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Energy Cost Minimization of a Compressor Station by Modified Genetic Algorithms

ENGINEERING LETTERS 2015年第4期23卷 258-268页

作者： Zhang, X. Wu, C. China Univ Petr Natl Engn Lab Pipeline Safety Beijing 102200 Peoples R China

Energy cost minimization of a compressor station is an integral part of operation optimization for gas pipelines. Given the suction flow rate, the suction pressure and temperature, and the required discharge pressure of a compressor station, the operator needs to figure out the optimal compressor combination and load distribution of the station. To investigate the feasibility of genetic algorithms for solving this problem and to examine how the coding sequence of a genetic algorithm influences its performance, four genetic algorithms which are different in aspect of coding method and coding sequence were devised for this problem. These four algorithms are tested on multiple case problems of two in-service compressor stations. Comparison of the four algorithms shows that the coding sequence of a genetic algorithm influences its ability to find a feasible solution. The weaker this ability is, the more severely the algorithm is impacted. However, once any feasible solution is found, the coding sequence just impacts slightly on how steady a genetic algorithm performs in solving a problem multiple times, and no obvious bias is observed. According to the comparison, one of the four genetic algorithms was chosen to compare with two global optimization approaches, and the results show that the genetic algorithm is comparable with these global optimization methods.

关键词： coding sequence compressor station genetic algorithm power optimization

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The N⁶-methyladenosine modification posttranscriptionally regulates hepatic UGT2B7 expression

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BIOCHEMICAL PHARMACOLOGY 2021年 189卷 114402页

作者： Ondo, Kyoko Isono, Motoki Nakano, Masataka Hashiba, Shiori Fukami, Tatsuki Nakajima, Miki Kanazawa Univ Fac Pharmaceut Sci Drug Metab & Toxicol Kakuma Machi Kanazawa Ishikawa 9201192 Japan Kanazawa Univ WPI Nano Life Sci Inst WPI NanoLSI Kakuma Machi Kanazawa Ishikawa 9201192 Japan

UDP-glucuronosyltransferases (UGTs) are enzymes catalyzing the glucuronidation of various endogenous and exogenous compounds. In this study, we examined the possibility that N-6-methyladenosine (m(6)A) modification affects hepatic UGT expression. Treatment of HepaRG cells with 3-deazaadenosine, an inhibitor of RNA methylation, significantly increased UGT1A1, UGT1A3, UGT1A4, UGT1A9, UGT2B7, UGT2B10, and UGT2B15 mRNA levels (1.3- to 2.6-fold). Among them, we focused on UGT2B7 because it most highly contributes to glucuronidation of clinically used drugs. Methylated RNA immunoprecipitation assays revealed that UGT2B7 mRNA in HepaRG cells and human livers is subjected to m(6)A modification mainly at the 5' untranslated region (UTR) and secondarily at the 3'UTR. UGT2B7 mRNA and protein levels in Huh-7 cells were significantly increased by double knockdown of methyltransferase-like 3 (METTL3) and METTL14, whereas those were decreased by knockdown of fat mass and obesity-associated protein (FTO) or alkB homolog 5, RNA demethylase (ALKBH5), suggesting that m(6)A modification downregulates UGT2B7 expression. By experiments using actinomycin D, an inhibitor of transcription, it was demonstrated that ALKBH5-mediated demethylation would attenuate UGT2B7 mRNA degradation, whereas METTL3/METTL14 or FTO-mediated m(6)A modification would alter the transactivity of UGT2B7. Luciferase assays revealed that the promoter region at -118 to -106 has a key role in the decrease in transactivity of UGT2B7 by FTO knockdown. We found that hepatocyte nuclear factor 4 alpha (HNF4 alpha) expression was significantly decreased by knockdown of FTO, indicating that this would be the underlying mechanism of the decreased transactivity of UGT2B7 by knockdown of FTO. Interestingly, treatment with entacapone, which is used for the treatment of Parkinson's disease and is an inhibitor of FTO, decreased HNF4 alpha and UGT2B7 expression. In conclusion, this study clarified that RNA methylation posttranscrip

