Comparison Of Nucleic Acid Sequences Research Articles

Discovered differentially expressed lncRNA AC010973.2 can act as a diagnostic and prognostic biomarker for colon adenocarcinoma.

BackgroundThe identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Recent studies show that long noncoding RNAs (lncRNAs) might act as prognostic biomarkers in a variety of cancers. This study aimed to identify and assess a prognostic lncRNA signature in patients with colon adenocarcinoma (COAD).MethodsWe downloaded expression profiles and corresponding clinicopathological data from The Cancer Genome Atlas (TCGA) database. We selected samples with lncRNA expression data and relevant clinical prognostic data for subsequent analysis. The association between lncRNA and prognostic function was analyzed by Cox regression analysis. The potential biofunctions of target lncRNA were investigated through bioinformatic analysis.ResultsLncRNAs expression profiles and corresponding clinicopathological data of 480 COAD patients and 41 normal samples were obtained from TCGA database. A multivariate Cox analysis model was used to identify the lncRNA signature. AC010973.2 lncRNA was found to be significantly related to the survival of COAD patients. The area under the curve (0.758) and the C-index (0.753) further confirmed the prediction accuracy of our model. Through nucleic acid sequence comparison and literature search, we found that the homologous host gene SLC4A2 of AC010973.2 is significantly related to COAD.ConclusionsWe provide here a new biomarker for COAD diagnosis and a new direction for further research on the pathogenesis of COAD.

Four Fallacies and an Oversight: Searching for Martian Life.

While it is anticipated that future human missions to Mars will increase the amount of biological and organic contamination that might be distributed on that planet, robotic missions continue to grow in capability and complexity, requiring precautions to be taken now to protect Mars, and particularly areas of Mars that might be Special Regions. Such precautionary cleanliness requirements for spacecraft have evolved over the course of the space age, as we have learned more about planetary environments, and are the subject of regular deliberations and decisions sponsored by the Committee on Space Research (COSPAR). COSPAR's planetary protection policy is maintained as an international consensus standard for spacecraft cleanliness that is recognized by the United Nations Committee on the Peaceful Uses of Outer Space. In response to the paper presented in this issue by Fairén et al. (2017), we examine both their concept of evidence for possible life on Mars and their logic in recommending that spacecraft cleanliness requirements be relaxed to access Special Regions “before it is too late.” We find that there are shortcomings in their plans to look for evidence of life on Mars, that they do not support their contention that appropriate levels of spacecraft cleanliness are unaffordable, that there are major risks in assuming martian life could be identified by nucleic acid sequence comparison (especially if those sequences are obtained from a Special Region contaminated with Earth life), and that the authors do not justify their contention that exploration with dirty robots, now, is preferable to the possibility that later contamination will be spread by human exploration. We also note that the potential effects of contaminating resources and environments essential to future human occupants of Mars are both significant and not addressed by Fairén et al. (2017). Key Words: Mars—Special Region—Mission—Life detection—Planetary protection. Astrobiology 17, 971–974.

Rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don’t-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/

Norovirus outbreak in a restaurant: investigation of the path of infection by sequence analysis of food and human samples

In September 2014, a small gastroenteritis outbreak occurred in a Greek restaurant. Primary investigations by official food surveillance revealed significant hygienic problems in the premises. Food samples and environmental samples were analyzed for the presence of bacterial and viral food pathogens. Norovirus genogroup I (GI) was detected in 2 environmental samples and in mixed salad. At the same time, stool samples from patients were analyzed and norovirus GI was detected. Further investigations revealed the presence of norovirus GI on some of the restaurant employees. Comparison of nucleic acid sequences revealed full sequence homology between norovirus RNA genotype 1.2 in food, environmental and stool samples, suggesting a common source of contamination and infection. Sequence analysis of food and environmental samples was facilitated by application of a system for total RNA amplification. Despite the fact that original source of contamination could be determined doubtlessly, observed weaknesses in the food production that caused this outbreak were discussed. The mixed salad could have been contaminated either by the lettuce contaminated at primary production or by one of the food-handlers. The investigation of the path of infection is necessary for the kind of legal consequences to be directed by authorities and may contribute to measures to eliminate possible sources of food contamination.

Phytoplasma strain collections: the Q-Bank database and the Q-collect project

The setting of the Q-Bank database freely available on line for quarantine phytoplasmas and also for general phytoplasma identification was linked with a new project Q-collect in order to made widely available the identification of relevant plant pests by nucleic acid sequence comparison of their barcodes and also by providing infected samples that are verified by quality standard for correct phytoplasma identification.

