bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of the mitochondrial targeting sequence and mechanism in human citrate synthase
Authors: Cheng Tsung‐Lin , Liao Ching‐Chun , Tsai Wen‐Hui , Lin Chin‐Chih , Yeh Chin‐Wei , Teng Chiao‐Fang , Chang Wen‐Tsan 
Published: May 2009

AbstractCitrate synthase (CS), the first and rate‐limiting enzyme of the tricarboxylic acid (TCA) cycle, plays a decisive role in regulating energy generation of mitochondrial respiration. Most mitochondrial proteins are synthesized in the cytoplasm as preproteins with an amino (N)‐terminal mitochondrial targeting sequence (MTS) that directs mitochondria‐specific sorting of the preprotein. However, the MTS and targeting mechanism of the human CS protein are not fully characterized. The human CS gene is a single nuclear gene which transcribes into two mRNA variants, isoform a (CSa) and b (CSb), by alternative splicing of exon 2. CSa encodes 466 amino acids, including a putative N‐terminal MTS, while CSb expresses 400 residues with a shorter N terminus, lacking the MTS. Our results indicated that CSa is localized in the mitochondria and the N‐terminal 27 amino acids, including a well‐conserved RXY ↓ (S/A) motif (the RHAS sequence), can efficiently target the enhanced green fluorescent protein (EGFP) into the mitochondria. Furthermore, site‐directed mutagenesis analysis of the conserved basic amino acids and serine/threonine residues revealed that the R9 residue is essential but all serine/threonine residues are dispensable in the mitochondrial targeting function. Moreover, RNA interference (RNAi)‐mediated gene silencing of the preprotein import receptors, including TOM20, TOM22, and TOM70, showed that all three preprotein import receptors are required for transporting CSa into the mitochondria. In conclusion, we have experimentally identified the mitochondrial targeting sequence of human CSa and elucidated its targeting mechanism. These results provide an important basis for the study of mitochondrial dysfunction due to aberrant CSa trafficking. J. Cell. Biochem. 107: 1002–1015, 2009. © 2009 Wiley‐Liss, Inc.
Interferon‐γ suppresses Na+–H+exchanger in cultured human endolymphatic sac epithelial cells
Authors: Son Eun Jin , Moon In Seok , Kim Sung Huhn , Kim Su Jin , Choi Jae Young 
Published: May 2009

AbstractAdequate regulation of endolymphatic pH is essential for maintaining inner ear function. The Na+–H+exchanger (NHE) is a major determinant of intracellular pH (pHi), and facilitates Na+and fluid absorption in various epithelia. We determined the functional and molecular expression of NHEs in cultured human endolymphatic sac (ES) epithelial cells and examined the effect of IFN‐γ on NHE function. Serial cultures of human ES epithelial cells were generated from tissue samples. The molecular expression of NHE1, ‐2, and ‐3 isoforms was determined by real‐time RT‐PCR. The functional activity of NHE isoforms was measured microfluorometrically using a pH‐sensitive fluorescent dye, 2′,7′‐bis(carbonylethyl)‐5(6)‐carboxyfluorescein (BCECF), and a NHE‐inhibitor, 3‐methylsulfonyl‐4‐piperidinobenzoyl guanidine methanesulfonate (HOE694). NHE1, ‐2, and ‐3 mRNAs were expressed in human ES epithelial cells. Functional activity of NHE1 and ‐2 was confirmed in the luminal membrane of ES epithelial cells by sequentially suppressing Na+‐dependent pHirecovery from intracellular acidification using different concentrations of HOE694. Treatment with IFN‐γ (50 nM for 24 h) suppressed mRNA expression of NHE1 and ‐2. IFN‐γ also suppressed functional activity of both NHE1 and ‐2 in the luminal membrane of ES epithelial cells. This study shows that NHEs are expressed in cultured human ES epithelial cells and that treatment with IFN‐γ suppresses the expression and functional activity of NHE1 and ‐2. J. Cell. Biochem. 107: 965–972, 2009. © 2009 Wiley‐Liss, Inc.
Using Gaussian model to improve biological sequence comparison
Authors: Dai Qi , Liu Xiaoqing , Li Lihua , Yao Yuhua , Han Bin , Zhu Lei 
Published: May 2009

