bluuebunny/crossref_metadata_2025 huggingface dataset:
cAMP/Ca2+ response element‐binding protein plays a central role in the biogenesis of respiratory chain proteins in mammalian cells
Authors: De Rasmo Domenico , Signorile Anna , Papa Francesco , Roca Emilio , Papa Sergio
Published: May 2010

In mammalian cells, promotion of mitochondrial biogenesis by various agents involves cAMP and Ca2+‐mediated signal transduction pathways. Recruitment of these pathways results in phosphorylation by cAMP and Ca2+‐dependent protein kinases of cAMP/Ca2+ response element‐binding protein (CREB). Phosphorylation of CREB, bound to transcriptional complexes of target genes, activates a down‐stream cascade of transcriptional complexes, which involve in sequence, the nuclear factors TORCs, PGC‐1, NRF1 and NRF2, and the mitochondrial factor mitochondrial transcriptional factor A. CREB also binds directly to the D‐loop of mitochondrial DNA and activates its expression. Activation of this network of transcriptional complexes results in concerted promotion of the expression of nuclear and mitochondrial genes encoding subunits of oxidative phosphorylation complexes. © 2010 IUBMB IUBMB Life, 62(6): 451–456, 2010
Specific ligands as pharmacological chaperones: The transport of misfolded G‐protein coupled receptors to the cell surface
Authors: Nakamura Motonao , Yasuda Daisuke , Hirota Nobuaki , Shimizu Takao
Published: May 2010

In the endoplasmic reticulum (ER), quality control mechanisms distinguish between correctly and incorrectly folded structures to ensure that aberrant proteins are not processed along the secretory pathway. Numerous studies have demonstrated the functional rescue of ER‐retained, aberrant proteins by small membrane permeable molecules called pharmacological chaperones. Pharmacological chaperones can bind to misfolded proteins, including G‐protein coupled receptors (GPCRs), and promote their correct folding and export from the ER. Recently, common structural features of GPCRs have been uncovered, including the eighth helical domain in the C‐terminal tail and conserved residues in the transmembrane domains. However, little is known about the importance of these features in signaling and intracellular trafficking, because receptors deficient in these domains are likely retained in the ER due to misfolding. In this review, we summarize the current knowledge about the requirement of these consensus domains and amino acid residues for the passing through the quality control of the ER. Furthermore, we propose the utilization of membrane permeable ligands for the transport of their cognate, ER‐retained GPCRs to the cell surface. The chaperone activity of these ligands allows us to perform functional analyses of the structure‐deficient receptors after their trafficking to the cell surface. © 2010 IUBMB IUBMB Life, 62(6): 457–463, 2010
Hormetic responses of thyroid hormone calorigenesis in the liver: Association with oxidative stress
Authors: Videla Luis A.
Published: May 2010

Thyroid hormone (L‐3,3′,5‐triiodothyronine, T3) exerts calorigenic effects by accelerating mitochondrial O2 consumption through transcriptional activation of respiratory genes, with consequent increased reactive oxygen species (ROS) production. In the liver, ROS generation occurs at different sites of hepatocytes and in the respiratory burst of Kupffer cells, triggering the activation of the transcription factors nuclear factor‐κB, signal transducer and activator of transcription 3, and activating protein 1. Under these conditions, the redox upregulation of Kupffer cell‐dependent expression of cytokines [tumor necrosis factor‐α, interleukin (IL)‐1, and IL‐6] is achieved, which upon interaction with specific receptors in hepatocytes trigger the expression of antioxidant enzymes (manganese superoxide dismutase, inducible nitric oxide synthase), antiapoptotic proteins (Bcl‐2), and acute‐phase proteins (haptoglobin, β‐fibrinogen). These responses and the promotion of hepatocyte and Kupffer cell proliferation observed represent hormetic effects re‐establishing redox homeostasis, promoting cell survival, and protecting the liver against ischemia–reperfusion (IR) injury. It is proposed that hormesis underlying T3 action may constitute a novel preconditioning strategy for IR injury during liver surgery in man or in liver transplantation using reduced‐size grafts from living donors, considering that (i) with the exception of the controversial ischemic preconditioning, all other studied strategies have failed to reach the clinical setting and (ii) T3 is a well‐tolerated therapeutic agent that either lacks major adverse effects or has minimal and controlled side effects. © 2010 IUBMB IUBMB Life, 62(6): 464–470, 2010
Human tissue distribution of paraoxonases 1 and 2 mRNA
Authors: Mackness Bharti , Beltran‐Debon Raul , Aragones Gerard , Joven Jorge , Camps Jordi , Mackness Mike
Published: May 2010

We have studied the distribution of mRNA for paraoxonases (PON) 1 and 2 in 24 human tissues using Gene Expression Panels. PON1 mRNA was restricted to adult kidney, liver, and colon as well as fetal liver, whereas PON2 mRNA was more widely distributed in adult human brain, heart, kidney, spleen, liver, colon, lung, small intestine, muscle, stomach, testis, placenta, salivary, thyroid and adrenal glands, pancreas, skin, and bone marrow, as well as fetal brain and liver. PON2 mRNA was not found in ovary, uterus, or plasma leukocytes using the panels. However, using real time PCR, we found PON2 mRNA expression in human plasma leukocytes. There were differences between the tissue distribution of mRNAs found in this study and the immunohistochemical localization of the PON1 and PON2 proteins reported previously. In particular, PON1 protein is much more widely distributed than its mRNA, possibly indicating the delivery of PON1 to various tissues by HDL. In addition, differences between PON2 mRNA and protein distributions could be due to missence mutations in the PON2 gene, causing nontranslation of mRNA to protein in some tissues. © 2010 IUBMB IUBMB Life, 62(6): 484–486, 2010
Endogenous antioxidants and Nasal human epithelium response to air pollutants: genotoxic and inmmunocytochemical evaluation
Authors: Fortoul T. I. , Rojas‐Lemus M. , Avila‐Casado M. C. , Rodriguez‐Lara V. , Montaño L. F. , Muñoz‐Comonfort A. , Lopez‐Zepeda L. S.
Published: May 2010

