scholarly journals Cryptosporidium occurrence in ruminants from the North Pioneer mesoregion of Paraná, Brazil

2018 ◽  
Vol 27 (2) ◽  
pp. 248-253 ◽  
Author(s):  
Luciane Holsback ◽  
Heloísa Eid Lima ◽  
Odilon Vidotto ◽  
Marcelo Alves da Silva ◽  
Thaís Helena Constantino Patelli ◽  
...  
Keyword(s):  
Beef Cows ◽  
18S Rrna Gene ◽  
Dairy Calves ◽  
P Value ◽  
Rrna Gene ◽  
Beef Calves ◽  
The North ◽  
Stool Samples ◽  
Pcr Techniques ◽  
Cattle And Sheep

Abstract The aim of this study was to investigate the occurrence of Cryptosporidium in cattle and sheep from the North Pioneer mesoregion of the state of Paraná. For this, 317 stool samples were collected from cattle and sheep on 16 properties in six municipalities in the North Pioneer mesoregion of Paraná. For detection of Cryptosporidium species, molecular analysis was performed using nested-PCR techniques targeting the 18S rRNA gene. Of the 37 beef cows and 115 calves analyzed, four (10.8%) and 14 (12.2%), respectively, were positive for Cryptosporidium. Of the 12 cows and 52 calves, one (8.3%) and 14 (26.9%), respectively, were positive for Cryptosporidium; and of the 42 ewes and 59 lambs, six (14.3%) and 12 (20.3%), respectively were positive for Cryptosporidium. Cattle (15.3%) and sheep (17.8%) were both susceptible to infection. All the properties of the municipalities of Assaí, Ibaiti and, Leópolis presented infected animals. The study showed that Cryptosporidium occurs in most municipalities assessed, that dairy calves had a higher risk (Odds Ratio=2,66, p-value=0,018) for infection than beef calves, and that sheep are just as susceptible to infection as are cattle, and that further Cryptosporidium studies are developed.

scholarly journals Fungi found in Mediterranean and North Sea sponges: how specific are they?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3722 ◽  
Author(s):  
Mohd Azrul Naim ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
North Sea ◽  
Ribosomal Rna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Operational Taxonomic Units ◽  
The North ◽  
Hypervariable Regions ◽  
The North Sea ◽  
Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

scholarly journals Real-time PCR detection and speciation of Cryptosporidium infection using Scorpion probes

2006 ◽  
Vol 55 (9) ◽  
pp. 1217-1222 ◽  
Author(s):  
Suzanne E. Stroup ◽  
Shantanu Roy ◽  
John Mchele ◽  
Venance Maro ◽  
Simon Ntabaguzi ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Rflp Analysis ◽  
18S Rrna Gene ◽  
Human Infection ◽  
Rrna Gene ◽  
Dna Extraction Method ◽  
Stool Samples ◽  
Stool Specimens ◽  
Human Stool

At least eight species of Cryptosporidium can cause human infection and disease. A real-time PCR (qPCR) assay based on the 18S rRNA gene and utilizing a Scorpion probe was developed to detect all human-pathogenic Cryptosporidium without the usual need for nested amplification. Sensitivity of detection in stool samples was highest using a glass bead-based DNA extraction method (under 103 oocysts per stool sample). The assay was validated against 123 human stool specimens from Bangladesh and Tanzania, exhibited a sensitivity and specificity of >91 % versus microscopy, and detected an additional eight microscopy-negative infections. Cryptosporidium parvum-specific and Cryptosporidium meleagridis-specific Scorpion qPCR assays that provided 100 % accurate speciation compared with VspI RFLP analysis and sequencing were developed subsequently. These Scorpion probe qPCR assays are simpler to perform than existing nested PCR and RFLP methods for diagnosis and epidemiological investigation of cryptosporidiosis.

scholarly journals Fungi found in Mediterranean and North Sea sponges: How specific are they?

