University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Construction and Analysis of Tissue-Specific Protein-Protein Interaction Networks in Humans 1 13 2687 10.22059/pbs.2013.2687 EN Mitra Mirzarezaee Department of Computer Engineering, Science and Research Branch , Islamic Azad University, Tehran, Iran Mehdi Sadeghi National Institute of Genetic Engineering and Biotechnology(NIGEB), Tehran, Iran.; School of Computer Sciences , Institute for Research in Fundamental Sciences, IPM, Tehran, Iran. Babak N. Araabi Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Iran.; School of Cognitive Sciences, Institute for Research in Fundamental Sciences, IPM, Tehran, Iran. Journal Article 2012 07 16 We have studied the changes in protein-protein interaction network of 38 different tissues of the human body. 123 gene expression samples from these tissues were used to construct human protein-protein interaction network. This network is then pruned using the gene expression samples of each tissue to construct different protein-protein interaction networks corresponding to different studied tissues of the body. This study is helpful for understanding how human protein interactions change in different tissues. In this way, similar tissues of the body and special functions of each tissue, corresponding to their individualized subnetworks, can be identified. We have calculated graph parameters for studying these protein-protein interaction networks and hubs and non-hubs of the studied protein-protein interaction networks are identified. We found a common subnetwork among protein-protein interaction networks of the studied tissues and a tree of tissue similarities has been constructed. We have also found that average correlation coefficient of hubs in human protein-protein interaction networks obeys a normal-like distribution though it is not possible to separate party and date hubs. https://pbiosci.ut.ac.ir/article_2687_657396842022b5508d6e760602656c53.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Comparing the Bidirectional Baum-Welch Algorithm and the Baum-Welch Algorithm on Regular Lattice 14 22 2690 10.22059/pbs.2013.2690 EN Vahid Rezaei Department of Mathematics, K.N.Toosi University of Technology. Tehran, Iran.; Bioinformatics Research Group, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran. Sima Naghizadeh The National Organization for Educational Testing (NOET), Ministry of Science, Research and Technology. Hamid Pezeshk School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Iran.; Bioinformatics Research Group, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran. Mehdi Sadeghi Department of Biophysics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. Changiz Eslahchi Faculty of Mathematical Science, Shahid-Beheshti University, G. C., Tehran, Iran. Journal Article 2012 07 21 A profile hidden Markov model (PHMM) is widely used in assigning protein sequences to protein families. In this model, the hidden states only depend on the previous hidden state and observations are independent given hidden states. In other words, in the PHMM, only the information of the left side of a hidden state is considered. However, it makes sense that considering the information of the both left and right sides of a hidden state can improve the assignment task. For this purpose, bidirectional profile hidden Markov model (BPHMM) can be used. Also, because of the evolutionary relationship between sequences in a protein family, the information of the corresponding amino acid in the preceding sequence of residues in the PHMM can be considered. For this purpose the hidden Markov random field on regular lattice (HMRFRL) is introduced. In a PHMM, the parameters are defined by the transition and emission probability matrices. The parameters are usually estimated using an EM (Expectation-Maximization) algorithm known as Baum-Welch algorithm. In this paper, the bidirectional Baum-Welch algorithm and theBaum-Welch algorithm on regular lattice are defined for estimating the parameters of the BPHMM and the HMRFRL respectively. We also compare the performance of common Baum-Welch algorithm, bidirectional Baum-Welch algorithm and the Baum-Welch algorithm on regular lattice by applying them to the real top ten protein families from Pfam database. Results show that using the lattice model for sequence assignment increases the number of correctly assigned protein sequences to profiles compared to BPHMM . https://pbiosci.ut.ac.ir/article_2690_021ceb98d7d4a88283de3287d351312d.