Nasal epithelium is a source for identifying atmospheric pollution impact. Antioxidants play a relevant role in the protection of the cells from environmental injury, but scarce information is available about the interaction of endogenous antioxidants and genotoxic damage in nasal epithelium from urban populations highly exposed to traffic‐generated air pollutants. An immunocytochemical and genotoxic evaluation was implemented in nasal cell epithelium in a population chronically exposed to atmospheric pollution from autumn 2004 to autumn 2005. Superoxide dismutase (SOD) and Catalase (CAT) were evaluated in nasal scrapings by morphometry and genotoxicity by comet assay. An increase in DNA damage correlates with a decrease in SOD and CAT in nasal cells during autumn and the inverse result was observed during summer (R = 0.88). Not only should exogenous antioxidant supplements be encouraged, but also a healthy diet to strengthen intracellular defenses against oxidative stress induced by exposure to air pollutants.
The effect of anatase TiO2 nanotube layers on MC3T3‐E1 preosteoblast adhesion, proliferation, and differentiation
Authors: Yu Wei‐qiang , Jiang Xing‐quan , Zhang Fu‐qiang , Xu Ling
Published: May 2010

Titanium oxide nanotube layers by anodization have received considerable attention in biomedical application. Previous studies have demonstrated increased osteoblast (bone‐forming cell) adhesion and function on nanotube layers compared with unanodized counterparts. More recently, one study showed amorphous TiO2 nanotube diameter determined cell fate. The anatase phase is known to be much more beneficial for bone growth than amorphous phase, so there is increasing demand to explore the response of osteoblast on anatase phase TiO2 nanotube layers. For this reason, we evaluated MC3T3‐E1 preosteoblast behavior on different diameter nanotube layers with anatase phase. The results showed that the diameter of 20–70 nm provided an effective length scale for cell adhesion, alkaline phosphatase activity, and mineralization. However, cell adhesion, alkaline phosphatase activity, and mineralization were severely impaired on nanotube layers with 100–120 nm. Interestingly, the filopodia seemed not spread into the nanotubular and like extending anatase nanotube walls, where there may be higher numbers of atoms at the surface compared to the nanotubular architecture. To our surprise, the proliferation rates of cells cultured on anatase nanotube layers increased with increasing tube diameter from 20 to 120 nm, which may be attributed to different length and nanometer‐scale roughness of the nanotube layers. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010
Fiber diameters control osteoblastic cell migration and differentiation in electrospun gelatin
Authors: Sisson Kristin , Zhang Chu , Farach‐Carson Mary C. , Chase D. Bruce , Rabolt John F.
Published: May 2010

Defined electrospinning conditions were used to create scaffolds with different fiber diameters to investigate their interactions with osteoblastic MG63 cells. Nonwoven gelatin scaffolds were electrospun with varied fiber diameters to investigate the effect of fiber size and resultant porosity on cell proliferation, viability, migration, and differentiation. The low toxicity solvent acetic acid:ethyl acetate:water ratio and gelatin concentrations were optimized to create small and large diameter fibers. The fiber diameters obtained by this procedure were 110 ± 40 nm for the small and 600 ± 110 nm for the large fibers. Cell viability assays showed that MG63 cells grew similarly on both fibers at the early time point (day 3) but preferred the scaffold with large diameter fibers by the later time points (day 5 and day 7). Confocal microscopic imaging showed that MG63 cells migrated poorly (maximum depth of 18 μm) into the scaffold of small diameter fibers, but readily penetrated (maximum depth of 50 μm) into the scaffold of large diameter fibers. Alkaline phosphatase (ALP) assays showed that MG63 cells differentiated on scaffolds made from both diameter fibers. In longer term experiments, MG63 cells differentiated to a greater extent on scaffolds made from small diameter fibers compared to large diameter fibers at days 3 and 7, but the ALP levels were the same for both diameter fibers by day 14. These results indicate that cells can perceive differences in the diameter and resultant pore size of electrospun gelatin fibers and that they process this information to alter their behavior. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010
Ab Initio and Quantum Chemical Topology studies on the isomerization of HONO to HNO2. Effect of the basis set in QCT
Authors: Berski Slawomir , Latajka Zdzislaw , Gordon Agnieszka J.
Published: May 2010

The article focus on the isomerization of nitrous acid HONO to hydrogen nitryl HNO2. Density functional (B3LYP) and MP2 methods, and a wide variety of basis sets, have been chosen to investigate the mechanism of this reaction. The results clearly show that there are two possible paths: 1) Uncatalysed isomerisation, trans‐HONO → HNO2, involving 1,2‐hydrogen shift and characterized by a large energetic barrier 49.7 ÷ 58.9 kcal/mol, 2) Catalysed double hydrogen transfer process, trans‐HONO + cis‐HONO → HNO2 + cis‐HONO, which displays a significantly lower energetic barrier in a range of 11.6 ÷ 18.9 kcal/mol. Topological analysis of the Electron Localization Function (ELF) shows that the hydrogen transfer for both studied reactions takes place through the formation of a ‘dressed’ proton along the reaction path.1 Use of a wide variety of basis sets demonstrates a clear basis set dependence on the ELF topology of HNO2. Less saturated basis sets yield two lone pair basins, V1(N), V2(N), whereas more saturated ones (for example aug‐cc‐pVTZ and aug‐cc‐pVQZ) do not indicate a lone pair on the nitrogen atom. Topological analysis of the Electron Localizability Indication (ELI‐D) at the CASSCF (12,10) confirms these findings, showing the existence of the lone pair basins but with decreasing populations as the basis set becomes more saturated (0.35e for the cc‐pVDZ basis set to 0.06e for the aug‐cc‐pVTZ). This confirms that the choice of basis set not only can influence the value of the electron population at the particular atom, but can also lead to different ELF topology. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Simulaid: A simulation facilitator and analysis program
Authors: Mezei Mihaly
Published: May 2010

