA enhances skeletal myogenesis and interacts with Wnt and BMP4 signalling during P19 or mouse embryonic stem (ES) cell differentiation.

Results

Treatment of P19 or mouse ES cells with low levels of RA led to an enhancement of skeletal myogenesis by upregulating the expression of the mesodermal marker, Wnt3a, the skeletal muscle progenitor factors Pax3 and Meox1, and the myogenic regulatory factors (MRFs) MyoD and myogenin. By chromatin immunoprecipitation, RA receptors (RARs) bound directly to regulatory regions in the Wnt3a, Pax3, and Meox1 genes and RA activated a β-catenin-responsive promoter in aggregated P19 cells. In the presence of a dominant negative β-catenin/engrailed repressor fusion protein, RA could not bypass the inhibition of skeletal myogenesis nor upregulate Meox1 or MyoD. Thus, RA functions both upstream and downstream of Wnt signalling. In contrast, it functions downstream of BMP4, as it abrogates BMP4 inhibition of myogenesis and Meox1, Pax3, and MyoD expression. Furthermore, RA downregulated BMP4 expression and upregulated the BMP4 inhibitor, Tob1. Finally, RA inhibited cardiomyogenesis but not in the presence of BMP4.

Conclusion

RA can enhance skeletal myogenesis in stem cells at the muscle specification/progenitor stage by activating RARs bound directly to mesoderm and skeletal muscle progenitor genes, activating β-catenin function and inhibiting bone morphogenetic protein (BMP) signalling. Thus, a signalling pathway can function at multiple levels to positively regulate a developmental program and can function by abrogating inhibitory pathways. Finally, since RA enhances skeletal muscle progenitor formation, it will be a valuable tool for designing future stem cell therapies.
In vivo99mTc-HYNIC-annexin V imaging of early tumor apoptosis in mice after single dose irradiation
Authors: Guo Ming-fang , Zhao Yaqing , Tian Rong , Li Lin , Guo Leiming , Xu Feng , Liu Yong-mei , He Yong-bo , Bai Sen , Wang Jin 
Published: October 2009

Abstract

Background
Apoptosis is a major mode of hematological tumor death after radiation. Early detection of apoptosis may be beneficial for cancer adaptive treatment. 99mTc-HYNIC-annexinV has been reported as a promising agent for in vivo apoptosis imaging. The purpose of this study is to evaluate the feasibility of in vivo99mTc-HYNIC-annexinV imaging of radiation- induced apoptosis, and to investigate its correlation with radiosensitivity.

Methods
Ten days after inoculation of tumor cells in the right upper limbs, the mice were randomly divided into two groups. The imaging group (4 mice each level, 4 dose levels) was injected with 4-8 MBq 99mTc-HYNIC-annexinV 24 hours after irradiation and imaged 1 hr post-injection, and the mice were sacrificed immediately after imaging for biodistribution analysis of annexin V. The observation group (4 mice each level, 2 dose levels) was only observed for tumor regression post-radiation. The number of apoptotic cells in a tumor was estimated with TUNEL assay.

Results
The 99mTc-HYNIC-annexin V uptake in E14 lymphoma significantly increased as the radiation dose escalated from 0 to 8 Gy, and significantly correlated with the number of TUNEL-positive cells (r = 0.892, P < 0.001). The Annexin-V uptake and the number of TUNEL-positive cells in El4 lymphoma were significantly greater than those in S180 sarcoma. With 8 Gy, S180 sarcoma tumor showed scanty apoptosis and less shrinkage while El4 lymphoma showed remarkable apoptosis and complete remission.

Conclusion

99mTc-HYNIC-annexinV in vivo imaging is a feasible method to detect early radiation-induced apoptosis in different tumors, and might be predictive for radiation sensitivity.
Perfusion-CT monitoring of cryo-ablated renal cells tumors
Authors: Squillaci Ettore , Manenti Guglielmo , Cicciò Carmelo , Nucera Francesca , Bove Pierluigi , Vespasiani Giuseppe , Russolillo Laura , Simonetti Giovanni 
Published: October 2009

Abstract

Background
No single and thoroughly validated imaging method in monitoring of cryoablated renal cell carcinoma (RCC) is available. The purpose of our study was to determine the feasibility of dynamic contrast-enhanced perfusion CT (pCT) in evaluating the hemodynamic response of RCC.