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Linkage of Parkinson’s disease in two very early onset siblings to a locus on chromosome 1 23 29 2702 10.22059/pbs.2013.2702 EN Maryam Malakouti Nejad Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran. Mehrdad Hashemi Department of Genetics, Islamic Azad University, Tehran Medical Branch, Tehran, Iran. Gholam Reza Shahidi Department of Neurology, Tehran University of Medical Sciences, Tehran, Iran. Elahe Elahi School of Biology, University College of Science, University of Tehran, Iran.; Department of Biotechnology, University College of Science, University of Tehran, Iran. Journal Article 2012 07 21 Parkinson’s disease (PD) is a prevalent neurodegenerative disease that usually affects individuals over 50 years of age. Age at onset in a small subset of PD cases is considerably lower, and these are considered early-onset PD (EOPD) patients. Most PD cases appear sporadic, but approximately 15% are familial, and some of the familial cases exhibit Mendelian inheritance. Genetic analysis of familial cases has led to identification of five major PD causing genes. Mutations in three of these, PRKN, PINK1, and DJ-1 are most often observed in EOPD patients belonging to families in which PD is inherited in an autosomal recessive fashion. Here, a PD family with two siblings whose ages of onset were 10 and 14 years was identified. Initially, PRKN, PINK1, and DJ-1 were screened, but a putative disease causing mutation was not found. Genome-wide homozygosity mapping using high density microarray chips led to identification of a 6.5 cM linked locus on locus on chromosome 1. ATP13A2 that encodes a lysosomal type 5 P-type ATPase is positioned within the linked locus. Mutations in ATP13A2 have previously been reported in a few EOPD patients, and this gene is an appropriate candidate as cause of PD in the pedigree here described. https://pbiosci.ut.ac.ir/article_2702_e2ee9d3d8382f5e06e2b645554273a96.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Polyethylene Glycol Repairs Damaged Membrane; Biophysical Application of Artificial Planar Bilayer to Mimic Biological Membrane 30 41 2703 10.22059/pbs.2013.2703 EN Sogolie Kouhzaei Saeid Hadi Alijanvand Hamid Mobasheri Journal Article 2012 07 02 Polyethylene glycol (PEG) is a hydrophilic polymer, known to be capable to fuse numerous single cells in vitro, to join the membranes of adjacent neurons and giant invertebrate axons, and to seal damaged neural membranes. The molecular mechanism of the action of PEG is still unknown. It is believed that PEG dehydrates membranes and enables their structural components to resolve and rearrange in a lamellar configurationfollowing rehydration. In this study, the effects of different sized PEGs (400, 1000, and 2000Da) at 10–30% w/w on different physical properties of intact and damaged artificial bilayers, including membrane conductivity (Gm), capacitance (Cm), and breakdown voltage (Vb), were studied by voltage clamp technique to address itsresealing capability at the molecular level. The unilamellar artificial planar bilayer was formed from soybean lecithin, based on the Montal and Mueller procedure. Our results show that in disrupted membrane, PEG2000 increased Gm and Cm significantly and decreased Vb. Furthermore, PEG1000 at 30% w/w significantly increased Gm and decreased Vb, but had no effect on Cm. PEG400 had no significant effect on Gm, Vb, or Cm. In addition, at the applied concentrations and molecular weights, the PEGs showed no effects on the stability, conductivity, or breakdown voltage of the intact bilayer. We conclude that PEGs repair membrane in concentration- and size-dependent manner; small PEG (400Da) is capable of repairing membrane and re-stabilizing its integrity at certain concentrations, while larger ones, such as PEG2000, destabilize the membrane and fail to re-establish its integrity. The results of this study might shed light on understanding the mechanism (s) by which PEGs repair damaged membranes of neural fibers, and might be considered in clinical treatment of brain and spinal cord injury in the near future. https://pbiosci.ut.ac.ir/article_2703_ede1693b2abb505fc36957b6d7e31ae1.