Analysis of the 16S–23S rDNA intergenic spacers (IGSs) of marine vibrios for species-specific signature DNA sequences

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

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Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽

10.1139/g10-065 ◽

2010 ◽

Vol 53 (10) ◽

pp. 769-777 ◽

Cited By ~ 1

Author(s):

Melanie Mehes-Smith ◽

Paul Michael ◽

Kabwe Nkongolo

Keyword(s):

Dna Sequences ◽

Random Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Pinus Monticola ◽

The Family ◽

Species Specific ◽

Rapd And Issr ◽

Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

Acta Botanica Croatica ◽

10.2478/v10184-012-0010-z ◽

2013 ◽

Vol 72 (1) ◽

pp. 1-133 ◽

Cited By ~ 2

Author(s):

Višnja Besendorfer ◽

Jelena Mlinarec

Keyword(s):

Dna Sequences ◽

Southern Hybridization ◽

Repeat Unit ◽

Similar Species ◽

Genomic Component ◽

Library Hypothesis ◽

Species Specific ◽

Eukaryotic Organisms ◽

Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

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Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽

10.1163/156854109x428016 ◽

2009 ◽

Vol 11 (6) ◽

pp. 847-857 ◽

Cited By ~ 21

Author(s):

Lieven Waeyenberge ◽

Nicole Viaene ◽

Maurice Moens

Keyword(s):

Internal Control ◽

Dna Sequences ◽

Rrna Gene ◽

Duplex Pcr ◽

Specific Primers ◽

5.8S Rrna Gene ◽

5.8S Rrna ◽

Wide Range ◽

Pcr Products ◽

Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

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Species specific DNA sequences in the Triticeae

Hereditas ◽

10.1111/j.1601-5223.1992.tb00204.x ◽

1992 ◽

Vol 116 (1-2) ◽

pp. 49-54 ◽

Cited By ~ 13

Author(s):

K. ANAMTHAWAT-JÓNSSON ◽

J. S. HESLOP-HARRISON

Keyword(s):

Dna Sequences ◽

Species Specific

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Isolation of a yeast gene involved in species-specific pre-tRNA processing

Molecular and Cellular Biology ◽

10.1128/mcb.8.12.5140-5149.1988 ◽

1988 ◽

Vol 8 (12) ◽

pp. 5140-5149

Author(s):

S S Wang ◽

A K Hopper

Keyword(s):

Dna Sequences ◽

Genomic Library ◽

Nonsense Suppression ◽

Suppressor Activity ◽

Specific Product ◽

Trna Processing ◽

Trna Splicing ◽

Trna Species ◽

Multiple Copies ◽

Species Specific

To identify genes involved in pre-tRNA processing, we searched for yeast DNA sequences that specifically enhanced the expression of the SUP4(G37) gene. The SUP4(G37) gene possesses a point mutation at position 37 of suppressor tRNA(Tyr). This lesion results in a reduced rate of pre-tRNA splicing and a decreased level of nonsense suppression. A SUP4(G37) strain was transformed with a yeast genomic library, and the transformants were screened for increased suppressor activity. One transformant contained a plasmid that encoded an unessential gene, STP1, that in multiple copies enhanced the suppression of SUP4(G37) and caused increased production of mature SUP4(G37) product. Disruption of the genomic copy of STP1 resulted in a reduced efficiency of SUP4-mediated suppression and the accumulation of pre-tRNAs. Not all intron-containing pre-tRNAs were affected by the stp1-disruption. At least five of the nine families of pre-tRNAs were affected. Two other species, pre-tRNA(Ile) and pre-tRNA(3Leu), were not. We propose that STP1 encodes a tRNA species-specific product that functions as a helper for pre-tRNA splicing. The STP1 product may interact with pre-tRNAs to generate a structure that is efficiently recognized by splicing machinery.

