Philippa Kaur

Fish and experimental protocolThree-hundred-fifty market-size (755–3865 g) common carp Cyprinus carpio were obtained from six sources at various times of year to for effects of variation in rearing conditions. The weight of collected carp corresponded to the weight of carp normally delivered to the market. Fish were obtained from the Faculty of Fisheries and Protection of Waters of the University of South Bohemia in Ceske Budejovice (FFPW USB), Vodnany and the fisheries Chlumec nad Cidlinou, Blatna, Hodonin, Klatovy, Lnare, and Tabor. Ten fish were collected from each fishery at the spring (March/April), summer (June/July), and autumn harvests (October/November) in 2018 and 2019. Carp were transported live to the laboratory of the FFPW, killed by a blow to the head, weighed, measured, and filleted. Two fillets, one with skin removed, from each fish were individually vacuum packed, immediately frozen, and stored at − 32 °C until chemical analysis.Ethics approvalAll the methods used in the present study followed relevant guidelines and regulations. Also, the competent authority (Ethical Committee for the Protection of Animals in Research of the University of South Bohemia, FFPW Vodnany) approved the fish sampling and protocols of the present study and reporting herein follows the recommendations in the ARRIVE guidelines.Chemical analysisSeven-hundred carp fillets were analysed for basic nutritional composition, dry matter, protein, fat, and ash. All samples were homogenized by grinding before analysis.The determination of dry matter followed ISO 1442:1997 Meat and meat products—Determination of moisture content (Reference method)26. The homogenized samples were dried with sand to constant weight at 103 ± 2 °C in a laboratory oven (Memmert UE 500, Memmert GmbH + Co. KG, Germany).The determination of ash was based on the standard ISO 936:1998 Meat and meat products—Determination of total ash27. The homogenized samples were burned in a muffle furnace (Nabertherm A11/HR, Nabertherm GmbH, Germany) at 550 ± 25 °C to a grey-white colour.The determination of total fat was based on the standard ISO 1443:1973 Meat and meat products—Determination of total fat content28. The homogenized samples were hydrolysed by hydrochloric acid, and fat was extracted by light petroleum in SOXTEC 2050 (FOSS Headquarters, Denmark).The determination of nitrogen used the Kjeldahl method based on the standard method ISO 937:1978 Meat and meat products—Determination of nitrogen content (Reference method)29. The homogenized samples were digested by sulphuric acid and a catalyser in a KjelROC Digestor 20 (OPSIS AB, Sweden) digestion unit at 420 ± 10 °C. Organically bound nitrogen was measured on the KJELTEC 8400 with KJELTEC sampler 8420 (FOSS Headquarters, Denmark). Calculation of protein content from nitrogen used the conversion factor for meat of 6.25.All analysis of dry matter, ash, and total fat were performed in duplicate and analysis of nitrogen (protein) was performed in triplicate for each sample.Calculation of fat-free nitrogen (Nff) in g/100 g used the formula24:$$ N_{ff} = frac{{100 times N { }}}{{100 – F { }}}. $$This formula was applied to nitrogen (N) and fat (F) content for all samples, providing a fat-free nitrogen value for each sample.Fish meat content calculated based on nitrogen factor Nf (total fillet) in g/100 g used the formula9:$$ Fish ;content_{Nf} = frac{N times 100}{{N_{f} }}. $$Fish meat content calculated based on fat-free nitrogen factor (Nff) and DCC (defatted carp content) in g/100 g used formulas11:$$ Fishc; content_{Nff} = DCC + F, $$$$ DCC = frac{N times 100}{{N_{ff} }}. $$Statistical analysisKolmogorov–Smirnov and Bartlett’s tests were applied to assess normal distribution data and the homoscedasticity of variance, respectively. A two-way ANOVA and Tukey’s test was conducted to analyse effects of season, weight, fishery, and difference between fillets with and without skin. The significance level was set at p  More

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In total, 13 culicoid species were found in the present study, with 45.5% of the collected specimens belonging to the Obsoletus Complex while species only occasionally present in previous collections in Germany, accounted for approximately 25% of the sampled individuals. Thus, the species composition is only partly in accordance to earlier studies on the German Culicoides fauna according to which 70 to over 90% of the specimens belonged to the Obsoletus Complex and up to 20% represented members of the Pulicaris Complex, while other culicoid species were present in negligible numbers only12,13. However, previous studies were based on UV-light trap catches12,13,14,15 and targeted active culicoid specimens16. The results obtained in this study are very specific as they represent the species compositions associated with the respective breeding substrates.The gender ratio differed strongly between species, revealing no pattern applicable to all species. The dominance of female Culicoides emerging from breeding sites corresponds to earlier results17,18, even though the sex ratio in the present study showed a much higher proportion of females with 70.7% or a female:male ratio of 2.4:1 than the above studies with 55.6%17 or a female:male ratio of 1.06:118.The evaluation of the diversity of each biotope (excluding the ungrazed meadow where no Culicoides were found) revealed clear differences between the agriculturally used habitats and the more natural biotopes. The Shannon–Weaver index depicted very low diversity for all three studied meadows where biting midges were found. The two meadows (with cattle and sheep) of region 2 reached the lowest possible diversity. This seems plausible as only one species was sampled within each biotope. The meadow with cattle of region 1 revealed at least two species. The Evenness factor of 0.24 depicts the dominance of one of them. The low number of species and unbalanced number of specimens within the biotope result in a low Shannon–Weaver index of 0.24, which describes the poor level of biodiversity.The