Gene regulation and systems biology最新文献

{"title":"Evolution and origin of HRS, a protein interacting with Merlin, the Neurofibromatosis 2 gene product.","authors":"Leonid V Omelyanchuk,&nbsp;Julia A Pertseva,&nbsp;Sarah S Burns,&nbsp;Long-Sheng Chang","doi":"10.4137/grsb.s3106","DOIUrl":"https://doi.org/10.4137/grsb.s3106","url":null,"abstract":"<p><p>Hepatocyte growth factor receptor tyrosine kinase substrate (HRS) is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2) gene product, and this interaction may be important for Merlin's tumor suppressor activity. Understanding the evolution, origin, and structure of HRS may provide new insight into Merlin function. We show that HRS homologs are present across a wide range of Metazoa with the yeast Vps27 protein as their most distant ancestor. The phylogenetic tree of the HRS family coincides with species evolution and divergence, suggesting a unique function for HRS. Sequence alignment shows that various protein domains of HRS, including the VHS domain, the FYVE domain, the UIM domain, and the clathrin-binding domain, are conserved from yeast to multicellular organisms. The evolutionary transition from unicellular to multicellular organisms was accompanied by the appearance of a binding site for Merlin, which emerges in the early Metazoa after its separation from flatworms. In addition to the region responsible for growth suppression, the Merlin-binding and STAM-binding domains of HRS are conserved among multicellular organisms. The residue equivalent to tyrosine-377, which is phosphorylated in the human HRS protein, is highly conserved throughout the HRS family. Three additional conserved boxes lacking assigned functions are found in the HRS proteins of Metazoa. While boxes 1 and 3 may constitute the Eps-15-and Snx1-binding sites, respectively, box 2, containing the residue equivalent to tyrosine-377, is likely to be important for HRS phosphorylation. While several functional domains are conserved throughout the HRS family, the STAM-binding, Merlin-binding, and growth suppression domains evolved in the early Metazoa around the time the Merlin protein emerged. As these domains appear during the transition to multicellularity, their functional roles may be related to cell-cell interaction.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"143-57"},"PeriodicalIF":0.0,"publicationDate":"2009-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s3106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28631418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HO1 mRNA and Protein do not Change in Parallel in Bronchial Biopsies of Patients After Long Term Exposure to Sulfur Mustard.","authors":"Mohammad Reza Nourani,&nbsp;Samaneh Yazdani,&nbsp;Mehryar Habibi Roudkenar,&nbsp;Majid Ebrahimi,&nbsp;Raheleh Halabian,&nbsp;Leila Mirbagheri,&nbsp;Mostafa Ghanei,&nbsp;Abbas Ali Imani Fooladi","doi":"10.4137/GRSB.S5871","DOIUrl":"https://doi.org/10.4137/GRSB.S5871","url":null,"abstract":"<p><p>Sulfur mustard (SM), is an alkylating agent and has been emerged as a chemical weapon in various battlefields. More recently, SM was employed in the Iraq conflict against Iranian military forces and civilians. Nowadays there are more than 40,000 people suffering from pulmonary lesions special chronic obstructive pulmonary disease (COPD) due to mustard gas in Iran. SM causes the endogenous production of reactive oxygen species (ROS).Heme oxygenases (HOs) are the rate-limiting enzyme for heme metabolism. Numerous studies have confirmed that HOs are concerned in diverse biological processes such as anti-oxidation.The present study was undertaken to consider the regulation of HO-1 and HO-2 n the human airway wall, and to suggest a probable role that HOs may play in cellular defense against oxidative stress due to SM.In this research ten unexposed SM individuals and twenty SM exposed patients were included. Evaluation of HO-1& HO -2 expressions in unexposed and SM exposed patients samples was performed by semiquantitative RT-PCR, real-time RT-PCR and Immunohistochemistry analysis.While unexposed SM samples expressed same levels of HOs, expression level of HO-1 was upregulated about 3.58 ± 1.93 folds in SM exposed patients in comparison with unexposed ones, we could not find any difference in expression of HO-2 n two groups. In contrast, Immunohistochemistry results showed negative HO-1 protein expression in SM injured patients.Our results revealed that HO1 may plays an important role in cellular protection against oxidative stress due to mustard gas toxicity in airway wall of SM exposed patients at mRNA level, but translational modifications might cause decrease in the amount of HO1 protein.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"4 ","pages":"83-90"},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S5871","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29382595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the role of FGF23 in mineral metabolism.","authors":"Hiroki Yokota,&nbsp;João F Raposo,&nbsp;Andy Chen,&nbsp;Chang Jiang,&nbsp;Hugo G Ferreira","doi":"10.4137/grsb.s2990","DOIUrl":"https://doi.org/10.4137/grsb.s2990","url":null,"abstract":"<p><p>Fibroblast growth factor 23 (FGF23) has recently been identified as a critical regulatory factor in phosphate (P) metabolism. Although the exact molecular mechanism of FGF23 synthesis through sensing the concentration of P is yet to be determined, experimental and clinical data indicate the influential role of FGF23 in P and calcium (Ca) homeostasis. Here, we extended our previous mathematical model in calcium regulation and examined the conceivable roles of FGF23 in mineral metabolism. We assumed that the level of FGF23 was controlled through the concentrations of P and calcitriol in serum, and its actions such as lowering of the renal threshold for P, inhibition of the production of calcitriol in the kidney tubule, and inhibition of the production of parathyroid hormone (PTH) were included. Comparisons between the models with and without FGF23 demonstrate a complex interplay of FGF23 with calcitriol and PTH. In consistent with the model, our in vitro experimentation indicates that expression of FGF23 is activated in the presence of P though a G-protein linked receptor. We expect that further efforts on modeling and experimental evaluation would contribute to diagnosing patients with metabolic diseases such as osteoporosis and chronic kidney diseases, and developing FGF23-linked treatment strategies.