A Web Application for Generation of Random DNA Sequences with a Single Open Reading Frame: Exemplars for Genetics and Bioinformatics Education

Coding sequences of DNA generate Open Reading Frames (ORFs) inside them with much higher frequency than random DNA sequences do, especially in the antisense strand. This is a specific feature of the genetic code. Since coding sequences are selected for their length, the generated ORFs are indirect results of this selection and their length is also influenced by selection. That is why ORFs found in any genome, even much longer ones than those spontaneously generated in random DNA sequences, should be considered as two different sets of ORFs: The first one coding for proteins, the second one generated by the coding ORFs. Even intergenic sequences possess greater capacity for generating ORFs than random DNA sequences of the same nucleotide composition, which seems to be a premise that intergenic sequences were generated from coding sequences by recombinational mechanisms.

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Expression of antibodies using single-open reading frame vector design and polyprotein processing from mammalian cells

Biotechnology Progress ◽

10.1002/btpr.182 ◽

2009 ◽

Vol 25 (3) ◽

pp. 735-744 ◽

Cited By ~ 7

Author(s):

Yune Z. Kunes ◽

Wendy R. Gion ◽

Emma Fung ◽

Jochen G. Salfeld ◽

Rong-Rong Zhu ◽

...

Keyword(s):

Mammalian Cells ◽

Open Reading Frame ◽

Single Open Reading Frame ◽

Reading Frame ◽

Polyprotein Processing

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Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis

Oto Rhino Laryngologica Indonesiana ◽

10.32637/orli.v44i1.83 ◽

2014 ◽

Vol 44 (1) ◽

pp. 52

Author(s):

Lenny Buana Wuriningtyas ◽

Dwi Reno Pawarti ◽

Achmad Chusnu Romdhoni

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Arithmetic Mean ◽

Recurrent Respiratory Papillomatosis ◽

Open Reading Frame ◽

Group Method ◽

Cross Sectional ◽

Reading Frame ◽

Pair Group ◽

Unweighted Pair Group Method

Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.

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Detection of Kaposi’s Sarcoma Herpesvirus DNA Sequences in Multiple Myeloma Bone Marrow Stromal Cells

Blood ◽

10.1182/blood.v93.5.1482.405a34_1482_1486 ◽

1999 ◽

Vol 93 (5) ◽

pp. 1482-1486 ◽

Cited By ~ 1

Author(s):

Dharminder Chauhan ◽

Ajit Bharti ◽

Noopur Raje ◽

Eric Gustafson ◽

Geraldine S. Pinkus ◽

...

Keyword(s):

Multiple Myeloma ◽

Bone Marrow ◽

Dna Sequences ◽

Stromal Cells ◽

Bone Marrow Stromal Cells ◽

Marrow Stromal Cells ◽

Open Reading Frame ◽

Sequence Analyses ◽

Reading Frame ◽

Kshv Gene

Whether Kaposi’s sarcoma herpesvirus (KSHV) is associated with multiple myeloma (MM) remains controversial. We assayed for KSHV DNA sequences in long-term bone marrow stromal cells (BMSCs) from 26 patients with MM and 4 normal donors. Polymerase chain reaction (PCR) using primers which amplify a KSHV gene sequence to yield a 233-bp fragment (KS330233 within open reading frame 26) was negative in all cases. Aliquots of these PCR products were used as templates in subsequent nested PCR, with primers that amplify a 186-bp product internal to KS330233. BMSCs from 24 of 26 (92%) patients with MM and 1 of 4 normal donors were KSHV PCR+. DNA sequence analyses showed interpatient specific mutations (2 to 3 bp). Both Southern blot and sequence analyses confirmed the specificity of PCR results. The presence of the KSHV gene sequences was further confirmed by amplifying T 1.1 (open reading frame [ORF] K7) and viral cyclin D (ORF 72), two other domains within the KSHV genome. Immunohistochemical studies of KSHV PCR+ MM BMSCs demonstrate expression of dendritic cell (DC) lineage markers (CD68, CD83, and fascin). Serological studies for the presence of KSHV lytic or latent antibodies were performed using sera from 53 MM patients, 12 normal donors, and 5 human immunodeficiency virus (HIV)/KSHV+ patients. No lytic or latent antibodies were present in sera from either MM patients or normal donors. Taken together, these findings show that KSHV DNA sequences are detectable in BMSCs from the majority of MM patients, but that serologic responses to KSHV are not present. Ongoing studies are defining whether the lack of antibody response is caused by the absence of ongoing infection, the presence of a novel viral strain associated with MM, or underlying immunodeficiency in these patients.

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Evolutionarily conserved regions in Caenorhabditis transposable elements deduced by sequence comparison

Genome ◽

10.1139/g91-002 ◽

1991 ◽

Vol 34 (1) ◽

pp. 6-12 ◽

Cited By ~ 17

Author(s):

Shiv S. Prasad ◽

Linda J. Harris ◽

David L. Baillie ◽

Ann M. Rose

Keyword(s):

Amino Acid ◽

Transposable Element ◽

Sequence Comparison ◽

Horizontal Transmission ◽

Protein A ◽

Open Reading Frame ◽

Single Open Reading Frame ◽

Major Open Reading Frame ◽

Reading Frame ◽

Caenorhabditis Species

In this paper we present the sequence of an intact Caenorhabditis briggsae transposable element, Tcb2. Tcb2 is 1606 base pairs in length and contains 80 base pair imperfect terminal repeats and a single open reading frame. We have identified blocks of T-rich repeats in the regions 150–200 and 1421–1476 of this element which are conserved in the Caenorhabditis elegans element Tc1. The sequence conservation of these regions in elements from different Caenorhabditis species suggests that they are of functional importance. A single open reading frame corresponding to the major open reading frame of Tc1 is conserved among Tc1, Tcb1, and Tcb2. Comparison of the first 550 nucleotides of the sequence among the three elements has allowed the evaluation of a model proposing an extension of the major open reading frame. Our data support the suggestion that Tc1 is capable of producing a 335 amino acid protein. A comparison of the sequence coding for the amino and carboxy termini of the 273 amino acid transposase from Caenorhabditis Tc1-like elements and Drosophila HB1 showed different amounts of divergence for each of these regions, indicating that the two functional domains have undergone different amounts of selection. Our data are not compatible with the proposal that Tc1-related sequences have been acquired via horizontal transmission. The divergence of Tc1 from the two C. briggsae elements, Tcb1 and Tcb2, indicated that all three elements have been diverging from each other for approximately the same amount of time as the genomes of the two species.Key words: Caenorhabditis, transposable element, sequence comparison.

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