关键词： ALKBH5 AlkB homolog 5 RNA demethylase CDS coding sequence COMT catechol- O -methyltransferase DAA 3-deazaadenosine DMEM Dulbecco’s modified Eagle’s medium DMSO dimethyl sulfoxide FBS fetal bovine serum FOXO1 forkhead box protein O1 FTO fat mass and obesity-associated protein G6Pase glucose-6-phosphatase GAPDH glyceraldehyde-3-phosphate dehydrogenase HNF hepatocyte nuclear factors m 6 A N 6 -methyladenosine m 6 Am N 6 2′- O -dimethyladenosine MeRIP m 6 A RNA immunoprecipitation METTL methyltransferase like miRNAs MicroRNAs P450 cytochrome P450 miRNA microRNAs SAM S -adenosylmethionine siRNA small interference RNA UGT UDP-glucuronosyltransferase UTR untranslated region YTH YT521-B homology

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PABPN1, a Target of p63, Modulates Keratinocyte Differentiation through Regulation of p63α mRNA Translation

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JOURNAL OF INVESTIGATIVE DERMATOLOGY 2020年第11期140卷 2166-+页

作者： Mohibi, Shakur Zhang, Jin Chen, Xinbin Univ Calif Davis Comparat Oncol Lab Sch Vet Med 2128A Tupper Hall Davis CA 95616 USA Univ Calif Davis Comparat Oncol Lab Sch Med 2128A Tupper Hall Davis CA 95616 USA

p63 is expressed from two promoters and produces two N-terminal isoforms, TAp63 and Delta Np63. Alternative splicing creates three C-terminal isoforms p63 alpha, p63 beta, and p63 delta, whereas alternative polyadenylation (APA) in coding sequence creates two more C-terminal isoforms p63 gamma and p63 epsilon. Although several transcription factors have been identified to differentially regulate the N-terminal p63 isoforms, it is unclear how the C-terminal p63 isoforms are regulated. Thus, we determined whether PABPN1, a key regulator of APA, may differentially regulate the C-terminal p63 isoforms. We found that PABPN1 deficiency increases p63 gamma mRNA through APA in coding sequence. We also found that PABPN1 is necessary for p63 alpha translation by modulating the binding of translation initiation factors eIF4E and eIF4G to p63 alpha mRNA. Moreover, we found that the p53 family, especially p63 alpha, regulates PABPN1 transcription, suggesting that the mutual regulation between p63 and PABPN1 forms a feedback loop. Furthermore, we found that PABPN1 deficiency inhibits keratinocyte cell growth, which can be rescued by ectopic Delta Np63 alpha. Finally, we found that PABPN1 controls the terminal differentiation of HaCaT keratinocytes by modulating Delta Np63 alpha expression. Taken together, our findings suggest that PABPN1 is a key regulator of the C-terminal p63 isoforms through APA in coding sequence and mRNA translation and that the p63-PABPN1 loop modulates p63 activity and the APA landscape.

关键词： APA alternative polyadenylation CDS coding sequence IP immunoprecipitation KD knockdown KO knockout PAS poly(A) sites PBST phosphate buffered saline with Tween 20 pcDNA3 plasmid cloning DNA3 RE response element RT-PCR reverse transcriptase PCR siRNA small interfering RNA UTR untranslated region

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Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol

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MOLECULAR & CELLULAR PROTEOMICS 2022年第8期21卷 100264页

作者： Bogaert, Annelies Fijalkowska, Daria Staes, An Van de Steene, Tessa Demol, Hans Gevaert, Kris VIB VIB Ctr Med Biotechnol Ghent Belgium Univ Ghent Dept Biomol Med Ghent Belgium

Ribosome profiling has revealed translation outside canonical coding sequences, including translation of short upstream ORFs, long noncoding RNAs, overlapping ORFs, ORFs in UTRs, or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling, and CRISPR-based screens showed that hundreds of ORFs derived from noncoding transcripts produce (micro)proteins, whereas other studies failed to find evidence for such types of noncanonical translation products. Here, we attempted to discover translation products from noncoding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from non -coding regions but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap-based interactome analysis of two N-terminal proteoforms originating from noncoding regions showed the functional potential of these novel proteins.

