Polymerase Chain Reaction Primer Pairs Research Articles

Development and Validation of Thinopyrum elongatum–Expressed Molecular Markers Specific for the Long Arm of Chromosome 7E

ABSTRACTThe ditelocentric addition line CS‐7EL of the spring wheat (Triticum aestivum L.) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS‐7EL), which confers high resistance to Fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS‐7EL, to develop 7EL‐specific molecular markers, and to validate their usefulness for characterizing recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High‐throughput sequencing of Fusarium graminearum–infected and control CS and CS‐7EL cDNA libraries was performed using RNA‐Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA‐Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. Polymerase chain reaction primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS‐7E(7D) × 2*CSph1b showed that these markers are useful for characterizing recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum.

HBV Genotyping and Phylogenetic Analysis through Multiplex PCR Using Type Specific Primer Pairs in Pakistani Population

Background: Hepatitis B virus causing acute and chronic hepatocellular carcinoma relics a serious health issue affecting more than 350 million people worldwide. Geographically, nine genotypes of HBV have been identified so far. Four open reading frames named (ORF P, S, F and X) renders it to specifically targets hepatocyte cells. Additionally, reverse transcription process present in the life cycle of HBV caused four order higher mutation rates as compared to adenovirus. The structural and functional differences between HBV genotypes are the mainstay to severity, complications, treatment and possibly vaccination against the virus. Hepatitis B genotyping is important for assessing its clinical implications and geographical distribution, but the sub-genotypes have been found useful for determination of specific genomic markers related to hepatocarcinogenesis and medical therapies. In Pakistan, there is no reported data available on molecular evolutionary analysis of HBV. A study was, therefore, much needed to evaluate the spectra of dominant strains prevalent here. Objectives: This study was aimed to figure out the prevalence of HBV genotypes among population in Pakistan. In this research, we focused to find out the new strains and sub genotypes of HBV. Pakistan is one of the HBV endemic countries but there is no data on subgenotypes and their recombination or the phylogenetic relatedness of the virus endemic in the country. The present study was carried out in this perspective. This study will help future researcher to study some other aspects of HBV related strains in Pakistan and also about its medical therapies. Place and duration of study: The present study was carried out at Polymerase Chain Reaction (PCR) lab, Nuclear Medicine, Oncology and Radiotherapy Institute [NORI], Islamabad, and the samples were collected between September 2012 to February 2014. Study design: A total of 450 Hepatitis B surface antigen HBsAg and HBV DNA positive samples were collected in the first step during the period of September 2012 to February 2014 and sent to Nuclear Medicine Oncology and Radiotherapy Institute [NORI], for further analysis. All the samples were genotyped by type specific nested PCR primer pair method for 8 HBV genotypes from A through H. The patients were randomly selected irrespective of their age and gender and a written consent (parental consent in case of less than 18 years of age) was obtained. The study was approved by ethical review committee. In our research, we have used the type specific primer technique to find out the dominant strain in Pakistani populations and furthermore its phylogenetic analysis with reference sequences retrieved from NCBI databases. Results: Our results showed a direct relationship between viral load and identified genotypes and pinpointed that genotype D is the most pre-dominant genotype and prevailing in high proportions among all genotypes in Pakistani population. Mix HBV genotype infections of genotype A with B & C, D with B and C constitute about 17 percent of all the samples. Subgenotypes of different HBV strains have been identified on the basis of differences in the complete nucleotide sequences. Positive PCR results were repeated twice for confirmation. Furthermore, phylogenetic analysis revealed a homology between our reported sequences and reference sequences. The phylogenetic method showed that genotypes/sub-genotypes varies in the geographical areas and correlate strongly with ethnicity. Conclusion: Genotype D was identified and come out to be the most dominant genotype in Pakistani community showing sub-genotypes of D1 & D3 in our study. Genotype A and D are present as co-infection with each other and contributed as the second prevailing genotypic group. Additionally, phylogenetic analysis revealed that genotypes varies in the geographical areas and correlate strongly with reference sequences from NCBI.

Analyzing the gene expression profile of anaplastic histology Wilms' tumor with real-time polymerase chain reaction arrays.