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Fungal Infection Alters Phosphate Level and Phosphatase Profiles in Arabidopsis 42 57 2704 10.22059/pbs.2013.2704 EN Tahmineh Lohrasebi Katayoun Zamani Mohammad S. Sabet Mohammad A. Malboobi Journal Article 2012 07 01 Phosphorus (P), in the form of phosphate ion (Pi), is a vital element contributing in biomolecule structures, metabolic reactions, signaling pathways and energy transfer within the living cells. The objective of the present study was to assess the influence of fungal infection on Pi metabolism in compare to the effects of phosphate stress in Arabidopsis. Quantification of total P contents showed higher storage of P in the shoots than in the roots of Pi-fed plants, while the homeostatic levels of soluble Pi was kept in a fairly narrow range in roots and shoots of both Pi-fed and Pi-starved. When the plants were subjected to Pi starvation, both total P and soluble Pi contents were reduced to minimal levels in roots and shoots. Total acid phosphatase (APase) activity was also affected by the level of available Pi such that it was higher in the starved plants than in the fed plants. When Pi-fed plants were subjected to fungal infections, a remarkable reduction was observed for the above indicators in roots but not shoots. Surprisingly, the analysis of APase expression profiling after inoculation with Alternaria brassicicola showed that the rates of transcription of several APase-encoding genes were affected by fungus infection. Atpap9, afungal inducible gene, promoter analysis also indicated alterations in tissue-specific expression patterns upon the fungal infections. These data clearly illustrate that how a nutrient distribution is affected by environmental conditions, even regardless of available phosphate. https://pbiosci.ut.ac.ir/article_2704_8b4d0c1523acc53e57c90ac05332a17c.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Analysis of N2-(2-carboxyethyl)-L-arginine, an Intermediate of Clavulanic Acid, by Liquid Chromatography Method Using Benzoin as aFluorogenic Reagent 58 65 2705 10.22059/pbs.2013.2705 EN Fatemeh Imanparast Faculty of Science, Department of Biology, Alzahra University, Tehran, Iran. Javad Hamedi Microbial Biotechnology Lab., Dept. of Microbiology, School of Biology, College of Science and UTMC (University of Tehran Microorganisms Collection, University of Tehran, Tehran, Iran. Behzad Laamerad Faculty of Science, Department of Biology, Alzahra University, Tehran, Iran. Majid M. Heravi Faculty of Science, Department of Chemistry, Alzahra University, Tehran, Iran. Journal Article 2012 10 06 Phosphorus (P), in the form of phosphate ion (Pi), is a vital element contributing in biomolecule structures, metabolic reactions, signaling pathways and energy transfer within the living cells. The objective of the present study was to assess the influence of fungal infection on Pi metabolism in compare to the effects of phosphate stress in Arabidopsis. Quantification of total P contents showed higher storage of P in the shoots than in the roots of Pi-fed plants, while the homeostatic levels of soluble Pi was kept in a fairly narrow range in roots and shoots of both Pi-fed and Pi-starved. When the plants were subjected to Pi starvation, both total P and soluble Pi contents were reduced to minimal levels in roots and shoots. Total acid phosphatase (APase) activity was also affected by the level of available Pi such that it was higher in the starved plants than in the fed plants. When Pi-fed plants were subjected to fungal infections, a remarkable reduction was observed for the above indicators in roots but not shoots. Surprisingly, the analysis of APase expression profiling after inoculation with Alternaria brassicicola showed that the rates of transcription of several APase-encoding genes were affected by fungus infection. Atpap9, afungal inducible gene, promoter analysis also indicated alterations in tissue-specific expression patterns upon the fungal infections. These data clearly illustrate that how a nutrient distribution is affected by environmental conditions, even regardless of available phosphate. https://pbiosci.ut.ac.ir/article_2705_75521f5fe36fe05f5ab2429c565adead.