AbstractOne of the major tasks in biological sequence analysis is to compare biological sequences, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Numerous efficient methods have been developed for sequence comparison, but challenges remain. In this article, we proposed a novel method to compare biological sequences based on Gaussian model. Instead of comparing the frequencies of k‐words in biological sequences directly, we considered the k‐word frequency distribution under Gaussian model which gives the different expression levels of k‐words. The proposed method was tested by similarity search, evaluation on functionally related genes, and phylogenetic analysis. The performance of our method was further compared with alignment‐based and alignment‐free methods. The results demonstrate that Gaussian model provides more information about k‐word frequencies and improves the efficiency of sequence comparison. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal
Authors: Hu Zhongqiao , Jiang Jianwen 
Published: May 2009

AbstractDifferent biomolecular force fields (OPLS‐AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the Ca atoms of lysozymes are about 0.1 to 0.2 nm from OPLS‐AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B‐factors, whereas OPLS‐AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten‐fold slower than in bulk phase. The directional and average water diffusivities from OPLS‐AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS‐AA and AMBER03 predict larger hydrophilic solvent‐accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS‐AA for lysozyme and the Kirkwood‐Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Computational studies on electron and proton transfer in phenol‐imidazole‐base triads
Authors: Yan Shihai , Kang Sunwoo , Hayashi Tomoyuki , Mukamel Shaul , Lee Jin Yong 
Published: May 2009

AbstractThe electron and proton transfer in phenol‐imidazole‐base systems (base = NH2− or OH−) were investigated by density‐functional theory calculations. In particular, the role of bridge imidazole on the electron and proton transfer was discussed in comparison with the phenol‐base systems (base = imidazole, H2O, NH3, OH−, and NH2−). In the gas phase phenol‐imidazole‐base system, the hydrogen bonding between the phenol and the imidazole is classified as short strong hydrogen bonding, whereas that between the imidazole and the base is a conventional hydrogen bonding. The n value in spn hybridization of the oxygen and carbon atoms of the phenolic CO sigma bond was found to be closely related to the CO bond length. From the potential energy surfaces without and with zero point energy correction, it can be concluded that the separated electron and proton transfer mechanism is suitable for the gas‐phase phenol‐imidazole‐base triads, in which the low‐barrier hydrogen bond is found and the delocalized phenolic proton can move freely in the single‐well potential. For the gas‐phase oxidized systems and all of the triads in water solvent, the homogeneous proton‐coupled electron transfer mechanism prevails. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
A‐type lamins and signaling: The PI 3‐kinase/Akt pathway moves forward
Authors: Marmiroli Sandra , Bertacchini Jessika , Beretti Francesca , Cenni Vittoria , Guida Marianna , De Pol Anto , Maraldi Nadir M. , Lattanzi Giovanna 
Published: May 2009

AbstractLamin A/C is a nuclear lamina constituent mutated in a number of human inherited disorders collectively referred to as laminopathies. The occurrence and significance of lamin A/C interplay with signaling molecules is an old question, suggested by pioneer studies performed in vitro. However, this relevant question has remained substantially unanswered, until data obtained in cellular and organismal models of laminopathies have indicated two main aspects of lamin A function. The first aspect is that lamins establish functional interactions with different protein platforms, the second aspect is that lamin A/C activity and altered function may elicit different effects in different cells and tissue types and even in different districts of the same tissue. Both these observations strongly suggest that signaling mechanisms targeting lamin A/C or its binding partners may regulate such a plastic behavior. A number of very recent data show involvement of kinases, as Akt and Erk, or phosphatases, as PP1 and PP2, in lamin A‐linked cellular mechanisms. Moreover, altered activation of signaling in laminopathies and rescue of the pathological phenotype in animal models by inhibitors of signaling pathways, strongly suggest that signaling effectors related to lamin A/C may be implicated in the pathogenesis of laminopathies and may represent targets of therapeutic intervention. In face of such an open perspective of basic and applied research, we review current evidence of lamin A/C interplay with signaling molecules, with particular emphasis on the lamin A‐Akt interaction and on the biological significance of their relationship. J. Cell. Physiol. 220: 553–561, 2009. © 2009 Wiley‐Liss, Inc.
MARCKS regulates lamellipodia formation induced by IGF‐I via association with PIP2 and β‐actin at membrane microdomains
Authors: Yamaguchi Hiroki , Shiraishi Mitsuya , Fukami Kiyoko , Tanabe Atsuhiro , Ikeda‐Matsuo Yuri , Naito Yasuhito , Sasaki Yasuharu 
Published: May 2009