Simulaid performs a large number of simulation‐related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB (Berman et al., Nucleic Acids Res 2000, 28, 235), Charmm (Brooks et al., J Comput Chem 4, 187) CRD, Amber (Case et al.), Macromodel (Mohamadi et al., J Comput Chem 1990, 11, 440), Gromos/Gromacs (Hess et al.), InsightII (InsightII. Accelrys Inc.: San Diego, 2005), Grasp (Nicholls et al., Proteins: Struct Funct Genet 1991, 11, 281) .crg, Tripos (Tripos International, S. H. R., St. Louis, MO) .mol2 (input only), and in the MMC (Mezei, M.; MMC: Monte Carlo program for molecular assemblies. Available at: http://inka.mssm.edu/∼mezei/mmc) formats; and trajectories in the formats of Charmm, Amber, Macromodel, and MMC. Analysis features include (but are not limited to): (1) simple distance calculations and hydrogen‐bond analysis, (2) calculation of 2‐D RMSD maps (produced both as text file with the data and as a color‐coded matrix) and cross RMSD maps between trajectories, (3) clustering based on RMSD maps, (4) analysis of torsion angles, Ramachandran (Ramachandran and Sasiskharan, Adv Protein Chem 1968, 23, 283) angles, proline kink (Visiers et al., Protein Eng 2000, 13, 603) angles, pseudorotational (Altona and Sundaralingam, J Am Chem Soc 1972, 94, 8205; Cremer and Pople, J Am Chem Soc 1975, 97, 1354) angles, and (5) analysis based on circular variance (Mezei, J Mol Graphics Model 2003, 21, 463). Torsion angle evolutions are presented in dial plots (Ravishanker et al., J Biomol Struct Dyn 1989, 6, 669). Several of these features are unique to Simulaid. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Association of circulating insulin‐like growth factor 1 with hepatocellular carcinoma: one cross‐sectional correlation study
Authors: Su Wei‐Wen , Lee King‐Teh , Yeh Yao‐Tsung , Soon Maw‐Soan , Wang Chao‐Ling , Yu Ming‐Lung , Wang Shen‐Nien
Published: May 2010

Deregulation of insulin‐like growth factor‐1 (IGF‐1) has been implicated in the pathogenesis of several malignancies. This study aimed to investigate the association of changes in circulating IGF‐1 with hepatocellular carcinoma (HCC). The radioimmunoassay was used to analyze serum IGF‐1 levels of 65 HCC patients and 165 healthy subjects. Serum IGF‐1 levels were significantly decreased in the HCC patients as compared with the healthy subjects (158.46±105.07 vs. 247.63±149.96 ng/mL, P<0.001). Furthermore, insulin resistance was significantly higher in the HCC patients than the healthy subjects (P=0.027). In addition, the significant correlations of serum IGF‐1 levels with age and insulin resistance in the healthy subjects were not noted in the HCC patients. Intriguingly, individuals with hepatitis C virus (HCV), not hepatitis B virus, had remarkably decreased IGF‐1 levels in both groups of the HCC patients and healthy subjects. Moreover, in the HCV subgroup, serum IGF‐1 levels were significantly reduced in the HCC patients than the healthy subjects (113.14±71.28 vs. 172.42±74.02 ng/mL, P=0.003). In conclusion, decreased serum IGF‐1 levels were associated with HCC and the decrease was remarkably noted in those patients concomitant with chronic hepatitis C. J. Clin. Lab. Anal. 24:195–200, 2010. © 2009 Wiley‐Liss, Inc.
Stability of hepatitis C virus RNA in blood samples by TaqMan real‐time PCR
Authors: Sener Kenan , Yapar Mehmet , Bedir Orhan , Gül Cem , Coskun Ömer , Kubar Ayhan
Published: May 2010

The storage conditions of blood samples for reliable results are very important in hepatitis C virus (HCV) RNA amplification tests used in routine HCV analyses. According to many studies, storage conditions could affect the RNA stability for HCV RNA detection. We have studied HCV RNA stability in blood samples stored at 4°C. Nineteen blood samples containing different HCV RNA levels were stored at 4°C and they were then analyzed by TaqMAN real‐time PCR method. HCV RNA levels remained almost stable (100%) at least for five weeks at this storage condition. However, among them, the stability period was up to 11 weeks in two of the samples. As with these findings, there was a slightly significant correlation between the positivity time and the beginning HCV RNA levels (r=0.474,P=0.040). We conclude that, blood samples can be stored at 4°C for five weeks without any significant difference in detected HCV RNA level by using TaqMan real‐time PCR. J. Clin. Lab. Anal. 24:134–138, 2010. © 2010 Wiley‐Liss, Inc.
Candida dubliniensis screening using the germ tube test in clinical yeast isolates and prevalence of C. dubliniensis in Korea
Authors: Kim Tae‐Hyoung , Park Bo‐Rae G. , Kim Hye Ryoun , Lee Mi‐Kyung
Published: May 2010

