Length Of Polymerase Chain Reaction Product Research Articles

MORPHOLOGICAL AND MOLECULAR IDENTIFICATION OF ZOONOTIC TREMATODE METACERCARIAE (Haplorchis taitui) IN FRESHWATER FISH IN IRAN

The intestinal trematode, Haplorchis taichui (Nishigori, 1924), is an important in public health that causes infection in humans and animals especially in Asia and in parts of Africa and the Americas. Haplorchis taitui metacercariae were found in the gills of Cyprinion macrostomus (Heckel) and Capoeta barroisi persica (Karaman) collected from the Shapour River. Morphological excysted metacercariae were identified as wet mounts under a stereomicroscope. Then, the samples were subjected to molecular analysis. The result showed that 69% of examined fish (n = 30) were diagnosed infected with encysted metacercariae in gills. The mean intensity was 8.3 ± 16.9 parasites per fish. The morphometrical values agree with the findings of other studies with the small differences and polymerase chain reaction product length and nucleotide sequence analysis of 18S ribosomal deoxyribonucleic acid gene showed a similarity of over 99% between the specimens and the Haplorchis taichui (Nishigori, 1924) recorded in GenBank.

The use of two pairs primer for CO1 gene amplification on traded stingray at fish auction Tasik Agung Rembang

Stingray provide a high economic contribution and increase in production and utilization. Conservation effort needed to identify molecularly using CO1 gene. The success of CO1 gene in identifying species can not be separated from amplification in polymerase chain reaction (PCR) technique. The use of primer FishF1, FishR1, FishF2, and FishR2 to amplify COI gene for stingray traded at fish auction Tasik Agung Rembang never been done, so it need to be researched. The purpose of this study is to amplify the COI gene of stingray traded at fish auction Tasik Agung Rembang using two pairs of primers. Five stingrays sample were obtained from fish auction Tasik Agung Rembang. Then its DNA was isolated using protocol from TIANamp Marine Animals DNA Kit and measured in quantity using nano spectrophotometer. Amplification of CO1 gene by PCR technique. Based on the results of the study showed that the five samples had good DNA purity, concentration, and quality. The 5 samples amplification result showed that the FishF1-FishR1 primer pair succeeded in amplifying samples a, b, d, and e, while the FishF2-FishR2 primer pair succeeded in amplifying samples b, c, d, and e with a PCR product length around 655 bp.

Influence of abaR gene knockout on growth metabolism and biofilm formation of Acinetobacter baumannii

Objective: To investigate the influence of abaR gene knockout on growth metabolism and biofilm formation of Acinetobacter baumannii. Methods: The abaR gene was knocked out from Acinetobacter baumannii standard strain ATCC 17978 (wild strain) by homologous recombination method, and then the ATCC 17978 abaR knockout strain (ATCC 17978/ΔabaR: : Kn) was obtained and verified by polymerase chain reaction (PCR) electrophoresis and sequencing. The growth curves of Acinetobacter baumannii wild strain and Acinetobacter baumannii knockout strain were determined by microplate reader within cultivation hour (CH) 18, and the biofilm formation ability was measured by crystal violet staining at CH 8, 24, and 48, respectively. The sample number at each time point was 3.The results were denoted as absorbance value. Data were processed with analysis of variance of factorial design, one-way analysis of variance, t test, and least-significant difference test. Results: (1) The length of PCR product of target fragment ΔabaR: : Kn was 3 029 bp. The abaR gene was knocked out to obtain the knockout strain ATCC 17978/ΔabaR: : Kn. The length of PCR product of the knockout strain was 3 300 bp. The abaR gene was successfully knocked out. (2) At CH 2, 3, and 4, the absorbance values of Acinetobacter baumannii wild strain were slightly higher than those of the knockout strain. The absorbance values of Acinetobacter baumannii wild strain and knockout strain were similar from CH 5 to 18. (3) At CH 8 and 24, the biofilm formation ability of Acinetobacter baumannii wild strains (0.644±0.066, 0.574±0.184) was similar to that of knockout strains (0.559±0.008, 0.394±0.030, t=2.209, 1.167, P>0.05). At CH 48, the biofilm formation ability of Acinetobacter baumannii wild strains (1.157±0.259) was significantly stronger than that of Acinetobacter baumannii knockout strains (0.576±0.026, t=3.865, P<0.05). The biofilm formation ability of Acinetobacter baumannii wild strains at CH 48 was significantly stronger than that at CH 8 and 24 (P<0.05). The biofilm formation ability of Acinetobacter baumannii knockout strains at CH 24 was significantly weaker than that at CH 8 and 48 (P<0.05). Conclusions: The abaR gene of Acinetobacter baumannii ATCC 17978 can be successfully knocked out by homologous recombination to obtain its knockout strain ATCC 17978/ΔabaR: : Kn. The abaR gene does not affect the growth and metabolism of Acinetobacter baumanniibut can weaken its biofilm formation ability.

