scholarly journals Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples

2021 ◽  
Vol 30 (3) ◽  
pp. 685-697
Author(s):  
Kara J. Andres ◽  
Suresh A. Sethi ◽  
David M. Lodge ◽  
Jose Andrés
Keyword(s):  
Allele Frequencies ◽  
Field Samples ◽  
Experimental Mesocosms

scholarly journals Development of high throughput method for the analysis of anthelmintic resistance allele frequencies in field populations of gastrointestinal nematodes

2019 ◽  
Author(s):  
Neil D. Sargison ◽  
Madison MacLeay ◽  
Alison A. Morrison ◽  
David J. Bartley ◽  
Mike Evans ◽  
...  
Keyword(s):  
Anthelmintic Resistance ◽  
Gastrointestinal Nematode ◽  
Gastrointestinal Nematodes ◽  
Allele Frequencies ◽  
Management Tool ◽  
Resistance Allele ◽  
Resistance Mutations ◽  
Field Samples ◽  
The Impact ◽  
Β Tubulin

AbstractDrug resistant helminths have become a major cause of poor health and production in sheep and goats, and there is a need for diagnostic markers and tools to determine the frequency of resistance alleles in field parasite populations. Gastrointestinal nematode resistance to benzimidazole drugs is caused by a mutation in one of three positions on the isotype 1 β-tubulin locus, and in the absence of markers for resistance to other broad spectrum anthelmintic classes, these provide a relevant study example. Determination of the prevalence of these single nucleotide polymorphisms in field gastrointestinal nematode populations can be impractical using conventional molecular methods, which may be error prone or lack sensitivity at low levels of resistance. Here, we report the development of a novel method based on an Illumina Mi-seq deep amplicon sequencing platform; to sequence the isotype 1 β-tubulin locus of the small ruminant gastrointestinal nematode,Teladorsagia circumcincta, and determine the frequency of the benzimidazole resistance mutations. We validated the method by assessing sequence representation bias in the isotype 1 β-tubulin locus, comparing the results of Illumina Mi-seq and pyrosequencing, and applying the method to populations containing known proportions of resistant and susceptible L3. Finally, we applied the method to field samples collected from ewes and lambs on over a period of one year on three farms, each highlighting different aspects of sheep management and approaches to parasite control. The results show opportunities to build hypotheses with reference to selection pressures leading to differences in resistance allele frequencies between sampling dates, farms and ewes or lambs, and to consider the impact of their genetic fixation or otherwise. This study provides proof of concept of a practical, accurate, sensitive and scalable method to determine frequency of anthelmintic drug resistance mutations in gastrointestinal nematodes in field studies and as a management tool for livestock farmers.

An experience of elaboration and implementation of systems of slag-forming mixtures mechanized feeding into CCM moulds

2020 ◽  
Vol 76 (10) ◽  
pp. 994-1003
Author(s):  
S. P. Eron’ko ◽  
M. Yu. Tkachev ◽  
E. V. Oshovskaya ◽  
B. I. Starodubtsev ◽  
S. V. Mechik
Keyword(s):  
Economic Effect ◽  
Three Dimensional ◽  
Movable Part ◽  
High Quality ◽  
Working Zone ◽  
Fine Material ◽  
Mixing Chamber ◽  
Field Samples ◽  
Technical Solutions ◽  
Feeding Systems

Effective application of slag-forming mixtures (SFM), being fed into continuous castingg machine (CCM) moulds, depends on their even distribution on the melt surface. Manual feeding of the SFM which is widely usedd does not provide this condition, resulting in the necessity to actualize the work to elaborate systems of SFM mechanized feedingg into moulds of various types CCM. A concept of the designing of a system of SFM feeding into CCM moulds presented with the ratte strictly correspondent to the casting speed and providing formation of an even layer of fine material of given thickness on the whoole surface of liquid steel. The proposed methods of designing of the SFM mechanized feeding systems based on three-dimensional computer simulation with the subsequent verification of the correctness of the adopted technical solutions on field samples. Informattion is presented on the design features of the adjusted facilities intended for continuous supply of finely granulated and powder mixtuures on metal mirror in moulds at the production of high-quality billets, blooms and slabs. Variants of mechanical and pneumo-mechaanical SFM supply elaborated. At the mechanical supply the fine material from the feeding hopper is moved at a adjusted distance bby a rigid horizontally located screw. At the pneumo-mechanical supply the metered doze of the granular mixture is delivered by a sshort vertical screw, the lower part of which is located in the mixing chamber attached from below to the hopper and equipped with ann ejector serving for pneumatic supply of the SFM in a stream of transporting gas. It was proposed to use flexible spiral screws in the ffuture facilities of mechanical SFM feeding. It will enable to eliminate the restrictions stipulated by the lack of free surface for locatiion of the facility in the working zone of the tundish, as well as to decrease significantly the mass of its movable part and to decreaase the necessary power of the carriage moving mechanism driver. The novelty of the proposed technical solutions is protected by thhree patents. The reduction of 10–15% in the consumption of slag-forming mixtures during the transition from manual to mechanizeed feeding confirmed. The resulting economic effect from the implementation of technical development enables to recoup the costs inncurred within 8–10 months.

