scholarly journals Distribution and Rate of Movement of the Curtovirus Beet mild curly top virus (Family Geminiviridae) in the Beet Leafhopper

2003 ◽  
Vol 93 (4) ◽  
pp. 478-484 ◽  
Author(s):  
Maria J. Soto ◽  
Robert L. Gilbertson
Keyword(s):  
Salivary Glands ◽  
Digestive Tract ◽  
Temporal Distribution ◽  
Virus Family ◽  
Beet Leafhopper ◽  
Beet Curly Top Virus ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Corn Plants ◽  
Rate Of Movement

A polymerase chain reaction (PCR)-based method for the detection of the curtovirus Beet mild curly top virus (BMCTV, previously named the Worland strain of Beet curly top virus) was developed and used to investigate the BMCTV-beet leafhopper interaction. Using PCR and a BMCTV-specific primer pair, an ≈1.1-kb BMCTV DNA fragment was amplified from adult leafhoppers and from the organs involved in circulative transmission: the digestive tract, hemolymph, and salivary glands. The temporal distribution of BMCTV in the leafhopper was determined using insects given acquisition access periods (AAPs) ranging from 1 to 48 h on BMCTV-infected shepherd's purse plants. BMCTV was detected in the digestive tract after all AAPs, in the hemolymph after AAPs of 3 h or greater, and in the salivary glands after AAPs of 4 h or greater. The amount of virus detected in the hemolymph and salivary glands increased with AAP length. The virus persisted for up to 30 days in leafhoppers (given a 3-day AAP on BMCTV-infected plants) maintained on corn plants, a nonhost for BMCTV, but transovarial transmission was not detected. These results are consistent with a persistent but nonpropagative mode of circulative transmission.

scholarly journals Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1373-1382 ◽  
Author(s):  
Carl A. Strausbaugh ◽  
Imad A. Eujayl ◽  
William M. Wintermantel
Keyword(s):  
Sugar Beet ◽  
Mixed Infections ◽  
Beet Leafhopper ◽  
Beet Curly Top Virus ◽  
Primary Means ◽  
Commercial Sugar ◽  
Polymerase Chain ◽  
Production Areas ◽  
Virus Strains ◽  
Contingency Test

Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2006-to-2007 collection but changes in disease severity suggested a need for reevaluation. Therefore, 406 leaf samples symptomatic for curly top were collected from sugar beet plants in commercial sugar beet fields in Idaho and Oregon from 2012 to 2015. DNA was isolated and BCTV strain composition was investigated based on polymerase chain reaction assays with strain-specific primers for the Severe (Svr) and California/Logan (CA/Logan) strains and primers that amplified a group of Worland (Wor)-like strains. The BCTV strain distribution averaged 2% Svr, 30% CA/Logan, and 87% Wor-like (16% had mixed infections), which differed from the previously published 2006-to-2007 collection (87% Svr, 7% CA/Logan, and 60% Wor-like; 59% mixed infections) based on a contingency test (P < 0.0001). Whole-genome sequencing (GenBank accessions KT276895 to KT276920 and KX867015 to KX867057) with overlapping primers found that the Wor-like strains included Wor, Colorado and a previously undescribed strain designated Kimberly1. Results confirm a shift from Svr being one of the dominant BCTV strains in commercial sugar beet fields in 2006 to 2007 to becoming undetectable at times during recent years.

scholarly journals A PCR-based Assay for Distinguishing between A1 and A2 Mating Types of Phytophthora capsici

2017 ◽  
Vol 142 (4) ◽  
pp. 260-264
Author(s):  
Ping Li ◽  
Dong Liu ◽  
Min Guo ◽  
Yuemin Pan ◽  
Fangxin Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating Type ◽  
Phytophthora Capsici ◽  
Mating Types ◽  
Sequence Repeat ◽  
Chain Reaction ◽  
Plant Parasite ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Microsatellite Diversity

Sexual reproduction in the plant parasite Phytophthora capsici Leonian requires the interaction of two distinct mating types, A1 and A2. Co-occurrence of these mating types can enhance the genetic diversity of P. capsici and alter its virulence or resistance characteristics. Using an intersimple sequence repeat (ISSR) screen of microsatellite diversity, we identified, cloned, and sequenced a novel 1121-base pair (bp) fragment specific to the A1 mating type of P. capsici. Primers Pcap-1 and Pcap-2 were designed from this DNA fragment to specifically detect the A1 mating type. Polymerase chain reaction (PCR) using these primers amplified an expected 997-bp fragment from known A1 mating types, but yielded a 508-bp fragment from known A2 mating types. This PCR-based assay could be adapted to accurately and rapidly detect the co-occurrence of A1 and A2 P. capsici mating types from field material.