Enzymatic synthesis of long double-stranded DNA labeled with haloderivatives of nucleobases in a precisely pre-determined sequence

BackgroundRestriction endonucleases are widely applied in recombinant DNA technology. Among them, enzymes of class IIS, which cleave DNA beyond recognition sites, are especially useful. We use BsaI enzyme for the pinpoint introduction of halogen nucleobases into DNA. This has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective.ResultsAn enzymatic method for synthesizing long double-stranded DNA labeled with the halogen derivatives of nucleobases (Hal-NBs) with 1-bp accuracy has been put forward and successfully tested on three different DNA fragments containing the 5-bromouracil (5-BrU) residue. The protocol assumes enzymatic cleavage of two Polymerase-Chain-Reaction (PCR) fragments containing two recognition sequences for the same or different class IIS restriction endonucleases, where each PCR fragment has a partially complementary cleavage site. These sites are introduced using synthetic DNA primers or are naturally present in the sequence used. The cleavage sites are not compatible, and therefore not susceptible to ligation until they are partially filled with a Hal-NB or original nucleobase, resulting in complementary cohesive end formation. Ligation of these fragments ultimately leads to the required Hal-NB-labeled DNA duplex. With this approach, a synthetic, extremely long DNA fragment can be obtained by means of a multiple assembly reaction (n × maximum PCR product length: n × app. 50 kb).ConclusionsThe long, precisely labeled DNA duplexes obtained behave in very much the same manner as natural DNA and are beyond the range of chemical synthesis. Moreover, the conditions of synthesis closely resemble the natural ones, and all the artifacts accompanying the chemical synthesis of DNA are thus eliminated. The approach proposed seems to be completely general and could be used to label DNA at multiple pre-determined sites and with halogen derivatives of any nucleobase. Access to DNAs labeled with Hal-NBs at specific position is an indispensable condition for the understanding and optimization of DNA photo- and radio-degradation, which are prerequisites for clinical trials of Hal-NBs in anticancer therapy.

Conserved PCR Primer Set Designing for Closely-Related Species to Complete Mitochondrial Genome Sequencing Using a Sliding Window-Based PSO Algorithm

BackgroundComplete mitochondrial (mt) genome sequencing is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. For long template sequencing, i.e., like the entire mtDNA, it is essential to design primers for Polymerase Chain Reaction (PCR) amplicons which are partly overlapping each other. The presented chromosome walking strategy provides the overlapping design to solve the problem for unreliable sequencing data at the 5′ end and provides the effective sequencing. However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA.Methodology/Principal FindingsThe purpose of this study is to develop an integrated primer design algorithm for entire mt genome in general, and for the common primer sets for closely-related species in particular. We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. Using a heuristic algorithm particle swarm optimization (PSO), all the designed primers were computationally validated to fit the common primer design constraints, such as the melting temperature, primer length and GC content, PCR product length, secondary structure, specificity, and terminal limitation. The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology. Finally, primer sets were designed within the overlapping region. The primer sets for the entire mtDNA sequences were successfully demonstrated in the example of two closely-related fish species. The pseudo code for the primer design algorithm is provided.Conclusions/SignificanceIn conclusion, it can be said that our proposed sliding window-based PSO algorithm provides the necessary primer sets for the entire mt genome amplification and sequencing.

