Development of a diagnostic molecular marker for Philonema spp. (Nematoda; Dracunculoidea) infecting salmonids in British Columbia

1995 ◽  
Vol 52 (S1) ◽  
pp. 129-133 ◽  
Author(s):  
L. Després ◽  
M.L. Adamson ◽  
T.E. McDonald
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Pcr Amplification ◽  
Base Substitution ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Nematode Parasites ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
In The Wild ◽  
Species Specific

We developed a species specific DNA probe based on differential PCR amplification that distinguishes two congeneric nematode parasites of salmonids in British Columbia: Philonema agubernaculum Simon and Simon, 1936, usually parasitic in lake resident rainbow trout, Oncorhynchus mykiss; and P. oncorhynchi Kuitunen-Ekbaum, 1933, parasitic in anadromous sockeye salmon, O. nerka. The region differentially amplified was the D3 expansion domain of the 28S rDNA. Sequences of the two species differ in two parts of the domain, one a single base substitution and the other a three base duplication in P. oncorhynchi. A primer specific to P. oncorhynchi (amplifying P. oncorhynchi, not P. agubernaculum) was defined in the duplication region. Using differential amplification, we showed that sockeye smolts are infected with P. agubernaculum, although returning adults harbour only P. oncorhynchi. This technique could conceivably be used to quantify the frequency of heterologous infections in the wild, before infecting worms are identifiable at the species level based on morphological criteria.

Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis

2005 ◽  
Vol 54 (11) ◽  
pp. 1031-1035 ◽  
Author(s):  
Niclas Grahn ◽  
Mounira Hmani-Aifa ◽  
Karin Fransén ◽  
Peter Söderkvist ◽  
Hans-Jürg Monstein
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Biopsy Specimens ◽  
16S Rdna Pcr ◽  
H Pylori ◽  
Species Specific ◽  
Pyrosequencing Analysis

Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding to H. pylori 26695 and H. pylori J99 were most commonly found. Intriguingly, one sequence belonged to Helicobacter mustelae, previously identified in ferrets. No significant correlations were found in the prevalence of Helicobacter DNA between colon and rectum tumour biopsies (P = 0.815), nor between Dukes’ classes A/B and C/D (P = 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identify Helicobacter species in human biopsy specimens.

Horizontal and vertical movements of telemetered rainbow trout (Oncorhynchus mykiss) in Lake Washington

1995 ◽  
Vol 73 (1) ◽  
pp. 146-153 ◽  
Author(s):  
Eric J. Warner ◽  
Thomas P. Quinn
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Average Velocity ◽  
Sockeye Salmon ◽  
Depth Distribution ◽  
Prey Species ◽  
Nearshore Zone ◽  
Vertical Movements ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Lake Washington

In summer and fall 1989, six rainbow trout (Oncorhynchus mykiss) were tracked in Lake Washington with ultrasonic transmitters for a total of 349 h to determine their movements in relation to the distribution of possible prey species. The trout moved primarily in the nearshore area at an average velocity of 12.4 cm/s (~ 0.25–0.3 body lengths/s). Five of the six fish made one more rapid (>1 body lengths/s) excursion across the lake, then continued moving in the nearshore zone. The trout were generally inactive, staying close (<50 m) to shore at night, and became more active near dawn; however, the highest average velocities were at dusk. They spent over 90% of their time in the top 3 m of the water column and 10% in brief (2 min), shallow (mean 6.6 m) dives. Dives occurred most frequently at dawn and during the day (0.8/h), less often near dusk (0.5/h), and seldom at night (0.1/h). The depth distribution and movement patterns suggest that the trout were feeding on Daphnia pulicaria during the day, in both nearshore and offshore areas, supplementing this diet with nearshore fishes such as prickly sculpins (Cottus asper). Predation on pelagic planktivores (longfin smelt, Spirinchus thaleichthyes, and juvenile sockeye salmon, Oncorhynchus nerka) was unlikely because the trout were primarily found nearshore and near the surface, whereas the planktivores are primarily offshore and closer to the bottom.

Bacterioplankton, Phytoplankton, and Zooplankton Communities in a British Columbia Coastal Lake Before and After Nutrient Reduction

1986 ◽  
Vol 43 (8) ◽  
pp. 1504-1514 ◽  
Author(s):  
F. Joan Hardy ◽  
Ken S. Shortreed ◽  
John G. Stockner
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Inorganic Nitrogen ◽  
Size Fraction ◽  
Growing Season ◽  
Nutrient Reduction ◽  
Nitrogen And Phosphorus ◽  
Coastal Lake ◽  
Before And After ◽  
High Concentrations

