Accurate Sequence Information Research Articles

In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D.

Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.

Development of a chemometric approach to improve the accuracy of copolymer sequence information obtained from pyrolysis gas-chromatography mass-spectrometry data

Number-average copolymer sequence length information can be obtained by pyrolysis-gas chromatography (Py-GC) by comparing the ratios of formed oligomers (i.e. dimers and trimers). The formation constants of the oligomers and their detection efficiency are not constant for all fragments, however. This can lead to unrepresentative peak ratios in the chromatogram. In these cases, calibration with an external method (e.g. NMR) is required. In this work, we introduce an algorithm that improves the copolymer sequence accuracy yielded from chromatograms with unrepresentative peak areas. The algorithm even functions in cases where oligomer data is missing as the rate of formation of certain oligomers is too low to detect them. One Py-GC measurement and one NMR measurement are required to train the developed algorithm for the determination of average monomer reactivity ratios and relative pyrolysis constants. Afterwards, Py-GC measurements of copolymers containing the same monomers, albeit with different compositions, can be corrected using the previously estimated constants. The algorithm was tested on various styrene-acrylate copolymers, yielding more accurate sequence information, even when limited oligomer information was available.

Facile de Novo Sequencing of Tetrazine-Cyclized Peptides through UV-Induced Ring-Opening and Cleavage from the Solid Phase.

While most FDA-approved peptide drugs are cyclic, the robust cyclization chemistry of peptides and the deconvolution of cyclic peptide sequences by using tandem mass spectrometry render cyclic peptide drug discovery difficult. Here we present the successful design of cyclic peptides on solid phase that addresses both of these problems. We demonstrate that this peptide cyclization method using dichloro-s-tetrazine on solid phase allows successful cyclization of a panel of random peptide sequences with various charges and hydrophobicities. The cyclic peptides can be linearized and cleaved from the solid phase by simple UV light irradiation, and we demonstrate that accurate sequence information can be obtained for the UV-cleaved linearized peptides by using tandem mass spectrometry. The tetrazine linker used in the cyclic peptides can further be explored for inverse electron-demand Diels-Alder (IEDDA) reactions for screening or bioconjugation applications in the future.

Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome

The genome sequences of unicellular holozoans, the closest relatives to animals, are shedding light on the evolution of animal multicellularity, shaping the genetic contents of the putative premetazoans. However, the assembly quality of the genomes remains poor compared to the major model organisms such as human and fly. Improving the assembly is critical for precise comparative genomics studies and further molecular biological studies requiring accurate sequence information such as enhancer analysis and genome editing. In this report, we present a new strategy to improve the assembly by fully exploiting the information of Illumina mate-pair reads. By visualizing the distance and orientation of the mapped read pairs, we could highlight the regions where possible assembly errors exist in the genome sequence of Capsaspora, a lineage of unicellular holozoans. Manual modification of these errors repaired 590 assembly problems in total and reassembled 84 supercontigs into 55. Our telomere prediction analysis using the read pairs containing the pan-eukaryotic telomere-like sequence identified at least 13 chromosomes. The resulting new assembly posed us a re-annotation of 112 genes, including 15 putative receptor protein tyrosine kinases. Our strategy thus provides a useful approach for improving assemblies of draft genomes, and the new Capsaspora genome offers us an opportunity to adjust the view on the genome of the unicellular animal ancestor.

Genome-wide identification of microRNA targets in the neglected disease pathogens of the genus Echinococcus

MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3′untranslated regions (3′UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs. However, current knowledge about their targets is limited. Since target prediction algorithms rely on complementarity between 3′UTRs and miRNA sequences, a major limitation is the lack of accurate sequence information of 3′UTR for most species including parasitic helminths. We performed RNA-seq and developed a pipeline that integrates the transcriptomic data with available genomic data of this parasite in order to identify 3′UTRs of Echinococcus canadensis. The high confidence set of 3′UTRs obtained allowed the prediction of miRNA targets in Echinococcus through a bioinformatic approach. We performed for the first time a comparative analysis of miRNA targets in Echinococcus and Taenia. We found that many evolutionarily conserved target sites in Echinococcus and Taenia may be functional and under selective pressure. Signaling pathways such as MAPK and Wnt were among the most represented pathways indicating miRNA roles in parasite growth and development. Genome-wide identification and characterization of miRNA target genes in Echinococcus provide valuable information to guide experimental studies in order to understand miRNA functions in the parasites biology. miRNAs involved in essential functions, especially those being absent in the host or showing sequence divergence with respect to host orthologs, might be considered as novel therapeutic targets for echinococcosis control.

HLA-B and HLA-C Supratyping by Pyrosequencing®.

Usually, HLA typing has been performed either by serology-based typing incubating a panel of known anti-HLA antibodies with viable lymphocytes of unknown HLA type or by molecular typing including medium-resolution HLA typing by Sequence Specific Oligonucleotide Probes (SSOP) or high-resolution HLA typing by Sequence Based Typing (SBT). Traditionally, HLA antigens have been defined using serological techniques, but these methods have several disadvantages, such as low resolution, the requirement for viable cells, and cell surface expression of HLA molecules. HLA type screening methods are categorized as low, medium, and high resolution, and only sequencing-based typing methods provide the highest resolution and are considered the gold standard for HLA typing.Among the HLA SBT based-methods, the Pyrosequencing(®) technique is an extremely versatile and accurate real-time sequencing technique with some advantages compared to classic Sanger method.Here, we describe a quick and inexpensive method that allows through the use of Pyrosequencing subtyping of HLA class I molecules, into HLA-Bw6, -Bw4 I80, or -Bw4 T80 and HLA-C1, or -C2 groups. In particular, this analysis is focused on the amino acids around residue 80. This method demonstrated good sensitivity, specificity, and reproducibility. Using a quantitative allele acquisition mode, the method provides accurate sequence information required for the definition of heterozygous and/or homozygous samples.

Whence Flavins? Redox-Active Ribonucleotides Link Metabolism and Genome Repair to the RNA World

Present-day organisms are under constant environmental stress that damages bases in DNA, leading to mutations. Without DNA repair processes to correct these errors, such damage would be catastrophic. Organisms in all kingdoms have repair processes ranging from direct reversal to base excision and nucleotide excision repair, and the recently characterized giant viruses also include these mechanisms. At what point in the evolution of genomes did active repair mechanisms become critical? In particular, how did early RNA genomes protect themselves from UV photodamage that would have hampered nonenzymatic replication and led to a mutation rate too high to pass on accurate sequence information from one generation to the next? Photolyase is a widespread and phylogenetically ancient enzyme that utilizes longer wavelength light to cleave thymine dimers in DNA produced via photodamage. The protein serves as a binding scaffold but does not contribute to the catalytic chemistry; the action of the dinucleotide cofactor FADH(2) breaks the chemical bonds. This small bit of RNA, hailed as a "fossil of the RNA World," contains the flavin heterocycle, whose redox activity has been harnessed for myriad functions of life from metabolism to DNA repair. In present-day biochemistry, flavin biosynthesis begins with guanosine and proceeds through seven steps catalyzed by protein-based enzymes. This leads to the question of how flavins originally evolved. Did the RNA world include ancestral RNA bases with greater redox activity than G, A, C, and U that were capable of photorepair of uracil dimers? Could those ancestral bases have chemically evolved to the current flavin structure? Or did flavins already exist from prebiotic chemical synthesis? And were they then co-opted as catalysts for repair sometime after metabolism was established? In this Account, we analyze simple derivatives of guanosine and other bases that show two prerequisites for flavin-like photolyase activity: a significantly lowered one-electron reduction potential and a red-shifted adsorption spectrum that facilitates excited-state electron transfer in a spectral window that does not produce cyclobutane pyrimidine dimers. Curiously, the best candidate for a primordial flavin is a base damage product, 8-oxo-7,8-dihydroguanine (8-oxoGua or "OG"). Other redox-active ribonucleotides include 5-hydroxycytidine and 5-hydroxyuridine, which display some of the characteristics of flavins, but might also behave like NADH.

