scholarly journals Characterization of Histone Genes from the Bivalve Lucina Pectinata

2018 ◽  
Vol 15 (10) ◽  
pp. 2170 ◽  
Author(s):  
Ingrid Montes-Rodríguez ◽  
Yesenia Rodríguez-Pou ◽  
Ricardo González-Méndez ◽  
Juan Lopez-Garriga ◽  
Alexander Ropelewski ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Aquatic Organisms ◽  
Histone Genes ◽  
Coding Region ◽  
Lucina Pectinata ◽  
Coding Regions ◽  
Semiconductor Sequencing ◽  
Amino Acid Sequence Conservation

Lucina pectinata is a clam that lives in sulfide-rich environments and houses intracellular sulfide-oxidizing endosymbionts. To identify new Lucina pectinata proteins, we produced libraries for genome and transcriptome sequencing and assembled them de novo. We searched for histone-like sequences using the Lucina pectinata histone H3 partial nucleotide sequence against our previously described genome assembly to obtain the complete coding region and identify H3 coding sequences from mollusk sequences in Genbank. Solen marginatus histone nucleotide sequences were used as query sequences using the genome and transcriptome assemblies to identify the Lucina pectinata H1, H2A, H2B and H4 genes and mRNAs and obtained the complete coding regions of the five histone genes by RT-PCR combined with automated Sanger DNA sequencing. The amino acid sequence conservation between the Lucina pectinata and Solen marginatus histones was: 77%, 93%, 83%, 96% and 97% for H1, H2A, H2B, H3 and H4, respectively. As expected, the H3 and H4 proteins were the most conserved and the H1 proteins were most similar to H1′s from aquatic organisms like Crassostrea gigas, Aplysia californica, Mytilus trossulus and Biomphalaria glabrata. The Lucina pectinata draft genome and transcriptome assemblies, obtained by semiconductor sequencing, were adequate for identification of conserved proteins as evidenced by our results for the histone genes.

scholarly journals Identification of Six Putative Novel Human Papillomaviruses (HPV) and Characterization of Candidate HPV Type 87

2001 ◽  
Vol 75 (23) ◽  
pp. 11913-11919 ◽  
Author(s):  
Stefano Menzo ◽  
Alessia Monachetti ◽  
Caterina Trozzi ◽  
Andrea Ciavattini ◽  
Guido Carloni ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Biological Data ◽  
Human Papillomaviruses ◽  
The Novel ◽  
Tissue Cultures ◽  
Coding Region ◽  
Coding Regions ◽  
Immunodeficiency Virus ◽  
E6 And E7

ABSTRACT Six putative novel human papillomavirus (HPV) types were detected by using general primers for a conserved L1 HPV region in patients examined in gynecologic centers. One of the isolates, detected in samples from 4 patients with koilocytic atypia at cervical cytology (3 of whom were also infected with human immunodeficiency virus type 1), was completely sequenced, identified as a new HPV genotype, and designated candidate HPV87 (candHPV87) by the Reference Center for Human Papillomavirus. candHPV87 shows the classic HPV genome organization and the absence of a functional E5 coding region. Phylogenetic analysis documented that thecandHPV87 genome clusters within the A3 group of HPVs, together with HPV61, HPV72, HPV83, HPV84 and candHPV86, which have been completely sequenced, and a number of other putative novel genotypes (two of which are described in this work), which have been partially characterized. To address the growth-enhancing potential of candHPV87, the E6 and E7 putative coding regions were cloned and expressed in tissue cultures. The data indicate that both proteins stimulate cell division in tissue cultures more than those of low-risk HPVs, though not as much as those of HPV16. Taken together, the clinical, molecular, and biological data suggest that the novel papillomavirus characterized in the present study is a low- to intermediate-risk HPV.