Isolation and identification of Marek’s disease virus (MDV) from feather follicle epithelium and internal organs of diseased chickens in Dakahlia Governorate, Egypt

2019 ◽  
Vol 20 (2) ◽  
pp. 6-11
Author(s):  
Aly El-Kenawy ◽  
Mohamed El-Tholoth ◽  
Emad A
Keyword(s):  
Real Time ◽  
Disease Virus ◽  
Real Time Pcr ◽  
Marek's Disease Virus ◽  
Marek's Disease ◽  
Marek’S Disease Virus ◽  
Marek’S Disease ◽  
Field Samples ◽  
Feather Follicle ◽  
Positive Results

In the present study, a total of 16 samples including feather follicle epithelium, ovary, spleen and kidney (4 samples for each organ) were collected from diseased chicken flocks suspected to be infected with Marek’s disease virus (MDV) at Dakahlia Governorate, Egypt during the period from October 2016 to October 2017. Each sample was pooled randomly from three to five birds (90 to 360 days old). The isolation of the suspected virus from the collected samples was carried out via chorioallantoic membranes (CAMs) of 12 days old embryonated chicken eggs (ECEs). Three egg passages were carried out for each sample. Hyperimmune serum was prepared against standard MDV. MDV in both field and egg passaged samples (after 3rd passage) was identified by agar gel precipitation test (AGPT) and indirect fluorescence antibody test (IFAT). Molecular identification of virus was carried out by conventional polymerase chain reaction (PCR) and real- time PCR in four selected samples. The results revealed that 14 samples (87.5%) including 4 (100%) samples from feather follicle epithelium, ovary and kidney and 2 (50%) samples from spleen, showed positive results in virus isolation after 3rd passage. The positive results percentage by AGPT for field samples were 50% (8 out of 16 samples), while after the 3rd passage in ECEs were 37.5% (6 out of 16 samples) and the positive results percentage by IFAT for field samples were 62.5% (10 out of 16 samples), while after the 3rd passage in ECEs were 81.25 % (13 out of 16 samples). Viral nucleic acid was detected in all selected samples by conventional and real- time PCR. The results indicate that feather follicle epithelium is the best organ for MDV detection. IFAT is superior over AGPT in virus detection. Conventional and real - time PCR could be efficiently used for molecular detection of the virus.

scholarly journals Inbreeding of Bottlenecked Butterfly Populations: Estimation Using the Likelihood of Changes in Marker Allele Frequencies

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1053-1063 ◽  
Author(s):  
Ilik J Saccheri ◽  
Ian J Wilson ◽  
Richard A Nichols ◽  
Michael W Bruford ◽  
Paul M Brakefield
Keyword(s):  
Linkage Disequilibrium ◽  
Probability Distribution ◽  
Reproductive Success ◽  
Genetic Markers ◽  
Allele Frequencies ◽  
Demographic Parameters ◽  
Bicyclus Anynana ◽  
Marker Allele ◽  
Wide Applicability ◽  
Per Gene

Abstract Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, σ2, the variance in the number of descendants left per gene. In all bottlenecked lines, σ2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in σ2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability.

scholarly journals The Epidemiology and Genetics of Hyperuricemia and Gout across Major Racial Groups: A Literature Review and Population Genetics Secondary Database Analysis

2021 ◽  
Vol 11 (3) ◽  
pp. 231
Author(s):  
Faven Butler ◽  
Ali Alghubayshi ◽  
Youssef Roman
Keyword(s):  
Literature Review ◽  
Risk Allele ◽  
Statistical Significance ◽  
Elevated Serum ◽  
The United States ◽  
Allele Frequencies ◽  
Racial Groups ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Risk Alleles