The aim of this study was to screen for C. dubliniensis using the germ tube test with human pooled serum (HPS) in clinical isolates and investigate the prevalence of C. dubliniensis in Korea. Among 1,854 yeast strains isolated, 1,404 strains of C. albicans (on the basis of positive results of the germ tube test) and 192 germ tube‐negative yeast strains were examined. All 1,596 clinical isolates were examined using the germ tube test with HPS, the differential temperature, and NaCl tolerance test. Only 81 isolates that did not grow at 45°C nor on Sabouraud 6.5% NaCl broth were selected and tested using the VITEK 2 ID‐YSTsystem and the multiplex‐PCR assay for the study. The two strains, C. dubliniensis ATCC MYA‐646 and KCTC 17427 failed to produce germ tubes in HPS but produced them in fresh rabbit serum (FRS) and fetal bovine serum (FBS). No C. dubliniensis was found in this study population. The results of this study suggest that the germ tube test with HPS in combination with FRS or FBS can be used for discriminating between C. albicans and C. dubliniensis strains and that the prevalence of C. dubliniensis appears to be extremely low in Korea. J. Clin. Lab. Anal. 24:145–148, 2010. © 2010 Wiley‐Liss, Inc.
Interleukin (IL)‐1β, IL‐1 receptor antagonist, IL‐6, IL‐8, IL‐10, and tumor necrosis factor α gene polymorphisms in patients with febrile seizures
Authors: Chou I‐Ching , Lin Wei‐De , Wang Chung‐Hsing , Tsai Chang‐Hai , Li Tsai‐Chung , Tsai Fuu‐Jen
Published: May 2010

Inflammation and genetics may play a role in the pathogenesis of febrile seizures (FSs). We aimed to test whether interleukin‐1β (IL‐1β), IL‐1 receptor antagonist (IL‐1 Ra), IL‐6 promoter, IL‐8, IL‐10, or tumor necrosis factor (TNF) gene polymorphisms could be used as markers of susceptibility to FSs. An association study was performed among a cohort of 104 patients with FSs and 143 normal control subjects. There was no significant difference between patients and controls in the distribution of allele frequencies of the IL‐1β promoter, IL‐1β exon 5, IL‐6 promoter, IL‐8, IL‐10, or TNF‐α gene polymorphisms. In contrast, the IL‐1 Ra‐I homozygote was more frequent in patients with FSs than in healthy controls (93.2% vs. 83.92%, χ2=4.51,P=0.034). In addition, individuals homozygous for the IL‐1 Ra‐I genotype were more than twice as likely to develop FSs than individuals heterozygous for the IL‐1 Ra‐I/II genotype (OR, 2.63, 95% CI: 1.08–6.39; χ2=4.55,P=0.033). We conclude that the IL‐1 Ra gene might be one of the useful markers for predicting susceptibility to FSs. J. Clin. Lab. Anal. 24:154–159, 2010. © 2010 Wiley‐Liss, Inc.
Neonatal screening for mucopolysaccharidoses by determination of glycosaminoglycans in the eluate of urine‐impregnated paper: preliminary results of an improved DMB‐based procedure
Authors: Alonso‐Fernández J.R. , Fidalgo J. , Colón C.
Published: May 2010

Background: The fact that mucopolysaccharidoses (MPSes) are now treatable, and that the earlier treatment is initiated the better, is an indication for neonatal screening. The most efficient approach seems likely to be a multi‐tier procedure in which screening for urinary glycosaminoglycan (GAG) is followed by enzyme determinations in heelprick blood of newborns screening positive. Hitherto the method of choice for the determination of GAG has been the measurement of absorbance by a complex of GAG and 1,9‐dimethylmethylene blue (DMB). Method: We evaluated a DMB method in which absorbance by DMB is measured following its addition to the eluate obtained from paper‐borne newborn urine samples and is normalized relative to urinary creatinine. Calibration is performed with chondroitin‐6‐sulfate (Ch‐6‐S). Results: The limits of detection and quantification of GAG were 1.98 and 5.94 mg/dl, respectively. The within‐run coefficients of variation (CVs) of the GAG/creatinine ratio for 25, 31, and 70 mg/dl solutions of Ch‐6‐S in urine were 21.8, 16.4, and 10.5%, respectively, and the corresponding between‐run CVs were 25.0, 13.5, and 10.1%. Recovery from the urine spiked with 31 mg Ch‐6‐S/dl was 94.8%. Accuracy was also acceptable for all other GAGs except hyaluronic acid. For neonatal screening, the diagnostic threshold was tentatively established as 800 mg GAG/g creatinine, the 95th centile of samples from 903 infants aged 3–28 days, but the value of the GAG/creatinine ratio was negatively correlated with age. Application of the new method to samples from older individuals with and without MPS achieved 100% sensitivity and specificity when used with an age‐dependent threshold taken from the literature on the original DMB method. Conclusion: If used in the first tier of a multi‐tier screening protocol, the proposed method would allow the detection of abnormal levels of all GAGs except hyaluronic acid. J. Clin. Lab. Anal. 24:149–153, 2010. © 2010 Wiley‐Liss, Inc.
Plasma osteopontin as a predictor of coronary artery disease: association with echocardiographic characteristics of atherosclerosis
Authors: Abdel‐Azeez Hala Abdel‐Hameed , Al‐Zaky Manar
Published: May 2010

