Database : MEDLINE
Search on : sequence and analysis [Words]
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[PMID]: 29524579
[Au] Autor:Liu L; Fu Y; Zhu F; Mu C; Li R; Song W; Shi C; Ye Y; Wang C
[Ad] Address:Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China.
[Ti] Title:Transcriptomic analysis of Portunus trituberculatus reveals a critical role for WNT4 and WNT signalling in limb regeneration.
[So] Source:Gene;, 2018 Mar 07.
[Is] ISSN:1879-0038
[Cp] Country of publication:Netherlands
[La] Language:eng
[Ab] Abstract:The swimming crab (Portunus trituberculatus) is among the most economically important seawater crustacean species in Asia. Despite its commercial importance and being well-studied status, genomic and transcriptomic data are scarce for this crab species. In the present study, limb bud tissue was collected at different developmental stages post amputation for transcriptomic analysis. Illumina RNA-sequencing was applied to characterise the limb regeneration transcriptome and identify the most characteristic genes. A total of 289,018 transcripts were obtained by clustering and assembly of clean reads, producing 150,869 unigenes with an average length of 956 bp. Subsequent analysis revealed WNT signalling as the key pathway involved in limb regeneration, with WNT4 a key mediator. Overall, limb regeneration appears to be regulated by multiple signalling pathways, with numerous cell differentiation, muscle growth, moult, metabolism, and immune-related genes upregulated, including WNT4, LAMA, FIP2, FSTL5, TNC, HUS1, SWI5, NCGL, SLC22, PLA2, Tdc2, SMOX, GDH, and SMPD4. This is the first experimental study done on regenerating claws of P. trituberculatus. These findings expand existing sequence resources for crab species, and will likely accelerate research into regeneration and development in crustaceans, particularly functional studies on genes involved in limb regeneration.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  2 / 727595 MEDLINE  
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[PMID]: 29524574
[Au] Autor:Zhang X; Li L; Jiang H; Ma J; Li J; Chen J
[Ad] Address:Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong 510260, People's Republic of China.
[Ti] Title:Identification and differential expression of microRNAs in testis and ovary of Amur sturgeon (Acipenser schrenckii).
[So] Source:Gene;, 2018 Mar 07.
[Is] ISSN:1879-0038
[Cp] Country of publication:Netherlands
[La] Language:eng
[Ab] Abstract:BACKGROUND: MicroRNAs (miRNAs) cooperate with sex-related genes in post-transcriptional regulation and play extremely important roles in the establishment of sexually dimorphic traits in animals. However, the gonad miRNAs and expression patterns of miRNAs in sturgeon have not been investigated. METHODS: In the present study, we used high-throughput small RNA sequencing (RNA-Seq) to discover gonad miRNAs from the ovaries and testes of Amur sturgeons (Acipenser schrenckii). Further, microarray and real-time PCR assays were performed to identify the expression patterns of gonad miRNAs. RESULTS: As a result, a total of 679 conserved and 51 novel miRNAs were successfully discovered in the gonads of A. schrenckii. Moreover, we found wide sequence variations (isomiRs) in gonad miRNAs, including 5' and 3' isomiRs. Our microarray analysis further characterized the 730 miRNAs expression profiles, which indicated that 117 differentially expressed miRNAs were detected with sex-biased patterns: 71 testis-biased and 46 ovary-biased miRNAs. Based on bioinformatics prediction, we found that there were functional differences between the testis-biased and ovary-biased miRNA targets involved in reproductive-related GO and KEGG pathways. Further, the association of the differentially expressed miRNAs and sex-related target mRNAs was uncovered. Finally, the expression patterns of 11 sex-biased miRNAs and 7 sex-related targets were validated in testes and ovaries using real-time PCR. Putative, negatively expressed miRNA-mRNA relationships were confirmed, such as Dmrt1 and asc-miR-2779, AR and asc-miR-203b-3p, foxl2 and asc-miR-30d. CONCLUSION: This study provides information regarding the gonad miRNAs in sturgeon. The differential expression miRNAs in the gonads will help us to further understand the role of miRNA-mediated post-transcriptional regulation in the ovary and testis of sturgeon.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  3 / 727595 MEDLINE  
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[PMID]: 29524546
[Au] Autor:Abdollahi S; Rasooli I; Gargari SLM
[Ad] Address:Department of Biology, Shahed University, Tehran-Qom Express Way, Tehran, Iran.
