Detection of Badnavirus in pineapple in northeastern Brazil

ABSTRACT: Brazil is one of the main global producers of pineapple (Ananas comosus L. Merril), with emphasis in the Northeastern region of the country. Pineapple is exposed to several phytosanitary problems, including viruses. Pineapple badnaviruses are caused by two distinct species: Pineapple bacilliform CO virus (PBCoV) and Pineapple bacilliform ER virus (PBErV). The present study aimed to detect possible species of the genus Badnavirus in pineapple samples in Northeastern Brazil, via PCR and sequencing of the RT/RNaseH region. Leaf samples of pineapples were collected in the states of Alagoas, Maranhão, Paraiba and Pernambuco, and subsequently subjected to total DNA extraction and amplification via PCR. Badnavirus positive samples were selected for sequencing. Analysis of pairwise comparisons revealed that all sequences obtained in this work showed an identity greater than 80% with the sequence of the species PBCoV (EU377664), from Australia, fully corroborating with phylogenetic analyzes. These results suggest the widespread of PBCoV in Northeastern Brazil and record the first report of Badnavirus in pineapple culture in Brazil. KEYWORDS: Caulimoviridae, Ananas comosus, molecular analysis.

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Simple modification to improve reliability of copro-DNA examinations for diagnosing Echinococcus multilocularis infections in red foxes

Journal of Helminthology ◽

10.1017/s0022149x20000255 ◽

2020 ◽

Vol 94 ◽

Author(s):

T. Irie ◽

T. Ito ◽

H. Kouguchi ◽

K. Uraguchi

Keyword(s):

Dna Extraction ◽

Echinococcus Multilocularis ◽

Epidemiological Studies ◽

Sequencing Analysis ◽

Red Foxes ◽

Simple Modification ◽

Pcr Inhibitors ◽

Examination Technique ◽

Modified Method ◽

Infection Pressure

Abstract Epidemiological studies of Echinococcus multilocularis infections in definitive hosts require a reliable and economic diagnostic method. In this study, the current copro-DNA examination technique was modified by increasing the faecal amounts tested and adding a step to neutralize the faeces before DNA extraction. Reliability of the modified method was evaluated using rectal faecal samples from red foxes and comparing them with intestinal worms detected using the sedimentation and counting technique (SCT) following necropsy. The modified copro-DNA examination method demonstrated 93.9% sensitivity (138/147) on the SCT. Its detectability increased depending on the worm burden, and the sensitivity was 100% in cases harbouring over 1000 worms. From 111 SCT-negative cases, six (5.4%) were copro-DNA-positive, and all were confirmed as E. multilocularis via sequencing analysis. Five of the remaining 105 SCT-negative cases (4.8%) retained polymerase chain reaction (PCR) inhibitors in the extracted solution, suggesting that approximately 5% of the red fox faeces retained these inhibitors after treatment with the present copro-DNA extraction method. Although further evaluation is needed for faeces deposited in the wild, the present copro-DNA examination technique will help monitor the E. multilocularis prevalence in definitive hosts. When used for detailed evaluations of endemicity (e.g. changes in infection pressure or spread in non-endemic areas), the absence of PCR inhibitors should be confirmed, and multiple trials on faecal subsamples are recommended.

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A fast and efficient method for total DNA extraction from soil filamentous fungi

Idesia (Arica) ◽

10.4067/s0718-34292014000200010 ◽

2014 ◽

Vol 32 (2) ◽

pp. 75-78 ◽

Cited By ~ 2

Author(s):

Wilson Huanca-Mamani ◽

Ricardo Salvatierra Martínez ◽

Germán Sepúlveda-Chavera

Keyword(s):

Dna Extraction ◽

Filamentous Fungi ◽

Efficient Method ◽

Total Dna

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First Report of Okra yellow mosaic Mexico virus in Okra in the United States

Plant Disease ◽

10.1094/pdis-94-7-0924b ◽

2010 ◽

Vol 94 (7) ◽

pp. 924-924 ◽

Cited By ~ 7

Author(s):

C. Hernandez-Zepeda ◽

T. Isakeit ◽

A. Scott ◽

J. K. Brown

Keyword(s):