Osteopontin (OPN), a bone‐related protein, is present within the atherosclerotic plaques, most strikingly in calcified plaques. Valvular calcifications are accepted as a part of the spectrum of atherosclerosis and are associated with atherosclerotic calcification in the coronary arteries. The study aimed to evaluate the association of plasma OPN with the presence and extent of coronary stenosis, mitral annular calcification (MAC), and aortic valve sclerosis in stable angina patients. We studied 120 subjects who underwent coronary angiography because of ischemic chest pain. Coronary artery disease (CAD) was defined as ≥50% stenosis in ≥1 coronary artery. MAC and aortic valve sclerosis were detected by echocardiography. Lipid profile, high sensitive C‐reactiveprotein (hsCRP), and OPN were measured in all studied subjects. Patients with CAD had increased plasma OPN when compared with those without CAD (P<0.001). Plasma OPN levels were significantly positively correlated with atherogenic lipid profile, hsCRP, MAC grading, aortic valve sclerosis grading, and the number of stenosed coronary vessels in CAD patients. In multivariate analysis, OPN was an independent predictor of CAD (P=0.01), MAC (P=0.01), and aortic valve sclerosis (P=0.04). In conclusion, OPN is an independent predictor of MAC and aortic valve sclerosis. Plasma OPN levels reflect the extent of coronary stenosis and can be used as a biomarker to identify patients with coronary atherosclerosis. J. Clin. Lab. Anal. 24:201–206, 2010. © 2010 Wiley‐Liss, Inc.
A comparison of Brucella IgG and IgM ELISA assays with agglutination methodology
Authors: Welch Ryan J. , Litwin Christine M.
Published: May 2010

Despite brucellosis having a low incidence rate in developed nations, it still remains the leading zoonotic disease in the world. Culturing of Brucella spp. provides good specificity but in cases where the fever is intermittent, sensitivity is problematic. This has led to the development of serological methods of detection. Brucella agglutination methods have been considered the serological gold‐standard since their inception, although commercial Brucella IgG and IgM enzyme‐linked immunosorbentassays are available to potentially aid in the diagnosis of the disease. In our study, anti‐Brucella IgG and IgM assays were compared with agglutination. Individually the IgG assay tested had an accuracy of 56% and the IgM assay had an accuracy of 77%. These poor accuracies reinforce Centers for Disease Control's conclusion that nonagglutination tests should not be used to confirm brucellosis. J. Clin. Lab. Anal. 24:160–162, 2010. © 2010 Wiley‐Liss, Inc.
Coagulopathy parameters in patients with Crimean‐Congo hemorrhagic fever and its relation with mortality
Authors: Onguru P. , Dagdas S. , Bodur H. , Yilmaz M. , Akinci E. , Eren S. , Ozet G.
Published: May 2010

Background: Crimean‐Congo hemorrhagic fever (CCHF) is an acute illness affecting multiple organ systems and characterized by ecchymosis, visceral bleeding, and hepatic dysfunction. In this study, we aimed to investigate the profile of coagulopathy markers (platelet count, activated partial tromboplastin time (aPTT), prothrombin time (PT), international normalized ratio (INR), fibrinogen, protein C, protein S, antithrombin III, activated protein C resistance (APCR), and D‐dimer) and their clinical significance in 83 CCHF‐infected patients.Subjects and methods: We studied 83 CCHF patients who were admitted to Ankara Numune Education and Research Hospital during the spring and summer of2007. We compared the coagulopathy markers of fatal CCHF patients (n=9) with nonfatal cases (n=74).Results: Platelet count, PT, aPTT, INR, and fibrinogen were prognostic factors associated with mortality for CCHF. Especially, platelet count<20×109 cells/l and aPTT>60 sec were important. Protein C, protein S, APCR, and antithrombin III levels were not associated with mortality.Conclusion: Laboratory tests including classical parameters (platelet count, PT, aPTT, INR, and fibrinogen) of coagulopathy seem to be enough for the followup of CCHF. Protein S, protein C, APCR, and D‐dimer levels were not associated with mortality. J. Clin. Lab. Anal. 24:163–166, 2010. © 2010 Wiley‐Liss, Inc.
The usefulness of multiplex PCR for the identification of bacteria in joint infection
Authors: Kim Hwanjung , Kim Jimyung , Ihm Chunhwa
Published: May 2010

Background: The diagnosis of septic arthritis (SA) relies on synovial analysis and conventional culture. But, these methods lack of sensitivity and culture is time consuming to establish a definite diagnosis. This study evaluated a new multiplex PCR assay which entailed screening PCR for Gram typing and identification PCR for species identification using two primer mixes. Methods: A total of 80 synovial fluid samples from patients with suspected SA were collected. Culture, multiplex PCR, and 16S rRNA gene PCR were performed. Results: The analytical sensitivity of multiplex PCR assay was 101 CFU/ml for each type of bacteria. There was no cross‐reactivity with common bacterial pathogens. Bacteria were detected in 20, 25, and 26 of 80 samples for culture, multiplex PCR, and 16S rRNA gene PCR, respectively. Nineteen (95%) of 20 culture‐positivesamples and 6 (10%) of 60 culture‐negative samples were positive for the multiplex PCR. Five of six samples which were positive only from multiplex PCR were also positive in 16S rRNA gene PCR. The multiplex PCR showed 2 false‐negative in 27 true‐positive samples but no false‐positive. The sensitivity and specificity of the multiplex PCR were 92.6 and 100%, and the agreement with culture and 16S rRNA gene PCR were 91.3 and 96.3%, respectively. The time to detection for multiplex PCR was a maximum of 6 hr. Conclusion: This multiplex PCR assay offers high sensitivity and improved detection speed relative to culture. The appropriate combination of this new multiplex PCR assay with culture may contribute to the accurate and rapid diagnosis of SA. J. Clin. Lab. Anal. 24:175–181, 2010. © 2010 Wiley‐Liss, Inc.
Evaluation of the alkaline wash/lysis procedure for the molecular diagnosis of a positive bacterial blood culture in clinical routine practice
Authors: Hsi Sheng‐Chuan , Sun Jun‐Ren , Chiueh Tzong‐Shi
Published: May 2010