[Ti] Title:An in silico structural and physicochemical characterization of TonB-dependent copper receptor in A. baumannii.
[So] Source:Microb Pathog;, 2018 Mar 07.
[Is] ISSN:1096-1208
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:Acinetobacter baumannii is an opportunistic multidrug resistant pathogen. TonB-dependent copper receptor is an outer membrane protein and has a role in binding of A. baumannii to host cell via attachment to fibronectin. Moreover, it is highly expressed in biofilm community. In this study the properties of copper receptor were analyzed in silico and its vaccine potential was investigated. TonB-dependent copper and iron receptor domains plus one plug domain at N-terminal were determined by domain analysis. Topology modeling showed 22 ß-strands, 11 loops and 10 periplasmic turns. Interaction of this protein with TonB2 energy transducer was also indicated. Beside the antigenicity, this protein could take part in bacterial virulence. The more preferable 3D structure was selected amongst all 26 predicted structures, refined and used in prediction of ligand binding site and conformational epitope. The results of B and T-cell epitope mapping indicated 8 potential areas in the protein sequence and structure that seems to be able to stimulate both humoral and cellular immune responses. Based on the alignment result, this protein and all selected epitopes are extremely conserved among A. baumannii strains which can be tested as sub unit vaccine by in vivo studies.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  4 / 727595 MEDLINE  
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[PMID]: 29524440
[Au] Autor:Wu C; Gao R; De Marinis Y; Zhang Y
[Ad] Address:School of Control Science and Engineering, Shandong University, Jinan, 250061, China.
[Ti] Title:A Novel Model for Protein Sequence Similarity Analysis Based on Spectral Radius.
[So] Source:J Theor Biol;, 2018 Mar 07.
[Is] ISSN:1095-8541
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:Advances in sequencing technologies led to rapid increase in the number and diversity of biological sequences, which facilitated development in the sequence research. In this paper, we present a new method for analyzing protein sequence similarity. We calculated the spectral radii of 20 amino acids (AAs) and put forward a novel 2-D graphical representation of protein sequences. To characterize protein sequences numerically, three groups of features were extracted and related to statistical, dynamics measurements and fluctuation complexity of the sequences. With the obtained feature vector, two models utilizing Gaussian Kernel similarity and Cosine similarity were built to measure the similarity between sequences. We applied our method to analyze the similarities/dissimilarities of four data sets. Both proposed models received consistent results with improvements when compared to that obtained by the ClustalW analysis. The novel approach we present in this study may therefore benefit protein research in medical and scientific fields.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  5 / 727595 MEDLINE  
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[PMID]: 29524415
[Au] Autor:Chen K; Wang Y; Sun J
[Ad] Address:School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin, 300387, China. Electronic address: chenke@tjpu.edu.cn.
[Ti] Title:A statistical analysis on transcriptome sequences: The enrichment of Alu-element is associated with subcellular location.
[So] Source:Biochem Biophys Res Commun;, 2018 Mar 07.
