scholarly journals Analysis of the Full-Length Pyriform Spidroin Gene Sequence

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 425 ◽  
Author(s):  
Kangkang Wang ◽  
Rui Wen ◽  
Qiupin Jia ◽  
Xiangqin Liu ◽  
Junhua Xiao ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Biomechanical Properties ◽  
Silk Protein ◽  
Full Length ◽  
Biological Functions ◽  
Repetitive Region ◽  
Long Distance ◽  
Silk Fibers ◽  
Silk Fibroins ◽  
Full Length Gene

Spiders often produce multiple types of silk, each with unique properties suiting them to certain tasks and biological functions. Orb-weaver spiders can generate more than six types of silk fibroins, with pyriform silk used to form attachment discs, adhering silk to other surfaces and substances. The unique higher-order structuring of silk fibroins has been cited as the source of their remarkable biomechanical properties. Even so, only one full-length gene sequence of pyriform silk protein 1 (PySp1) from Argiopeargentata has been reported, and studies on the mechanical properties of natural pyriform silk fibers are also lacking. To better understand the PySp1 family of genes, we used long-distance PCR (LD-PCR) to determine the sequence of PySp1 in the Araneusventricosus species. This full-length PySp1 gene is 11,931 bp in length, encoding for 3976 amino acids residues in non-repetitive N- and C-terminal domains with a central largely repetitive region made up of sixteen remarkably homogeneous units. This was similar to the previously reported A. argentata PySp1 sequence, with PySp1 from A. ventricosus also having a long repetitive N-linker that bridges the N-terminal and repetitive regions. Predictions of secondary structure and hydrophobicity of A. ventricosus PySp1 showed the pyriform silk fiber’s functional properties. The amino acid compositions of PySp1 is obviously distinct from other spidroins. Our sequence makes an important contribution to understand pyriform silk protein structure and also provides a new template for recombinant pyriform silk proteins with attractive properties.

scholarly journals Generation of Full-Length Class I Human Leukocyte Antigen Gene Consensus Sequences for Novel Allele Characterization

2016 ◽  
Vol 62 (12) ◽  
pp. 1630-1638 ◽  
Author(s):  
Peter M Clark ◽  
Jamie L Duke ◽  
Deborah Ferriola ◽  
Valia Bravo-Egana ◽  
Tunde Vago ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Human Leukocyte ◽  
Full Length ◽  
Class I ◽  
Hla Alleles ◽  
Consensus Sequences ◽  
Leukocyte Antigen ◽  
Novel Alleles ◽  
Full Length Gene

Abstract BACKGROUND Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs. METHODS We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased full-length gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline. RESULTS Our analysis revealed that 7.7% (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated full-length gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles. CONCLUSIONS The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.

scholarly journals A comprehensive overview of FCGR3A gene variability by full-length gene sequencing including the identification of V158F polymorphism

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Niken M. Mahaweni ◽  
Timo I. Olieslagers ◽  
Ivan Olivares Rivas ◽  
Stefan J. J. Molenbroeck ◽  
Mathijs Groeneweg ◽  
...  
Keyword(s):  
Gene Sequencing ◽  
Full Length ◽  
Comprehensive Overview ◽  
Gene Variability ◽  
Full Length Gene

scholarly journals Role of Main RNA Methylation in Hepatocellular Carcinoma: N6-Methyladenosine, 5-Methylcytosine, and N1-Methyladenosine

2021 ◽  
Vol 9 ◽  
Author(s):  
Yating Xu ◽  
Menggang Zhang ◽  
Qiyao Zhang ◽  
Xiao Yu ◽  
Zongzong Sun ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cellular Differentiation ◽  
Molecular Mechanisms ◽  
Gene Sequence ◽  
Epigenetic Modification ◽  
Biological Processes ◽  
Biological Functions ◽  
Rna Detection ◽  
Rna Methylation

RNA methylation is considered a significant epigenetic modification, a process that does not alter gene sequence but may play a necessary role in multiple biological processes, such as gene expression, genome editing, and cellular differentiation. With advances in RNA detection, various forms of RNA methylation can be found, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), and 5-methylcytosine (m5C). Emerging reports confirm that dysregulation of RNA methylation gives rise to a variety of human diseases, particularly hepatocellular carcinoma. We will summarize essential regulators of RNA methylation and biological functions of these modifications in coding and noncoding RNAs. In conclusion, we highlight complex molecular mechanisms of m6A, m5C, and m1A associated with hepatocellular carcinoma and hope this review might provide therapeutic potent of RNA methylation to clinical research.