Blood culture is commonly used to detect microorganisms in patients with a suspected blood infection. This study evaluated the alkaline wash/lysis procedure to extract DNA of microorganisms in a clinical blood culture. A multiplex polymerase chain reaction (PCR) targeting the 16S rDNA (ribosomal DNA) gene and the fungal ITS (internal transcribed spacer) gene was used as a reliable indicator for the presence of microorganism DNA in the extracts. A total of 535BacT/ALERT positive blood culture bottles were evaluated. Multiplex PCR showed positive results in 530 DNA extracts, but 5 DNA extracts gave negative results. We conclude that the alkaline wash/lysis procedure in combination with the multiplex PCR is a simple and sensitive method, which can be used in a standard diagnostic laboratory to detect microorganisms in blood culture material. J. Clin. Lab. Anal. 24:139–144, 2010. © 2010 Wiley‐Liss, Inc.
Automatic evaluation of nickel alloy secondary phases from SEM images
Authors: de Albuquerque Victor Hugo C. , Silva Cleiton Carvalho , Menezes Thiago Ivo de S. , Farias Jesualdo Pereira , Tavares João Manuel R. S.
Published: May 2010

Quantitative metallography is a technique to determine and correlate the microstructures of materials with their properties and behavior. Generic commercial image processing and analysis software packages have been used to quantify material phases from metallographic images. However, these all‐purpose solutions also have some drawbacks, particularly when applied to segmentation of material phases. To overcome such limitations, this work presents a new solution to automatically segment and quantify material phases from SEM metallographic images. The solution is based on a neuronal network and in this work was used to identify the secondary phase precipitated in the gamma matrix of a Nickel base alloy. The results obtained by the new solution were validated by visual inspection and compared with the ones obtained by a commonly used commercial software. The conclusion is that the new solution is precise, reliable and more accurate and faster than the commercial software. Microsc. Res. Tech. 74:36‐46, 2011. © 2010 Wiley‐Liss, Inc.
Texture analysis of TEM micrographs of alginate gels for cell microencapsulation
Authors: Brun Francesco , Accardo Agostino , Marchini Maurizio , Ortolani Fulvia , Turco Gianluca , Paoletti Sergio
Published: May 2010

In this work, the morphological characteristics of a calcium alginate gel and a binary (gel) mixture composed of (calcium) alginate and lactose‐modified chitosan (chitlac) are evaluated and compared to quantify the differences between the two three‐dimensional (3D) structures. A set of textural descriptors based on histogram analysis as well as on gray level co‐occurrence matrix and on fractal dimension is extracted from transmission electron microscopy micrographs to describe the morphological differences that the images present. The obtained results reveal significant quantitative morphological differences between the calcium alginate gel and the binary gel mixture that were already inferred from rheological experiments, so as to provide a structural basis for developing new encapsulation systems based on such mixed polymer gels. Microsc. Res. Tech. 74:58‐66, 2011. © 2010 Wiley‐Liss, Inc.
10th international symposium on the synthesis and applications of isotopes and isotopically labelled compounds—applications of isotopes in pharmaceutical research and development, Session 7, Tuesday, June 16, 2009
Authors: Lavey Carolee , Hesk David
Published: May 2010

The use of a Na125I‐Iodo‐Gen system for the labelling of oxidation sensitive peptides was discussed. The question was posed as to whether the concern about reactive metabolites was warranted. In addition, the use of tritium labelling in the evaluation of a potential new nucleoside analog was discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Selectively weakened binding of methotrexate by human dihydrofolate reductase allows rapid ex vivo selection of mammalian cells
Authors: Volpato Jordan P. , Mayotte Nadine , Fossati Elena , Guerrero Vanessa , Sauvageau Guy , Pelletier Joelle N.
Published: May 2010

Ex vivo selection of transduced hematopoietic stem cells (HSC) with drug‐resistance genes offers the possibility to enrich transduced cells prior to engraftment, toward increased reconstitution in transplant recipients. We evaluated the potential of highly methotrexate (MTX)‐resistant variants of human dihydrofolate reductase (hDHFR) for this application. Two subsets of hDHFR variants with reduced affinity for MTX that had been previously identified in a bacterial system were considered: those with substitutions at positions 31, 34, and/or 35, and those with substitutions at position 115. The variants were characterized for their resistance to pemetrexed (PMTX), an antifolate that is related to MTX. We observed a strong correlation between decreased binding to both antifolates, although the identity of specific sequence variations modulated the correlation. We chose a subset of hDHFR variants for tests of ex vivo MTX resistance, taking into consideration their residual specific activity and their decrease in affinity for the related antifolates. Murine myeloid progenitors and other differentiated hematopoietic cells were transduced and exposed to MTX in a nucleotide‐free medium. Bone marrow (BM) cells including 15% cells infected with F31R/Q35E were enriched to 98% transduced cells within 6 days of ex vivo selection. hDHFR variant F31R/Q35E allowed a strong ex vivo enrichment upon a short exposure to MTX relative to a less resistant variant of hDHFR, L22Y. We have thus demonstrated that bacterial selection of highly antifolate‐resistant hDHFR variants can provide selectable markers for rapid ex vivo enrichment of hematopoietic cells. Copyright © 2010 John Wiley & Sons, Ltd.
Predicting and monitoring cancer treatment response with diffusion‐weighted MRI
Authors: Thoeny Harriet C. , Ross Brian D.
Published: May 2010