关键词： proteomics protein N termini proteoforms novel proteins AA amino acid ACN acetonitrile AGC automatic gain control aTIS annotated TIS CDS coding sequence CHX cycloheximide COFRADIC combined fractional diagonal chromatography DMEM Dulbecco's modified Eagle's medium eDHFR Escherichia coli dihydrofolate reductase FA formic acid f.c. final concentration FDR false discovery rate HEK293 human embryonic kidney 293 cell line iBAQ intensity-based absolute quantification I.D. internal diameter iMet initiator methionine lncRNA long noncoding RNA LTM lactimidomycin MC missed cleavage MetAp methionine aminopeptidase MS mass spectrometry NCE normalized collision energy NHS N -hydroxysuccinimide Nt N-terminal NTR noncoding transcript PSM peptide-to-spectrum match Ribo-Seq ribosome sequencing sORF small ORF TBS-T TBS supplemented with 0.1% Tween-20 TIS translation initiation site uORF upstream ORF VLP viral-like particle VSV-G vesicular stomatitis virus G protein

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Effect of Different Types of sequence Data on Palaeognath Phylogeny

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GENOME BIOLOGY AND EVOLUTION 2023年第6期15卷 evad092页

作者： Takezaki, Naoko Kagawa Univ Fac Med Lab Life Sci Takamatsu Kagawa Japan

Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements, introns, and ultraconserved elements. Using the noncoding loci together with protein-coding loci, this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene tree-based approaches supported rheas as the group that diverged first among groups (1)-(4). Whereas gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than noncoding loci. Regarding the relationships of (1)-(4), the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogeneous model and suggested the clustering of kiwi and cassowaries and emu the most likely with similar to 40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.

关键词： coding sequence noncoding sequence outgroup nucleotide composition RY-coding gene tree

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Widespread non-modular overlapping codes in the coding regions*

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PHYSICAL BIOLOGY 2020年第3期17卷 031002页

作者： Bergman, Shaked Tuller, Tamir Tel Aviv Univ Dept Biomed Engn Tel Aviv Israel Tel Aviv Univ Sagol Sch Neurosci Tel Aviv Israel

Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5 ' UTR and 3 ' UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.

关键词： gene expression coding sequence molecular evolution

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EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies

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MOLECULAR ECOLOGY RESOURCES 2012年第5期12卷 967-971页

作者： Li, Chenhong Riethoven, Jean-Jack M. Naylor, Gavin J. P. Shanghai Ocean Univ Coll Fisheries & Life Sci Shanghai 201306 Peoples R China Univ Nebraska Bioinformat Core Res Facil Lincoln NE 68588 USA Coll Charleston Grice Marine Lab Charleston SC 29412 USA

Recent innovations in next-generation sequencing have lowered the cost of genome projects. Nevertheless, sequencing entire genomes for all representatives in a study remains expensive and unnecessary for most studies in ecology, evolution and conservation. It is still more cost-effective and efficient to target and sequence single-copy nuclear gene markers for such studies. Many tools have been developed for identifying nuclear markers, but most of these have focused on particular taxonomic groups. We have built a searchable database, EvolMarkers, for developing single-copy coding sequence (CDS) and exon-primed-intron-crossing (EPIC) markers that is designed to work across a broad range of phylogenetic divergences. The database is made up of single-copy CDS derived from BLAST searches of a variety of metazoan genomes. Users can search the database for different types of markers (CDS or EPIC) that are common to different sets of input species with different divergence characteristics. EvolMarkers can be applied to any taxonomic group for which genome data are available for two or more species. We included 82 genomes in the first version of EvolMarkers and have found the methods to be effective across Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata and plants. We demonstrate the effectiveness of searching for CDS markers within annelids and show how to find potentially useful intronic markers within the lizard Anolis.

关键词： coding sequence comparative genomics exon-primed-intron-crossing nuclear markers phylogenetics single-copy gene

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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

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MOLECULAR & CELLULAR PROTEOMICS 2023年第9期22卷 100631页

作者： Prensner, John R. Abelin, Jennifer G. Kok, Leron W. Clauser, Karl R. Mudge, Jonathan M. Ruiz-Orera, Jorge -Sternberg, Michal Bassani Moritz, Robert L. Deutsch, Eric W. van Heesch, Sebastiaan Univ Michigan Dept Pediat Div Pediat Hematol Oncol Med Sch Ann Arbor MI 48109 USA Univ Michigan Med Sch Dept Biol Chem Ann Arbor MI 48109 USA Broad Inst MIT & Harvard Cambridge MA USA Princess Maxima Ctr Pediat Oncol Utrecht Netherlands European Mol Biol Lab European Bioinformat Inst Wellcome Genome Campus Cambridge England Helmholtz Assoc MDC Cardiovasc & Metab Sci Max Delbruck Ctr Mol Med Berlin Germany Univ Lausanne Ludwig Inst Canc Res Agora Ctr Bugnon 25A Lausanne Switzerland Ctr Hosp Univ Vaudois CHUV Dept Oncol Lausanne Switzerland Agora Canc Res Ctr Lausanne Switzerland Inst Syst Biol ISB Seattle WA USA

Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has the potential to expand the number of human protein CDSs by 30%, from similar to 19,500 annotated CDSs to over 26,000 annotated CDSs. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of noncanonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome but searching for guidance on how to proceed. Here, we discuss the current state of noncanonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein coding."