BackgroundWilms’ tumor (WT) is one of the most common malignant neoplasms of the urinary tract in children. Anaplastic histology (unfavorable histology) accounts for about 10% of whole WTs, and it is the single most important histologic predictor of treatment response and survival in patients with WT; however, until now the molecular basis of this phenotype is not very clearly.MethodsA real-time polymerase chain reaction (PCR) array was designed and tested. Next, the gene expression profile of pediatric anaplastic histology WT and normal adjacent tissues were analyzed. These expression data were anlyzed with Multi Experiment View (MEV) cluster software further. Datasets representing genes with altered expression profiles derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool (IPA).Results88 real-time PCR primer pairs for quantitative gene expression analysis of key genes involved in pediatric anaplastic histology WT were designed and tested. The gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal controls; we identified 15 genes that are up-regulated and 16 genes that are down-regulated in the former. To investigate biological interactions of these differently regulated genes, datasets representing genes with altered expression profiles were imported into the IPA for further analysis, which revealed three significant networks: Cancer, Hematological Disease, and Gene Expression, which included 27 focus molecules and a significance score of 43. The IPA analysis also grouped the differentially expressed genes into biological mechanisms related to Cell Death and Survival 1.15E−12, Cellular Development 2.84E−11, Cellular Growth and Proliferation 2.84E-11, Gene Expression 4.43E−10, and DNA Replication, Recombination, and Repair 1.39E−07. The important upstream regulators of pediatric anaplastic histology WT were TP53 and TGFβ1 signaling (P = 1.15E−14 and 3.79E−13, respectively).ConclusionsOur study demonstrates that the gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal tissues with real-time PCR array. We identified some genes that are dysregulated in pediatric anaplastic histology WT for the first time, such as HDAC7, and IPA analysis showed the most important pathways for pediatric anaplastic histology WT are TP53 and TGFβ1 signaling. This work may provide new clues into the molecular mechanisms behind pediatric anaplastic histology WT.Electronic supplementary materialThe online version of this article (doi:10.1186/s12935-015-0197-x) contains supplementary material, which is available to authorized users.

First Report of Phytoplasma (16SrI) Associated with Yellow Decline Disease of Royal Palms [Roystonea regia (Kunth) O. F. Cook] in Malaysia

AbstractRoyal Palms (Roystonea regia) with symptoms such as severe chlorosis, stunting, collapse of older fronds and general decline were observed in the state of Selangor, Malaysia. Using polymerase chain reaction (PCR) amplification with phytoplasma universal primer pair P1/P7 followed by R16F2N/R16R2 and fU5/rU3 as nested PCR primer pairs, all symptomatic plants tested positively for phytoplasma. Results of phylogenetic and virtual RFLP analysis of the 16S rRNA gene sequences revealed that the phytoplasma associated with Royal Palm yellow decline (RYD) was an isolate of ‘Candidatus Phytoplasma asteris’ belonging to a new 16SrI‐subgroup. These results show that Roystonea regia is a new host for the aster yellows phytoplasma (16SrI). This is the first report on the presence of 16SrI phytoplasma on Royal Palm trees in Malaysia.

A multiplex PCR assay for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in Korean ready-to-eat food.

A multiplex polymerase chain reaction (PCR) assay was developed for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in various Korean ready-to-eat foods. The six specific primer pairs for multiplex PCR were selected based on the O157 antigen (rfbE) gene of E. coli O157:H7, the DNA gyrase subunit B (gyrB) gene of B. cereus, the toxin regulatory protein (toxR) gene of V. parahaemolyticus, the invasion protein A (invA) gene of Salmonella spp., the hemolysin (hly) gene of L. monocytogenes, and the thermonuclease (nuc) gene of S. aureus. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity assays for multiplex primer pairs were investigated by testing different strains. When this multiplex PCR assay was applied to evaluate the validity of detecting six foodborne pathogens in artificially inoculated several ready-to-eat food samples, the assay was able to specifically simultaneously detect as few as 1 colony-forming unit/mL of each pathogen after enrichment for 12 h. Their presence in naturally contaminated samples also indicates that the developed multiplex PCR assay is an effective and informative supplement for practical use.