DEVELOPMENT OF PRIMERS FOR DETECTION OF MULTIPLE CERVID SPECIES IN ANIMAL FEED

ABSTRACT Polymerase chain reaction (PCR) detection of mammal or ruminant tissue is used for ensuring compliance with animal feed regulations for BSE protection. In the event of a positive result using the group‐specific primers for mammal or ruminant, it is necessary to identify likely species sources of the contamination. To investigate contaminated species tissue, species‐specific primer can be used such as primers for cattle, sheep or deer. Although primers for single cervid species were reported, there are risks such as false negative result or non‐availability for feed, because they are not designed for inspection of feed and for detection of multiple cervid species. In this study, we have developed primers to detect multiple cervid species in feed. The primers we developed were designed from the whole mtDNA sequences of eleven cervid species. This primer set created 133‐bp DNA fragment from various deer mtDNA, and no amplification were observed from nontarget species, several feed materials and formula feed at the same length of the target PCR product. The detection limit was 0.1 pg of the mtDNA. PRACTICAL APPLICATIONBecause existing PCR primers for cervid species are designed to detect specific cervid species, they may produce false negative results when they are used for detecting deer in general. Moreover, animal feed contains various kinds of materials and some of them may become a inhibitor of the primers. The PCR method in this study is available to be used for an investigation for the contaminated cervid species in feed or feed materials. To avoid the false negative result, a consensus sequence for designing group‐specific primers was created from 11 cervid mtDNA sequences, using a computer program. This primer set differentiates various cervid species from non‐cervid species in feed.

Vibrio tapetis의 검출을 위한 PCR specific primer의 제작

Brown Ring Disease (BRD) is a bacterial disease caused by Vibrio tapetis which affects cultured clam Ruditapes philippinarum and causes heavy economic losses on Atlantic coasts of france, Spain and England. In this study, to evaluate the effective detection of the pathogen, specific primer set based on 16S ribosomal RNA (rRNA) sequences designed for rapid detection of V. tapetis. Polymerase chain reaction (PCR) with this primer set produced the specific band for each V. tapetis. The length of PCR product using designed primer set of Vbts-F and Vbts-R was about 400 bp. Therefore, these primers will be provided with a basic tool for rapid detection of V. tapetis in the various cases such as examination of imported aquatic products, diagnosis of aquatic organisms, and etc.

The association of −627 interleukin-10 promoter polymorphism in Chinese patients with systemic lupus erythematosus

The objective of the study is to examine whether interleukin-10 (IL-10) promoter polymorphism is a marker of susceptibility of systemic lupus erythematosus (SLE) in Chinese patients in Taiwan. The study included 119 Chinese patients with SLE. One hundred unrelated healthy individuals living in central Taiwan served as control subjects. Each polymorphism was detected as a result of a polymerase chain reaction (PCR)-based restriction analysis. The PCR product length was determined to be 412 bp (CC) whereas two fragments of 236 and 176 bp were determined to be excisable lengths (AA). The relationship between the IL-10 gene polymorphism and clinical manifestations of SLE was evaluated. For the genotype and allelic frequency, there were statistically significant differences between the SLE patients and the normal control subjects (p=0.007 and 0.003, respectively). But we did not detect any association of carriage rate of the IL-10 polymorphism and the normal control subjects (p=0.077). Furthermore, we did not detect any association of IL-10 genotype with antinuclear antibody, malar rash, photosensitivity, discoid lupus, mucosal ulcer, arthritis, serositis, hematology, immunology, involvement of central nervous system, and renal disease involvement in the SLE patients. The significant relation of -627 IL-10 genotype and allelic frequency with SLE implies that the IL-10 gene polymorphism can serve as a candidate gene marker for further study in patients with SLE in Taiwan.