Retrospective Comparison of Nucleic Acid Sequence–Based Amplification, Real-Time PCR, and Galactomannan Test for Diagnosis of Invasive Aspergillosis

Invasive aspergillosis is a life-threatening infection in immunocompromised patients, and treating these infections at an early stage is often crucial for a favorable outcome. Early diagnosis, however, remains challenging. We performed a retrospective comparison of three methods: real-time quantitative PCR (qPCR), nucleic acid sequence-based amplification (NASBA), and galactomannan enzyme-linked immunosorbent assay (GM-ELISA); these detect circulating Aspergillus DNA, RNA, and galactomannan, respectively. Blood samples from 80 patients at high risk for invasive aspergillosis were tested by each assay. The sensitivity of NASBA, qPCR, and GM-ELISA was 76.47% (95% CI, 58.4-88.6%), 67.65% (95% CI, 49.4-82.0%), and 52.94% (95% CI, 35.4-69.8%), respectively, and the specificity was 80.43% (95% CI, 65.6-90.1%), 89.13% (95% CI, 75.6-95.9%), and 80.43% (95% CI, 65.6-90.1%), respectively. We also evaluated the efficiency of the three tests in various combinations. Perfect specificity (100%; 95% CI, 90.4-100%) and perfect positive predictive value (100%; 95% CI, 77.1-100%) were achieved by combining NASBA and qPCR testing in series. Testing with both NASBA and qPCR in parallel was the most sensitive and had the highest Youden index. Our data support the great potential of NASBA and qPCR, singly or in combination, for diagnosis of invasive aspergillosis in high-risk populations.

Q-bank phytoplasma database

The setting of the Q-Bank database free available on line for quarantine phytoplasma and also for general phytoplasma identification is described. The tool was developed in the frame of the EU-FP7 project Qbol and is linked with a new project Q-collect in order to made widely available the identification of relevant plant pests by nucleic acid sequence comparison of their barcodes.

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration.

BackgroundScientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services.MethodsWe selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info.ResultsA total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST).ConclusionsThe need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high priority data from local, independent, idiosyncratic data schemas to common shared concepts as implemented in web-accessible ontologies. These mappings are then amenable for use in semantic web services. Our implementation of approximately two dozen services means that biological data at three large information resources (Gramene, SoyBase, and LIS) is available for programmatic access, semantic searching, and enhanced interaction between the separate missions of these resources.

Dicarboximide resistance in field isolates of Alternaria alternata is mediated by a mutation in a two-component histidine kinase gene

Isolates of Alternaria alternata collected from a field site which had previously been treated with the dicarboximide fungicide iprodione were found to demonstrate a high level of resistance to iprodione and the phenylpyrrole fungicide, fludioxonil in plate assays. In order to determine the genetic basis for this fungicide resistance a partial length clone of a two-component histidine kinase (HK) was isolated from genomic DNA of a fungicide-sensitive A. alternata isolate using degenerate primers by PCR. Analysis of the AaHK1 gene structure indicates the presence of six 90 amino acid repeat domains upstream of a kinase domain as found in the homologous HK genes from other fungal species. Comparison of nucleic acid sequences from the fungicide-sensitive and fungicide-resistant A. alternata isolates confirmed the presence of mutations leading to premature termination of the translated HK protein. The possible role of the two-component HK in the development of dicarboximide resistance in A. alternata is discussed.

First Report of Tomato spotted wilt virus and Impatiens necrotic spot virus in Slovenia.

In July 2000, concentric necrotic rings and patterns were observed on greenhouse-grown pepper (Capsicum anuum L. 'Blondi'). Symptoms were present only on lower leaves, not on young leaves or fruits. Typical tospovirus particles using electron microscopy were observed in leaf-dip preparations of symptomatic leaves. Impatiens necrotic spot virus (INSV) was detected in symptomatic but not in asymptomatic tissues using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with polyclonal antiserum (Loewe Biochemica, Sauerlach, Germany). Nicotiana benthamiana, N. rustica, and Petunia sp. were mechanically inoculated with sap of symptomatic leaves. Local and systemic symptoms were observed only on N. benthamiana. Tomato spotted wilt virus (TSWV) infections were later confirmed in some pepper and tomato plants with distinct systemic symptoms and in greenhouse-grown chrysanthemums, calla lilies, cyclamen and spatiphylum using DAS-ELISA with polyclonal antiserum. Severe systemic symptoms were observed only on some chrysanthemum cultivars, where the infection rate of TSWV was between 80 and 100%. Such TSWV-infected plants were not marketable. Symptomless infections by the same virus were also found. At one location, calla lilies were heavily infected by TSWV, but only local symptoms on leaves were observed. INSV was also confirmed using DAS-ELISA on different chrysanthemum cultivars. Mixed infections of TSWV and INSV were detected using DAS-ELISA on calla lilies with local necrotic rings and patterns on leaves and on Impatiens walerana with systemic necrosis. A limited number of weeds from the vicinity of greenhouses containing symptomatic plants were tested for the presence of TSWV using DAS-ELISA, and only Artemisia vulgaris was infected. Both viruses, TSWV from chrysanthemum and INSV from pepper, were isolated on test plants, and their identity was confirmed using DAS-ELISA. For further verification of TSWV and INSV infection, immunocapture reverse-transcription polymerase chain reaction was performed using general tospovirus primers (1). Amplification products of the expected size were detected and sequenced. Comparison of nucleic acid sequences of amplification products with viral sequence databases confirmed the identities of both viruses. To our knowledge, this is the first report of TSWV and INSV infection in ornamental and vegetable plants in Slovenia. Reference: (1) R. J. Weekes et al. Acta Hortic. 431:159, 1996.