AbstractMyristoylated alanine‐rich C kinase substrate (MARCKS) is considered to participate in formation of F‐actin‐based lamellipodia, which represents the first stage of neurite formation. However, the mechanism of how MARCKS is involved in lamellipodia formation is not precisely unknown. Using SH‐SY5Y cells, we demonstrated here that MARCKS was translocated from cytosol to detergent‐resistant membrane microdomains, known as lipid rafts, within 30 min after insulin‐like growth factor‐I (IGF‐I) stimulation, which was accompanied by MARCKS dephosphorylation, β‐actin accumulation in lipid rafts, and lamellipodia formation. The protein kinase C inhibitor, Ro‐31‐8220, and Rho‐kinase inhibitors, HA1077 and Y27632, themselves decreased basal phosphorylation levels of MARCKS and coincidently elicited translocation of MARCKS to lipid rafts. On the other hand, the phosphoinositide 3‐kinase inhibitor, LY294002, abolished IGF‐I‐induced dephosphorylation, translocation of MARCKS to lipid rafts, and lamellipodia formation. Treatment of cells with neomycin, a PIP2‐masking reagent, attenuated the translocation of MARCKS to lipid rafts and the lamellipodia formation induced by IGF‐I, although dephosphorylation of MARCKS was not affected. Immunocytochemical and immunoprecipitation analysis indicated that IGF‐I stimulation induced the translocation of MARCKS to lipid rafts in the edge of lamellipodia and formation of the complex with PIP2. Moreover, we demonstrated that knockdown of endogenous MARCKS resulted in significant attenuation of IGF‐I‐induced β‐actin accumulation in the lipid rafts and lamellipodia formation. These results suggest a novel role for MARCKS in lamellipodia formation induced by IGF‐I via the translocation of MARCKS, association with PIP2, and accumulation of β‐actin in the membrane microdomains. J. Cell. Physiol. 220: 748–755, 2009. © 2009 Wiley‐Liss, Inc.
Characterization of calcium signaling pathways in human preadipocytes
Authors: Hu Rui , He Mu‐lan , Hu Hao , Yuan Bing‐Xiang , Zang Wei‐Jin , Lau Chu‐Pak , Tse Hung‐Fat , Li Gui‐Rong 
Published: May 2009

AbstractIntracellular free Ca2+ (Ca) is an important regulator of many cellular activities; however, Ca2+ signaling is not well studied in human preadipocytes. The purpose of the present study was to characterize Ca2+ signal pathways using a confocal scanning technique and RT‐PCR. It was found that spontaneous Ca oscillations were observed in 12.1% preadipocytes, and number of cells with Ca2+ oscillations was increased to 47.9% by 1% fetal bovine serum. Ca oscillations were dependent on Ca2+ entry mainly via stored‐operated Ca2+ (SOC) entry. They were suppressed by the SOC entry channel blocker La3+, the phospholipase C (PLC) inhibitor U73122, the inositol trisphosphate receptor (IP3R) blocker 2‐amino‐ethoxydiphenyl borate, or the sarcoplasmic/endoplasmic reticulum Ca2+ pump (SERCA) inhibitors thapsigargin and cyclopiazonic acid, but not by ryanodine. The IP3R activator thimerosal increased Ca oscillations. In addition, the plasma membrane Ca2+ pump (PMCA) inhibitor carboxyeosin and Na+–Ca2+ exchanger (NCX) inhibitor Ni2+ both suppressed Ca2+ oscillations. RT‐PCR revealed that the mRNAs for IP3R1‐3, SERCA1,2, NCX3 and PMCA1,3,4, CaV1.2, and TRPC1,4,6, STIM1 and Orai1 (for SOC entry channels) were significant in human preadipocytes. The present study demonstrates that multiple Ca2+ signal pathways are present in human preadipocytes, and provides a basis for investigating how Ca2+ signals regulate biological and physiological activities of human preadipocytes. J. Cell. Physiol. 220: 765–770, 2009. © 2009 Wiley‐Liss, Inc.
High level of laccases production by Trametes trogii culture on olive mill wastewater‐based media, application in textile dye decolorization
Authors: Chakroun Hanen , Sayadi Sami , Mechichi Tahar , Dhouib Abdelhafidh 
Published: May 2009