Methods
15 patients (14 male, 1 female; age range, 43-81 years; mean age, 62 years) with cryoablated RCC via a transperitoneal approach, underwent to pCT 6-8 months after cryo-therapy. pCT was performed for 65 seconds after intravenous injection of contrast medium (80 mL, 370 mg iodine per millilitre, 4 mL/sec). Perfusion parameters (Time/Density curve; Blood flow, BF; Blood Volume, BV; Mean Transit Time, MTT; Permeability-Surface Area Product, PS) were sampled in the cryoablated tumor area and in ipsilateral renal cortex using deconvolution-based method. A tumor was considered to be not responsive to treatment by CT evidence of pathological contrast enhancement in the cryoablated area or renal mass persistence compared with the preoperative CT control. Written informed consent was obtained from all participants before the study.

Results
After cryotherapy, successfully ablated tumor (n = 13) showed decrease in BV (5,39 +/- 1,28 mL/100 g), BF (69,92 +/- 20,12 mL/100 g/min) and PS (16,66 +/- 5,67 mL/100 g/min) value and increased value of MTT (25,35 +/- 4,3 sec) compared with those of normal renal cortex (BV: 117,86 +/- 31,87 mL/100 g/min; BF: 392,39 +/- 117,32 mL/100 g/min; MTT: 18,02 +/- 3,6 sec; PS: 81,68 +/- 22,75 mL/100 g/min). In one patient, assessment of perfusion parameters was not feasible for breathing artifacts. One tumor showed poor response to treatment by the evidence of nodular contrast enhancement in the region encompassing the original lesion. Two typical enhancement patterns were obtained comparing the Time-Density curves of responsive and not responsive ablated tumors.

Conclusion
Perfusion CT seems to be a feasible and promising technique in monitoring the effects of cryoablation therapy.
Genomic DNA k-mer spectra: models and modalities
Authors: Chor Benny , Horn David , Goldman Nick , Levy Yaron , Massingham Tim 
Published: October 2009

Abstract
Background
The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is now possible.

Results
We have studied the k-mer spectra of more than 100 species from Archea, Bacteria, and Eukaryota, particularly looking at the modalities of the distributions. As expected, most species have a unimodal k-mer spectrum. However, a few species, including all mammals, have multimodal spectra. These species coincide with the tetrapods. Genomic sequences are clearly very complex, and cannot be fully explained by any simple probabilistic model. Yet we sought such an explanation for the observed modalities, and discovered that low-order Markov models capture this property (and some others) fairly well.

Conclusions
Multimodal spectra are characterized by specific ranges of values of C+G content and of CpG dinucleotide suppression, a range that encompasses all tetrapods analyzed. Other genomes, like that of the protozoa Entamoeba histolytica, which also exhibits CpG suppression, do not have multimodal k-mer spectra. Groupings of functional elements of the human genome also have a clear modality, and exhibit either a unimodal or multimodal behaviour, depending on the two above mentioned values.
Growth and Layer Characterization of SrTiO3 by Atomic Layer Deposition using Sr(tBu3Cp)2 and Ti(OMe)4
Authors: Popovici Mihaela , Van Elshocht Sven , Menou Nicolas , Swerts Johan , Pierreux Dieter , Delabie Annelies , Opsomer Karl , Brijs Bert , Faelens Gerrit , Franquet Alexis , Conard Thierry , Maes Jan , Wouters Dirk , Kittl Jorge 
Published: October 2009

AbstractStrontium titanate (STO) thin films (45-67 % Sr) were deposited by atomic layer deposition using Sr(tBu3Cp)2/Ti(OMe)4/H2O as precursors. The Sr content of the layers is well controlled by the precursor pulse ratio, as indicated by Rutherford backscattering spectroscopy (RBS). The amount of Sr and Ti deposited depends on the Sr:Ti pulse ratio and indicates the enhancement of the Ti precursor reactivity in the presence of Sr-OH. STO compositions that are closer to stoichiometric SrTiO3 result in denser films with correspondingly higher index of refraction. The increase (decrease) of the Sr content over (below) 50 % leads to an expansion (contraction) of the lattice parameter corresponding to cubic SrTiO3 with a perovskite structure. The dielectric constant (extracted from film thickness series) and leakage current strongly depends both on the Sr content and the crystalline state of the films.
Successful Field Application of Novel, Nonsilicone Antifoam Chemistries for High-Foaming Heavy-Oil Storage Tanks in Northern Alberta
Authors: Wylde Jonathan J. 
Published: October 2009