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Quantitative Detection of Species-Specific DNA in Feedstuffs and Fish Meals

Journal of Food Protection ◽

10.4315/0362-028x-68.6.1217 ◽

2005 ◽

Vol 68 (6) ◽

pp. 1217-1221 ◽

Cited By ~ 27

Author(s):

PAVEL KRCMAR ◽

EVA RENCOVA

Keyword(s):

Mitochondrial Dna ◽

Real Time ◽

Dna Sequences ◽

Real Time Pcr ◽

Single Species ◽

Absolute Quantification ◽

Quantitative Detection ◽

Vertebrate Species ◽

Target Species ◽

Species Specific

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species–derived material in concentrate feed mixtures and fish meals.

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Development and Application of a New PCR Method for Detection of Blumeria graminis f. sp. tritici

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000494432 ◽

2018 ◽

Vol 28 (3) ◽

pp. 137-146 ◽

Cited By ~ 1

Author(s):

Adam Kuzdraliński ◽

Hubert Szczerba ◽

Anna Kot ◽

Agnieszka Ostrowska ◽

Michał Nowak ◽

...

Keyword(s):

Dna Sequences ◽

Puccinia Triticina ◽

Blumeria Graminis ◽

Pyrenophora Tritici Repentis ◽

Field Samples ◽

Expected Length ◽

Pcr Assays ◽

Primer Sets ◽

Wheat Leaves ◽

Species Specific

We developed new PCR assays that target beta-tubulin (TUB2) and 14 alpha-demethylase (CYP51) genes and used them for the species-specific detection of Blumeria graminis f. sp. tritici (Bgt). Based on fungi DNA sequences available in the NCBI (National Center for Biotechnology Information) GenBank database we developed simplex and duplex PCR assays. The specificities of the primer sets were evaluated using environmental samples of wheat leaves collected during the 2015/2016 growing season across Poland. Primer sets LidBg17/18 and LidBg21/22 strongly amplified fragments of the expected length for all 67 tested samples. Primer specificity was confirmed using field samples of Zymoseptoria tritici, Puccinia triticina (syn. P. recondita f. sp. tritici), P. striiformis f. sp. tritici, and Pyrenophora tritici-repentis.

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Community assessment of crustose calcifying red algae as coral recruitment substrates

10.1101/2021.09.27.461929 ◽

2021 ◽

Author(s):

Mari E. Deinhart ◽

Matthew S. Mills ◽

Tom Schils

Keyword(s):

Dna Sequences ◽

Red Algae ◽

Taxonomic Diversity ◽

Coralline Algae ◽

Crustose Coralline Algae ◽

Coral Recruitment ◽

Successful Recruitment ◽

Ecological Roles ◽

Coral Reef Ecosystems ◽

Species Specific

AbstractSuccessful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) have been identified as important recruitment substrates for scleractinian corals. As such, CCRA as a whole or subgroups (e.g., crustose coralline algae, CCA) are often used at the functional group level in experimental, ecological, and monitoring studies. Species of CCRA, however, differ in their ecological roles and their value as coral recruitment substrates. Here, we (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles, and (2) assess if there is a recruitment preference of the coral Acropora surculosa for any of these CCRA species. 27 species of two orders of CCRA (Corallinales and Peyssonneliales) were identified from the recruit tiles. None of the DNA sequences of these species matched released sequences in GenBank or sequences of CCRA collected from natural reef systems in Guam. The similarity in CCRA communities between the recruitment tiles was high. Two species of CCRA were significantly preferred as recruitment substrates over the other CCRA species. Both of these species belonged to the subfamily of the Lithophylloideae. These two species are closely related to Pacific species that have been referred to as Titanoderma -but probably have to be assigned to another genus- and many of the latter have been attributed to be preferred coral recruitment substrates. Of all CCRA, Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and was the most preferred recruitment substrate. These findings highlight the high taxonomic diversity of CCRA communities and provide insight into species-specific ecological roles of CCRA that are often overlooked.

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Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65449 ◽

2021 ◽

Vol 4 ◽

Author(s):

O. Nurul Fizatul Nabilah ◽

A. R. Ramizah ◽

A. B. Adibah ◽

S. Syazwan ◽

A.G. Intan Faraha ◽

...

Keyword(s):

Dna Sequences ◽

Environmental Dna ◽

Coi Gene ◽

Alien Invasive Species ◽

Survey Method ◽

Specific Primers ◽

Invasive Fishes ◽

Specific Amplification ◽

Species Specific ◽

High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

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