United States ◽

The United States ◽

Full Length ◽

Bipartite Begomoviruses ◽

Economic Losses ◽

Growth Stages ◽

First Report ◽

Total Dna ◽

Hidalgo County ◽

Whitefly Vector

During the okra growing season from August to November of 2009, symptoms reminiscent of geminivirus infection were observed on 75% of ‘Green Emerald’ Abelmoschus esculentus (L.) Moench, plants in a 0.2-km2 field in Hidalgo County, TX. Visible symptoms consisted of irregular yellow patches on leaves, distinctive yellow borders on leaf edges, and chlorosis of subsequently developing leaves. The whitefly vector of begomoviruses, Bemisia tabaci (Genn.), infested okra plants in the early growth stages during late July 2009. Total DNA was isolated from the leaves of three symptomatic okra plant samples (1) and used as the PCR template to amplify a 575-bp fragment of the coat protein gene (CP) using the universal begomovirus primers AV494 and AC1048 (2). PCR products of the expected size were cloned into the pGEM-T Easy (Promega, Madison, WI) and sequenced using the universal M13F and M13 R primers. ClustalV alignment indicated 99 to 100% shared nucleotide (nt) identity, and BLAST analysis revealed that the closest relative was Okra yellow mosaic Mexico virus - Tetekalitla (OkYMMV) (GenBank Accession No. EF591631) at 98%. To amplify the full-length DNA-A and a possible cognate DNA-B component, one plant that was positive by CP-PCR and DNA sequencing was selected for further analysis. Total DNA from this plant was used as template for a second detection method that consisted of rolling circle amplification (RCA) using the TempliPhi 100 Amplification System (GE Healthcare). RCA is a non-sequence-specific approach that permits amplification of circular DNA. The RCA products were linearized to release unit length ~2.6 kb DNA-A and DNA-B components using BamHI, and EcoRI, respectively. These products were cloned into pGEM3zf+ (Promega) and sequenced using M13F and M13 R primers and then by primer walking (>300 base overlap). Full-length DNA-A and DNA-B components were obtained, respectively, at 2,613 bp (GenBank Accession No. HM035059) and 2,594 bp (GenBank Accession No HM035060). Alignment of the DNA-A component using ClustalV (MegAlign, DNASTAR, Madison, WI) with begomoviral sequences available in GenBank indicated that it was 99% identical to OkYMMV DNA-A (GenBank Accession No. DQ022611). The closest relative to the DNA-B component (ClustalV) was Sida golden mosaic virus (SiGMV) (GenBank Accession No. AJ250731) at 73%. The nt identity of the 172-nt ‘common region’ present in the DNA-A and DNA-B components was 99%, and the iterons (predicted Rep binding motif) were identical for the two components, indicating that they are a cognate pair. The genome organization was typical of other New World bipartite begomoviruses. The economic losses due to infection by this virus could not be determined because an early freeze killed the plants. Hidalgo County is adjacent to Tamaulipas, Mexico, where ~50 km2 of okra are grown and the whitefly vector is also present. The identification of OkYMMV based on two independent detection methods, and the presence of begomovirus-like symptoms together with the whitefly vector, provide robust evidence for the association of OkYMMV-TX with diseased okra plants. To our knowledge, this is the first report of OkYMMV-TX infecting okra crops in Texas and in the continental United States. References: (1) J. J. Doyle and J. L. Doyle. Focus 12:13, 1990. (2) S. Wyatt and J. K. Brown. Phytopathology 86:1288, 1996.

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First Report of Anthracnose of Onion Caused by Colletotrichum coccodes in Ohio

Plant Disease ◽

10.1094/pdis-01-14-0032-pdn ◽

2014 ◽

Vol 98 (9) ◽

pp. 1271-1271 ◽

Cited By ~ 2

Author(s):

F. Baysal-Gurel ◽

N. Subedi ◽

D. P. Mamiro ◽

S. A. Miller

Keyword(s):