AbstractBACKGROUND: Laccases are receiving increasing attention as potential industrial enzymes in various applications. Therefore, it is important to find inexpensive and optimized media for large‐scale commercial production. The present work aims to valorize olive mill wastewater (OMW) by its use as base media for laccases production by Trametes trogii and use of the laccases produced for decolorizing textile dyes.RESULTS: A high yield of 25 120 U L−1 of laccases was obtained at an OMW:water ratio of 80:20 enriched with 2 g L−1 of urea corresponding to initial biochemical oxygen demand (BOD5), chemical oxygen demand (COD) and total phenol concentrations of 18.4, 46 and 4.6 g L−1 respectively. The partially purified laccases resulted in 85% decolorization of blue tubantin GLL 300 and black tubantin VSF 600, and 45% decolorization of blue solophenyl after 6 h of incubation. Subsequent additions of the same dye dose to the reaction mixture resulted in a very significant decrease in laccases activity after the third dye addition.CONCLUSION: The use of OMW for laccases production is a cost effective process. The laccases produced can be applied to the decolorization of textile wastewaters. Copyright © 2009 Society of Chemical Industry
Contributions of electrochemical oxidation to waste‐water treatment: fundamentals and review of applications
Authors: Anglada Ángela , Urtiaga Ane , Ortiz Inmaculada 
Published: May 2009

AbstractOVERVIEW: This paper provides an overview of some fundamental aspects of electrochemical oxidation and gives updated information on the application of this technology to waste‐water treatment. In recent years, electrochemical oxidation has gained increasing interest due to its outstanding technical characteristics for eliminating a wide variety of pollutants normally present in waste‐waters such as refractory organic matter, nitrogen species and microorganisms.IMPACT: The strict disposal limits and health quality standards set by legislation may be met by applying electrochemical oxidation. However, treatment costs have to be cut down before full‐scale application of this technology. Deployment of electrochemical oxidation in combination with other technologies and the use of renewable sources to power this process are two steps in this direction.APPLICATIONS: Effluents from landfill and a wide diversity of industrial effluents including the agro‐industry, chemical, textile, tannery and food industry, have been effectively treated by this technology. Its high efficiency together with its disinfection capabilities makes electro‐oxidation a suitable technology for water reuse programs. Copyright © 2009 Society of Chemical Industry
Microwave photocatalysis III. Transition metal ion‐doped TiO2thin films on mercury electrodeless discharge lamps: preparation, characterization and their effect on the photocatalytic degradation of mono‐chloroacetic acid and Rhodamine B
Authors: Žabová Hana , Církva Vladimír 
Published: May 2009

AbstractBACKGROUND:Mercury electrodeless discharge lamps (Hg‐EDLs) were used to generate UV radiation when exposed to a microwave field. EDLs were coated with doped TiO2in the form of thin films containing transition metal ions Mn+(M = Fe, Co, Ni, V, Cr, Mn, Zr, Ag). Photocatalytic degradation of mono‐chloroacetic acid (MCAA) to HCl, CO2, and H2O, and decomposition of Rhodamine B on the thin films were investigated in detail.RESULTS:Polycrystalline thin doped TiO2films were prepared by dip‐coating of EDL via a sol–gel method using titaniumn‐butoxide, acetylacetone, and a transition metal acetylacetonate. The films were characterized by Raman spectroscopy, UV/Vis absorption spectroscopy, X‐ray photoelectron spectroscopy (XPS), electron microprobe analysis and by atomic force microscopy (AFM). The photocatalytic activity of doped TiO2films was monitored in the decomposition of Rhodamine B in water. Compared with the pure TiO2film, the UV/Vis spectra of V, Zr and Ag‐doped TiO2showed significant absorption in the visible region, and hence the photocatalytic degradation of MCAA had increased. The best apparent degradation rate constant (0.0125 min−1), which was higher than that on the pure TiO2film by a factor of 1.7, was obtained with the Ag(3%)/TiO2photocatalyst. The effect of doping level of vanadium acetylacetonate on the photocatalytic efficiency of the V‐doped TiO2was determined.CONCLUSIONS:Transition metal ion‐doped TiO2thin films showed significant absorption in the visible region. The metal doped TiO2photocatalyst (with an appropriate amount of V, Zr and Ag) on the Hg‐EDLs increased the degradation efficiency of MCAA in a microwave field. Copyright © 2009 Society of Chemical Industry
Microwave‐assisted immobilization of lipase from Candida rugosa on Eupergit® supports
Authors: Bezbradica Dejan , Mijin Dušan , Mihailović Mladen , Knežević‐Jugović Zorica 
Published: May 2009