[Is] ISSN:1090-2104
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:The Alu-element plays important roles in mediating alternative splicing, RNA editing and translation regulation. However, the distribution and function of the Alu-element are never analysed at the transcriptome level. This study presents a statistical analysis of the Alu-element on human transcriptome. We found that mRNAs and lncRNAs share the same sequence form for the Alu-element. The Alu-element covers 5.8% of the coding transcripts and 17.1% of the coding genes for mRNAs, and covers 9.3% of the transcripts and 13.6% of the genes for lncRNAs. The Alu-element is preferentially located at the 3' end. Statistical analysis demonstrates that the enrichment of Alu-element is associated with subcellular location. For instance, Alu-inclusive transcripts are overexpressed in nucleus, mitochondrion and Golgi apparatus membrane while under-expressed in cell membrane and extracellular space. We found that genes contain both Alu-element and S- domains of 7SL RNA are all associated with cellular activities carried out in mitochondrion.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  6 / 727595 MEDLINE  
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[PMID]: 29524380
[Au] Autor:Tuma Sabah J; Zulkifli RM; Shahir S; Ahmed F; Abdul Kadir MR; Zakaria Z
[Ad] Address:Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Malaysia.
[Ti] Title:In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool.
[So] Source:Anal Biochem;, 2018 Mar 06.
[Is] ISSN:1096-0309
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Distinctive bioactivities possessed by luteolin (3', 4', 5, 7-tetrahydroxy-flavone) are advantageous for sundry practical applications. This paper reports the in vitro selection and characterization of single stranded-DNA (ssDNA) aptamers, specific for luteolin (LUT). 76-mer library containing 1015 randomized ssDNA were screened via systematic evolution of ligands by exponential enrichment (SELEX). The recovered ssDNA pool from the 8th round was amplified with unlabeled primers and cloned into PSTBlue-1 vector prior to sequencing. 22 of LUT-binding aptamer variants were further classified into one of the seven groups based on their N40 random sequence regions, wherein one representative from each group was characterized. The dissociation constant of aptamers designated as LUT#28, LUT#20 and LUT#3 was discerned to be 107, 214 and 109 nM, respectively with high binding affinity towards LUT. Prediction analysis of the secondary structure suggested discrete features with typical loop and stem motifs. Furthermore, LUT#3 displayed higher specificity with insignificant binding toward kaempferol and quercetin despite its structural and functional similarity compared to LUT#28 and LUT#20. Further LUT#3 can detect free luteolin within 0.2-1 mM in solution. It was suggested that LUT#3 aptamer were the most suitable for LUT recognition tool at laboratory scale based on the condition tested.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  7 / 727595 MEDLINE  
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[PMID]: 29512653
[Au] Autor:Scapin G; Dandey VP; Zhang Z; Prosise W; Hruza A; Kelly T; Mayhood T; Strickland C; Potter CS; Carragher B
[Ad] Address:Merck & Co., Inc., Department of Biochemical Engineering & Structure, 2000 Galloping Hill Rd. Kenilworth, NJ, 07033, USA.
[Ti] Title:Structure of the Insulin Receptor-Insulin Complex by Single Particle CryoEM analysis.
[So] Source:Nature;, 2018 Feb 28.
[Is] ISSN:1476-4687
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:The insulin receptor (IR) is a dimeric protein that plays a crucial role in controlling glucose homeostasis, regulating lipid, protein and carbohydrate metabolism, and modulating brain neurotransmitter levels . IR dysfunction has been associated with many diseases, including diabetes, cancer, and Alzheimer's disease . The primary sequence has been known since the 1980s , and is composed of an extracellular portion (ectodomain, ECD), a single transmembrane helix and an intracellular tyrosine kinase domain. Insulin binding to the dimeric ECD triggers kinase domain auto-phosphorylation and subsequent activation of downstream signaling molecules. Biochemical and mutagenesis data have identified two putative insulin binding sites (S1 and S2) . While insulin bound to an ECD fragment containing S1 and the apo ectodomain have been characterized structurally , details of insulin binding to the full receptor and the signal propagation mechanism are still not understood. Here we report single particle cryoEM reconstructions for the 1:2 (4.3 Å) and 1:1 (7.4 Å) IR ECD dimer:Insulin complexes. The symmetric 4.3 Å structure shows two insulin molecules per dimer, each bound between the Leucine-rich sub domain L1 of one monomer and the first fibronectin-like domain (FnIII-1) of the other monomer, and making extensive interactions with the α subunit C-terminal helix (α-CT helix). The 7.4 Å structure has only one similarly bound insulin per receptor dimer. The structures confirm the S1 binding interactions and define the full S2 binding site. These insulin receptor states suggest that recruitment of the α-CT helix upon binding of the first insulin changes the relative subdomain orientations and triggers downstream signal propagation.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:Publisher
[do] DOI:10.1038/nature26153

  8 / 727595 MEDLINE  
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[PMID]: 29511176
[Au] Autor:Piguet F; Ouldali H; Pastoriza-Gallego M; Manivet P; Pelta J; Oukhaled A
[Ad] Address:LAMBE UMR 8587, Université de Cergy-Pontoise, 95300, Pontoise, France. fabien.piguet@u-cergy.fr.
