The effect of water source and soil supplementation on parasite contamination in organic vegetable gardens

Abstract The objective of this study was to determine factors associated with vegetable contamination with zoonotic protozoan. Samples of water, soil and vegetables were collected from July/2014 to May/2016, totaling 83 samples, 21 properties of Londrina region, Paraná, Brazil. DNA amplification of Toxoplasma gondii, Cryptosporidium spp. and Giardia intestinalis in the samples was conducted using polymerase chain reaction (PCR). The PCR results were positive for T. gondii in 12.9% (8/62), Cryptosporidium spp. in 11.3% (7/62) and G. intestinalis in 25.8% (16/62) of the samples. DNA sequencing identified C. parvum in five samples and G. intestinalis Assemblage E in three. The statistical associations demonstrated greater probability of positive samples for T. gondii and for at least one of the three protozoa when the source of irrigation water was the river; a greater chance of positive samples for Cryptosporidium spp. when deer were present on the property; and a smaller chance of positive samples for at least one of the three etiologic agents when soil was supplemented with limestone. The results expose some critical contamination points, providing support for training farmers on good management practices during the production process.

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PCR BY THERMAL CONVECTION

Modern Physics Letters B ◽

10.1142/s0217984904007049 ◽

2004 ◽

Vol 18 (16) ◽

pp. 775-784 ◽

Cited By ~ 37

Author(s):

DIETER BRAUN

Keyword(s):

Polymerase Chain Reaction ◽

Thermal Convection ◽

Dna Amplification ◽

Reaction Vessel ◽

Cold Region ◽

Chain Reaction ◽

Heating And Cooling ◽

Highly Sensitive ◽

Specific Amplification ◽

Polymerase Chain

The Polymerase Chain Reaction (PCR) allows for highly sensitive and specific amplification of DNA. It is the backbone of many genetic experiments and tests. Recently, three labs independently uncovered a novel and simple way to perform a PCR reaction. Instead of repetitive heating and cooling, a temperature gradient across the reaction vessel drives thermal convection. By convection, the reaction liquid circulates between hot and cold regions of the chamber. The convection triggers DNA amplification as the DNA melts into two single strands in the hot region and replicates into twice the amount in the cold region. The amplification progresses exponentially as the convection moves on. We review the characteristics of the different approaches and show the benefits and prospects of the method.

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Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers

Genome ◽

10.1139/g93-092 ◽

1993 ◽

Vol 36 (4) ◽

pp. 686-693 ◽

Cited By ~ 23

Author(s):

Benoit Van Coppenolle ◽

Iwao Watanabe ◽

Charles Van Hove ◽

Gerard Second ◽

Ning Huang ◽

...

Keyword(s):

Principal Component Analysis ◽

Polymerase Chain Reaction ◽

Principal Component ◽

Dna Amplification ◽

Component Analysis ◽

Genetic Distances ◽

Group Method ◽

Chain Reaction ◽

Arbitrary Primers ◽

Polymerase Chain

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the worldwide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla–Anabaena complex. Twenty-two primers were used and each primer gave 4–10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla–Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.Key words: Azolla–Anabaena symbiosis, genetic distances, polymerase chain reaction, principal component analysis.

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HTLV-I-induced lymphoma mimicking Hodgkin's disease. Diagnosis by polymerase chain reaction amplification of specific HTLV-I sequences in tumor DNA

Blood ◽

10.1182/blood.v71.4.1027.1027 ◽

1988 ◽

Vol 71 (4) ◽

pp. 1027-1032 ◽

Cited By ~ 87

Author(s):

DB Duggan ◽

GD Ehrlich ◽

FP Davey ◽

S Kwok ◽

J Sninsky ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Hodgkin's Disease ◽

Polymerase Chain Reaction Amplification ◽

Hodgkin’S Disease ◽

Dna Amplification ◽

Disease Diagnosis ◽

Lymphoproliferative Disease ◽

Enzyme Linked Immunosorbent Assay ◽

Chain Reaction ◽

Polymerase Chain

Abstract A patient with a localized HTLV-I-associated lymphoproliferative disease that was misdiagnosed as Hodgkin's disease is presented. The patient's serum was negative for HTLV-I antibodies by enzyme-linked immunosorbent assay (ELISA), Western blot, and radioimmunoprecipitation. Tumor tissue DNA was negative for HTLV-I by Southern blotting but was positive for distinct HTLV-I sequences when subjected to DNA amplification using the polymerase chain reaction. We conclude that the clinical and pathologic diagnosis of HTLV-I-related lymphoma can be difficult and can be confused with Hodgkin's disease. Extremely sensitive molecular biological techniques may be required to establish a diagnosis of HTLV-I-induced lymphoma.