Extraction of DNA from plant and fungus tissues in situ

BackgroundWhen samples are collected in the field and transported to the lab, degradation of the nucleic acids contained in the samples is frequently observed. Immediate extraction and precipitation of the nucleic acids reduces degradation to a minimum, thus preserving accurate sequence information. An extraction method to obtain high quality DNA in field studies is described.FindingsDNA extracted immediately after sampling was compared to DNA extracted after allowing the sampled tissues to air dry at 21°C for 48 or 72 hours. While DNA extracted from fresh tissues exhibited little degradation, DNA extracted from all tissues exposed to 21°C air for 48 or 72 hours exhibited varying degrees of degradation. Yield was higher for extractions from fresh tissues in most cases. Four microcentrifuges were compared for DNA yield: one standard electric laboratory microcentrifuge (max rcf = 16,000×g), two battery-operated microcentrifuges (max rcf = 5,000 and 3,000 ×g), and one manually-operated microcentrifuge (max rcf = 120×g). Yields for all centrifuges were similar. DNA extracted under simulated field conditions was similar in yield and quality to DNA extracted in the laboratory using the same equipment.ConclusionsThis CTAB (cetyltrimethylammonium bromide) DNA extraction method employs battery-operated and manually-operated equipment to isolate high quality DNA in the field. The method was tested on plant and fungus tissues, and may be adapted for other types of organisms. The method produced high quality DNA in laboratory tests and under simulated field conditions. The field extraction method should prove useful for working in remote sites, where ice, dry ice, and liquid nitrogen are unavailable; where degradation is likely to occur due to the long distances between the sample site and the laboratory; and in instances where other DNA preservation and transportation methods have been unsuccessful. It may be possible to adapt this method for genomic, metagenomic, transcriptomic and metabolomic projects using samples collected in situ.

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Cyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3-62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means.

NaiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing

Immense amounts of raw instrument data (i.e., images of fluorescence) are currently being generated using ultra high-throughput sequencing platforms. An important computational challenge associated with this rapid advancement is to develop efficient algorithms that can extract accurate sequence information from raw data. To address this challenge, we recently introduced a novel model-based base-calling algorithm that is fully parametric and has several advantages over previously proposed methods. Our original algorithm, called BayesCall, significantly reduced the error rate, particularly in the later cycles of a sequencing run, and also produced useful base-specific quality scores with a high discrimination ability. Unfortunately, however, BayesCall is too computationally expensive to be of broad practical use. In this article, we build on our previous model-based approach to devise an efficient base-calling algorithm that is orders of magnitude faster than BayesCall, while still maintaining a comparably high level of accuracy. Our new algorithm is called naive-BayesCall, and it utilizes approximation and optimization methods to achieve scalability. We describe the performance of naiveBayesCall and demonstrate how improved base-calling accuracy may facilitate de novo assembly and SNP detection when the sequence coverage depth is low to moderate.

Flower: extracting information from pyrosequencing data

Summary: The SFF file format produced by Roche's 454 sequencing technology is a compact, binary format that contains the flow values that are used for base and quality calling of the reads. Applications, e.g. in metagenomics, often depend on accurate sequence information, and access to flow values is important to estimate the probability of errors. Unfortunately, the programs supplied by Roche for accessing this information are not publicly available. Flower is a program that can extract the information contained in SFF files, and convert it to various textual output formats.Availability: Flower is freely available under the General Public License.Contact: ketil.malde@imr.no

Helicos single molecule sequencing: unique capabilities and importance for molecular diagnostics

