Cellular & Molecular Biology Letters

International Scientific Journal
Established 1996

Volume 10 (2005) No. 4

Volume 10 (2005) pp 563-569
Title	EXPLORING THE EFFECT OF XENON ON BIOMEMBRANES
Authors	Lorna M. Stimson¹*, Ilpo Vattulainen², Tomasz Róg^1,3 and Mikko Karttunen¹
Abstract	We report the initial findings of 100 ns molecular dynamics simulations of the role of cellular membranes in general anaesthesia. The effect of xenon on hydrated dipalmitoylphosphatidylcholine bilayers is described. The xenon atoms were found to prefer the interfacial and central regions of the bilayer. The presence of xenon was observed to lead to a small increase in the surface area, membrane thickness, and order of the acyl chains.
Adress and Contact Informations	¹Biophysics & Statistical Mechanics Group, Laboratory of Computational Engineering, P.O.B. 9203, 02015 Helsinki University of Technology, Finland, ²Laboratory of Physics and Helsinki Institute of Physics, P.O.B. 1100, 02015 Helsinki University of Technology, Finland, and MEMPHYS-Center of Biomembrane Physics, Physics Department, University of Southern Denmark, ³Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland * Corresponding author, e-mail: lorna@lce.hut.fi

Volume 10 (2005) pp 571-594
Title	REGULATION OF MITOCHONDRIAL TRANSLATION IN YEAST
Authors	Joanna Towpik*
Abstract	This review provides an overview of the current state of knowledge regarding the control of very unusual mechanism of mitochondrial gene expression and the structure of mitochondrial ribosomes, with emphasis on the potential of the yeast Saccharomyces cerevisiae as a model organism.
Adress and Contact Informations	Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland * Corresponding author; e-mail: viva@ibb.waw.pl

Volume 10 (2005) pp 595-612
Title	FOLDING OF SPECTRIN’S SH3 DOMAIN IN THE PRESENCE OF SPECTRIN REPEATS
Authors	Joacim Robertsson¹, Katja Petzold¹, Lars Lofvenberg² and Lars Backman^1,*
Abstract	The multifunctional protein spectrin contains several different structural motifs, such as spectrin repeats and a SH3 domain. Both triple-helix spectrin repeats and the SH3 domain are believed to form independent structural entities. In a-spectrins the SH3 domain is localized to repeat 9, where it is positioned between helix B and helix C in the repeat unit. The presence of SH3 in repeat 9 decreases the thermal stability considerably of this repeat unit while another insert in helix C does not seem to affect the stability. Addition of one or two adjacent repeat units increases the thermal stability from ca 25°C to ~41 and ~48°C, respectively. Despite the differences in thermal stability, the folding properties of peptides comprising the SH3 domain only or together with one or more repeats are more or less the same.
Adress and Contact Informations	Biochemistry, Umeå University, SE-901 87 Umeå, Sweden and Department of Microbiology, University Hospital of Trondheim, N-7006 Trondheim, Norway * Corresponding author, e-mail: lars.backman@chem.umu.se

Volume 10 (2005) pp 613-623
Title	THE SYNTHESIS, PHYSICOCHEMICAL PROPERTIES AND IMMUNOLOGICAL ACTIVITY OF 5-AMINO-3- METHYLISOXAZOLO[5,4-D]4-PYRIMIDINONE DERIVATIVES
Authors	Marcin Mączyński¹*, Michał Zimecki², Ewa Drozdszczygieł¹ and Stanisław Ryng¹
Abstract	A series of 5-amino-3-methylisoxazole[5,4-d]4-pyrimidinone derivatives were obtained by reacting substituted 5-amino-3-methylisoxazol-4- carboxylic acid hydrazide with ethyl ortho-formate. The compounds were tested using the models of in vivo cellular and humoral immune response in mice and pokeweed mitogen-induced (PWM-induced) polyclonal antibody production in a culture of human peripheral blood mononuclear cells (PBMC). The compounds exhibited differential inhibitory activities in the described models, depending on the character and location of the substituted groups. We suggest that the compounds affect the early stages of the immune response.
Adress and Contact Informations	¹Wrocław Medical University, Faculty of Pharmacy, Department of Organic Chemistry, Grodzka 9, 50-137 Wrocław, Poland, ²Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Experimental Therapy, R. Weigla 12, 53-114 Wrocław, Poland *Corresponding author: fax: +48 71 784-03-41, e-mail: marcinm@bf.uni.wroc.pl