The association between fibromyalgia and polymorphism of monoamine oxidase A and interleukin-4

Because fibromyalgia (FM) is often comorbid with anxiety, and monoamine oxidase A (MAOA) was reported to be associated with anxiety, we determine if there is MAOA gene polymorphism associated with FM patients. Moreover, interleukin 4 (IL-4) was found to be an important cytokine participating in the immunologic pathway of T-helper 2 (Th-2) cells, in this study, we search if the genetic polymorphism of IL-4 intron3 could be demonstrated in FM patients. The genotype of sixty-two FM patients was compared with that of control subjects. The polymorphism of IL-4 intron3 variable number of tandem repeats (VNTR) was demonstrated by performing the genomic polymerase chain reaction (PCR) and analyzing the length of PCR product. Furthermore, the MAOA 941 G to T polymorphism was also determined by PCR-RFLP (restriction fragment length polymorphism) analysis. The MAOA 941 position genotype polymorphism between FM and control subjects was found neither statistically different in male (p=0.60) or female (p=0.52), nor total allelic frequency (p=0.52). Similarly, the difference of IL-4 intron3 polymorphism between FM and control was neither existing in genotype (p=0.06), nor allele frequency (p=0.07). The result suggests either the genetic linkage between FM and anxiety or that between FM and immunologic diseases are weak. Accordingly, the MAOA 941 position and IL-4 intron3 polymorphisms are not susceptible markers to predict FM.

Doubly uniparental transmission of mitochondrial DNA length variants in the mussel Mytilus trossulus

Doubly uniparental inheritance of mitochondrial DNA (mtDNA) is an unusual feature found in marine mussels and a few other bivalve species. In addition to a mitochondrial genome (F) inherited through the female line, heteroplasmic individuals (males) contain a second highly diverged genome (M) that is inherited through the paternal line. The Baltic mussel Mytilustrossulus is characterized by the presence of two phylogenetically close female and male genomes. We examined M. trossulus sampled from the Gulf of Gdansk, southern Baltic. Somatic tissues and gametes were surveyed for the presence of different types of mtDNA. Length variants were identified using PCR (polymerase chain reaction) amplification of the mtDNA fragment containing the major noncoding region. Seventeen length variants present in homo- and heteroplasmic individuals were found in a sample of 343 individuals analyzed. Two length variants of the major noncoding region (PCR product lengths: 1520 and 1370 bp) were the most frequent. Length heteroplasmy was found in 46.8% of males, and was mostly caused by the presence of the short length variant (PCR product length: 1370 bp) of the major noncoding region. MtDNA variants were also detected by restriction analysis of a 1.3 kb segment of coding region (ND2–COIII) amplified by PCR. This study provides evidence that the short length variant is always transmitted to sperm and has taken over the role of the M genome. The remaining length variants were present in both males and females. Longer length variants were transmitted mainly through the female line. A possibility of much higher incidence of genome role reversals in Baltic M. trossulus, in comparison with other populations of mussels is discussed.

Association of vitamin D receptor gene BsmI polymorphisms in Chinese patients with systemic lupus erythematosus.