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"131-42"},"PeriodicalIF":0.0,"publicationDate":"2009-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s2990","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28446016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The goldfish SG2NA gene encodes two alpha-type regulatory subunits for PP-2A and displays distinct developmental expression pattern.","authors":"Hai-Li Ma, Yun-Lei Peng, Lili Gong, Wen-Bin Liu, Shuming Sun, Jiao Liu, Chun-Bing Zheng, Hu Fu, Dan Yuan, Junqiong Zhao, Pei-Chao Chen, Si-si Xie, Xiao-Ming Zeng, Ya-Mei Xiao, Yun Liu, David Wan-Cheng Li","doi":"10.4137/grsb.s2764","DOIUrl":"10.4137/grsb.s2764","url":null,"abstract":"<p><p>SG2NA is a member of the striatin protein family. In human and mouse, the SG2NA gene encodes two major protein isoforms: SG2NA alpha and SG2NA beta. The functions of these proteins, except for acting as the regulatory subunits for PP-2A, remain largely unknown. To explore the possible functions of SG2NA in lower vertebrates, we have isolated two SG2NA cDNAs from goldfish, Carassius auratus. Our results reveal that the first cDNA contains an ORF of 2118 bp encoding a deduced protein with 705 amino acids, and the second one 2148 bp coding for a deduced protein of 715 amino acids. Comparative analysis reveals that both isoforms belong to the alpha-type, and are named SG2NA alpha and SG2NA alpha(+). RT-PCR and western blot analysis reveal that the SG2NA gene is differentially expressed in 9 tissues examined. During goldfish development, while the SG2NA mRNAs remain relatively constant in the first 3 stages and then become decreased and fluctuated from gastrula to larval hatching, the SG2NA proteins are fluctuated, displaying a peak every 3 to 4 stages. Each later peak is higher than the earlier one and the protein expression level becomes maximal at hatching stage. Together, our results reveal that SG2NA may play an important role during goldfish development and also in homeostasis of most adult tissues.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"115-29"},"PeriodicalIF":0.0,"publicationDate":"2009-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28446015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of Petri nets in bone remodeling.","authors":"Lingxi Li,&nbsp;Hiroki Yokota","doi":"10.4137/grsb.s2881","DOIUrl":"https://doi.org/10.4137/grsb.s2881","url":null,"abstract":"<p><p>Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"105-14"},"PeriodicalIF":0.0,"publicationDate":"2009-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s2881","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28446014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Letter to the editor: Does dicer expression affect shRNA processing?","authors":"Neil Senzer,&nbsp;Donald Rao,&nbsp;John Nemunaitis","doi":"10.4137/grsb.s2551","DOIUrl":"https://doi.org/10.4137/grsb.s2551","url":null,"abstract":"<p><p>Elevated Dicer and Drosha mRNA levels have been documented across a range of tumor types (including ovarian carcinoma) by a number of investigators without any demonstrable correlation with patient survival nor evidence of interference with shRNA processing. A recent publication by Merritt et al. (NEJM 359(25):2641-50, 2008) reporting their findings in patients with ovarian carcinoma reach opposite conclusions. Further study will be needed to resolve this issue.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"103-4"},"PeriodicalIF":0.0,"publicationDate":"2009-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s2551","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28446013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Safety and in vivo expression of a GNE-transgene: a novel treatment approach for hereditary inclusion body myopathy-2.","authors":"Anagha P Phadke,&nbsp;Chris Jay,&nbsp;Salina J Chen,&nbsp;Courtney Haddock,&nbsp;Zhaohui Wang,&nbsp;Yang Yu,&nbsp;Derek Nemunaitis,&nbsp;Gregory Nemunaitis,&nbsp;Nancy S Templeton,&nbsp;Neil Senzer,&nbsp;Phillip B Maples,&nbsp;Alex W Tong,&nbsp;John Nemunaitis","doi":"10.4137/grsb.s2210","DOIUrl":"https://doi.org/10.4137/grsb.s2210","url":null,"abstract":"<p><p>Hereditary inclusion body myopathy-2 (HIBM2) is an adult-onset, muscular disease caused by mutations in the GNE gene. HIBM2-associated GNE mutations causing hyposialyation have been proposed to contribute to reduced muscle function in patients with HIBM2, though the exact cause of this disease is unknown. In the current studies we examined pre-clinical in vivo toxicity, and expression of the plasmid-based, CMV driven wild-type GNE plasmid vector. The plasmid vector was injected intramuscularly (IM) or systemically (IV) into BALB/c mice, following encapsulation in a cationic liposome (DOTAP:Cholesterol). Single IM injections of the GNE-lipoplex