Molecular evolution and phylogeny of dengue-4 viruses.

Nucleotide sequences of the envelope protein genes of 19 geographically and temporally distinct dengue (DEN)-4 viruses were determined. Nucleic acid sequence comparison revealed that the identity among the DEN-4 viruses was greater than 92%. Similarity among deduced amino acids was between 96 and 100%; in most cases identical amino acid substitutions occurred among viruses from similar geographical regions. Alignment of nucleic acid sequences followed by parsimony analysis generated phylogenetic trees, which indicated that geographically independent evolution of DEN-4 viruses had occurred. DEN-4 viruses were separated into two genetically distinct subtypes (genotypes). Genotype-1 contains viruses from the Philippines, Thailand and Sri Lanka; genotype-2 consists of viruses from Indonesia, Tahiti, the Caribbean Islands (Puerto Rico, Dominica) and Central and South America.

Features of the hmg 1 subfamily of genes encoding HMG-CoA reductase in potato

3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes a key step in isoprenoid metabolism leading to a range of compounds that are important for the growth, development and health of the plant. We have isolated 7 classes of genomic clones encoding HMGR from a potato genomic library. Comparison of nucleic acid sequences reveals a high degree of identity between all seven classes of clones and the potato hmg 1 gene described by Choi et al. (Plant Cell 4: 1333, 1992), indicating that all are members of the same subfamily in potato. A representative member (hmg 1.2) of the most abundant class of genomic clones was selected for further characterization. Transgenic tobacco and potato containing the beta-glucuronidase (GUS) reporter gene under the control of the hmg 1.2 promoter expressed GUS activity constitutively at a low level in many plant tissues. High levels of GUS activity were observed only in the pollen. GUS assays of isolated pollen, correlations of GUS activity with the HMGR activity of anthers, hmg 1.2 promoter deletion studies, and segregation analysis of the expression of hmg 1.2::GUS among the R2 pollen of R1 progeny plants demonstrated that the hmg 1.2 promoter controls pollen expression.

Short duplication in a cDNA clone of the rbcL gene from Picea abies.

The plastidic rbcL gene encodes the LSU of Rubisco (EC 4.1.1.39), the enzyme that catalyzes CO, fixation during photosynthesis (Hallick and Bottomley, 1983). In higher plants the enzyme structure is commonly given as a hexadecameric structure composed of eight LSUs and eight small subunits. Nucleotide sequence data from the rbcL gene have been used extensively in studies of plant phylogeny and molecular evolution (Morden and Golden, 1991; Pasternak and Glick, 1992). To investigate the expression of the rbcL gene in damaged and undamaged Norway spruce trees (Picea abies), we have isolated a rbcL cDNA clone via reverse transcriptasePCR (Table I). Using the proofreading ability of the DNA polymerase from the hyperthermophilic archaebacterium Pyrococcus furiosus (Pfu DNA polymerase) we have minimized the number of mutations obtained from amplifications performed with Taq DNA polymerase (Lundberg et al., 1991). The primer sequences were determined by sequence alignment of coniferous rbcL genes using the EMBL data library. The clone was sequenced by the dideoxynucleotide chain termination method using deletion subclones and additional primers. Sequence analysis of the cDNA clone revealed an ORF encoding a 475-amino acid polypeptide, highly homologous to the deduced protein sequences from the two conifers Pinus thunbergii and Pseudotsuga menziesii (Hipkins et al., 1990; Mukai et al., 1991). Furthermore, nucleic acid sequence comparison with the rbcL genes of these two species revealed no possible RNA editing site. In addition to the whole coding region (1425 bp) the sequence contains 28 bp of the 5’ leader including the possible ribosome binding site, 38 bp of the 3’ trailer, and the two PCR primer sites. Moreover, a short, 19-bp duplication was found at the 3’ end of the ORF, which seems to be a specific feature of the genus Picea. This duplication causes a frameshift that creates a new stop codon. It was also found in the North American species Picea pungens (Doerksen et al., 19911, but not in other coniferous or angiosperm species.