2017 ◽  
Author(s):  
Mohd Azrul Naim ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
North Sea ◽  
Ribosomal Rna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Operational Taxonomic Units ◽  
The North ◽  
Hypervariable Regions ◽  
The North Sea ◽  
Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point into the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

scholarly journals Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray

2008 ◽  
Vol 74 (17) ◽  
pp. 5305-5316 ◽  
Author(s):  
Christine Gescher ◽  
Katja Metfies ◽  
Stephan Frickenhaus ◽  
Britta Knefelkamp ◽  
Karen H. Wiltshire ◽  
...  
Keyword(s):  
Community Composition ◽  
Dna Microarrays ◽  
Time Series Data ◽  
Sampling Site ◽  
18S Rrna Gene ◽  
Series Data ◽  
Rrna Gene ◽  
The North ◽  
Algal Group ◽  
The North Sea

ABSTRACT The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.

scholarly journals Prevalence and species identification of Cryptosporidium spp. in the newborn dairy calves from Muang District, Khon Kaen Province, Thailand

2019 ◽  
Vol 12 (9) ◽  
pp. 1454-1459 ◽  
Author(s):  
Phennarin Doungmala ◽  
Patchara Phuektes ◽  
Weerapol Taweenan ◽  
Somboon Sangmaneedet ◽  
Ornampai Japa
Keyword(s):  
18S Rrna ◽  
Polymerase Chain Reaction Amplification ◽  
18S Rrna Gene ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Nested Polymerase Chain Reaction ◽  
Cryptosporidium Spp ◽  
Cryptosporidium Oocysts ◽  
Khon Kaen ◽  
Acid Fast Staining

Aim: This study aims to determine the prevalence of Cryptosporidium spp. infection and to identify the species of Cryptosporidium spp. in newborn dairy calves between December 2016 and March 2017 in Muang District, Khon Kaen Province, Thailand. Materials and Methods: A total of 200 fecal samples from newborn dairy calves of the ages 1 day up to 28 days were collected and the presence of Cryptosporidium oocysts was examined microscopically using the modified Kinyoun's acid-fast staining technique. Then, Cryptosporidium species were identified using nested polymerase chain reaction amplification of 18S rRNA gene and sequencing. Results: The modified Kinyoun's acid-fast staining revealed the presence of Cryptosporidium oocysts in 51% (102/200). Sequence analysis of the 18S rRNA gene identified two species, namely, Cryptosporidium bovis (n=11) and Cryptosporidium ryanae (n=11) and one isolated strain could not be identified. Conclusion: This study indicated that newborn dairy calves aging up to 4 weeks were highly infected with Cryptosporidium spp., and the infection mostly occurred in diarrheic dairy calves. This is the first report of Cryptosporidium in dairy calves in Khon Kaen Province and the results provide baseline information for further studies and control of Cryptosporidium infection in dairy calves in the study area.

scholarly journals  Recovery of Cryptosporidium from spiked water and stool samples measured by PCR and real time PCR

2012 ◽  
Vol 57 (No. 5) ◽  
pp. 224-232 ◽  
Author(s):  
M. Adamska ◽  
A. Leonska-Duniec ◽  
M. Sawczuk ◽  
A. Maciejewska ◽  
B. Skotarczak
Keyword(s):  
Real Time ◽  
Water Samples ◽  
Real Time Pcr ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
High Concentration ◽  
Intestinal Protozoan ◽  
Wide Range ◽  
Stool Samples