Volume 10 (2005) pp 625-630
Title	MODELING GLYCOLIPIDS: TAKE ONE
Authors	Tomasz Róg^1,2*, Ilpo Vattulainen^3,4 And Mikko Karttunen¹
Abstract	Molecular dynamics simulations of glycolipid bilayers consisting of 1,2-di-O-palmitoyl-3-O-b-D-glucosyl-sn-glycerol were performed using five different force field parameterizations. Comparing the results with experimental data revealed that only the all-atom model correctly reproduces both the phase behavior and the surface area per lipid. Only one of the united atom models studied reproduces the correct phase behavior.
Adress and Contact Informations	¹Biophysics and Statistical Mechanics Group, Laboratory of Computational Engineering, POB 9203, 02015, Helsinki University of Technology, Finland; ²Department of Biophysics, Gronostajowa 7, 30-387, Kraków, Jagiellonian University, Poland; ³Laboratory of Physics and Helsinki Institute of Physics, POB 1100, 02015, Helsinki University of Technology, Finland; ⁴MEMPHYSCenter for Biomembrane Physics, University of Southern Denmark * Corresponding author; e-mail: tomekr@mol.uj.edu.pl

Volume 10 (2005) pp 631-647
Title	THE ROLE OF MAMMALIAN DNA METHYLTRANSFERASES IN THE REGULATION OF GENE EXPRESSION.
Authors	Justyna Turek-Plewa and Paweł P. Jagodziński*
Abstract	The term epigenetic modification denotes reversible traits of gene expression that do not include alterations to the DNA sequence. These epigenetic alterations are responsible for chromatin structure stability, genome integrity, modulation of tissue-specific gene expression, embryonic development, genomic imprinting and X-chromosome inactivation in females. Epigenetic changes include reversible DNA methylation and histone acetylation or methylation. The modification of mammalian genomic DNA includes the methylation at the 5-position of the cytosine (C) residue within cytosine-guanine dinucleotides (CpG), resulting in the formation of 5-methylcytosine (m5C). Regulatory DNA sequences in vertebrates often have little or no methylation. The methylation of mammalian genomic DNA is catalyzed by DNA methyltransferases (DNMTs), which play a special role in the initiation of chromatin remodeling and gene expression regulation. The mammalian DNMTs are DNMT1, DNMT3A and DNMT3B, which together with accessory proteins, like DNMT3L, are responsible for methylation pattern acquisition during gametogenesis, embryogenesis and somatic tissue development. Reversible epigenetic alterations lead to selective utilization of genome information through the activation or inactivation of transcription of functional genes during gametogenesis, embryogenesis and cell differentiation. Recently, several disparate isoforms of DNMT1 were identified in human somatic and female and male germ cells. Recent advances in the investigation of DNMT function in epigenetic DNA changes have formed the basis of the understanding of various disorder etiopathogeneses, and as a result, have facilitated and enabled new therapies with respect to these diseases.
Adress and Contact Informations	Karol Marcinkowski University of Medical Sciences, ul. Święcickiego 6, 60-781 Poznań, Poland * Corresponding author: fax: (48 61) 865 95 86, e-mail: pjagodzi@am.poznan.pl