Leaf Tissue ◽

Its Region ◽

The United States ◽

Tween 20 ◽

Colletotrichum Coccodes ◽

Academic Press ◽

Conidial Suspension ◽

First Report ◽

Allium Cepa L ◽

Total Dna

Dry bulb onion (Allium cepa L. cvs. Pulsar, Bradley, and Livingston) plants with symptoms of anthracnose were observed in three commercial fields totaling 76.5 ha in Huron Co., Ohio, in July 2013. Symptoms were oval leaf lesions and yellowing, curling, twisting, chlorosis, and death of leaves. Nearly half of the plants in a 32.8-ha field of the cv. Pulsar were symptomatic. Concentric rings of acervuli with salmon-colored conidial masses were observed in the lesions. Conidia were straight with tapered ends and 16 to 23 × 3 to 6 μm (2). Colletotrichum coccodes (Wallr.) S. Hughes was regularly isolated from infected plants (2). Culturing diseased leaf tissue on potato dextrose agar (PDA) amended with 30 ppm rifampicin and 100 ppm ampicillin at room temperature yielded white aerial mycelia and salmon-colored conidial masses in acervuli. Numerous spherical, black microsclerotia were produced on the surface of colonies after 10 to 14 days. To confirm pathogen identity, total DNA was extracted directly from a 7-day-old culture of isolate SAM30-13 grown on PDA, using the Wizard SV Genomic DNA Purification System (Promega, Madison, WI) following the manufacturer's instructions. The ribosomal DNA internal transcribed spacer (ITS) region was amplified by PCR using the primer pair ITS1 and ITS4 (2), and sequenced. The sequence, deposited in GenBank (KF894404), was 99% identical to that of a C. coccodes isolate from Michigan (JQ682644) (1). Ten onion seedlings cv. Ebenezer White at the two- to three-leaf stage of growth were spray-inoculated with a conidial suspension (1 × 105 conidia/ml containing 0.01% Tween 20, with 10 ml applied/plant). Plants were maintained in a greenhouse (21 to 23°C) until symptoms appeared. Control plants were sprayed with sterilized water containing 0.01% Tween 20, and maintained in the same environment. After 30 days, sunken, oval lesions each with a salmon-colored center developed on the inoculated plants, and microscopic examination revealed the same pathogen morphology as the original isolates. C. coccodes was re-isolated consistently from leaf lesions. All non-inoculated control plants remained disease-free, and C. coccodes was not re-isolated from leaves of control plants. C. coccodes was reported infecting onions in the United States for the first time in Michigan in 2012 (1). This is the first report of anthracnose of onion caused by C. coccodes in Ohio. Unusually wet, warm conditions in Ohio in 2013 likely contributed to the outbreak of this disease. Timely fungicide applications will be necessary to manage this disease in affected areas. References: (1) A. K. Lees and A. J. Hilton. Plant Pathol. 52:3. 2003. (2) L. M. Rodriguez-Salamanca et al. Plant Dis. 96:769. 2012. (3) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

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First Report of Xylella fastidiosa in Peach in New Mexico

Plant Disease ◽

10.1094/pdis-10-10-0719 ◽

2011 ◽

Vol 95 (7) ◽

pp. 871-871 ◽

Cited By ~ 1

Author(s):

J. J. Randall ◽

J. French ◽

S. Yao ◽

S. F. Hanson ◽

N. P. Goldberg

Keyword(s):

New Mexico ◽

Prunus Persica ◽

Xylella Fastidiosa ◽

Its Region ◽

23S Rrna ◽

Pcr Analysis ◽

Sequencing Analysis ◽

First Report ◽

Dark Green ◽

Branch Dieback

Xylella fastidiosa is a gram-negative bacterium that causes disease in a wide variety of plants such as grapes, citrus trees, oleanders, and elm and coffee trees. This bacterium is xylem limited and causes disease symptoms such as leaf scorch, stunting of plant growth, branch dieback, and fruit loss. The presence of X. fastidiosa was previously reported in New Mexico where it was found to be infecting chitalpa plants and grapevines (3). In the summer of 2010, peach (Prunus persica (L.) Batsch) trees from two locations in northern New Mexico exhibited leaf deformity and stunting, dark green venation, slight mottling, and branch dieback. Preliminary viral diagnostic screening was performed by Agdia (Elkhart, IN) on one symptomatic tree and it was negative for all viruses tested. Three trees from two different orchards tested positive for X. fastidiosa by ELISA and PCR analysis using X. fastidiosa-specific primer sets HL (1) and RST (2). Bacterial colonies were also cultured from these samples onto periwinkle wilt media. Eight colonies obtained from these three plants tested PCR positive using the X. fastidiosa-specific primers. The 16S ribosomal and 16S-23S rRNA internal transcribed spacer (ITS) region (557 nucleotides) (GenBank Accession No. HQ292776) along with the gyrase region (400 nucleotides) (GenBank Accession No. HQ292777) was amplified from the peach total DNA samples and the bacterial colonies. Sequencing analysis of these regions indicate that the X. fastidiosa found in peach is 100% similar to other X. fastidiosa multiplex isolates including isolates from peach, pecan, sycamore, and plum trees and 99% similar to the X. fastidiosa isolates previously found in New Mexico. Further analysis of the 16S ribosomal and 16S-23S rRNA ITS sequences with maximum likelihood phylogenetic analysis using Paup also groups the peach isolates into the X. fastidiosa multiplex subspecies. The gyrase sequence could not be used to differentiate the peach isolates into a subspecies grouping because of the lack of variability within the sequence. This X. fastidiosa multiplex subspecies could possibly be a threat to the New Mexico pecan industry since pecan infecting X. fastidiosa isolates belong to the same bacterial subspecies. It is not known if X. fastidiosa subspecies multiplex isolates from peach are capable of infecting pecans but they are closely genetically related. It is interesting to note that the isolates from peach are different than previously described X. fastidiosa isolates in New Mexico that were infecting chitalpa and grapes (3). X. fastidiosa has previously been described in peach; the disease is called “phony peach”. The peach trees exhibited stunting and shortened internodes as reported for “phony peach”. They also exhibited slight mottling and branch dieback that may be due to the environment in New Mexico or perhaps they are also exhibiting mineral deficiency symptoms in association with the X. fastidiosa disease. To our knowledge, this is the first report of X. fastidiosa in peach in New Mexico. References: (1) M. H. Francis et al. Eur. J. Plant Pathol. 115:203, 2006. (2) G. V. Minsavage et al. Phytopathology 84:456, 1994. (3) J. J. Randall et al. Appl. Environ. Microbiol. 75:5631, 2009.