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Molecular Phylogeny ofthe Puntius (Hamilton, 1822) Based on Nuclear Gene RAG2 66 75 2706 10.22059/pbs.2013.2706 EN Faezeh Yazdani Moghaddam Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. Mansour Aliabadian Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. Siti Khalijah Daud Biology Department, Faculty of Science, Universiti Putra Malaysia, 43400UPM Serdang, Selangor, Malaysia. Mahvash Seifali Department of Biology, Faculty of Science, University Alzahra, Tehran, Iran. Journal Article 2012 09 11 The tropical Asian cyprinid genus Puntius is a major part of the ichthyofauna in Southeast Asia. Systematic status of the genus Puntius among Cyprinidae, the most prominent freshwater fish all over the world, remain to be substantiated. The molecular phylogenetic analyses derived from Recombination activating genesequences (RAG2) for 35 representative samples of Malaysian Puntius and their allies, indicated paraphyly of the genus Puntius among common cyprinid groups of Southeast Asia. At a larger scale, while the monophyly of Cyprinidae and the subfamily Cyprininae were confirmed, the monophyly of the tribe Barbinini, Cyprinini, or Puntius (Systomus) were not supported. https://pbiosci.ut.ac.ir/article_2706_9a21bd394753fd53d533ec3a65902dc1.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Responses of Transgenic Tobacco (Nicotiana plambaginifolia) Over-Expressing P5CS Gene Underin vitroSalt Stress 76 84 2708 10.22059/pbs.2013.2708 EN Mahboobeh Riahi Ali Akbar Ehsanpour Journal Article 2012 07 01 Salinity is a major limiting factor for plant growth and development. To evaluate the impact of P5CS gene expression under in vitro salt stress condition, transgenic tobacco (Nicotiana plumbaginifolia) carrying P5CS gene and non-transgenic plants were treated with 0, 100, 150, 200 or 250 mM NaCl for 28 days. Proline content, lipid peroxidation and the activity of some antioxidant enzymes after salt treatment were measured. At 150 mM NaCl or higher, plant’s leaf and root showed an increase in proline content significantly. Malondialdehyde (MDA) level in non-transgenic plants was considerably higher than the transgenic tobacco plant at 100 mM NaCl and higher. Activities of ascorbateperoxidase (APX) and catalase (CAT) was increased in transgenic as well as non-transgenic plants by increasing salt concentrations. However, transgenic plants showed higher level of antioxidant enzymes activity than non transgenic plants. Salinity tolerance of Nicotine plumbaginifolia transgenic P5CS gene might be closely related to the accumulation of proline, CAT and APX activity and consequently suppressed level of lipid peroxidation. https://pbiosci.ut.ac.ir/article_2708_cd5713eaae0e282571a434b3a1957c5a.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Production ofHalothermotolerant α-Amylase from aModerately Halophilic Bacterium, NesterenkoniaStrain F. 85 97 2710 10.22059/pbs.2013.2710 EN Mohammad Ali Amoozegar Extremophile lab, Department. of Microbiology , School of Biology and center of excellence in philogeny of living organisms, College of Science , University of Tehran , Tehran , Iran. Bardia Samareh-Abolhasani Extremophile lab, Department. of Microbiology , School of Biology and center of excellence in philogeny of living organisms, College of Science , University of Tehran , Tehran , Iran. Mohammad Shafiei Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Iran. Maryam Didari Extremophile lab, Department. of Microbiology , School of Biology and center of excellence in philogeny of living organisms, College of Science , University of Tehran , Tehran , Iran. Javad Hamedi Microbial Biotechnology Lab., Dept. of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran Journal Article 2012 10 07 Production of extracellular amylase was demonstrated under conditions of high salinity in aerobically cultivated culture of a newly isolated moderately halophilic Gram-positive coccus, designated strain F in basal medium containing peptone from meat, yeast extract, NaCl (7% w/v) and starch. Biochemical and physiological characterization along with 16S rRNA sequence analysis placed F in the genus Nesterenkonia. The enzyme production was synchronized bacterial growth and reached a maximum level during the early-stationary phase in the basal medium. Maximum yield production was observed when the soluble starch, yeast extract and NaCl (1%, 0.75% and 10% w/v, respectively) were used in the fermentation medium with pH 8.0, inoculated with 7% (v/v) pre-culture medium and incubated in 30°C for 72 h with aeration of 250 rpm (299.25 U/ml). The potential of different carbohydrates in amylase production was in the order: starch> maltose>dextrin>fructose>lactose=glucose>sodium acetate>sodium citrate. The production yield in the presence of different salts was as follows: NaCl> KCl> NaNO3> Na2SO4. Maximum activity for enzyme was assayed in 3.0 M NaCl, pH: 5-7, and 40°C. α-amylase hydrolyzed starch, dextrin and glycogen to form maltose, maltotriose and maltotetraose as major products, and has no effect on amylose and pullulan as substrates. These results suggest that the amylase secreted by Nesterenkonia sp. strain F is industrially important from the perspective of its tolerance to a broad temperature range and its high tolerance to a wide range of salt concentrations (0–3 M NaCl). https://pbiosci.ut.ac.ir/article_2710_fecaa08ce61523dc56ab112a47e76563.