An imaging biomarker that would provide for an early quantitative metric of clinical treatment response in cancer patients would provide for a paradigm shift in cancer care. Currently, nonimage based clinical outcome metrics include morphology, clinical, and laboratory parameters, however, these are obtained relatively late following treatment. Diffusion‐weighted MRI (DW‐MRI) holds promise for use as a cancer treatment response biomarker as it is sensitive to macromolecular and microstructural changes which can occur at the cellular level earlier than anatomical changes during therapy. Studies have shown that successful treatment of many tumor types can be detected using DW‐MRI as an early increase in the apparent diffusion coefficient (ADC) values. Additionally, low pretreatment ADC values of various tumors are often predictive of better outcome. These capabilities, once validated, could provide for an important opportunity to individualize therapy thereby minimizing unnecessary systemic toxicity associated with ineffective therapies with the additional advantage of improving overall patient health care and associated costs. In this report, we provide a brief technical overview of DW‐MRI acquisition protocols, quantitative image analysis approaches and review studies which have implemented DW‐MRI for the purpose of early prediction of cancer treatment response. J. Magn. Reson. Imaging 2010. © 2010 Wiley‐Liss, Inc.
An APCI LC‐MS/MS method for routine determination of capecitabine and its metabolites in human plasma
Authors: Montange Damien , Bérard Michel , Demarchi Martin , Muret Patrice , Piédoux Sarah , Kantelip Jean Pierre , Royer Bernard
Published: May 2010

The anticancer drug capecitabine and its metabolites [including the active metabolite 5‐fluorouracil (5‐FU)] display high pharmacokinetic inter‐patient variability. Such variability, which may lead to treatment failure or toxicity, could need drug concentration measurement to individualize dosing regimen. However, usual assay methods are often long and fastidious. A simultaneous and cost‐effective method was thus developed for the determination of the concentrations of these compounds in human plasma. Compounds were extracted via a classic liquid–liquid extraction. Chromatographic analysis was performed on a C18 reverse phase column with detection by atmosphere pressure chemical ionization LC‐MS/MS. Our method allows a good chromatographic separation of the compounds and was fully validated following Food and Drug Administration (FDA) recommendations (good selectivity, no carry‐over, linearity of the calibration curves without weighting, deviations from nominal concentrations of standard samples lower than 15%, intra‐ and inter‐assay precision and accuracy lower than 15%). Recovery and stability were also acceptable following the FDA guidelines. A matrix effect impairing the determination of 5‐FU was avoided by using a stable isotopic derivative of 5‐FU as internal standard. Interestingly, this method allows detection of TetraHydroUridine, an inhibitor of ex vivo degradation of metabolites, which is essential for the stability, the adequate conditioning of blood samples and for good laboratory practice, essential in routine determination. This method seems usable to routinely determine concentrations of capecitabine and its metabolites in blood and may be helpful in further studies aiming at performing therapeutic drug monitoring. Copyright © 2010 John Wiley & Sons, Ltd.
Modeling of cylindrical resonators by wave concept iterative process in cylindrical coordinates
Authors: Houaneb Z. , Zairi H. , Gharsallah A. , Baudrand H.
Published: May 2010

The purpose of this study is the formulation of a wave concept iterative process for the analysis of the microwave planar circuits printed between two dielectric mediums in a cylindrical metallic box. This method is based on the transverse wave formulation. It also uses the Hankel Transform to express the integral relation in a spectral domain. An example of circular patch has been studied and the obtained results validate the new approach. The good agreement between the simulation results and the experimental published data justifies the design procedure and validates the present analysis approach. Copyright © 2010 John Wiley & Sons, Ltd.
Physiological studies on endorhizospheric establishment of Azotobacter chroococcum in wheat
Authors: Thekkiniath Jose , Paul Sangeeta , Dureja Prem , Dhar Dolly Wattal
Published: May 2010

Ten strains of Azotobacter chroococcum were studied for their ability to invade the endorhizosphere of wheat. Strain W‐5 exhibited ability to invade endorhizosphere as shown in the microscopic observations. This strain was compared with the strain OA‐3 which did not invade the endorhizosphere zone. Strain W‐5 showed higher production of cellulase and pectinase than OA‐3. Both the strains induced defense enzymes in the host plant. However, induction of peroxidase and phenylalanine ammonia lyase activities (PAL) was higher in OA‐3 than W‐5. Quantitative differences in flavonoid like compounds obtained from root extracts and root exudates of plants inoculated with these strains were observed. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of pfkA chromosomal interruption on growth, sporulation, and production of organic acids in Bacillus subtilis
Authors: Muñoz‐Márquez María‐Enriqueta , Ponce‐Rivas Elizabeth
Published: May 2010

Phosphofructokinase (Pfk) plays a key role in the regulation of carbohydrate metabolism. Its activity can be used as an indicator of glycolytic flux in a microorganism. We have cloned and characterized the pfkA gene from Bacillus subtilis, which encodes the enzyme phosphofructokinase. This gene was insertionally inactivated at the chromosomal level in a wild type strain and in strains lacking the PEP:sugar phosphotranferase system (PTS). Although the pykA gene is immediately downstream of the pfkA gene, forming a constitutive operon in B. subtilis, the pyruvate kinase activity was not altered in the pfkA mutant. The inactivation of the pfkA gene had a strong impact on the growth of the B. subtilis wild type strain and PTS mutants in Spizizen's minimal media and Schaeffer's sporulation media. Pfk inactivation was also reflected by the timing and percentage of sporulation of the wild type and PTS mutants in sporulation media as well as in the production of organic by‐products (pyruvate, lactate, and acetate). (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ultrastructure of Aphanomyces cochlioides zoospores and changes during their developmental transitions triggered by the host‐specific flavone cochliophilin A
Authors: Tofazzal Islam M.
Published: May 2010