Molecular cloning and expression of early T cell costimulatory molecule-1 and its characterization as B7-2 molecule.

The interaction of T cell CD28/CTLA-4 receptors with B7-1 activation Ag on APC represents an important costimulatory pathway in T cell activation. However, it is now evident that this costimulatory pathway is neither unique nor universal for the activation of T cells. Our previous study indicated that a 60-kDa membrane protein, recognized by mAb 2D10, was expressed before B7 by activated murine B cells. This molecule was critically involved in activation of T cells in response to auto- and alloantigens. In the present study, we report on the isolation of a cDNA for this early T cell costimulatory molecule (ETC-1). ETC-1, like B7-1, is a member of the Ig supergene family and is composed of 303 amino acids. Nucleic acid sequence comparison indicated that ETC-1 is identical to the B7-2 molecule. When expressed in Chinese hamster ovary cells, ETC-1 showed profound T cell costimulatory activity as demonstrated by its ability to enhance CD4 T cell proliferation in response to Con A or anti-CD3 stimulation. Furthermore, ETC-1 also bound to both CD28-Ig and CTLA4-Ig fusion proteins. These results strongly support the notion that the interaction of ETC-1/B7-2 with CD28 or CTLA-4 receptors represents an alternative T cell costimulatory pathway.

Molecular evolution and epidemiology of dengue-3 viruses.

The nucleic acid sequences of the pre-membrane/membrane and envelope protein genes of 23 geographically and temporally distinct dengue (DEN)-3 viruses were determined. This was accomplished by reverse transcriptase-PCR amplification of the structural genes followed by automated DNA sequence analysis. Comparison of nucleic acid sequences revealed that similarity among the viruses was greater than 90%. The similarity among deduced amino acids was between 95% and 100%, and in many cases identical amino acid substitutions occurred among viruses from similar geographical regions. Alignment of nucleic acid sequences followed by parsimony analysis allowed the generation of phylogenetic trees, demonstrating that geographically independent evolution of DEN-3 viruses had occurred. The DEN-3 viruses were separated into four genetically distinct subtypes. Subtype I consists of viruses from Indonesia, Malaysia, the Philippines and the South Pacific islands; subtype II consists of viruses from Thailand; subtype III consists of viruses from Sri Lanka, India, Africa and Samoa; subtype IV consists of viruses from Puerto Rico and the 1965 Tahiti virus. Phylogenetic analysis has also contributed to our understanding of the molecular epidemiology and worldwide distribution of DEN-3 viruses.

Improved sensitivity of nucleic acid database searches using application-specific scoring matrices

Scoring matrices for nucleic acid sequence comparison that are based on models appropriate to the analysis of molecular sequencing errors or biological mutation processes are presented. In mammalian genomes, transition mutations occur significantly more frequently than transversions, and the optimal scoring of sequence alignments based on this substitution model differs from that derived assuming a uniform mutation model. The information from sequence alignments potentially available using an optimal scoring system is compared with that obtained using the BLASTN default scoring. A modified BLAST database search tool allows these, or other explicitly specified scoring matrices, to be utilized in computationally efficient queries of nucleic acid databases with nucleic acid query sequences. Results of searches performed using BLASTN's default score matrix are compared with those using scores based on a mutational model in which transitions are more prevalent than transversions.

Segmentation and Segmental Differentiation in the Development of the Central Nervous Systems of Leeches and Flies

There are two current views regarding the phyletic organization of the arthropods. In one view, all arthropods [chelicerates, crustaceans, and uniramians (onychophorans, myriapods, and hexapods)] belong to a single phylum, arising through a complex evolutionary radiation that occurred some 500 to 600 million years ago; the second view holds that the arthro­ pods are polyphyletic, since embryological features suggest separate evo­ lutionary relationships between polychaetes and crustaceans, and between oligochaetes and uniramians (Anderson 1 973, Gupta 1979). Regardless which of these is correct, the metamerism of annelids and arthropods is generally thought to have arisen in a common ancestor of both groups, and both structural and embryological analyses provide evidence for a close relationship between the two groups. One such analysis of several shared features has led to the proposal of a particular phylogenetic affinity between leeches and insects (Sawyer 1 984). The relative closeness of these relationships has been somewhat compromised, however, by recent cross­ species comparisons of nucleic acid sequences. Metamery is also a feature of the chordates, and, interestingly, sequence analysis of 18s rRNA does not indicate that, among the eucoelomates, annelids and arthropods are

General methods of sequence comparison

Mathematical methods for comparison of nucleic acid sequences are reviewed. There are two major methods of sequence comparison: dynamic programming and a method referred to here as the regions method. The problem types discussed are comparison of two sequences, location of long matching segments, efficient database searches and comparison of several sequences.