Summary
Substantial foam formation was being experienced by two operators in several heavy-oil leases in northern Alberta. This 10 to 12°API crude had a large foaming potential and a unique foam-formation mechanism. Crude oil passed from the wellhead through a short flowline to a pair of hydrostatically balanced and heated storage tanks. The storage tanks heated the crude oil from approximately 50 to 85°C. In doing so, it caused gas breakout and degassing, which resulted in the formation of a thick, persistent foam in the top of the tanks. The foam would enter the transportation trucks and end up at the local battery and create carry-over and separation problems in the process systems.
Silicone antifoam products were not acceptable because of their poor environmental profile and the influence these large molecules had at the refinery where the crude oil was shipped for (predominantly) asphalt manufacture.
A wide range of chemistries was tested including phosphate-based products, ethoxylated and propoxylated esters, polyethylene glycol esters and oleates, alcohols, fatty alcohols, and ethoxylated and propoxylated alcohols. One of the major challenges detailed in this paper is that all products had to be freeze protected to −40°C. This was significant because many antifreeze chemicals affect the efficacy of antifoam chemicals.
This paper details evolution of testing leading to the field application of this combined defoamer/antifoam chemistry. Initial laboratory screening is included, which describes a laboratory test method designed to mimic the foam-formation environment in the field more accurately. The paper also illustrates the field-trial evaluation, as well as the case histories of full field implementation of the highest-efficacy products.
Parental Origin and Cell Stage Errors in X-Chromosome Polysomy 49, XXXXY
Authors: Guzel A , Demirhan O , Pazarbasi A , Yuksel B 
Published: October 2009

Parental Origin and Cell Stage Errors in X-Chromosome Polysomy 49, XXXXYPolysomy 49, XXXXY is a rare sex chromosome aneuploidy syndrome characterized by mental retardation, severe speech impairment, craniofacial abnormalities, multiple skeletal defects and genital abnormalities. We describe a patient with 49, XXXXY syndrome who had many characteristics of Fraccaro syndrome; language impairment, mongoloid slant, epicanthal folds, cryptorchidism, umbilical hernia and dysmyelinization in his brain. A GTG-banding technique was used for karyotype analysis of peripheral blood cell cultures. The parental origin of polysomy X was identified by using quantitative fluorescent polymerase chain reaction (QF-PCR) with seven short tandem repeat (STR) markers specific for the X/Y-chromosome which revealed that all the X-chromosomes were of maternal origin. This report provides evidence for successive non disjunctions in maternal meiosis I and II.
Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic Groups
Authors: Ozkorkmaz A , Baransel Isir A , Pehlivan S , Özkorkmaz E 
Published: October 2009

Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic GroupsAllele frequencies of the 10 short tandem repeats (STRs) loci (D16S539, D2S1338, D3S1358, vWA, D18S51, D21S11, D8S1179, D19S433, FGA, THO1) included in the AmpFISTR SGM Plus kit, were obtained from biological samples from 100 unrelated individual residing in different part of Turkey. The χ2 test showed that all these loci agreed with Hardy-Weinberg equilibrium, The results were compared with the previously published data from Turkish and other ethnic groups. Suggest that these loci with their high heterozygosity and combined power of discrimination (PD) values are useful for forensic identifications.
Immature Dendritic Cell-Derived Exosomes Rescue Septic Animals Via Milk Fat Globule Epidermal Growth Factor VIII
Authors: Miksa Michael , Wu Rongqian , Dong Weifeng , Komura Hidefumi , Amin Dhruv , Ji Youxin , Wang Zhimin , Wang Haichao , Ravikumar Thanjavur S. , Tracey Kevin J. , Wang Ping 
Published: October 2009

Abstract
Sepsis, a highly lethal systemic inflammatory syndrome, is associated with increases of proinflammatory cytokines (e.g., TNF-α, HMGB1) and the accumulation of apoptotic cells that have the potential to be detrimental. Depending on the timing and tissue, prevention of apoptosis in sepsis is beneficial; however, thwarting the development of secondary necrosis through the active removal of apoptotic cells by phagocytosis may offer a novel anti-sepsis therapy. Immature dendritic cells (IDCs) release exosomes that contain milk fat globule EGF factor VIII (MFGE8), a protein required to opsonize apoptotic cells for phagocytosis. In an experimental sepsis model using cecal ligation and puncture, we found that MFGE8 levels decreased in the spleen and blood, which was associated with impaired apoptotic cell clearance. Administration of IDC-derived exosomes promoted phagocytosis of apoptotic cells and significantly reduced mortality. Treatment with recombinant MFGE8 was equally protective, whereas MFGE8-deficient mice suffered from increased mortality. IDC exosomes also attenuated the release of proinflammatory cytokines in septic rats. Liberation of HMGB1, a nuclear protein that contributes to inflammation upon release from unengulfed apoptotic cells, was prevented by MFGE8-mediated phagocytosis in vitro. We conclude that IDC-derived exosomes attenuate the acute systemic inflammatory response in sepsis by enhancing apoptotic cell clearance via MFGE8.