Volume 10 (2005) pp 649-657
Title	*ISOLATION OF A cDNA ENCODING THE a-SUBUNIT OF CAAXPRENYLTRANSFERASES FROM Catharanthus roseus* AND THE EXPRESSION OF THE ACTIVE RECOMBINANT PROTEIN FARNESYLTRANSFERASE**
Authors	Vincent Courdavault^1,*, Vincent Burlat¹, Benoit Stpierre¹, Pascal Gantet² and Nathalie Giglioli-Guivarc’h¹
Abstract	Crfta/ggt_Ia (AF525030), a cDNA encoding the a-subunit of the two types of CaaX-prenyltransferase (CaaX-PTase), i.e. protein farnesyltransferase (PFT) and type I protein geranylgeranyltransferase, was cloned from Catharanthus roseus via a PCR strategy. Crfta/ggt_Ia is 1381-bp long and bears a 999-bp open reading frame encoding a protein of 332 residues (FTA) that shares 66% identity with its Lycopersicon esculentum orthologue. Southern blot analysis revealed that FTA is encoded by a single gene copy per haploid genome. Co-expression of Crfta/ggt_Ia and Crftb encoding the b-subunit of PFT yielded purified active recombinant PFT. This enzyme is able to prenylate proteins from C. roseus, and could be used as a potent tool for prenylated protein identification.
Adress and Contact Informations	¹Université François-Rabelais de Tours, EA 2106 Biomolécules et Biotechnologies Végétales, UFR Sciences et Techniques, Parc de Grandmont, 37200 Tours, France, ²Université Montpellier II, Equipe analyse fonctionnelle du génome du riz, C.C. 002, 34095 Montpellier Cedex 5, France * Corresponding author; tel: +33.2.47.36.69.88; fax: +33.2.47.36.70.42; e-mail: courdavault@univ-tours.fr

Volume 10 (2005) pp 659-668
Title	MOLECULAR CLONING AND CHARACTERIZATION OF A PEROXIREDOXIN FROM Phanerochaete chrysosporium
Authors	Quan Jiang, Yong-Hong Yan, Guo-Ku Hu and Yi-Zheng Zhang*
Abstract	Peroxiredoxins (Prxs) are a ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Here, we report on the cloning and functional characterization of a cDNA designated PcPrx-1, encoding peroxiredoxin from the white-rot fungus Phanerochaete chrysosporium. The full-length PcPrx-1 cDNA (932 bp) contains an open reading frame of 200 amino acid residues with a molecular mass of 22.1 kDa. The deduced primary structure of PcPrx-1 polypeptide shows a high level of sequence identity to other recently identified 2-cys peroxiredoxins. The recombinant PcPrx-1 protein was expressed as a histidine fusion protein in Escherichia coli and purified with a Ni2+-column. The purified protein was shown to have a protective effect against plasmid DNA cleavage by reactive oxygen species. The PcPrx-1 protein displays the ability to remove H2O2 in a ferrithiocyanate system. The results of this study suggest that PcPrx-1 may play a protective role against oxidative stress in P. chrysosporium.
Adress and Contact Informations	College of Life Sciences, Sichuan University, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu 610064, P.R. China *Corresponding author; fax: +86 28 85412738; e-mail: Quan Jiang: jiangquan@blazemail.com, YiZheng Zhang: nic3602@scu.edu.cn

Volume 10 (2005) pp 669-676
Title	REPEATED ADMINISTRATION OF LEAD DECREASES BRAIN 5-HT METABOLISM AND PRODUCES MEMORY DEFICITS IN RATS
Authors	Saida Haider*, Saima Shameem, Shahida P. Ahmed, Tahira Perveen and Darakhshan J. Haleem
Abstract	Long-term exposure to low levels of lead (Pb²⁺) has been shown to produce learning and memory deficits in rodents and humans. These deficits are thought to be associated with altered brain monoamine neurotransmission. Increased brain 5-HT (5-hydroxytryptamine; serotonin) activity is thought to be a prerequisite for maintaining control over the cognitive information process, and is said to have a role in learning and memory. This study was designed to investigate the effects of Pb²⁺ administration on brain 5-HT metabolism and memory function in rats. Rats were injected daily for three weeks with Pb²⁺- acetate at a dose of 100mg/kg body weight. The assessment of memory was done using the Radial arm maze (RAM) and Passive avoidance tests. The results showed spatial working memory (SWM) deficits as well as decreased brain 5- HT metabolism. Increased serotonin activity is considered to be an indication of improved cognitive performance. The results are discussed in the context of lead-induced decreases in 5-HT metabolism playing a role in the impairment of memory.
Adress and Contact Informations	Department of Biochemistry, Neurochemistry and Biochemical Neuropharmacology Research Unit, University of Karachi, Pakistan * Corresponding author; e-mail: aapa1@hotmail.com or aapa_saira@yahoo.com