Aphanomyces cochlioides is a serious damping‐off causing pathogen of sugar beet, spinach and some other members of Chenopodiaceae and Amaranthaceae. The biflagellated motile zoospores of the pathogen locate their host roots by perceiving the host‐specific flavone cochliophilin A (5‐hydroxy‐6,7‐methylenedioxyflavone), transiently modify into cystospores that germinate prior to penetration. This study for the first time illustrated ultrastructure of the zoospores and morphological modification during their developmental transitions triggered by cochliophilin A using transmission electron microscopy (TEM). TEM revealed that zoospores had two heterokont flagella inserted laterally into a ventral groove of their body where each is attached to a kinetosome. In the cross sections of flagellar axonemes, two single and nine peripheral microtubules in doublets were clearly observed. Mitochondria, the Golgi complexes, finger print vesicles, and vesicles with striated electron opaque inclusion and vesicles containing a granular cortex and center were also detected. The latter vesicles disappeared and two flagella were shed when zoospores converted to spherical cystsopores. The shape, size and number of mitochondria were dynamically changed during the encystment of zoospores presumably through fission and fusion processes. The dynamics of mitochondria observed in this study indicated its distinct role in the signal transduction pathway of the zoospore encystment. This study also revealed the transformation of shape of nuclei from pyriform in zoospores to spherical in cystospores and lanceolate in the hyphae. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Diversity of Frankia strains nodulating HippÖphae salicifolia D. Don using FAME profiling as Chemotaxonomic markers
Authors: Mishra Arun Kumar , Singh Anju , Singh Satya Shila
Published: May 2010

Twelve Frankia strains isolated from HippÖphae salicifolia D. Don or Alnus glutinosa or Comptonia peregrine, showed the significant variation in fatty acid composition viz. palmitic acid (16:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), arachidic acid (20:0) and erucic acid (22:1) suggesting the strain specific variability among the Frankia strains. Presence of Erucic acid (22:1), a major component of the oil obtained from the seeds of Brassica sp., albeit in lesser amount in the few studied frankial strains, is the first report. Cluster analysis on the basis of fatty acid composition suggests the presence of two distinct clusters with similitude coefficient ranging from 0.75 to 1.00. Cluster I with HsIi2 showed great divergence from other 11 frankial strains (Cluster II). The two sub groups were distinguished in cluster II: IIa contained five strains isolated from H. salicifolia and these strains are distantly related to the strains of cluster IIb isolated from different host. There is high degree of similarity among the frankial strains of Cluster IIb which suggests that the frankial strains might be evolved from the same ancestor. FAME profiling might be useful tool in the study of polyphasic approach based taxonomy and phylogenetic relationship. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Novel linear megaplasmid from Brevibacterium sp. isolated from extreme environment
Authors: Dib Julián Rafael , Wagenknecht Martin , Hill Russell T. , Farías María Eugenia , Meinhardt Friedhelm
Published: May 2010

Brevibacterium sp. Ap13, isolated from flamingo's feces in Laguna Aparejos, a high‐altitude lake located at approximately 4,200 m in the northwest of Argentina was previously found to be resistant to multiple antibiotics, and was therefore screened for plasmids that may be implicated in antibiotic resistance. Brevibacterium sp. Ap13 was found to contain two plasmids of approximately 87 and 436 kb, designated pAP13 and pAP13c, respectively. Only pAP13 was stably maintained and was extensively characterized by pulsed‐field gel electrophoresis to reveal that this plasmid is linear and likely has covalently linked terminal proteins associated with its 5′ ends. This is the first report of a linear plasmid in the genus Brevibacterium and may provide a new tool for genetic manipulation of this commercially important genus. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Production of laccase from Pleurotus florida NCIM 1243 using Plackett–Burman Design and Response Surface Methodology
Authors: Palvannan T. , Sathishkumar P.
Published: May 2010

Statistically‐based experimental designs were applied to optimize the fermentation for the production of laccase by Pleurotus florida NCIM 1243. Eleven components were screened for their significant effect on laccase production using Plackett–Burman factorial design. Glucose (carbon source), asparagine (nitrogen source), CuSO4(inducer) and incubation period were found to have highest positive influence on the laccase production. The combined effect of these factors on laccase production was studied using central composite design of Response surface methodology. The optimal point of variables for maximum laccase production using Response surface methodology are glucose (15.21 g/l), asparagine (6.40 g/l), CuSO4 (91.78 μM) and incubation period (178.55 h), respectively. The maximum enzyme activity predicted by the model was 5.0 U/ml which was in perfect agreement with the actual experimental value (4.8 U/ml). Further, partially purified laccase from the optimized cultural condition was used for the decolorization of reactive dyes, Reactive Blue 198 and Reactive Red 35. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Morphological and genetic diversity of symbiotic cyanobacteria from cycads
Authors: Thajuddin Nooruddin , Muralitharan Gangatharan , Sundaramoorthy Mariappan , Ramamoorthy Rengasamy , Ramachandran Srinivasan , Akbarsha Mohamed Abdulkadar , Gunasekaran Muthukumaran
Published: May 2010

The morphological and genetic diversity of cyanobacteria associated with cycads was examined using PCR amplification techniques and 16S rRNA gene sequence analysis. Eighteen symbiotic cyanobacteria were isolated from different cycad species. One of the symbiotic isolates was a species of Calothrix, a genus not previously reported to form symbioses with Cycadaceae family, and the remainder were Nostoc spp. Axenic cyanobacterial strains were compared by DNA amplification using PCR with either short arbitrary primers or primers specific for the repetitive sequences. Based on fingerprint patterns and phenograms, it was revealed that cyanobacterial symbionts exhibit important genetic diversity among host plants, both within and between cycad populations. A phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that most of the symbiotic cyanobacterial isolates fell into well‐separated clades. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)