Cryptosporidium parvum is a common intestinal protozoan parasite infecting humans and a wide range of animals, whose diagnostics present considerable difficulties. These arise from the exceptionally robust nature of the oocyst’s walls, which necessitates more stringent treatments for disruption and recovery of DNA for analysis using molecular methods. In the case of water, which is the major source of Cryptosporidium oocysts, investigations concern the detection of the presence of the oocysts. Their concentration in water is very low, and moreover, many substances that may have significance as inhibitors of DNA amplification, are present in environmental water and stool. We have carried out trials in order to assess the effectiveness of recovery of C. parvum oocysts, from spiked environmental and distilled water samples, filtrated and concentrated with the use of special laboratory equipment. Inactivation of inhibitors was carried out with use of bovine serum albumin (BSA) in PCR mixes at ten different concentrations. DNA extraction was carried out from stool samples spiked with C. parvum oocysts, concentrated using two methods, and unconcentrated. Nested PCR and a TaqMan nested real time PCR assay, targeting the 18S rRNA gene, was used to detect C. parvum DNA in spiked water and additionally in spiked stool samples. The obtained results showed that losses of C. parvum oocysts occur during the filtration and concentration of spiked water samples. The addition of small amounts of BSA (5–20 ng/µl) to PCR and TaqMan PCR mixes increases the sensitivity of both methods, but a high concentration of BSA (100 ng/µl and above) has an inhibiting effect on the polymerase reaction. The extraction of DNA from C. parvum oocysts from spiked stool samples preceded by concentration with PBS, ether and Percoll resulted in a higher copy number of the 18S rRNA gene.  

scholarly journals Diversity and Distribution of Marine Microbial Eukaryotes in the Arctic Ocean and Adjacent Seas

2006 ◽  
Vol 72 (5) ◽  
pp. 3085-3095 ◽  
Author(s):  
C. Lovejoy ◽  
R. Massana ◽  
C. Pedr�s-Ali�
Keyword(s):  
Arctic Ocean ◽  
18S Rrna Gene ◽  
Ocean Basin ◽  
Significant Loss ◽  
Canada Basin ◽  
The Arctic ◽  
Rrna Gene ◽  
The North ◽  
The Arctic Ocean ◽  
Upper Mixed Layer

ABSTRACT We analyzed microbial eukaryote diversity in perennially cold arctic marine waters by using 18S rRNA gene clone libraries. Samples were collected during concurrent oceanographic missions to opposite sides of the Arctic Ocean Basin and encompassed five distinct water masses. Two deep water Arctic Ocean sites and the convergence of the Greenland, Norwegian, and Barents Seas were sampled from 28 August to 2 September 2002. An additional sample was obtained from the Beaufort Sea (Canada) in early October 2002. The ribotypes were diverse, with different communities among sites and between the upper mixed layer and just below the halocline. Eukaryotes from the remote Canada Basin contained new phylotypes belonging to the radiolarian orders Acantharea, Polycystinea, and Taxopodida. A novel group within the photosynthetic stramenopiles was also identified. One sample closest to the interior of the Canada Basin yielded only four major taxa, and all but two of the sequences recovered belonged to the polar diatom Fragilariopsis and a radiolarian. Overall, 42% of the sequences were <98% similar to any sequences in GenBank. Moreover, 15% of these were <95% similar to previously recovered sequences, which is indicative of endemic or undersampled taxa in the North Polar environment. The cold, stable Arctic Ocean is a threatened environment, and climate change could result in significant loss of global microbial biodiversity.

scholarly journals Blastocystis spp. subtype 10 infected beef cattle in Kamal and Socah, Bangkalan, Madura, Indonesia

2020 ◽  
Vol 13 (2) ◽  
pp. 231-237 ◽  
Author(s):  
Lucia Tri Suwanti ◽  
Yuli Susana ◽  
Poedji Hastutiek ◽  
Endang Suprihati ◽  
Nunuk Dyah Retno Lastuti
Keyword(s):  
Beef Cattle ◽  
Dna Analysis ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Zoonotic Parasite ◽  
Blastocystis Spp ◽  
Stool Samples ◽  
Polymerase Chain ◽  
Zoonotic Parasites ◽  
Fresh Stool