Remodeling of Marrow Hematopoietic Stem and Progenitor Cells by Non-self ST6Gal-1 Sialyltransferase

Glycans occupy the critical cell surface interface between hematopoietic cells and their marrow niches. Typically, glycosyltransferases reside within the intracellular secretory apparatus, and each cell autonomously generates its own cell surface glycans. In this study, we report an alternate pathway to generate cell surface glycans where remotely produced glycosyltransferases remodel surfaces of target cells and for which endogenous expression of the cognate enzymes is not required. Our data show that extracellular ST6Gal-1 sialyltransferase, originating mostly from the liver and released into circulation, targets marrow hematopoietic stem and progenitor cells (HSPCs) and mediates the formation of cell surface α2,6-linked sialic acids on HSPCs as assessed by binding to the specific lectins Sambucus nigra agglutinin and Polysporus squamosus lectin and confirmed by mass spectrometry. Marrow HSPCs, operationally defined as the Lin-c-Kit+ and Lin-Sca-1+c-Kit+ populations, express negligible endogenous ST6Gal-1. Animals with reduced circulatory ST6Gal-1 have marrow Lin-Sca-1+c-Kit+ cells with reduced S. nigra agglutinin reactivity. Bone marrow chimeras demonstrated that α2,6-sialylation of HSPCs is profoundly dependent on circulatory ST6Gal-1 status of the recipients and independent of the ability of HSPCs to express endogenous ST6Gal-1. Biologically, HSPC abundance in the marrow is inversely related to circulatory ST6Gal-1 status, and this relationship is recapitulated in the bone marrow chimeras. We propose that remotely produced, rather than the endogenously expressed, ST6Gal-1 is the principal modifier of HSPC glycans for α2,6-sialic acids. In so doing, liver-produced ST6Gal-1 may be a potent systemic regulator of hematopoiesis.

Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp) and its wild progenitor species Saccharum spontaneum L.

A striking characteristic of modern sugarcane is that all sugarcane cultivars (Saccharum spp) share a common cytoplasm from S. officinarum. To explore the potential value of S. spontaneum cytoplasm, new Saccharum hybrids with an S. spontaneum cytoplasm were developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Laboratory, through a combination of conventional and molecular breeding approaches. In this study, we analyzed the genetic variability among the chloroplast genomes of four sugarcane cultivars, eight S. spontaneum clones, and three F1 progeny containing an S. spontaneum cytoplasm. Based on the complete chloroplast genome sequence information of two sugarcane cultivars (NCo 310 and SP 80-3280) and five related grass species (barley, maize, rice, sorghum, and wheat), 19 polymerase chain reaction primer pairs were designed targeting various chloroplast DNA (cpDNA) segments with a total length varying from 4781 to 4791 bp. Ten of the 19 cpDNA segments were polymorphic, harboring 14 mutation sites [a 15-nt insertion/deletion (indel), a 5-nt indel, two poly (T) tracts, and 10 single nucleotide polymorphisms]. We demonstrate for the first time that the chloroplast genome of S. spontaneum was maternally inherited. Comparative sequence homology analyses clustered sugarcane cultivars into a distinctive group away from S. spontaneum and its progeny. Three mutation sites with a consistent, yet species-specific, nucleotide composition were found, namely, an A/C transversion and two indels. The genetic variability among cpDNA of sugarcane cultivars and S. spontaneum will be useful information to determine the maternal origin in the Saccharum genus.

Short communication: development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon.

Oriental persimmon (Diospyros kaki Thunb.) (2n = 6x = 90) is a major commercial and deciduous fruit tree that is believed to have originated in China. However, rare transcriptomic and genomic information on persimmon is available. Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed. A total of 1,250,893 reads were generated and 83,898 unigenes were assembled. A total of 42,711 SSR loci were identified from 23,494 unigenes and 289 polymerase chain reaction primer pairs were designed. Of these 289 primers, 155 (53.6%) showed robust PCR amplification and 98 revealed polymorphism between 15 persimmon genotypes, indicating a polymorphic rate of 63.23% of the productive primers for characterization and genotyping of the genus Diospyros. Transcriptome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no genomic sequence information available.