Isolation and characterization of an expressed napin gene fromBrassica rapa

1991 ◽  
Vol 1 (4) ◽  
pp. 209-219 ◽  
Author(s):  
Jean C. Kridl ◽  
David W. McCarter ◽  
Ronald E. Rose ◽  
Donna E. Scherer ◽  
Deborah S. Knutzon ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Storage Protein ◽  
Protein Gene ◽  
Coding Region ◽  
Coding Regions ◽  
Endogenous Expression ◽  
Isolation And Characterization ◽  
Glucuronidase Reporter ◽  
Transgenic Rapeseed

AbstractAn expressed napin storage protein gene fromBrassica rapa, BcNA1, has been cloned and sequenced. The gene is a member of a family of four to seven napin genes inB. rapaand is highly expressed in developing seeds. An expression cassette containing the DNA flanking the napin coding region of BcNA1 has been engineered and demonstrated to function appropriately, as compared with the gene's endogenous expression, in transgenic rapeseed using the β-glucuronidase reporter gene. TheB. rapaBcNA1 gene and aB. napusnapin gene, gNa, share extremely high nucleotide homology not only throughout their coding regions, but over a DNA locus comprising 4.3 kb. We suggest the gNa gene was contributed by the originalB. rapaprogenitor of the amphidiploidB. napus.

scholarly journals Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain

2014 ◽  
Vol 104 (11) ◽  
pp. 1241-1250 ◽  
Author(s):  
María Bergua ◽  
Marisol Luis-Arteaga ◽  
Fernando Escriu
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Geographic Origin ◽  
Alfalfa Mosaic Virus ◽  
Polymorphism Analysis ◽  
Coding Region ◽  
Coding Regions ◽  
Low Genetic Diversity ◽  
Genetic Types

The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions—P1, P2, movement protein (MP), and coat protein (CP)—revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.

scholarly journals First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis

2018 ◽  
Author(s):  
Luana Ferreira Afonso ◽  
Danielle Amaral ◽  
Marcela Uliano-Silva ◽  
André Luiz Quintanilha Torres ◽  
Daniel Reis Simas ◽  
...  
Keyword(s):  
De Novo ◽  
Pfam Domain ◽  
Draft Genome ◽  
Atlantic Rainforest ◽  
Volatile Fraction ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
Limonene Synthase ◽  
Molecular Bases

BackgroundProtium species produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.ResultsHere we present (i) the first draft genome of an endemic tree of the Brazil’s Atlantic Rainforest (Mata Atlântica), Protium kleinii Cuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resin’s volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenes α-terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resin’s volatile fraction identified four monoterpenes: terpinolene, limonene, α-pinene and α-phellandrene.ConclusionThese results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.

Molecular Characterization of the T(14;18)(q32;q21) Involving the IGH Locus and the MALT1 Gene in MALT Lymphomas

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4145-4145
Author(s):  
Eva Maria Murga Penas ◽  
Evelyne Callet-Bauchu ◽  
Nadine Albert ◽  
Sophie Gazzo ◽  
Françoise Berger ◽  
...  
Keyword(s):  
Malt Lymphoma ◽  
De Novo ◽  
Molecular Genetic ◽  
Molecular Characteristics ◽  
Coding Region ◽  
Long Distance ◽  
Igh Locus ◽  
First Case ◽  
Igh Genes