Inorganic nitrogen and phosphorus were applied weekly during the growing season from 1980 to 1982 and twice weekly in 1983 to Hobiton Lake, a warm monomictic coastal lake in British Columbia. The lake was not fertilized in 1984. Average numbers of bacteria during the growing season decreased from a high of 1.53 × 106∙mL−1 in the fertilized condition to 0.84 × 106∙mL−1 in the unfertilized condition. Chlorophyll a concentrations decreased from a maximum seasonal average of 2.69 μg∙L−1 (1981) to 1.30 μg∙L−1 (1984), and algal numbers decreased from 5.83 × 104∙mL−1 (1983) to 2.29 × 104∙mL−1 (1984). Although the numbers of phytoplankton in each size fraction (picoplankton, nanoplankton, or microplankton) decreased in the unfertilized condition, the greatest change was an almost fourfold decrease in picoplankton, which consisted of 90% cyanobacteria (primarily Synechococcus spp.). Abundance of the large diatoms Rhizosolenia spp. and Melosira spp. increased in 1984, resulting in an increase in average seasonal algal volume. Average densities of medium (0.15–0.84 mm) and large (0.85–1.5 mm) zooplankton were greatest in 1982, while rotifers and small zooplankton (0.10–0.14 mm) were most dense in 1984 following nutrient reduction. The lake had relatively high concentrations of planktivorous juvenile sockeye salmon (Oncorhynchus nerka) that appeared to minimize any direct effect of nutrient additions on zooplankton densities.

Fecundity and Egg Retention of Some Sockeye Salmon (Oncorhynchus nerka) Stocks in British Columbia

1986 ◽  
Vol 43 (8) ◽  
pp. 1643-1655 ◽  
Author(s):  
J. I. Manzer ◽  
I. Miki
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Absolute Fecundity ◽  
Egg Retention ◽  
Inadequate Sample Size ◽  
Egg Number ◽  
The Mean ◽  
The Relationship ◽  
Individual Fecundity

The fecundity and egg retention of anadromous female sockeye salmon (Oncorhynchus nerka) collected during 1971–82 from several stocks in British Columbia undergoing controlled fertilization to enhance adult sockeye production were examined. The relationship between egg number and postorbital–hypural length based on 863 females representing 14 stocks was not consistent between all age-types, stocks, and years, probably because of inadequate sample size in some instances. Combined samples, however, revealed a significant positive relationship between postorbital–hypural length and egg number for age 1.2, 1.3, and 2.2 females. Mean absolute fecundity for the respective age-types was 3218, 4125, and 3544 eggs. For samples of 10 or more females, significant stock and annual differences were detected when individual mean absolute fecundity was adjusted to a postorbital–hypural length of 447 mm, but not for females of different age. A comparison of mean fecundities for coastal stocks with historical data for interior British Columbia stocks suggests that coastal stocks are 18% more fecund than interior stocks. Possible causal mechanisms for this regional difference are hypothesized. Examination of 796 carcasses (representing five stocks) for egg retention revealed a range from totally spawned to totally unspawned females, with 56% of the carcasses containing 20 eggs or less and 68% containing 50 eggs or less. The mean egg retention based on all samples combined was estimated to be 6.5% of the mean individual fecundity. This value was reduced to 3.9% when stock means were averaged.

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals Importance of sample size for estimating prevalence: A case example of infectious hematopoietic necrosis viral RNA detection in mixed-stock Fraser River Sockeye salmon (Oncorhynchus nerka), British Columbia, Canada.

2020 ◽  
Author(s):  
Emilie Laurin ◽  
Julia Bradshaw ◽  
Laura Hawley ◽  
Ian A. Gardner ◽  
Kyle A Garver ◽  
...  
Keyword(s):  
British Columbia ◽  
Sample Size ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Small Sample ◽  
Viral Rna ◽  
Sample Sizes ◽  
Apparent Prevalence ◽  
Infectious Hematopoietic Necrosis ◽  
Mixed Stock

Proper sample size must be considered when designing infectious-agent prevalence studies for mixed-stock fisheries, because bias and uncertainty complicate interpretation of apparent (test)-prevalence estimates. Sample size varies between stocks, often smaller than expected during wild-salmonid surveys. Our case example of 2010-2016 survey data of Sockeye salmon (Oncorhynchus nerka) from different stocks of origin in British Columbia, Canada, illustrated the effect of sample size on apparent-prevalence interpretation. Molecular testing (viral RNA RT-qPCR) for infectious hematopoietic necrosis virus (IHNv) revealed large differences in apparent-prevalence across wild salmon stocks (much higher from Chilko Lake) and sampling location (freshwater or marine), indicating differences in both stock and host life-stage effects. Ten of the 13 marine non-Chilko stock-years with IHNv-positive results had small sample sizes (< 30 samples per stock-year) which, with imperfect diagnostic tests (particularly lower diagnostic sensitivity), could lead to inaccurate apparent-prevalence estimation. When calculating sample size for expected apparent prevalence using different approaches, smaller sample sizes often led to decreased confidence in apparent-prevalence results and decreased power to detect a true difference from a reference value.

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

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