scholarly journals DETEKSI BAKTERI PENYEBAB PENYAKIT TYPHUS PADA MANUSIA DENGAN POLYMERASE CHAIN REACTION

2011 ◽  
Vol 1 (1) ◽  
pp. 45
Author(s):  
Muktiningsih Nurjayadi ◽  
Fera Kurnia Dewi ◽  
Dahlia Dahlia ◽  
S, Restu.N S ◽  
Fitri W
Keyword(s):  
Polymerase Chain Reaction ◽  
Detection Method ◽  
Serological Test ◽  
Research Result ◽  
Salmonella Typhi ◽  
Detection Methods ◽  
Chain Reaction ◽  
Specificity And Sensitivity ◽  
Dna Fragment ◽  
Polymerase Chain

Salmonella typhi is bacteria that cause typhoid disease in humans. In Indonesia, the morbidity number of typhoid disease tends to be increase. Thus, it has been requiring the alternative for handling or preventing that disease. Recently, the detection method commonly uses for S. typhi detection is Serological test. The weakness of this method is often producing less accurate and not specific detection. The previous research was successfully discovered S. typhi gene that codes protein which is contributed at adherents or colonization those bacteria in epithelial human cell. That result was base to develop detection on S. typhi method by Polymerase chain reaction (PCR). The aim of this research is developing a specific and accurate detection method for S. typhi bacteria by PCR. The research result is performed successfully to amplify the fimbrial-C S. typhi gene using pairs of primer FW-INT 2- REV-1A NEW which was designed and synthesized in previous step. That success showed by the finding of the DNA fragment of 0.2 kilobase (kb) proffers to size of DNA fragment which is hopefully in using S. typhi genome as a template. Specificity and sensitivity test for those primers are still conducting to reproducibility results. Base on the results can be concluded that the research have successfully conducted in developing S. typhi detection method using pairs of S. typhi fimbrial-C primer. Hopefully, the studied of developing detection methods was conducted better compare with former detection methods.Keywords: S. typhi detection method, fim-C S. typhi gene, PCRAbstrakSalmonella typhi merupakan bakteri penyebab penyakit tifus pada manusia. Di Indonesia, angka morbiditas penderita penyakit typhus cenderung meningkat, sehingga diperlukan suatu alternatif untuk penanganan atau pencegahan penyakit tersebut. Sampai saat ini metode deteksi S. typhi yang banyak digunakan adalah uji serologi. Kelemahan metode ini adalah sering menghasilkan deteksi yang kurang akurat dan tidak spesifik. Pada penelitian yang dilakukan sebelumnya, telah berhasil ditemukan gen fimbrial-C S. typhi pengkode protein yang berperan dalam penempelan S. typhi pada usus manusia, hasil ini dijadikan landasan untuk pengembangan metode deteksi menggunakan teknik PCR. Tujuan penelitian ini mengembangkan metode deteksi yang akurat dan spesifik untuk bakteri penyebab penyakit typhus pada manusia. Hasil penelitian menunjukkan bahwa telah berhasil dilakukan amplifikasi gen fimbrial-C S. typhi menggunakan pasangan primer hasil perancangan yaitu FW-INT 2- REV-1A NEW. Keberhasilan tersebut ditunjukkan dengan diperolehnya pita DNA berukuran 0.2 kilo basa (kb) sesuai dengan ukuran pita DNA yang diharapkan dengan menggunakan template DNA genom bakteri S. typhi. Uji sensitivitas dan spesifisitas terhadap primer hasil rancangan sedang di kaji lebih lanjut untuk memperoleh reprodusibiltas hasil pengujian. Berdasarkan hasil yang diperoleh dapat disimpulkan bahwa telah berhasil dilakukan pengembangan metode deteksi S. typhi menggunakan pasangan primer fimbrial-C S. typhi. Pengkajian pengembangan metode deteksi yang dihasilkan ini diharapkan dapat lebih baik dibanding beberapa metode deteksi yang sudah ada.Kata Kunci: Metode Deteksi Bakteri typhus, fim-C S. typhi, PCR

scholarly journals Histochemical localisation of carbonic anhydrase in the digestive tract and salivary glands of the house cricket, Acheta domesticus