at 40 microg did not produce overt toxicity or deaths, indicating that the no observable adverse effect level (NOAEL) dose for IM injection was >or=40 microg. Single intravenous (IV) infusion of GNE-lipoplex was lethal in 33% of animals at 100 microg dose, with a small proportion of animals in the 40 microg cohort demonstrating transient toxicity. Thus the NOAEL dose by the IV route was greater than 10 microg and less than or equal to 40 microg. Real-time RT-qPCR analysis demonstrated recombinant human GNE mRNA expression in 100% of muscle tissues that received IM injection of 40 microg GNE-lipoplex, at 2 weeks. These results indicate that GNE-lipoplex gene transfer is safe and can produce durable transgene expression in treated muscles. Our findings support future exploration of the clinical efficacy of GNE-lipoplex for experimental gene therapy of HIBM2.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"89-101"},"PeriodicalIF":0.0,"publicationDate":"2009-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s2210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28445475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sigma factors for cyanobacterial transcription.","authors":"Sousuke Imamura,&nbsp;Munehiko Asayama","doi":"10.4137/grsb.s2090","DOIUrl":"https://doi.org/10.4137/grsb.s2090","url":null,"abstract":"<p><p>Cyanobacteria are photosynthesizing microorganisms that can be used as a model for analyzing gene expression. The expression of genes involves transcription and translation. Transcription is performed by the RNA polymerase (RNAP) holoenzyme, comprising a core enzyme and a sigma (sigma) factor which confers promoter selectivity. The unique structure, expression, and function of cyanobacterial sigma factors (and RNAP core subunits) are summarized here based on studies, reported previously. The types of promoter recognized by the sigma factors are also discussed with regard to transcriptional regulation.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"65-87"},"PeriodicalIF":0.0,"publicationDate":"2009-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s2090","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28445474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An effective tri-clustering algorithm combining expression data with gene regulation information.","authors":"Ao Li,&nbsp;David Tuck","doi":"10.4137/grsb.s1150","DOIUrl":"https://doi.org/10.4137/grsb.s1150","url":null,"abstract":"<p><strong>Motivation: </strong>Bi-clustering algorithms aim to identify sets of genes sharing similar expression patterns across a subset of conditions. However direct interpretation or prediction of gene regulatory mechanisms may be difficult as only gene expression data is used. Information about gene regulators may also be available, most commonly about which transcription factors may bind to the promoter region and thus control the expression level of a gene. Thus a method to integrate gene expression and gene regulation information is desirable for clustering and analyzing.</p><p><strong>Methods: </strong>By incorporating gene regulatory information with gene expression data, we define regulated expression values (REV) as indicators of how a gene is regulated by a specific factor. Existing bi-clustering methods are extended to a three dimensional data space by developing a heuristic TRI-Clustering algorithm. An additional approach named Automatic Boundary Searching algorithm (ABS) is introduced to automatically determine the boundary threshold.</p><p><strong>Results: </strong>Results based on incorporating ChIP-chip data representing transcription factor-gene interactions show that the algorithms are efficient and robust for detecting tri-clusters. Detailed analysis of the tri-cluster extracted from yeast sporulation REV data shows genes in this cluster exhibited significant differences during the middle and late stages. The implicated regulatory network was then reconstructed for further study of defined regulatory mechanisms. Topological and statistical analysis of this network demonstrated evidence of significant changes of TF activities during the different stages of yeast sporulation, and suggests this approach might be a general way to study regulatory networks undergoing transformations.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"49-64"},"PeriodicalIF":0.0,"publicationDate":"2009-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/grsb.s1150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28445472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel function of ethylene.","authors":"Aiko Amagai","doi":"10.4137/grsb.s2202","DOIUrl":"10.4137/grsb.s2202","url":null,"abstract":"<p><p>The cellular slime mold, Dictyostelium mucoroides-7 (Dm7) exhibits clear dimorphism; macrocyst formation as a sexual process and sorocap formation as an asexual process. These two life cycles are regulated by two regulators, ethylene and cyclic AMP (cAMP). This is the first report demonstrating a novel function of ethylene at the cellular level. That is, ethylene induces a zygote formed by cell fusion and subsequent nuclear fusion. Recently, the function of ethylene at the molecular level has been clarified as it induces zygote formation through an enhanced expression of a novel gene, zyg1. The signaling pathway for induction or inhibition of zygote formation is now trying to be clarified focusing on the ZYG1 protein.</p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"3 ","pages":"21-30"},"PeriodicalIF":0.0,"publicationDate":"2009-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28445471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}