The purpose of this study was to evaluate whether vitamin D receptor (VDR) genes BsmI polymorphisms were markers for susceptibility to or severity of systemic lupus erythematosus (SLE) in Chinese patients in Taiwan. The study included 47 Chinese patients with SLE. In addition, 90 unrelated, healthy individuals living in central Taiwan served as control subjects. Each polymorphism was detected as a result of polymerase chain reaction (PCR)-based restriction analysis. A PCR product length was determined to be 580bp (BB) whereas two fragments of 405 and 175bp were determined to be excisable lengths (bb) by BsmI endonuclease. The relationship between Bsm polymorphisms and clinical manifestations of SLE was evaluated. We found that BB was significantly more common and bb less common in SLE than in control group (chi2 = 54.2, P < 0.0001). In addition, the frequency of B allele was also significantly more common in patients with SLE than in the healthy control subjects (chi2 = 38.7, P < 0.0001), giving an odds ratio of 7.14 (95% confidence interval 3.53-14.4). In the SLE patients, we did not detect any associations of VDR genotype with the clinical, laboratory profiles, or lupus nephritis (chi2 = 2.34, P = 0.3). This study indicated an increased distribution of VDR BB genotype and B allelic frequencies in the Chinese SLE patients in Taiwan. However, there were no associations between the frequency of VDR allelic variations and clinical manifestations, laboratory profiles, or lupus nephritis.

Identification of mycorrhizal fungi from single pelotons of Dactylorhiza majalis (Orchidaceae) using single-strand conformation polymorphism and mitochondrial ribosomal large subunit DNA sequences.

The mitochondrial ribosomal large subunit (Ls) DNA was used to identify the orchid mycorrhizal fungi found in roots of Dactylorhiza majalis. The gene was amplified using DNA extracted from single pelotons obtained from fresh and silica gel dried roots. Furthermore, sequencing a variety of well-characterized orchid isolates expanded the fungal database of the mitochondrial ribosomal LsDNA. Polymerase chain reaction product length variants present in D. majalis were sequenced and identified using the expanded database. These analyses revealed two different peloton-forming fungi in samples from D. majalis, which sometimes occurred together as a single two-taxa peloton within the same cortex cell. The first taxon belonged to the genus Tulasnella and the second taxon was distantly related to Laccaria.

No association of vitamin D receptor gene BsmI polymorphisms with calcium oxalate stone formation.

The formation of urinary stones is reported to be associated with the vitamin D receptor (VDR). As the most frequently seen polymorphism within the VDR gene is BsmI, it has been used as a genetic marker in searching for the cause of urolithiasis. We aimed to evaluate the association between calcium stone disease and the BsmI polymorphisms. A control group of 90 healthy people and a group of 124 patients with calcium oxalate stones were examined. The polymorphism was detected using polymerase chain reaction (PCR)-based restriction analysis. A PCR product length was determined to be 580 bp (BB) whereas two fragments of 405 bp and 175 bp were determined to be excisable (bb) by BsmI endonuclease. Associations between calcium stone disease and BsmI polymorphisms were evaluated. The results revealed no significant difference between normal individuals and stone patients (P = 0.891). The allelic distribution of B and b were similar within both the normal group and the stone patients. Therefore, the BsmI polymorphism of the VDR gene at intron 8 is not a suitable genetic marker for urinary stone disease.

Mutational and genetic origin of LDL receptor gene mutations detected in both Belgian and Dutch familial hypercholesterolemics.

DNA samples from 100 unrelated Belgian patients with familial hypercholesterolemia (FH) were screened for the presence of specific low-density lipoprotein receptor (LDLR) gene mutations, previously shown to be prevalent in related populations. Two point mutations, viz., P664L and a G to A splicing defect at position 1359-1, were detected in single Flemish-speaking families. A long-distance polymerase chain reaction (PCR) assay, used to screen for the 4-kb and 2.5-kb deletions previously identified by Southern blot analyses in different parts of The Netherlands, revealed a 3-kb deletion in two Belgian patients. Comparison of PCR product length showed that both Dutch deletions of exons 7-8 are identical to that found in Belgians, but different from the 2.5-kb deletion previously described in South Africans of mixed ancestry. The Belgian patients probably share a common ancestor, for each mutation identified, with FH patients from The Netherlands, since all three mutations were associated with the same LDLR gene haplotype as described for the Dutch population. Analysis of the deletion junctions demonstrated the role of a 31-bp repetitive sequence in the generation of large rearrangements involving exons 7 and 8 of the LDLR gene. The finding that only 4 out of 100 analyzed Belgian hypercholesterolemics carry a known LDLR mutation that is prevalent in related populations suggests that the Belgian FH population has its own spectrum of mutations.