AbstractBACKGROUND: Immobilization of lipase (triacylglycerol acylhydrolase EC 3.1.1.3) from Candida rugosa on Eupergit® C and Eupergit® C 250L was performed under microwave irradiation in order to reduce immobilization time. Lipase loading, hydrolytic activity, esterification activity and operational stability in organic solvent of immobilized lipase preparation were determined.RESULTS: The microwave‐assisted procedure resulted in a 29% lower lipase loadings, compared with immobilized lipase obtained without microwaves. In hydrolytic activity assay, lipase immobilized under microwaves exhibited a 23% higher specific activity. Slight activation of lipase by microwave‐assisted immobilization was observed, since specific activity was around 5% higher than for free lipase. Lipase of highest activity was obtained after 2 min immobilization on Eupergit® C. The same preparation exhibited high esterification activity in organic medium and a half life of 212 h was determined in multiple use assay.CONCLUSION: The application of microwave irradiation leads to reduction of immobilization time from 2 days to only 2 min. The immobilized lipase obtained has prospects for further application due to its high retained activity and stability. Copyright © 2009 Society of Chemical Industry
Removal of dyes by Moringa oleifera seed extract. Study through response surface methodology
Authors: Beltrán‐Heredia J. , Sánchez‐Martïn J. , Delgado‐Regalado A. 
Published: May 2009

AbstractBACKGROUND: The effect of pH and initial dye concentration (IDC) on dye removal by coagulation/flocculation process with Moringa oleifera seed extract has been studied. The study was carried out by using the response surface methodology (RSM) in an orthogonal and rotatable design of experiments. Three types of dye were studied: anthraquinonic (Alizarin Violet 3R); indigoid (Indigo Carmine); and azoic (Palatine Fast Black WAN).RESULTS: The interaction level of the two variables studied is higher in the case of azo dye, while it is almost null in the case of anthraquinonic dye. Indigoid dye presents an intermediate situation. pH has a negative influence on dye removal, and by raising IDC q capacity tends to be higher. Polynomic regression of the surface plot was carried out and the adjusted r2 found for each case, this being 0.99 in the case of anthraquinonic dye, 0.94 in the case of indigoid dye, and 0.74 in the case of azoic dye.CONCLUSIONS: Moringa oleifera is an interesting natural coagulation agent for use in dye removal. pH should be taken into account in the cases of indigoid and azo dyes, while its influence is rather small in the case of anthraquinonic dye. Copyright © 2009 Society of Chemical Industry
Comparing phenanthrene degradation by alginate‐encapsulated and free Pseudomonas sp. UG14Lr cells in heavy metal contaminated soils
Authors: Somtrakoon Khanitta , Suanjit Sudarat , Pokethitiyook Prayad , Kruatrachue Maleeya , Cassidy Michael B. , Trevors Jack T. , Lee Hung , Upatham Suchart 
Published: May 2009

AbstractBACKGROUND: Many polycyclic aromatic hydrocarbon (PAH) contaminated sites also contain high levels of toxic heavy metals. The presence of heavy metals can adversely affect PAH biodegradation. Encapsulation of bacterial cells has been shown to improve survival and activity of cells under various environmental stresses. This study examined if encapsulation of a phenanthrene‐mineralizing bacterial strain could improve its survival and phenanthrene degradation in heavy metal contaminated soils.RESULTS: Alginate encapsulation did not improve survival and phenanthrene degradation by Pseudomonas sp. UG14Lr in heavy metal contaminated soil. Phenanthrene degradation by, and survival of, free cells and alginate‐encapsulated cells were similar in soil contaminated with 5 mg kg−1 dry soil of As, Cd, or Pb. The number of UG14Lr cells decreased to undetectable level when the concentration of each heavy metal was increased to 100 mg kg−1 dry soil. UG14Lr, when inoculated as free cells, survived the best and they were detected over 60 days of incubation in soil. Cells in both wet and dry alginate beads survived less well than free cells at the higher metal concentrations. Correspondingly, phenanthrene degradation in soil inoculated with free UG14Lr was better than that in soil inoculated with alginate‐encapsulated cells.CONCLUSION: Alginate encapsulation adversely affected the survival and phenanthrene degradation ability of UG14Lr cells in heavy metal contaminated soil. It is postulated that alginate may have concentrated the metals which in turn increased the toxicity to UG14Lr cells. The results are of interest to those interested in the use of encapsulation technology to formulate microbial cells for bioremediation purposes. Copyright © 2009 Society of Chemical Industry