Gout is an inflammatory condition caused by elevated serum urate (SU), a condition known as hyperuricemia (HU). Genetic variations, including single nucleotide polymorphisms (SNPs), can alter the function of urate transporters, leading to differential HU and gout prevalence across different populations. In the United States (U.S.), gout prevalence differentially affects certain racial groups. The objective of this proposed analysis is to compare the frequency of urate-related genetic risk alleles between Europeans (EUR) and the following major racial groups: Africans in Southwest U.S. (ASW), Han-Chinese (CHS), Japanese (JPT), and Mexican (MXL) from the 1000 Genomes Project. The Ensembl genome browser of the 1000 Genomes Project was used to conduct cross-population allele frequency comparisons of 11 SNPs across 11 genes, physiologically involved and significantly associated with SU levels and gout risk. Gene/SNP pairs included: ABCG2 (rs2231142), SLC2A9 (rs734553), SLC17A1 (rs1183201), SLC16A9 (rs1171614), GCKR (rs1260326), SLC22A11 (rs2078267), SLC22A12 (rs505802), INHBC (rs3741414), RREB1 (rs675209), PDZK1 (rs12129861), and NRXN2 (rs478607). Allele frequencies were compared to EUR using Chi-Square or Fisher’s Exact test, when appropriate. Bonferroni correction for multiple comparisons was used, with p < 0.0045 for statistical significance. Risk alleles were defined as the allele that is associated with baseline or higher HU and gout risks. The cumulative HU or gout risk allele index of the 11 SNPs was estimated for each population. The prevalence of HU and gout in U.S. and non-US populations was evaluated using published epidemiological data and literature review. Compared with EUR, the SNP frequencies of 7/11 in ASW, 9/11 in MXL, 9/11 JPT, and 11/11 CHS were significantly different. HU or gout risk allele indices were 5, 6, 9, and 11 in ASW, MXL, CHS, and JPT, respectively. Out of the 11 SNPs, the percentage of risk alleles in CHS and JPT was 100%. Compared to non-US populations, the prevalence of HU and gout appear to be higher in western world countries. Compared with EUR, CHS and JPT populations had the highest HU or gout risk allele frequencies, followed by MXL and ASW. These results suggest that individuals of Asian descent are at higher HU and gout risk, which may partly explain the nearly three-fold higher gout prevalence among Asians versus Caucasians in ambulatory care settings. Furthermore, gout remains a disease of developed countries with a marked global rising.

scholarly journals Performance of a Handheld Chlorophyll-a Fluorometer: Potential Use for Rapid Algae Monitoring

Water ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1409
Author(s):  
Hamdhani Hamdhani ◽  
Drew E. Eppehimer ◽  
David Walker ◽  
Michael T. Bogan
Keyword(s):  
Chlorophyll A ◽  
Surface Waters ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Water Quality Monitoring ◽  
Ambient Light ◽  
Calibration Equation ◽  
Field Samples ◽  
Potential Use

Chlorophyll-a measurements are an important factor in the water quality monitoring of surface waters, especially for determining the trophic status and ecosystem management. However, a collection of field samples for extractive analysis in a laboratory may not fully represent the field conditions. Handheld fluorometers that can measure chlorophyll-a in situ are available, but their performance in waters with a variety of potential light-interfering substances has not yet been tested. We tested a handheld fluorometer for sensitivity to ambient light and turbidity and compared these findings with EPA Method 445.0 using water samples obtained from two urban lakes in Tucson, Arizona, USA. Our results suggested that the probe was not sensitive to ambient light and performed well at low chlorophyll-a concentrations (<25 µg/L) across a range of turbidity levels (50–70 NTU). However, the performance was lower when the chlorophyll-a concentrations were >25 µg/L and turbidity levels were <50 NTU. To account for this discrepancy, we developed a calibration equation to use for this handheld fluorometer when field monitoring for potential harmful algal blooms in water bodies.

scholarly journals Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 363
Author(s):  
Sulochana K. Wasala ◽  
Dana K. Howe ◽  
Louise-Marie Dandurand ◽  
Inga A. Zasada ◽  
Dee R. Denver
Keyword(s):  
Genetic Variation ◽  
Potato Production ◽  
Globodera Pallida ◽  
Fixation Index ◽  
Parasitic Nematodes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Field Samples ◽  
Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

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