FIRST REPORT ON Cryptococcus neoformans IN PIGEON EXCRETA FROM PUBLIC AND RESIDENTIAL LOCATIONS IN THE METROPOLITAN AREA OF CUIABÁ, STATE OF MATO GROSSO, BRAZIL

SUMMARYCryptococcosis is a severe systemic mycosis caused by two species of Cryptococcus that affect humans and animals: C. neoformans and C. gattii. Cosmopolitan and emergent, the mycosis results from the interaction between a susceptible host and the environment. The occurrence of C. neoformans was evaluated in 122 samples of dried pigeon excreta collected in 49 locations in the City of Cuiabá, State of Mato Grosso, Brazil, including public squares (n = 5), churches (n = 4), educational institutions (n = 3), health units (n = 8), open areas covered with asbestos (n = 4), residences (n = 23), factory (n = 1) and a prison (n = 1). Samples collected from July to December of 2010 were seeded on Niger seed agar (NSA). Dark brown colonies were identified by urease test, carbon source assimilation tests and canavanine-glycine-bromothymol blue medium. Polymerase chain reaction primer pairs specific for C. neoformans were also used for identification. Cryptococcus neoformans associated to pigeon excreta was isolated from eight (6.6%) samples corresponding to six (12.2%) locations. Cryptococcus neoformans was isolated from urban areas, predominantly in residences, constituting a risk of acquiring the disease by immunocompromised and immunocompetent individuals.

Point Mutation in Syntaxin-1A Causes Abnormal Vesicle Recycling, Behaviors, and Short Term Plasticity

Syntaxin-1A is a t-SNARE that is involved in vesicle docking and vesicle fusion; it is important in presynaptic exocytosis in neurons because it interacts with many regulatory proteins. Previously, we found the following: 1) that autophosphorylated Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), an important modulator of neural plasticity, interacts with syntaxin-1A to regulate exocytosis, and 2) that a syntaxin missense mutation (R151G) attenuated this interaction. To determine more precisely the physiological importance of this interaction between CaMKII and syntaxin, we generated mice with a knock-in (KI) syntaxin-1A (R151G) mutation. Complexin is a molecular clamp involved in exocytosis, and in the KI mice, recruitment of complexin to the SNARE complex was reduced because of an abnormal CaMKII/syntaxin interaction. Nevertheless, SNARE complex formation was not inhibited, and consequently, basal neurotransmission was normal. However, the KI mice did exhibit more enhanced presynaptic plasticity than wild-type littermates; this enhanced plasticity could be associated with synaptic response than did wild-type littermates; this pronounced response included several behavioral abnormalities. Notably, the R151G phenotypes were generally similar to previously reported CaMKII mutant phenotypes. Additionally, synaptic recycling in these KI mice was delayed, and the density of synaptic vesicles was reduced. Taken together, our results indicated that this single point mutation in syntaxin-1A causes abnormal regulation of neuronal plasticity and vesicle recycling and that the affected syntaxin-1A/CaMKII interaction is essential for normal brain and synaptic functions in vivo.

Identification of Veillonella tobetsuensis in tongue biofilm by using a species-specific primer pair

Veillonella atypica, Veillonella denticariosi, Veillonella dispar, Veillonella parvula, and Veillonella rogosae have been reported to be isolated from human oral cavities. The recently detected Veillonellatobetsuensis in human tongue biofilms was proposed as a novel Veillonella sp.In this study, to determine the distribution and frequency of V. tobetsuensis, we established a method for the detection and identification of V. tobetsuensis by using polymerase chain reaction (PCR) using a species-specific primer pair. The primer pair for V. tobetsuensis was designed on the basis of the nucleotide sequence of the 70-kDa heat shock protein (dnaK) gene of V. tobetsuensis JCM 17976T (=ATCC BAA-2400T). The primer pair generated a specific PCR product for V. tobetsuensis but not for other oral Veillonella spp. With the PCR procedure using the primer pair, we could detect less than 10 ng of genomic DNA extracted from V. tobetsuensis. Thus, the PCR method using this primer pair is suitable for the specific detection and identification of V. tobetsuensis. The distribution and frequency of V. tobetsuensis were investigated by PCR using this species-specific primer pair. V. tobetsuensis was detected in 5 of 27 subjects. V. tobetsuensis was recovered from 19% (5/27) of subjects with other Veillonella species. And, prevalence of V. tobetsuensis ranged from 7.6% to 20.0% in these subjects. V. tobetsuensis is likely to coexist with other Veillonella spp. in tongue biofilm.In this study, the species-specific PCR primer pair for V. tobetsuensis was designed using partial sequences of the dnaK gene. This is the first report using a species-specific primer pair for PCR to determine the distribution and frequency of V. tobetsuensis in tongue biofilm.