Background and Aim: Blastocystis spp. is a gastrointestinal parasite that can infect both humans and animals and has the potential to become a zoonotic parasite. This study analyzed a subtype (ST) of Blastocystis spp. that had infected beef cattle in Kamal and Socah, Bangkalan, Madura, Indonesia. Materials and Methods: Fresh stool samples were collected from 108 beef cattle at Kamal and Socah, Bangkalan, Madura, Indonesia. Blastocystis spp. were detected both morphologically and genetically based on the 18S rRNA gene. The morphology of Blastocystis spp. from the stool samples and cultured samples were observed under a light microscope. Blastocystis spp. from 20 positive cultures were amplified through polymerase chain reaction, and the resultant sequences were identified by ST. Results: One hundred and eight (100%) fecal samples from the fresh or cultured stools were positive morphologically for Blastocystis spp. Molecularly, all 20 of the samples selected for DNA analysis were found to be Blastocystis spp. ST 10. Conclusion: Based on morphological and molecular detection, the prevalence of Blastocystis spp. infection in beef cattle within Kamal and Socah, Bangkalan, Madura, Indonesia, was high. About 100% were non-zoonotic parasites. This was the first report of Blastocystis spp. ST 10 found in infected beef cattle in Kamal and Socah, Bangkalan, Madura, Indonesia.

scholarly journals Fungi found in Mediterranean and North Sea sponges: How specific are they?

2017 ◽  
Author(s):  
Mohd Azrul Naim ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
North Sea ◽  
Ribosomal Rna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Operational Taxonomic Units ◽  
The North ◽  
Hypervariable Regions ◽  
The North Sea ◽  
Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point into the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

scholarly journals Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer

2012 ◽  
Vol 9 (6) ◽  
pp. 6219-6259 ◽  
Author(s):  
S. Balzano ◽  
P. Gourvil ◽  
R. Siano ◽  
M. Chanoine ◽  
D. Marie ◽  
...  
Keyword(s):  
18S Rrna ◽  
Gene Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
28S Rrna ◽  
28S Rrna Gene ◽  
North East ◽  
The North ◽  
Green Algal ◽  
Rrna Gene Sequencing

Abstract. During the MALINA cruise (summer 2009) an extensive effort was undertaken to isolate phytoplankton strains from the North East (NE) Pacific Ocean, the Bering Strait, and the Beaufort Sea. Strains were isolated by flow cytometry sorting (FCS) and pipetting before or after phytoplankton enrichment of seawater samples. Strains were isolated both onboard and back in the laboratory and cultured at 4 °C under light/dark conditions. Overall, we isolated and characterised by light microscopy and 18S rRNA gene sequencing 104 strains of photosynthetic flagellates which grouped into 21 genotypes (defined by 99.5% 18S rRNA gene sequence similarity) mainly affiliated to Chlorophyta and Heterokontophyta. The taxon most frequently isolated was an Arctic ecotype of the green algal genus Micromonas (Arctic Micromonas) which was almost the only phytoplankter recovered within picoplankton (≤ 2 μm) size range. Strains of Arctic Micromonas as well as three unidentified strains related to the same genus were identified in further details by sequencing the Internal Transcribed Spacer (ITS) region of the rRNA operon. The MALINA Micromonas strains share identical 18S rRNA and ITS sequences suggesting high genetic homogeneity within Arctic Micromonas. The unidentified strains form a genotype likely belonging to a new genus within the family Mamiellaceae to which Micromonas belongs. Other green algae genotypes from the genera Nephroselmis, Chlamydomonas, Pyramimonas were also isolated whereas Heterokontophyta included Pelagophyceae, Dictyochophyceae and Chrysophyceae. Dictyochophyceae included Pedinellales which could not be identified to the genus level whereas Chrysophyceae comprised Dinobryon faculiferum. Moreover, we isolated Rhodomonas sp. as well as a few Haptophyta and dinoflagellates. We identified the dinoflagellate Woloszynskia cincta by Scanning Electron Microscopy (SEM) and 28S rRNA gene sequencing. Our morphological analyses show that this species possess the diagnostic features of the genus Biecheleria, and the 28S rRNA gene topology corroborates this affiliation. We thus propose the transfer of W. cincta to the genus Biecheleria and its recombination as Biecheleria cincta.

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