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Diagnosis of Blastocystis sp., Cryptosporidium sp., and Giardia intestinalis by Multiplex PCR: An Optimization Study

Türk Mikrobiyoloji Cemiyeti Dergisi ◽

10.5222/tmcd.2021.20981 ◽

2021 ◽

Author(s):

Ali Ahmet Kilimcioğlu ◽

Nogay Girginkardeşler ◽

Tuba Oyur ◽

Selin Bölük Sabuncu ◽

Didem Düzyol Azak ◽

...

Keyword(s):

Multiplex Pcr ◽

Dna Isolation ◽

Giardia Intestinalis ◽

Molecular Method ◽

Chain Reaction ◽

Optimization Study ◽

Optimized Protocol ◽

Blastocystis Sp ◽

Stool Samples ◽

Polymerase Chain

Objective: It was aimed to develop a new Multiplex Polymerase Chain Reaction (PCR) protocol with isolates obtained from local patients for the diagnosis of Blastocystis sp., Cryptosporidium sp. and Giardia intestinalis, which can cause severe gastrointestinal system complaints especially in immunocompromised patients and children. Method: DNA isolation was performed with a commercial kit from three stool samples of different patients whose microscopic examination showed dense amounts of Blastocystis sp., Cryptosporidium sp. and Giardia intestinalis. First, a special PCR protocol has been developed for each protozoon. Then, the multiplex PCR protocol, in which these three protozoa can be diagnosed together, was optimized. Results: In the multiplex PCR protocol performed after DNA isolation, bands of 95 bp., 227 bp. and 258 bp. were obtained for Cryptosporidium sp., Blastocystis sp. and G. intestinalis, respectively. Conclusion: Blastocystis sp., Cryptosporidium sp. and Giardia intestinalis were diagnosed by multiplex PCR with the original protocol developed. Due to the difficulties in using different methods in parasitological examination, by adding other protozoa important for public health to this optimized protocol, it will be possible to detect a large number of parasites with a single molecular method.

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Factors Associated with HIV prevalence among HIV-exposed Infants with HIV DNA Polymerase Chain Reaction Tests in Malawi: 2013-2020

10.1101/2021.10.06.21264671 ◽

2021 ◽

Author(s):

Wingston Ng'ambi ◽

Janne Estill ◽

Fatma Aziza Merzouki ◽

Erol Orel ◽

Tiwonge Chimpandule ◽

...

Keyword(s):

Hiv Infection ◽

Temporal Trends ◽

Chain Reaction ◽

Factors Associated ◽

Hiv Dna ◽

Polymerase Chain ◽

Hiv Exposed ◽

Spatial And Temporal Trends ◽

Dna Pcr ◽

Test Result

Background: Despite the high availability of individual-level data of infants accessing HIV DNA polymerase chain reaction (DNA-PCR) testing service, there has been little in-depth analysis of such data. Therefore, we describe spatial and temporal trends in risk of HIV infection among Malawi HIV-exposed infants (HEI) with DNA-PCR HIV test result from 2013 to 2020. Methods: This is an implementation study using routinely collected patient-level HIV DNA-PCR test result data extracted from the national Laboratory Management Information System database managed by the Department of HIV/AIDS between 1 January 2013 and 30 June 2020. We calculated frequencies, proportions and odds ratios (OR) with their associated 95% confidence intervals (95%CI). We performed a random-effects logistic regression to determine the risk factors associated with HIV infection in infants, controlling for the spatial autocorrelation between districts and adjusting for other variables. Results: We evaluated 255,229 HEI across 750 facilities in 28 districts. The overall risk of HIV infection among all tested HEI between 2013 and 2020 was 7.2% (95%CI: 7.1-7.3). We observed a decreasing trend in the proportion of HEI that tested HIV positive from 7.0% (95%CI: 6.6-7.4) in 2013 to 5.7% (95%CI: 5.4-5.9) in 2015 followed by an increase to 9.9% (95%CI: 9.6-10.2) in 2017 and then a decreasing trend to 4.2% (95%CI: 3.7-4.6) in 2020. The risk of HIV infection increased by age of the HEI. There was spatial heterogeneity of HIV prevalence between districts of Malawi. Conclusion: We summarised spatial and temporal trends of risk of HIV infection amongst HEI in Malawi between 2013 and 2020. There is need for further strengthening of EID program to ensure that all the HEI are enrolled in care by eight weeks of age in order to further reduce mother-to-child transmission of HIV.