Improving PCR detection of prey in molecular diet studies: importance of group‐specific primer set selection and extraction protocol performances

While the morphological identification of prey remains in predators' faeces is the most commonly used method to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase chain reaction-based methods are increasingly used to detect prey DNA in the predator food bolus and have proven efficient, delivering highly accurate results. When studying complex diet samples, the extraction of total DNA is a critical step, as polymerase chain reaction (PCR) inhibitors may be co-extracted. Another critical step involves a careful selection of suitable group-specific primer sets that should only amplify DNA from the targeted prey taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analysed using both morphological and molecular methods. We tested a panel of 31 PCR primer pairs targeting bird, invertebrate and plant sequences; four of them were selected to be used as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols (QIAamp(®) DNA stool mini kit, DNeasy(®) mericon food kit and two of cetyltrimethylammonium bromide-based methods) were compared using four variables: DNA concentration, A(260) /A(280) absorbance ratio, food compartment analysed (stomach or faecal contents) and total number of prey-specific PCR amplification per sample. Our results clearly indicate that the A(260) /A(280) absorbance ratio, which varies between extraction protocols, is positively correlated to the number of PCR amplifications of each prey taxon. We recommend using the DNeasy(®) mericon food kit (QIAGEN), which yielded results very similar to those achieved with the morphological approach.

Identification of ‘Candidatus Phytoplasma solani’ Associated with Tree Peony Yellows Disease in China

AbstractTree peony (Paeonia suffruticosais) plants with yellowing symptoms suggestive of a phytoplasma disease were observed in Shandong Peninsula, China. Typical phytoplasma bodies were detected in the phloem tissue using transmission electron microscopy. The association of a phytoplasma with the disease was confirmed by polymerase chain reaction (PCR) using phytoplasma universal primer pair R16mF2/R16mR1 followed by R16F2n/R16R2 as nested PCR primer pair. The sequence analysis indicated that the phytoplasma associated with tree peony yellows (TPY) was an isolate of ‘Ca. Phytoplasma solani’ belonging to the stolbur (16SrXII) group. This is the first report of a phytoplasma associated with tree peony.

Sequence Variations in Equine Candidate Genes For XX and XY Inherited Disorders of Sexual Development

Inherited disorders of sexual development (DSD) cause sterility and infertility in horses. Mutations causing such disorders have been identified in other mammals, but there is little information on the molecular causes in horses. While the equine genome sequence has made it possible to identify candidate genes, additional tools are needed to routinely screen them for causative mutations. In this study, we designed a screening panel of polymerase chain reaction primer pairs for 15 equine genes. These are the candidate genes for testicular or ovotesticular XX DSD and XY DSD, the latter of which includes gonadal dysgenesis, androgen insensitivity syndrome (AIS), persistent Mullerian duct syndrome and isolated cryptorchidism. Six horses with testicular or ovotesticular XX DSD and controls were screened. In addition, candidate genes for androgen insensitivity syndrome, persistent Mullerian duct syndrome and isolated cryptorchidism were screened in normal horses. While no sequence variants were uniquely associated with XX DSD, the 38 sequence variants identified can serve as intragenic markers in genome-wide association studies or linkage studies to hasten mutation identification in equine XX DSD and XY DSD.