Association of the IVR Gene with Virus Localization and Resistance

1995 ◽  
Author(s):  
Gad Loebenstein ◽  
William Dawson ◽  
Abed Gera
Keyword(s):  
Amino Acids ◽  
Coat Protein ◽  
Plant Viruses ◽  
Full Length ◽  
N Gene ◽  
Complete Suppression ◽  
Coat Proteins ◽  
Nicotiana Glutinosa ◽  
Nicotiana Debneyi ◽  
Full Length Gene

We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi. During the present grant we found that TMV production is enhanced in protoplasts and plants of local lesion responding tobacco cultivars exposed to 35oC, parallel to an almost complete suppression of the production of IVR. We also found that IVR is associated with resistance mechanisms in pepper cultivars. We succeeded to clone the IVR gene. In the first attempt we isolated a clone - "101" which had a specific insert of 372 bp (the full length gene for the IVR protein of 23 kD should be around 700 bp). However, attempts to isolate the full length gene did not give clear cut results, and we decided not to continue with this clone. The amino acid sequence of the N-terminus of IVR was determined and an antiserum was prepared against a synthetic peptide representing amino acids residues 1-20 of IVR. Using this antiserum as well as our polyclonal antiserum to IVR a new clone NC-330 was isolated using lamba-ZAP library. This NC-330 clone has an insert of about 1 kB with an open reading frame of 596 bp. This clone had 86.6% homology with the first 15 amino acids of the N-terminal part of IVR and 61.6% homology with the first 23 amino acids of IVR. In the QIA expression system and western blotting of the expressed protein, a clear band of about 21 kD was obtained with IVR antiserum. This clone was used for transformation of Samsun tobacco plants and we have presently plantlets which were rooted on medium containing kanamycin. Hybridization with this clone was also obtained with RNA from induced resistant tissue of Samsun NN but not with RNA from healthy control tissue of Samsun NN, or infected or healthy tissue of Samsun. This further strengthens the previous data that the NC 330 clone codes for IVR. In the U.S. it was shown that IVR is induced in plants containing the N' gene when infected with mutants of TMV that elicit the HR. This is a defined system in which the elicitor is known to be due to permutations of the coat protein which can vary in elicitor strength. The objective was to understand how IVR synthesis is induced after recognition of elicitor coat protein in the signal transduction pathway that leads to HR. We developed systems to manipulate induction of IVR by modifying the elicitor and are using these elicitor molecules to isolate the corresponding plant receptor molecules. A "far-western" procedure was developed that found a protein from N' plants that specifically bind to elicitor coat proteins. This protein is being purified and sequenced. This objective has not been completed and is still in progress. We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi.

scholarly journals Analysis of the Impact of Known SPINK1 Missense Variants on Pre-mRNA Splicing and/or mRNA Stability in a Full-Length Gene Assay

Genes ◽  
2017 ◽  
Vol 8 (10) ◽  
pp. 263 ◽  
Author(s):  
Hao Wu ◽  
Arnaud Boulling ◽  
David Cooper ◽  
Zhao-Shen Li ◽  
Zhuan Liao ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Mrna Splicing ◽  
Full Length ◽  
Missense Variants ◽  
Gene Assay ◽  
The Impact ◽  
Full Length Gene

scholarly journals Full-Length Minor Ampullate Spidroin Gene Sequence

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e52293 ◽  
Author(s):  
Gefei Chen ◽  
Xiangqin Liu ◽  
Yunlong Zhang ◽  
Senzhu Lin ◽  
Zijiang Yang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Full Length

scholarly journals Isolation and characterization by asymmetric PCR of the ENDO1 gene for glucan endo-1,3-β-D-glucosidase in Phytophthora cinnamomi associated with the ink disease of Castanea sativa Mill

2010 ◽  
Vol 53 (3) ◽  
pp. 513-518 ◽  
Author(s):  
Sofia Meirinho ◽  
Marisa Carvalho ◽  
Ángel Dominguez ◽  
Altino Choupina
Keyword(s):  
Genomic Dna ◽  
Gene Sequence ◽  
Phytophthora Cinnamomi ◽  
Castanea Sativa ◽  
European Regions ◽  
Asymmetric Pcr ◽  
Isolation And Characterization ◽  
Castanea Sativa Mill ◽  
Full Length Gene ◽  
Ink Disease

Ink disease is one of the most destructive diseases in Castanea sativa. The most common symptoms are root necrosies and a reduction in root growth, which invariably lead to the death of the trees. Phytophthora cinnamomi is an oomycete associated with this disease whose life cycle develops integrally in the soil. In the present work, was a fragment with 1231bp of the glucan endo-1,3-β-D-glucosidase gene obtained by amplification, using conserved primers and the full-length gene sequence by flanking this known sequence by asymmetric PCR. This fragment was obtained from genomic DNA of Phytophthora cinnamomi isolated in the European Regions of Castilla-Leon (Spain) and Trás-os-Montes (Portugal) and associated with the ink disease of Castanea sativa Mill.

scholarly journals A novel full-length gene of human ribosomal protein L14.22 related to human glioma

2006 ◽  
Vol 119 (16) ◽  
pp. 1353-1358
Author(s):  
Zhen-yu QI ◽  
Guo-zhen HUI ◽  
Yao LI ◽  
Zong-xiang ZHOU ◽  
Shao-hua GU ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Full Length ◽  
Human Glioma ◽  
Human Ribosomal Protein ◽  
Full Length Gene
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