Background Helicos Single Molecule Sequencing provides a unique view of genome biology through direct sequencing of cellular nucleic acids in an unbiased manner, providing both quantitative and accurate sequence information. The simple sample preparation involves no ligation or PCR amplification, allowing direct sequencing of targeted DNA or RNA molecules. DNA and RNA can be directly hybridized to the flow cell, eliminating many intermediary steps that can introduce sample loss or bias. From these methods, a diverse array of applications have been successfully demonstrated on the HeliScope Sequencer. For example, human genome sequencing for accurate variant detection; multiplexing of DNA for targeted resequencing; copy number variation studies from both fresh tumor tissue and formalinfixed paraffin-embedded tissue samples; RNA-seq studies demonstrating the unexplored biology that exists in the transcriptome; small RNA studies leading to the identification of new classes of RNAs [1]; and the direct capture and sequencing of nucleic acid from as few as 400 cells with the end goal of single cell measurements [2]. Current efforts now focus on applying these unique attributes to develop novel substrate for molecular diagnostic tests.

Termination of DNA synthesis by N6 -alkylated, not 3′- O -alkylated, photocleavable 2′-deoxyadenosine triphosphates

The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the ‘next-generation’ technologies, cyclic reversible termination (CRT) is a promising method with the goal of producing accurate sequence information at a fraction of the cost and effort. The foundation of this approach is the reversible terminator (RT), its chemical and biological properties of which directly impact the performance of the sequencing technology. Here, we have discovered a novel paradigm in RT chemistry, the attachment of a photocleavable, 2-nitrobenzyl group to the N6-position of 2′-deoxyadenosine triphosphate (dATP), which, upon incorporation, terminates DNA synthesis. The 3′-OH group of the N6-(2-nitrobenzyl)-dATP remains unblocked, providing favorable incorporation and termination properties for several commercially available DNA polymerases while maintaining good discrimination against mismatch incorporations. Upon removal of the 2-nitrobenzyl group with UV light, the natural nucleotide is restored without molecular scarring. A five-base experiment, illustrating the exquisite, stepwise addition through a homopolymer repeat, demonstrates the applicability of the N6-(2-nitrobenzyl)-dATP as an ideal RT for CRT sequencing.

Reliable and accurate sequencing of lambda, cosmid and P1 DNAs using modified dye terminator reaction parameters

▼Many laboratories still find the direct sequencing of large DNA templates (i.e. lambda, cosmid and bacteriophage P1 clones) problematic. To date, only limited amounts of sequence information, which in many cases is of poor quality, can be generated from such molecules, even when using polymerase chain reaction (PCR)-based cycle sequencing protocols (Ref. 1, 3, 4, 5, 6, 7). To obtain reliable nucleotide data, it is usually necessary to subclone portions of the DNA of interest into either a high copy-number plasmid or a single-strand bacteriophage, such as M13. It would be advantageous to have a simple and rapid protocol that could reliably yield large amounts of accurate sequence information and that could be employed in conjunction with an automated fluorescence-based DNA-sequencing apparatus. Here, we describe optimized reaction parameters (template concentration, primer length and cycling conditions) for use with a commercially available dye terminator DNA sequencing kit, and show the excellent quality of the data that can be obtained from either lambda, cosmid or bacteriophage P1 DNAs. This procedure is performed in a single tube, using unmodified oligonucleotide primers, on templates that do not require extensive purification.

Imaging as a tool for improving length and accuracy of sequence analysis in automated fluorescence‐based DNA sequencing

A new method of signal analysis for automated fluorescence-based DNA sequencing is presented. Signal resolution is a limiting factor in obtaining accurate sequence information beyond 400-450 nucleotides per gel lane. We have developed a computer program for the imaging of DNA bands in sequencing gels. The image analysis shows that distortions in the shapes of the bands decrease resolution of peaks observed served in the standard data plots. Reconstruction of the undistorted band shape prior to signal analysis substantially improves the resolution of peaks and may improve the accuracy and length of the contiguous sequence read. Image analysis identified other factors limiting the accuracy and length of automated DNA sequence analysis and provided a tool for evaluating various remedies. Our techniques should also be applicable in other systems, for example, in gel electrophoresis of proteins and DNA restriction fragments, and in scranning densitometry.