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Familial Prion Disease Cases Without Mutation in PRNPGene 98 103 2713 10.22059/pbs.2013.2713 EN Sahar Jelodari-Mamaghani Gholam Ali Shahidi Mohammad Roohani Farzad Sina Journal Article 2012 09 05 Phosphorus (P), in the form of phosphate ion (Pi), is a vital element contributing in biomolecule structures, metabolic reactions, signaling pathways and energy transfer within the living cells. The objective of the present study was to assess the influence of fungal infection on Pi metabolism in compare to the effects of phosphate stress in Arabidopsis. Quantification of total P contents showed higher storage of P in the shoots than in the roots of Pi-fed plants, while the homeostatic levels of soluble Pi was kept in a fairly narrow range in roots and shoots of both Pi-fed and Pi-starved. When the plants were subjected to Pi starvation, both total P and soluble Pi contents were reduced to minimal levels in roots and shoots. Total acid phosphatase (APase) activity was also affected by the level of available Pi such that it was higher in the starved plants than in the fed plants. When Pi-fed plants were subjected to fungal infections, a remarkable reduction was observed for the above indicators in roots but not shoots. Surprisingly, the analysis of APase expression profiling after inoculation with Alternaria brassicicola showed that the rates of transcription of several APase-encoding genes were affected by fungus infection. Atpap9, afungal inducible gene, promoter analysis also indicated alterations in tissue-specific expression patterns upon the fungal infections. These data clearly illustrate that how a nutrient distribution is affected by environmental conditions, even regardless of available phosphate. https://pbiosci.ut.ac.ir/article_2713_457b620bdca939e940d007262a1a5dcf.pdf

University of Tehran Press Progress in Biological Sciences 1016-1058 2 2 2013 03 01 Expression and Purification of Human Interferon Gamma Using a Plant Viral Vector 104 115 2715 10.22059/pbs.2013.2715 EN Sayed Mohsen Nassaj Hosseini Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Masoud Shams-Bakhsh Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Ali-Hatef Salamanian National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. Shyi-Dong Yeh Plant Pathology Department, National Cheng Hsing University, Taichnug, Taiwan. Journal Article 2012 10 29 A plant viral vector engineered from an in vivo infectious clone of zucchini yellow mosaic virus(ZYMV) was used to express the human interferon-gamma (INF-γ) in planta. The INF-γ gene was in frame inserted between the P1 and HC-Pro ORFs of the ZYMV vector. The infectious activity of the vector was approved by rubbing the plasmid on Chenopodium quino a and observing local lesions. Individual lesions were mechanically transferred to the systemic host plant zucchini squash at the stage of cotyledonary leaf. The stability of INF-γ expression was assessed by successive passages of recombinant viruses from infected plant and throughout the period of 35 days after inoculating in a single plant. Then, the leaf tissues ofinoculated plant were analyzed for the presence of transgene by RT-PCR and western blot analysis. The recombinant protein was purified using affinity chromatography method. The results showed approximately 1–1.2 mg INF-γ per 100 g tissues were purified from leaves two weeks post inoculation. Also, the vector was remarkably stable in squash after six serial passages and 35 days. The procedure provides a convenient and fast method for production of large quantities of pure INF-γin planta. The system also has a potential for production of other proteins of interest in cucurbits to use as immunogen to produce antiserum or use for other purposes. https://pbiosci.ut.ac.ir/article_2715_453ce9e33a4c3c0f49074c9d15a8aad9.pdf