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Methods for identification of causative agents of dangerous and particularly dangerous infections based on the analysis of nucleic acids

Journal of NBC Protection Corps ◽

10.35825/2587-5728-2018-2-4-22-35 ◽

2018 ◽

Vol 2 (4) ◽

pp. 22-35

Keyword(s):

Nucleic Acids ◽

Dna Amplification ◽

Rapid Identification ◽

Chain Reaction ◽

Biological Contamination ◽

Laboratory Facilities ◽

Trained Personnel ◽

Causative Agents ◽

Polymerase Chain ◽

Goals And Objectives

One of the main tasks of the NBC Protection Troops is accurate and rapid identification of infectious disease causative agents in case of establishing the fact of biological contamination. Different methods based on the analysis of nucleic acids are most preferred for this purpose. Most of them are based on DNA amplification by polymerase chain reaction (PCR). The result is detected by electrophoretic separation of amplification products, as well as by registration of endpoint fluorescent signal (FLASH modification) or in real time (PCR-RT). Other methods of DNA amplification, such as ligase chain reaction (LCR) and isothermal amplification, are also applicable in practice. The article also describes some identification methods based on nucleic acid sequencing: multilocus sequence typing (MLST) method, sequencing of individual genes and complete genome sequencing. It is concluded that the choice of identification method should be based on the goals and objectives, laboratory facilities, availability of trained personnel and funding levels. Despite the fact that the most informative are methods based on sequencing nucleotide sequences, their implementation in the field is difficult so far due to technological requirements

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Molecular diagnosis of the curly lettuce parasitic contamination from hydroponic cultivation from supermarkets

Revista Brasileira de Parasitologia Veterinária ◽

10.1590/s1984-29612020095 ◽

2020 ◽

Vol 29 (4) ◽

Author(s):

Fernanda Pinto-Ferreira ◽

Jonatan Batista Reis ◽

Aline Ticiani Pereira Paschoal ◽

Letícia Santos Balbino ◽

Amanda Bertão-Santos ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Toxoplasma Gondii ◽

Dna Extraction ◽

Chain Reaction ◽

Cryptosporidium Spp ◽

Hydroponic Cultivation ◽

Polymerase Chain ◽

Fluctuation Method ◽

The City ◽

Commercial Kit

Abstract The consumption of vegetables has increased in recent years due to the search for a healthier diet that is rich in fiber and has fewer calories. To assess the parasitic contamination of lettuce sold in markets, a survey of parasites was carried out from a supermarket chain in the city of Londrina, Paraná. A total of thirty samples of lettuce were purchased in the ten markets visited, three in each, of which ten were conventionally cultivated, ten were hydroponically cultivated, and ten were organically cultivated. All samples were analyzed using the sedimentation methods of Hoffman, Pons and Janer and the fluctuation method of Faust and colleagues and Willis with adaptations. In addition, the samples were subjected to DNA extraction by a commercial kit and polymerase chain reaction to detect Toxoplasma gondii, Cryptosporidium spp. and Giardia spp., which are protozoa that cause food and waterborne parasitic outbreaks. All samples were negative for sedimentation and flotation techniques. One of the hydroponically cultivated samples was positive for T. gondii. The results demonstrate the risk of curly lettuce contamination from hydroponic cultivation and the need for proper cleaning of these foods before consumption.

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