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A first case of hemoglobin Castilla [Beta 32(B14) Leu>Arg; HBB: c.98T>G] associated with [IVS-I-1 (G>A); HBB:c.92+1G>A] mutation found in a Syrian betathalassemia patient

Thalassemia Reports ◽

10.4081/thal.2020.8396 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ahmad Shoujaa ◽

Yasser Mukhalalaty ◽

Hossam Murad ◽

Faizeh Al-Quobaili

Keyword(s):

Molecular Analysis ◽

Clinical Case ◽

Globin Gene ◽

Thalassemia Major ◽

Beta Thalassemia ◽

Blood Transfusions ◽

Beta Globin ◽

First Report ◽

Beta Thalassemia Major ◽

First Case

Beta thalassemia (β-thal) is one of the most common worldwide inherited hemoglobinopathies. Proper identification and diagnosis of hemoglobin (Hb) variants provide a major challenge. In this report, we describe a 1-year-old boy, presented with the diagnosis of β-TM (beta thalassemia major), has received regular blood transfusions. The molecular analysis revealed the presence of rare Hb Castilla [Beta 32(B14) Leu>Arg; HBB: c.98T>G] variant associated with β0 [IVS-I-1 (G>A); AG^GTTGGT- >AGATTGGT beta0] (HBB:c.92+1G>A) Mutation in beta-globin (β-globin) gene. To our knowledge, this is the first report of Hb Castilla [Beta 32(B14) Leu>Arg] in ExonII of β-globin gene which were found in Syrian male proband. However, we should investigate abnormal hemoglobins in patients with beta thalassemia to determine whether they have involvement with β-thalassemia mutations in the clinical case of the patients or not.

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Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765201420130314 ◽

2014 ◽

Vol 86 (4) ◽

pp. 1711-1718 ◽

Cited By ~ 5

Author(s):

CLÁUDIA ROHDE ◽

DIVA MARIA IZABEL O. SILVA ◽

GEÓRGIA F. OLIVEIRA ◽

LIV S. MONTEIRO ◽

MARTÍN A. MONTES ◽

...

Keyword(s):

High Altitude ◽

Atlantic Forest ◽

Northeastern Brazil ◽

High Abundance ◽

Northeastern Region ◽

Mangrove Swamps ◽

Historical Relationship ◽

First Time ◽

High Diversity

Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments.

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Plant Total DNA Extraction

Molecular Tools for Screening Biodiversity ◽

10.1007/978-94-009-0019-6_2 ◽

1998 ◽

pp. 10-14 ◽

Cited By ~ 1

Author(s):

Julia Rueda ◽

Rosario Linacero ◽

Ana M. Vázquez

Keyword(s):

Dna Extraction ◽

Total Dna

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Synchronous Wilms Tumor and Fibrolamellar Hepatocellular Carcinoma: Report of a Case

Pediatric and Developmental Pathology ◽

10.1007/s100240010096 ◽

2000 ◽

Vol 3 (5) ◽

pp. 492-496 ◽

Cited By ~ 6

Author(s):

Anirban Maitra ◽

Dharamdas M. Ramnani ◽

Linda R. Margraf ◽

Adi F. Gazdar

Keyword(s):

Hepatocellular Carcinoma ◽

Solid Tumors ◽

Molecular Analysis ◽

Wilms Tumor ◽

P53 Mutation ◽

Malignant Neoplasms ◽

Fibrolamellar Hepatocellular Carcinoma ◽

First Report ◽

Second Malignant Neoplasms

Fibrolamellar hepatocellular carcinoma (FHCC) is a unique histologic variant of HCC that occurs in a younger subset of patients than classical HCC, and is associated with a better prognosis. Wilms tumor (WT) is a malignant embryonal neoplasm of the kidney and is one of the most common solid tumors of childhood, occurring at an estimated frequency of 1 in 8000 to 10,000 births. Although second malignant neoplasms (SMNs) following therapy for WTs have been reported in the liver, the coexistence of HCC and WT is extremely rare. We present the first report of a synchronous ana-plastic WT and FHCC in a previously healthy 4-year-old girl. Despite the presence of focal immunohistochemical positivity for p53 in the WT, molecular analysis failed to reveal a germline or somatic p53 mutation, and was inconclusive in establishing a clonal relation between the two tumors.

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