Abstract The t(14;18)(q32;q21) involving the MALT1 and IGH genes is a recurrent abnormality in MALT lymphomas. So far, molecular genetic characterization of the t(14;18)/IGHMALT1 has only been performed in 2 cases and revealed a fusion of the entire coding region of MALT1 to the IGH locus. We herein report the molecular genetic analyses of 2 new cases of MALT lymphoma harboring the t(14;18)/IGH-MALT1 using fluorescence in situ hybridization (FISH) and we determined the molecular characteristics at the IGH-MALT1 junctions using long-distance PCR (LD-PCR). The first case, a 71-year-old female, presented with an extranodal MALT lymphoma of the conjunctiva, stage IEA. The second case, a 53-year-old-male patient, was diagnosed as having a MALT lymphoma originating from the lung. FISH with PAC clones 117B5 and 59N7 revealed a translocation involving MALT1. Further FISH assays with probes hybridizing to MALT1 and IGH showed the t(14;18)(q32;q21)/IGH-MALT1. By FISH with specific probes for the P53, P16, RB1, and ATM genes no deletions of these genes were found. The IGH-MALT1 fusion was confirmed by LD-PCR on patients’ DNA with nested primers for the MALT1 and IGH genes. Cloning and sequencing of the purified PCR products revealed a fusion of sequences upstream of the coding region of MALT1 to the JH segment of the IGH locus in both cases. The breaks on chromosome 18 were located in the 5′ non-coding region of MALT1, only 13 nucleotides apart from each other. The breaks at IGH were located in the JH4 joining segment in both cases and showed features of a V(D)J-mediated recombination. Deletion and “de novo” nucleotides additions at the point of joining were observed in case 1. Furthermore, a detailed analysis of the “de novo” nucleotides additions in this case revealed the presence of DH segments of the DH gene D3-10 in the JH/MALT1 junction. Our findings indicate that the pathomechanism underlying the t(14;18)/IGH-MALT1 in MALT lymphomas is probably based on an illegitimate V(D)J recombination at IGH, similar to other IGH-associated translocations, such as the t(14;18)/IGH-BCL2 in follicular lymphomas and the t(11;14)/CCND1-IGH in mantle cell lymphomas and that the events leading to the t(14;18)/IGH-MALT1 might take place during an initial DH-to-JH or a later VH-to-DJH joining.

scholarly journals Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data

2021 ◽  
pp. gr.271627.120
Author(s):  
Zhaozhao Zhao ◽  
Qiushi Xu ◽  
Ran Wei ◽  
Weixu Wang ◽  
Dong Ding ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Significance ◽  
Rna Seq ◽  
Coding Region ◽  
Dynamic Changes ◽  
Cancer Tumor ◽  
Tumor Types ◽  
Pan Cancer ◽  
Intronic Poly

Intronic polyadenylation (IpA) usually leads to changes in coding region of an mRNA, and its implication in diseases has been recognized, though at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2. Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m6A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.

Characterization of the Original Christmas Disease Mutation (Cysteine 206 → Serine): From Clinical Recognition to Molecular Pathogenesis

1992 ◽  
Vol 67 (01) ◽  
pp. 063-065 ◽  
Author(s):  
Sherryl A M Taylor ◽  
Jacalyn Duffin ◽  
Cherie Cameron ◽  
Jerome Teitel ◽  
Bernadette Garvey ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Novel Mutation ◽  
Factor Ix ◽  
Causative Mutation ◽  
Coding Region ◽  
Body Of Knowledge ◽  
Polymerase Chain ◽  
Splice Junctions

SummaryChristmas disease was first reported as a distinct clinical entity in two manuscripts published in 1952 (1, 2). The eponym associated with this disorder, is the surname of the first patient examined in detail and reported by Biggs and colleagues in a paper describing the clinical and laboratory features of seven affected individuals (3). This patient has severe factor IX coagulant deficiency (less than 0.01 units/ml) and no detectable circulating factor IX antigen (less than 0.01 units/ml). Coding sequence and splice junctions of the factor IX gene from this patient have been amplified in vitro through the polymerase chain reaction (PCR). One nucleotide substitution was identified at nucleotide 30,070 where a guanine was replaced by a cytosine. This mutation alters the amino acid encoded at position 206 in the factor IX protein from cysteine to serine. The non conservative nature of this substitution, the absence of this change in more than 200 previously sequenced factor IX genes and the fact that the remainder of the coding region of this gene was normal, all provide strong circumstantial evidence in favour of this change being the causative mutation in this patient. The molecular characterization of this novel mutation in the index case of Christmas disease, contributes to the rapidly expanding body of knowledge pertaining to Christmas disease pathogenesis.

scholarly journals Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44911 ◽  
Author(s):  
Tingjuan Gao ◽  
Jitka Petrlova ◽  
Wei He ◽  
Thomas Huser ◽  
Wieslaw Kudlick ◽  
...  
Keyword(s):  
De Novo

scholarly journals Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Marios Lange ◽  
Rodiola Begolli ◽  
Antonis Giakountis
Keyword(s):  
Disease Onset ◽  
Cancer Genome ◽  
Driver Mutations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Coding Regions ◽  
Functional Variants ◽  
Coding Variants ◽  
Clinical Potential

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.

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