[Ti] Title:Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore.
[So] Source:Nat Commun;9(1):966, 2018 Mar 06.
[Is] ISSN:2041-1723
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:In-Data-Review
[do] DOI:10.1038/s41467-018-03418-2

  9 / 727595 MEDLINE  
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[PMID]: 29510665
[Au] Autor:Sugiaman-Trapman D; Vitezic M; Jouhilahti EM; Mathelier A; Lauter G; Misra S; Daub CO; Kere J; Swoboda P
[Ad] Address:Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
[Ti] Title:Characterization of the human RFX transcription factor family by regulatory and target gene analysis.
[So] Source:BMC Genomics;19(1):181, 2018 Mar 06.
[Is] ISSN:1471-2164
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:BACKGROUND: Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS: We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS: The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:In-Data-Review
[do] DOI:10.1186/s12864-018-4564-6

  10 / 727595 MEDLINE  
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[PMID]: 29506527
[Au] Autor:Liu Y; Zhou RM; Zhang YL; Wang DQ; Li SH; Yang CY; Qian D; Zhao YL; Zhang HW; Xu BL
[Ad] Address:Henan Center for Disease Control and Prevention, Zhengzhou, Henan, China. liuying@hncdc.com.cn.
[Ti] Title:Analysis of polymorphisms in the circumsporozoite protein gene of Plasmodium vivax isolates from Henan Province, China.
[So] Source:Malar J;17(1):103, 2018 Mar 05.
[Is] ISSN:1475-2875
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:BACKGROUND: Plasmodium vivax malaria has historically been a major source of disease in Henan, China. In the 1970s, the morbidity of malaria was highest in the country. With support from the government and the efforts of healthcare personnel, the reported malaria cases have declined dramatically and a national elimination programme was launched in 2010. To achieve the goal, it is essential to study the diversity of autochthonous malaria and transmission of Plasmodium parasites, which will provide baseline data for disease control and management. METHODS: Thirty-two P. vivax isolates from Henan province were collected from 2008 to 2011, and circumsporozoite protein (csp) genes were analysed to estimate the genetic diversity of this parasite. RESULTS: The assessment of csp sequences indicated that all the isolates were the VK210 type, however, none of them was identical to the VK210 strain. The sequences displayed variations in the central region, and eight sub-types were observed. Among the sub-types, HN7 was the most prevalent (37.5%), followed by HN3 (34.4%). A total of 653 repeat units were discovered in 32 Henan isolates. Nucleotide sequences were grouped in 13 unique repeat nucleotide sequence allotypes that coded for 7 different repeated amino acid allotypes. B (GNGAGGQAA) and D (GDRAAGQPA) were more frequent based on the results; they represented 53.9% (352/653) of the total. In comparison to the basic repeat units of VK210, more than 75% of the central repeat units had at least one non-synonymous nucleotide change. CONCLUSIONS: Recent P. vivax populations in Henan province showed some degree of genetic diversity in csp, with 8 sub-types among 32 samples. Meantime, the results also suggested its relative conserved parasite populations. This could provide interesting baseline data that allow identifying whether potential new cases differ from the parasites already circulating in the area.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:In-Data-Review
[do] DOI:10.1186/s12936-018-2237-1


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