关键词： Ribo-Seq mass spectrometry immunopeptidomics microprotein noncanonical ORF CDS coding sequence DIA data-independent acquisition doORF downstream overlapping ORF dORF downstream ORF FDR false discovery rate HLA human leukocyte antigen HUPO/HPP Human Proteome Organization/Human Proteome Project intORF internal ORF lncRNA long noncoding RNA MS mass spectrometry NIH National Institutes of Health PSM peptide-spectrum match PTM post-translational modification uORF upstream ORF uoORF upstream overlapping ORF

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CLONING AND SEQUENCING OF A CDNA-ENcoding THE MOUSE BRAIN-TYPE CANNABINOID RECEPTOR PROTEIN

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DNA sequence 1995年第6期5卷 385-388页

作者： CHAKRABARTI, A ONAIVI, ES CHAUDHURI, G MEHARRY MED COLL DIV BIOMED SCINASHVILLETN 37208 MEHARRY MED COLL DEPT PHARMACOLNASHVILLETN 37208

Mouse brain-type cannabinoid receptor (CB1) cDNA was cloned and sequenced. Comparison to rat and human CB1 sequences showed extensive homology (>96%) both at the nucleotide and protein levels implicating the import... 详细信息

关键词： coding sequence PEPTIDE sequence ACTIVE SITE

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Post-Transcriptional and Post-Translational Regulation of PTEN by Transforming Growth Factor-β1

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JOURNAL OF CELLULAR BIOCHEMISTRY 2009年第6期106卷 1102-1112页

作者： Yang, Yong Zhou, Feng Fang, Zengyu Wang, Liying Li, Zengxia Sun, Lidong Wang, Can Yao, Wantong Cai, Xiumei Jin, Jiawei Zha, Xiliang Fudan Univ Dept Biochem & Mol Biol Shanghai Med Coll Shanghai 200032 Peoples R China Minist Hlth Key Lab Glycoconjugate Res Shanghai 200032 Peoples R China

PTEN is a critical tumor suppressor gene mutated frequently in various human cancers. Previous studies have showed that PTEN mRNA expression is down-regulated by TGF-beta 1 in various cell lines. In present study, we have found that TGF-beta 1 down-regulates PTEN mRNA and protein expression in a dose- and time-dependent manner in hepatocarcinoma cell line SMMC-7721. Based on the PTEN promoter dual-luciferase report assay, we have found that PTEN transcription is not affected by TGF-beta 1. By using transcriptional inhibitor actinomycin D (Act D), the turnover rate of PTEN transcripts appeared to be accelerated during TGF-beta 1 stimulation, which indicated that down-regulation of PTEN by TGF-beta 1 was post-transcriptional. What interested us was that transfection of PTEN coding sequence increased TGF-beta 1-induced degradation of PTEN mRNA, suggesting that PTEN coding region was account for TGF-beta 1-mediated down-regulation of PTEN. In addition, TGF-beta 1 down-regulated PTEN expression was blocked by the T beta IR inhibitor SB43 1542 and the p38 inhibitor SB203580, suggesting Smad and p38 MAPK signal pathways played crucial roles in PTEN down-regulation via TGF-beta 1 stimulation. In this study, we also found TGF-beta 1 accelerated down-regulation of PTEN through the ubiquitin-proteasome pathway. Collectively, our data clearly demonstrated that TGF-beta 1 mediated down-regulation of PTEN was post-transcriptional and post-translational, depending on its coding sequence, Smad and p38-MAPK signal pathways were involved in this down-regulation. J. Cell. Biochem. 106: 1102-1112, 2009. (c) 2009 Wiley-Liss, Inc.

关键词： POST-TRANSCRIPTIONAL TGF-beta 1 PTEN coding sequence SMAD

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