The use of microsatellite DNA markers for soybean genotype identification

Conventional morphological and pigementation traits, as well as disease resistance, have been used to distinguish the uniqueness of new soybean cultivars for purposes of plant variety protection. With increasing numbers of cultivars and a finite number of conventional characters, it has become apparent that such traits will not suffice to establish uniqueness. The objective of this work was to provide an initial evaluation of microsatellite or simple-sequence-repeat (SSR) DNA markers to develop unique DNA profiles of soybean genotypes. Microsatellites are DNA sequences such as (AT) n /(TA) n and (ATT) n /(TAA) n that are composed of tandemly repeated 2-5-basepair DNA core sequences. The DNA sequences flanking microsatellites are generally conserved allowing the selection of polymerase chain reaction (PCR) primers that will amplify the intervening SSR. Variation in the number of tandem repeats, "n", results in PCR product length differences. The SSR alleles present at three (AT) n /(TA) n and four (ATT) n /(TAA) n loci were determined in each of 96 diverse soybean genotypes. Between 11 and 26 alleles were found at each of the seven loci. Only two genotypes had identical SSR allelic profiles and these had very similar pedigrees. The gene diversity for the seven markers averaged 0.87 for all 96 genotypes and 0.74 for a subset of 26 North American cultivars. These are much higher than soybean gene diversity values obtained using RFLP markers, and are similar to the average values obtained for human microsatellite markers. SSR markers provide an excellent complement to the conventional markers that are currently used to characterize soybean genotypes.

Sequence variability of the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus

Sequence analysis of polymerase chain reaction (PCR) amplified products from the presumed tetranucleotide repeat at the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus shows far greater variability in both PCR product length and sequence than has been previously reported. Alleles differing in size by 1 bp exist, and accurate sizing is required if the locus is to be used to its full potential.

Molecular analysis of pseudorabies viral vaccines and their rapid differentiation from wild-type isolates using DNA-amplified glycoprotein I and thymidine kinase gene segment polymorphisms

Several conventional and genetically recombinant modified-live viral (MLV) vaccines are used to control pseudorabies virus infections (Aujeszky's disease, PRV) in swine. Differentiating vaccinal PRV (V-PRV) from wild PRV (WT-PRV) is important for herd health, regulatory and forensic purposes, and for studies of PRV latency and epidemiology. All PRV vaccines used currently contain glycoprotein I (gl) and/or thymidine kinase (TK) gene deletions, whereas WT-PRV typically contain intact gl and TK genes. Utilizing these differences we developed an effective but simple differential polymerase chain reaction (PCR) approach based upon the amplification of gl and TK gene polymorphisms. The primary immunoreactive epitope-encoding region of the gl gene and nearly the entire TK gene were amplified and analyzed using nested PCR procedures. TK and gl PCR products were cleaved with Sal I and Sac I, and Nco I restriction enzymes respectively. PCR product and restriction fragment length polymorphisms enabled most V-PRV to be clearly distinguished from each other, and all of them, as a group, clearly differentiated from typical WT-PRV. Mixtures of V-PRV and WT-PRV could be identified as such. The uncommon but occasional occurrence of atypical WT-PRV containing altered gl and/or TK genes indicates the need for interpretive caution, particularly if aberrant gene segment polymorphisms are observed. This rapid and precise molecular approach will facilitate regulatory monitoring, epidemiological investigations, diagnostic differentiation, purity testing and latency/recrudescence studies with the class of biologicals and offers a model for similar analyses of other MLV biologicals as well.