A multiplex polymerase chain reaction coupled with high-performance liquid chromatography assay for simultaneous detection of six foodborne pathogens

A multiplex polymerase chain reaction (PCR) coupled with high-performance liquid chromatography (HPLC) assay was developed to simultaneously detect Salmonella, Campylobacter jejuni, Listeria monocytogenes, Yersinia enterocolitica, Streptococcus hemolyticus and Staphylococcus aureus from foods. Six pairs of specific PCR primers were designed according to Salmonella invA, C. jejuni cdtA, L. monocytogenes pfrA, S. aureus femA, Y. enterocolitica 16S rRNA and St. hemolyticus cfb. Following the development of multiplex PCR, the PCR products were subjected to HPLC analysis. Unique HPLC peak profile for each PCR product represented corresponding bacterial strain, suggesting a better alternative to conventional PCR gel electrophoresis with ethidium bromide (EB) staining. The specificity analysis of the multiplex PCR-HPLC with 121 bacterial strains and 4 yeast strains showed that the method was highly specific for the target pathogens. One thousand and three hundred ninety-four blind samples were used to evaluate the practical diagnostic capability of the method, and results showed that eighty-eight food samples contaminated with single or multiple pathogens were detected by the method, which accorded with the testing results via conventional method. All data demonstrated that the multiplex PCR-HPLC is an efficient diagnostic method for rapid identification of the six foodborne pathogens. The simplicity and high sensitivity of the method may lead to improved management of food safety and foodborne diseases.

DEVELOPMENT AND CLINICAL VALIDATION OF A MULTIPLEX POLYMERASE CHAIN REACTION‐DENATURING HIGH‐PERFORMANCE LIQUID CHROMATOGRAPHY METHOD FOR THE IDENTIFICATION OF FOODBORNE DIARRHEAGENIC ESCHERICHIA COLI

ABSTRACTA multiplex polymerase chain reaction (PCR) combined with denaturing high‐performance liquid chromatography (DHPLC) method to simultaneously detect foodborne enterotoxigenic Escherichia coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC) and enteroinvasive E. coli (EIEC) were described. Following the design of PCR primer pairs specific for ETEC, EPEC, EHEC and EIEC, respectively, the multiplex PCR was developed, and then PCR products were subjected to DHPLC analysis under nondenaturing condition. The specificity and potential diagnostic capability of the multiplex PCR‐DHPLC method were evaluated, and results demonstrated that the multiplex PCR‐DHPLC is an effective method to rapidly identify the major four categories of diarrheagenic E. coli, simultaneously.PRACTICAL APPLICATIONSIn practice, we collected 690 import and export food samples including beef, pork, sausage, chicken and milk and 189 samples of patients' fecal materials, which were used to evaluate the potential diagnostic capability of the multiplex PCR‐DHPLC method. The results showed that a total of 60 positive samples were detected by the method established in this work, which accorded with the testing results of conventional diagnosis method, indicating that the PCR‐DHPLC is an efficient method for rapid identification of the main four diarrheagenic E. coli.

A Multiplex PCR for the Detection of Phytophthora nicotianae and P. cactorum, and a Survey of Their Occurrence in Strawberry Production Areas of Japan.

We aimed to simultaneously detect two pathogens causing strawberry diseases, Phytophthora nicotianae and P. cactorum, by multiplex polymerase chain reaction (PCR), and to survey their occurrence in the main strawberry production areas of Japan. Due to the need to combine different primer pairs for multiplex PCR and the low specificity of published specific primers for P. nicotianae and P. cactorum, new species-specific primers for P. nicotianae and P. cactorum were designed based on the internal transcribed spacer regions of ribosomal DNA and the ras-related protein gene Ypt1, respectively. Specificity of the designed primers was demonstrated using 68 isolates, including Phytophthora spp., Pythium spp., and other soilborne pathogens. Multiplex PCR discriminated between P. nicotianae and P. cactorum in DNA mixtures of mycelia of the two species. Moreover, both species were detected in artificially and naturally infested soils, indicating that these markers can be used in diagnosis of strawberry diseases. For investigation of the geographic distribution of the two pathogens in Japan, soil samples were collected in 89 strawberry fields from eight prefectures (Gifu, Saga, Nara, Tochigi, Chiba, Shizuoka, Yamanashi, and Hokkaido) of Japan. The method that was developed was successfully applied to survey P. nicotianae and P. cactorum, and distribution of the two pathogens in strawberry plantings in Japan was determined.