2020 ◽  
Vol 6 (2) ◽  
pp. 191-198
Author(s):  
E. Thorsson ◽  
A. Jansson ◽  
M. Vaga ◽  
L. Holm
Keyword(s):  
Carbonic Anhydrase ◽  
Salivary Glands ◽  
Digestive Tract ◽  
Cell Types ◽  
Acheta Domesticus ◽  
Ph Gradient ◽  
House Cricket ◽  
Main Cell ◽  
Cellular Localisation ◽  
Luminal Ph

The house cricket (Acheta domesticus) is one of several cricket species with great potential to be farmed as a sustainable protein source. In order to succeed in large-scale cricket farming, knowledge of cricket digestion is essential. The digestive tract morphology of A. domesticus is well documented, but knowledge of the salivary glands is lacking. In the digestive tract of insects, the carbonic anhydrase (CA) enzyme family is believed to contribute to the luminal pH gradient. Presence of CA in the digestive tract of A. domesticus has been reported, but not the cellular localisation. This study examined the digestive tract of A. domesticus, including salivary glands, and the cellular localisation and activity of CA in fed or starved (48 h) males and females. Tissues were collected from third-generation offspring of wild A. domesticus captured in Sweden and the histology of the salivary glands and the cellular localisation of CA in the digestive tract of A. domesticus were determined, to our knowledge for the first time. The salivary glands resembled those of grasshoppers and locusts, and we suggest the two main cell types present to be parietal and zymogenic cells. Histochemical analysis revealed that CA activity was localised in midgut epithelium, both main cell types of salivary gland, and muscle along the entire digestive tract. These findings support the suggestion that CA contributes to digestive tract luminal pH gradient, by driving acidic secretions from the salivary glands and alkaline secretions from the midgut. Starvation resulted in significantly reduced body size and weight, but neither starvation nor sex had any effect on CA activity or localisation.

scholarly journals Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 246 ◽  
Author(s):  
Wycliff M. Kinoti ◽  
Narelle Nancarrow ◽  
Alison Dann ◽  
Brendan C. Rodoni ◽  
Fiona E. Constable
Keyword(s):  
Polymerase Chain Reaction ◽  
High Throughput Sequencing ◽  
Mottle Virus ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Virus Family ◽  
First Report ◽  
Hop Stunt Viroid ◽  
Polymerase Chain ◽  
Stem Pitting

One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.

scholarly journals Prediction of Early Season Beet Leafhopper Populations in Southern New Mexico

2020 ◽  
Vol 21 (1) ◽  
pp. 71-76
Author(s):  
Erik Lehnhoff ◽  
Rebecca Creamer
Keyword(s):  
New Mexico ◽  
Weed Management ◽  
Broad Host Range ◽  
Insect Vector ◽  
Early Season ◽  
Beet Leafhopper ◽  
Beet Curly Top Virus ◽  
Circulifer Tenellus ◽  
Sisymbrium Irio ◽  
The Relationship

Curly top is an important widespread disease in semiarid regions that can be caused by several Curtovirus and Becurtovirus species. The strains of beet curly top virus (BCTV) have been some of the most widely reported to be associated with curly top. The viruses causing curly top are phloem limited and transmitted by the beet leafhopper (BLH), Circulifer tenellus Baker (Hemiptera: Cicadellidae). The BLH can also transmit other important pathogens such as phytoplasmas. Both the virus and insect vector have a broad host range of crops and weeds, including the winter annual weed London rocket (Sisymbrium irio L.). Prior prediction of disease would allow growers a window of opportunity to make informed management choices. A prediction model of BLH abundance was developed for southern New Mexico based on fall precipitation, which corresponds with London rocket emergence, and BLH sticky trap catch data for 2001 to 2018. Regression analyses showed positive associations between BLH numbers and October + November rainfall (P < 0.001) for two areas within southern New Mexico. A third area, where good weed management was used, had lower BLH numbers, and the relationship with precipitation was not significant (P = 0.190). Cumulative-season BLH abundance was correlated with BLH abundance in late April (r = 0.43) and late May (r = 0.56), indicating that early season knowledge of BLH abundance is useful for planning later season management. Although models based on October + November precipitation are good predictors of BLH abundance through June, they may not predict year-long BLH abundance because other environmental and biological factors contribute to subsequent BLH success and movement.