Volume 10 (2005) pp 677-687
Title	THE OVERPRODUCTION OF NITRIC OXIDE ASSOCIATED WITH NEUTROPHILIC PREDOMINANCE IS RELEVANT TO AIRWAY MYCOTIC INFECTIONS IN ASTHMATICS UNDERGOING PROLONGED GLUCOCORTICOID TREATMENT
Authors	Monika Cembrzyńska-Nowak¹*, Jerzy Liebhart², Małgorzata Bieńkowska-Haba¹, Ewa Liebhart², Aleksandra Kulczak², Iwona Siemieniec¹, Rafał Dobek², Anna Dor², Wojciech Barg ² and Bernard Panaszek²
Abstract	The complex relationship between the local inflammatory response and the spread of airway mycosis during prolonged glucocorticoid therapy in bronchial asthma patients remains unclear. We assessed the ability of airway leukocytes to produce nitric oxide (NO) in relation to differential inflammatory cell counts, levels of asthma severity, and coexisting airway mycotic infections. The study was carried out on leukocytes from the induced sputa (IS) of 14 patients with asthma complicated by mycotic airway infections undergoing prolonged glucocorticoid therapy (group FcA). Three groups of subjects without airway fungal infections were also studied: 18 glucocorticoid-treated asthmatics (group cA), 11 steroid-free asthmatics (group A), and 13 healthy control subjects (group H). In group FcA, both the level of spontaneous production of NO and the percentages of neutrophils in the IS were significantly higher than in all the remaining groups. Additionally, a significant positive correlation was noticed between the NO levels and both the percentages of neutrophils in the IS and the symptom intensity scores. The results suggest a possible predominant role of neutrophils in the overproduction of NO related to asthma severity and coexisting fungal infections in glucocorticoid-treated patients.
Adress and Contact Informations	¹Laboratory of Virology, Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wrocław, Poland, ²Department of Internal Medicine and Allergology, Wrocław Medical University, Traugutta 57, 50-417 Wrocław, Poland * Corresponding author; tel.: (+48 71) 370 99 23, e-mail: nowak@iitd.pan.wroc.pl

Volume 10 (2005) pp 689-696
Title	*THE CLONING AND CHARACTERIZATION OF Tetrahymena pyriformis* TRANSLATION ELONGATION FACTOR 1B a AND g SUBUNITSR**
Authors	Violeta Jonusiene*, Sofija Sasnauskiene and Benediktas Juodka
Abstract	The multi-subunit eukaryotic translation elongation factor 1 (eEF1) consists of two functionally distinct parts: G-protein eEF1A and guanine nucleotide exchange factor eEF1B. Here, we report on the cloning of cDNAs of both the a and g subunits of the eEF1B from the ciliated protozoan Tetrahymena pyriformis. The open reading frame of the eEF1Bg cDNA encodes a 399-amino acid long polypeptide with a calculated molecular mass of 45.2 kDa. The eEF1Ba cDNA contains an open reading frame encoding a polypeptide of 228 amino acids. The calculated molecular mass of this protein is 25.2 kDa. The overall deduced amino acid sequences of eEF1Ba and eEF1Bg show a considerable homology with the families of a and g proteins from other eukaryotic organisms. We demonstrated that eEF1Bg is an RNA-binding protein which is able to bind to different RNAs.
Adress and Contact Informations	Department of Biochemistry and Biophysics, Vilnius University, Ciurlionio 21, LT-03101 Vilnius, Lithuania *Corresponding author: Fax +370 5 823931; e-mail: violeta.jonusiene@gf.vu.lt