A rapid and simple PCR method for identifying isolates of the genus Azospirillum within populations of rhizosphere bacteria

To develop a rapid and simple genus-specific polymerase chain reaction (PCR) method for detecting and identifying isolates of the genus Azospirillum which is well-recognized as plant growth-promoting rhizobacterium. Nine pairs of PCR primers were designed based on the Azospirillum 16S rRNA, ipdC, nifA and nifH genes to assess their genus specificity by testing against 12 Azospirillum (from seven species) and 15 non-Azospirillum reference strains, as compared with the fAZO/rAZO pair reported by Baudoin et al. (J Appl Microbiol, 108, 2010, 25). Among the primer pairs assessed, the Az16S-A pair designed on the 16S rRNA gene sequence showed the highest genus specificity: it successfully yielded a single amplicon of the expected size in all the 12 Azospirillum strains and for a close relative, Rhodocista centenaria. The PCR with the Az16S-A primers generated a detectable amount of the amplicon from ≥10³ CFU ml⁻¹ of Azospirillum cell suspensions even in the presence of contaminants and accurately discriminated Azospirillum and non-Azospirillum species in both 35 Azospirillum-like and 70 unknown isolates from plant roots and rhizosphere soils. We developed a rapid and simple PCR method for detecting and identifying Azospirillum isolates within populations of rhizosphere bacteria. The method developed would serve as a useful tool for isolating a variety of indigenous Azospirillum bacteria from agricultural samples.

ERBB2 juxtamembrane domain (trastuzumab binding site) gene mutation is a rare event in invasive breast cancers overexpressing the ERBB2 gene

The recent development of targeted therapies using monoclonal antibodies has added new dimensions to breast cancer treatment. Trastuzumab has been added to the regimens that contain chemotherapeutic agents, which has improved the clinical outcomes of patients in both the adjuvant and metastatic settings. However, trastuzumab resistance, both de novo and acquired, continues to be problematic. There have been scattered studies reporting ERBB2 gene mutation, but nothing is currently known about the ERBB2 binding site mutations. In the current study, we examined the ERBB2 juxtamembrane domain trastuzumab binding site for mutations in invasive breast cancers overexpressing ERBB2. Pure tumor cells of 54 breast cancer patients were procured using laser capture microdissection. Two polymerase chain reaction primer pairs were designed to amplify the trastuzumab binding site sequence. The polymerase chain reaction product was sequenced. Standard clinicopathological data were recorded. For the 54 patients, there was one (2%) case that showed missense point mutation in exon 17 (H559A). There were nine patients treated with trastuzumab in the metastatic setting, none of which had gene mutation. Therefore, we conclude that ERBB2 juxtamembrane domain (trastuzumab binding site) gene mutation is a rare event in breast cancer. Although it is unclear whether this substitution would result in trastuzumab target therapy resistance, this would not account for the relatively high frequency of this resistance encountered clinically.

Sodium channel genes and their differential genotypes at the L-to-F kdr locus in the mosquito Culex quinquefasciatus

The para-type sodium channel in insects is the primary target of pyrethroid and DDT insecticides. However, modifications in the target protein structure such as point mutations or substitutions, resulting from single nucleotide polymorphisms (SNP), cause insensitivity of the insect’s nervous system to pyrethroids and DDT and, in turn, result in insecticide resistance. Among these mutations, substitution of leucine to phenylalanine (L to F) in the 6th segment of domain II (IIS6) has been clearly associated with pyrethroid and DDT resistance in many insect species, including mosquitoes. Here, multiple copies of the sodium channel gene were identified in the mosquito Culex quinquefasciatus by Southern blot analysis and polymerase chain reaction (PCR) analysis. Two genomic DNA fragments of the mosquito sodium channel gene (509 and 181bp) were detected by a single PCR primer pair. Sequence analysis indicated the lack of an intron sequence in the 181bp sodium channel fragment. Single nucleotide polymorphism (SNP) analysis revealed a strong correlation among the frequencies of L-to-F allelic (T) expression at the RNA level, the frequencies and resistance allele (T) at the L-to-F site of the 509bp genomic DNA fragment, which did include an intron sequence, and the levels of insecticide resistance. Taking together, this study, for the first time, not only revealed multiple copies of the sodium channel gene presented in the Culex mosquito genome but also suggested that the one with the intro sequence may be a functional copy of the sodium channel gene in the Culex mosquitoes.