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ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
Explore the co-localization of CTCF and ZNF143. Where are the co-bound regions located? Which sequence motifs do they contain? Download the ChIA-pet data for the GM12878 cell line, and look at the 3D interaction between different classes of binding sites. [Difficulty: Advanced]
A Comprehensive HLA-DRB, -DQB, and -DPB Oligotyping Procedure by Hybridization with Sequence-Specific Oligonucleotide Probes
Published in M. Kam, Jeffrey L. Bidwell, Handbook of HLA TYPING TECHNIQUES, 2020
The six subtypes of DR13 can be identified by hybridization with nine SSOs including the probes E71, K71, and N37 found within the DR generic typing protocol. An example of DR13 subtyping of 16 individuals is shown in Figure 4. For the discrimination of 1305 from 1306 and of 0801 from 0803, §SO I67 is used instead of 167-2, which identifies the I-DE sequence motif.
Immunoglobulins
Published in Constantin A. Bona, Francisco A. Bonilla, Textbook of Immunology, 2019
Constantin A. Bona, Francisco A. Bonilla
As is evident in Figure 4–6, many sequence motifs are found in promoters and enhancers. Each sequence motif interacts with one or more binding factors; each binding factor may interact with one or more sequence motifs. Furthermore, binding factors may dimerize or heterodimerize with varying effects on their binding specificity; non-DNA-binding proteins may also associate with sequence-specific factors and either positively or negatively affect their interaction with DNA. The relative concentrations of all of these interacting factors fluctuates with the pattern of development, differentiation and activation of the cell. In fact, it is the coordinated activation and repression of various groups of genes determined through the interplay of these transcription-regulating factors which leads to phenotypic changes in the cell.
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
To further characterize the extracted enolase data sets, sequence motifs were discovered and analyzed using the MOTIF search program (https://www.genome.jp/tools/motif/). Furthermore, we used GhostKOALA, an annotation and KEGG mapping web server, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways. To identify the number of regions encoding the protein and the variants of introns within the enolase gene, the intron-exon map of enolase was identified based on the method previously described (Salabi and Jafari 2022). Briefly, the genomic DNA sequence of Centruroides sculpturatus (NW_019386438.1) was aligned with mRNA sequences of enolase genes from C. sculpturatus enolase (XM_023356340.1), A. crassicauda (MW366377.1), and H. lepturus (MW366378.1). The MAFFT multiple sequence alignment software version 7 was used to create multiple sequence alignments.
Development and Evaluation of Novel Aptamers Specific for Human PD1 Using Hybrid Systematic Evolution of Ligands by Exponential Enrichment Approach
Published in Immunological Investigations, 2020
Mostafa Khedri, Khalil Abnous, Houshang Rafatpanah, Maryam Sadat Nabavinia, Seyed Mohammad Taghdisi, Mohammad Ramezani
Phylogenetic tree was illustrated by MEGA7 software using unweighted pair group method with arithmetic mean (UPGMA) program in which a rooted phylogenetic tree was calculated (Figure 3). Binding of the random candidate aptamers was evaluated and then selected sequences were synthesized for further characterization. According to the binding results, cell SELEX colonies such as C52, C42 and C72 showed more binding in comparison to protein SELEX colonies; P36 and P30. This finding was further supported by the enrichment of binding affinity of colonies to cellular PD1 through cell SELEX steps. As seen in Figurer 2, some sequence motifs such as motif 2 have high relative prevalence in selected aptamers. Although this motif was repeated in the selected aptamer several times (17 times), a significant relationship between aptamers containing this motif and aptamers binding affinity was not detected, and the results can be observed in binding images in Figure 3.
Deamidation and isomerization liability analysis of 131 clinical-stage antibodies
Published in mAbs, 2019
Xiaojun Lu, R. Paul Nobrega, Heather Lynaugh, Tushar Jain, Kyle Barlow, Todd Boland, Arvind Sivasubramanian, Maximiliano Vásquez, Yingda Xu
Historical review of the literature reveals that certain sequence motifs are particularly labile to modification under the stress conditions used in this study.17-19 Previously reported canonical motifs are NG, NS, NN, NT, NH and DG, DS, DD, DT, and DH for deamidation and isomerization modification under our conditions, respectively.23,32 Three publications contain the INNs (enabling unambiguous identification of the amino acid sequence) of the mAbs being investigated and study chemical modifications under reaction conditions similar to those used in this study. Sydow et al., is the most comprehensive, with isomerization and deamidation data (resulting post-incubation at pH 6.0 and 40 °C for two weeks) for 37 mAbs, 13 of which are identified by their INN.23Huang et al., provides high pH stress (pH 10.4 at 25 °C for 7 days) data for the Fc fusion etanercept,50 and Yang et al., published low pH data (pH 6.0 at 40 °C for 14 days) on trastuzumab.40 All other available publications either do not include a molecule’s name, do not have comparable reaction conditions, investigate the constant region, or interrogate the reactions of interest with peptides or antibody fragments (instead of full-length mAbs).