Volume 10 (2005) pp 697-710
Title	THE METABOLIC PROFILES OF TRANSGENIC CUCUMBER LINES VARY WITH DIFFERENT CHROMOSOMAL LOCATIONS OF THE TRANSGENE
Authors	Norikazu Tagashira^{1, 2}, Wojciech Plader², Marcin Filipecki^2,*, Zhimin Yin³, Anita Wiśniewska^{2, 4}, Paweł Gaj², Maria Szwacka², Oliver Fiehn⁵, Yoshikazu Hoshi⁶, Katsuhiko Kondo⁷ and Stefan Malepszy²
Abstract	The metabolic profiles of five transgenic cucumber lines were compared taking into consideration their transgene integration sites. The plants analyzed were homozygous and contained transgenes integrated in a single locus on chromosomes I, II, III or IV. The transgenes were preferentially located in the euchromatic regions. Each of these locations possessed a specific metabolic profile. The number of altered compounds in the transgenic lines varied between 9 and 23 of the 47 metabolites identified. These alterations seem to be specific for each independent transgene integration. However, some changes are common: a decrease in the levels of phenylalanine, aspartate, ethanolamine and pipecolate, and an increase in the level of benzoic acid. The observed effects of transgene introduction are discussed in this paper.
Adress and Contact Informations	¹Faculty of Human Life Science, Hiroshima Jogakuin University, 4-13-1 Ushita- Higashi, Higashi-ku, Hiroshima 732-0063, Japan, ²Department of Plant Genetics, Breeding and Biotechnology, Warsaw Agricultural University, Nowoursynowska 159, 02-776 Warsaw, Poland, ³Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland, ⁴Department of Plant Physiology, Warsaw Agricultural University, Nowoursynowska 159, 02-776 Warsaw, Poland, ⁵Max-Planck-Institute for Plant Molecular Physiology, Am Muehlenberg 1, D-14476 Golm/Potsdam, Germany, ⁶Dept. of Chemical and Biological Engineering, Ariake National College of Technology, 150 Higashi-Hagio, Omuta, Fukuoka 836-8585, Japan, ⁷Laboratory of Plant Chromosome and Gene Stock, Graduate School of Science, Hiroshima University, Higashi-Hiroshima City, Japan * Corresponding author, e-mail: filipecki@alpha.sggw.waw.pl

Volume 10 (2005) pp 711-719
Title	LIPOSOMES: AN OVERVIEW OF MANUFACTURING TECHNIQUES
Authors	M. Reza Mozafari *
Abstract	During the last few decades liposomes have attracted great interest as ideal models for biological membranes as well as efficient carriers for drugs, diagnostics, vaccines, nutrients and other bioactive agents. The extensive and ever increasing literature covering the field of liposomology written by researchers with diverse backgrounds is an indication of increasing interest in this field. Many techniques and methodologies have evolved for the manufacture of liposomes, on small and large scales, since their introduction to the scientific community around 40 years ago. This article intends to provide an overview of the advantages and disadvantages of liposome preparation methods in general with particular emphasis on the heating method, developed in our laboratory, as a model technique for fast production of the lipid vesicles.
Adress and Contact Informations	Riddet Centre, Massey University, Private Bag 11 222, Palmerston North, New Zealand * e-mail: R.Mozafari@massey.ac.nz

Volume 10 (2005) pp 721-732
Title	THE INCREASE IN MITOCHONDRIAL DNA COPY NUMBER IN THE TISSUES OF Γ-IRRADIATED MICE
Authors	Ludmila Malakhova, Vladimir G. Bezlepkin*, Valeria Antipova, Tat’yana Ushakova, Ludmila Fomenko, Nikolai Sirota and Azhub I. Gaziev
Abstract	Changes in the number of mitochondrial DNA (mtDNA) copies in the brain and spleen tissues of gamma-irradiated (3 Gy) mice were studied by comparative analysis of the long-extension PCR products of mtDNA (15.9 kb) and a fragment of the cluster nuclear β-globin gene (8.7 kb) amplified simultaneously in one and the same test-tube within total DNA. The analysis showed that, compared to the nuclear β-globin gene, an increase in mtDNA copy number (polyploidization) took place in the brain and spleen cells of mice exposed to gamma-radiation. This data led to the suggestion that the major mechanism for maintenance of the mitochondrial genome, which is constantly damaged by endogenous ROS and easily affected by ionizing radiation or other exogenous factors, is the induction of synthesis of new mtDNA copies on intact or little affected mtDNA templates because the repair systems in the mitochondria function at a low level of efficiency.
Adress and Contact Informations	Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences, RAS, Pushchino, Moscow Region, 142290, Russia * Corresponding author; tel: +7-0967-731886, fax: +7-0967-330553, e-mail: bezlepkin@iteb.ru