Plasma vs. serum in circulating tumor DNA measurement: characterization by DNA fragment sizing and digital droplet polymerase chain reaction

2020 ◽  
Vol 58 (4) ◽  
pp. 527-532 ◽  
Author(s):  
Jee-Soo Lee ◽  
Miyoung Kim ◽  
Moon-Woo Seong ◽  
Han-Sung Kim ◽  
Young Kyung Lee ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Circulating Tumor Dna ◽  
Analytical Sensitivity ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Specimen Type ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Ctdna Analysis ◽  
Tumor Dna

AbstractBackgroundChoosing the specimen type is the first step of the pre-analytical process. Previous reports suggested plasma as the optimal specimen for circulating tumor DNA (ctDNA) analysis. However, head-to-head comparisons between plasma and serum using platforms with high analytical sensitivity, such as droplet digital polymerase chain reaction (ddPCR), are limited, and several recent studies have supported the clinical utility of serum-derived ctDNA. This study aimed to compare the DNA profiles isolated from plasma and serum, characterize the effects of the differences between specimens on ctDNA measurement, and determine the major contributors to these differences.MethodsWe isolated cell-free DNA (cfDNA) from 119 matched plasma/serum samples from cancer patients and analyzed the cfDNA profiles by DNA fragment sizing. We then assessed KRAS mutations in ctDNA from matched plasma/serum using ddPCR.ResultsThe amount of large DNA fragments was increased in serum, whereas that of cfDNA fragments (<800 bp) was similar in both specimens. ctDNA was less frequently detected in serum, and the KRAS-mutated fraction in serum was significantly lower than that in plasma. The differences in ctDNA fractions between the two specimen types correlated well with the amount of large DNA fragments and white blood cell and neutrophil counts.ConclusionsOur results provided detailed insights into the differences between plasma and serum using DNA fragment sizing and ddPCR, potentially contributing to ctDNA analysis standardization. Our study also suggested that using plasma minimizes the dilution of tumor-derived DNA and optimizes the sensitivity of ctDNA analysis. So, plasma should be the preferred specimen type.

scholarly journals MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors

2020 ◽  
Vol 36 (11) ◽  
pp. 3322-3326
Author(s):  
Michael Schwarz ◽  
Marius Welzel ◽  
Tolganay Kabdullayeva ◽  
Anke Becker ◽  
Bernd Freisleben ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Web Application ◽  
De Novo ◽  
Supplementary Information ◽  
Dna Fragments ◽  
Synthetic Dna ◽  
Custom Made ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Error Probabilities

Abstract Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. Availability and implementation MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Rusted Root of Ginseng (Panax quinquefolius) Is Caused by a Species of Rhexocercosporidium

2006 ◽  
Vol 96 (11) ◽  
pp. 1243-1254 ◽  
Author(s):  
R. D. Reeleder ◽  
S. M. T. Hoke ◽  
Yun Zhang
Keyword(s):  
Its Region ◽  
Root Tissue ◽  
Panax Quinquefolius ◽  
Oligonucleotide Primers ◽  
Infected Root ◽  
Culture Independent ◽  
Pathogenicity Tests ◽  
Agar Media ◽  
Dna Fragment ◽  
Polymerase Chain

Rusted root (also known as rusty root) of ginseng (Panax quinquefolius) was first described over 70 years ago, but the causal agent has not been clearly established. The disease is characterized by slightly raised reddish-brown to black root lesions of varying size. The lesions, regardless of size, remain superficial; however, peridermal tissue is ruptured and sloughed off, giving the root a scabbed appearance. Culture-independent techniques were used to demonstrate that a fungal internal transcribed spacer (ITS) region DNA fragment was strongly associated with diseased but not healthy root tissue. The fragment (≈ 650 bp in length) was cloned. Restriction enzyme digests of cloned DNA indicated that the 650-bp fragment represented a single taxon. BLAST analysis following sequencing of the fragment found that the nearest matches in GenBank were anamorphic genera associated with discomycetes, in particular Rhexocercosporidium spp. This putative identification was supported further by isolating fungi from diseased tissue using a semiselective agar medium. With this procedure, a Rhexocercosporidium-like fungus was isolated; DNA extracted from fungal cultures and amplified using ITS oligonucleotide primers was found to be identical to similarly amplified DNA from the 650-bp bands. However, the isolates were distinct, with respect to growth rate on agar media and ITS sequence, from Rhexocercosporidium carotae, the only described species in this genus. The ability to reproduce symptoms on ginseng roots was confirmed in pathogenicity tests. Oligonucleotide primers based on ITS sequences were designed to amplify DNA of Rhexocercosporidium spp. Polymerase chain reaction assays on DNA extracted from naturally infected root tissue showed that the fungus was present in nearly all symptomatic roots but was infrequent in healthy-appearing roots. The most probable cause of rusted root of ginseng is a previously undescribed species of Rhexocercosporidium.

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