Volume 10 (2005) pp 733
Title	W. MEJBAUM-KATZENELLENBOGEN’S MOLECULAR BIOLOGY SEMINARS 11. AMPHIPHILES AND THEIR AGGREGATES IN BASIC AND APPLIED SCIENCE, MAY 15-19, 2005, WROCŁAW / KLICZKÓW, POLAND Commentary: AMPHIPHILES AND THEIR AGGREGATES IN BASIC AND APPLIED SCIENCE. A POST-CONFERENCE THOUGHT ON NOMENCLATURE
Authors	M. Reza Mozafari *
	It was very good to be in Poland after three years, for the second time, meeting peers and colleagues in a beautiful Polish castle. The opportunity to meet world class senior scientists in the field as well as young enthusiasts has always been such that I could hardly miss. Being face to face with people like T. Allen, G. Scherphof, V. Torchilin, I. Uchegbu and Z. Zawada whose articles have been guiding me in studies and research was inspiring. Applications of amphiphiles in drug targeting and delivery (and in a wider context bioactive entrapment and release), biomembrane research, origin of life, nanomedicine and nanotherapy were among the many titles presented. It was interesting (at least for me) to see a large number of studies devoted to the computerised modelling in the elucidation of (bio)molecular interactions and their mechanism of function. Prof. Kozubek, conference chairman, at the closing talk mentioned presence of people from as far as New Zealand from one side of the world to Brazil at the other side, making the meeting a real international one. Returning from the conference site to Wroclaw, during a friendly discussion, Prof. Kozubek emphasised the necessity for proper and specific use of technical nomenclature in the field. He stressed the requirement to use terminologies such as liposome(s), which in Greek mean fat bodies, correctly. Along with the advances in the field the necessity to distinguish liposomes from other lipid-based structures including bilayer discs, micelles, hexagonal and cubic phases is increasing. As a result more specific and exclusive definitions are being proposed, such as ‘Liposomes are closed, continuous bilayered structures made mainly of lipid and/or phospholipid molecules’ [Mozafari et al, 9. Liposomes: From Models to Applications, Wroclaw, Poland, 2002]. A more concise description would be: “liposomes are bilayer vesicles made mainly of lipid molecules”. It should be noted that while lipids are the main components of liposomes (and this need to be included in their description to distinguish them from non-lipid vesicles) they can contain other molecules such as proteins and polymers in their structure. With respect to the formation and preparation of liposomes the commonly used expression ‘liposomes are formed spontaneously when lipids are introduced to an aqueous medium’ does not seem to be correct since liposomes are not formed without input of sufficient amount of energy. On the other hand, with the progress in nanotechnology there is an increasing need to differentiate between microscale and nanoscale liposomes. Indeed liposomes have always been a crucial tool in nanotechnology in general and in the field of nanotherapy in particular. Towards this end, the recently introduced term ‘nanoliposomes’ should be used in reference to nanometric vesicles exclusively. Due to the fact that liposomes are dynamic entities and tend to aggregate, fuse and precipitate and as a result increase in size, vesicles prepared in nanometric size ranges may end up becoming micrometric particles upon storage. Nevertheless, nanoliposomes should have adequate stability to retain their sizes and could be defined as: “nanoliposomes are bilayer lipid vesicles possessing and maintaining nanometric size ranges during storage and application”.
Adress and Contact Informations	Riddet Centre, Massey University, Private Bag 11 222, Palmerston North, New Zealand * e-mail: R.Mozafari@massey.ac.nz

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