Simpson index measures the probability that two individuals, randomly selected from a sample, belong to the same species. As only one species was sampled on each meadow from region 2, the probability to choose two specimens which belong to one species is 100% (displayed by the value of D = 1.0). The meadow with cattle of region 2 revealed at least two culicoid species, but the dominance of one species leads to a high Simpson index of 0.92 as well.Opposite to the very low biodiversity of all meadows, the four more natural biotopes of region 3 show an overall high level of biodiversity: according to the Shannon–Weaver index, the level of biodiversity is highest within the AFS (H = 2.96). Compared to the other biotopes of region 3, the AFS revealed by far the highest numbers of culicoid species and specimens. This and the relatively high Evenness factor (E = 0.89) lead to the high H value. The Shannon–Weaver indices for CW and MA are 1.91 and 1.92, respectively. Based on the low numbers of species and specimens in both biotopes, the relatively high H value is mainly caused by its high Evenness values of 0.95 (CW) and 0.96 (MA), respectively. Therefore, the almost equal numbers of all present species leads to the relatively high biodiversity, rather than a high number of species.The Shannon–Weaver index of the DW is the lowest of the four biotopes of region 3 with H = 1.42 and rates this biotope as the one with the lowest diversity of region 3. Though the number of species equal the one of the CW and MA, the higher number of specimens and especially the much lower Evenness factor of 0.71 reduces the H value.Other than the Shannon–Weaver index, the Simpson index rates both, the AFS and the MA, as the two most diverse biotopes. With values of D = 0.13, the probability to randomly select two species of the same species is rather low in both biotopes. As the AFS revealed more than double as many species than the MA, the lower number of caught specimens of the MA must have led to the same biodiversity rate.Study 1—Influence of domestic animals on meadows: up to date, dung-breeding Culicoides have been investigated more thoroughly18,19,20 than most other culicoid species. Most studies have focused on examining selectively either dungheaps or cowpats, rather than conducting a direct comparison between grazed and ungrazed meadows under field conditions. In the present study, we were able to show that the ungrazed meadow seems to be an unsuitable breeding habitat for Culicoides. Therefore, it seems plausible that the suitability of meadows as culicoid breeding sites can be largely, if not completely, attributed to the influence of livestock pasturing.The strong dominance of Obsoletus Complex specimens sampled on grazed meadows is not surprising as this species complex is known to contain typical dung-breeders19,20. The high potential of manure as a breeding substrate has been demonstrated before21,22 and explains the high quantity of Culicoides developing on meadows used by cattle in the present study. While 0.83 midges/sample were found on the meadow with cattle in region 1, only 0.21 midges/sample were collected on the meadow with cattle in region 2. The quantitative differences between these two study sites might be caused by the differing time periods of sampling (April to July for region 1 and August to October for region 2). Previous studies observed population peaks of Obsoletus Complex midges in October, though23, giving reason to expect even higher numbers of midges for region 2 than for region 1, particularly so, as region 2 is an agriculturally dominated area with a higher abundance of potential blood hosts and more suitable breeding habitats than region 1.Compared to the much higher total number of midges emerging from cowpats, sheep dung produced only two specimens. The very low number of midges originating from sheep faeces might be due to the very quick decomposition and desiccation of the rather small droppings, which likely reduces the quality of these remains as culicoid breeding sites. Therefore, it can be assumed that, contrary to pastures with cattle dung, sheep-runs might not play an essential role in promoting the distribution of Culicoides. For modeling approaches, it should be considered, though, that this might only apply to single scattered pieces of faeces as the longer persistence of higher volumes of sheep dung, i.e. on muckheaps, might very likely raise its quality as potential breeding sites as observed by21.All grazed meadows revealed very few culicoid species. Besides members of the Obsoletus Complex, only one individual of C. comosioculatus was found. The present investigation represents a case study though as merely one habitat of each type was sampled. More research to confirm the present results is therefore strongly recommended, even more, as ceratopogonid communities of terrestrial ecosystems have been barely investigated24, with the consequence that breeding sites of Culicoides spp. are still poorly known25.Study 2—Quality of forest-dominated biotopes as culicoid breeding sites: In the present study, the AFS turned out to be very productive as a culicoid breeding site in regards to the number of caught specimens and species diversity. Ten of the 13 collected species were found in the AFS. This is 2.5 times as many species as in the three other biotopes of region 3, which contained four species each in different compositions. Therefore, species-specific requirements for larval development seem to be met for more culicoid species in the AFS than in any of the other study sites.The measured pH values are in accordance to soil analyses conducted in German forests26. As the top layers usually are the most acidic ones, the chosen depth of soil sampling in the present study (upper 0–5 cm) persistently produced low pH values. Additionally, the used solvent (CaCl2) is less sensitive to fast changing weather conditions, but also lowers the measured pH value significantly compared to distilled water26—a solvent often used in earlier studies analyzing the distribution of Ceratopogonidae.The wide variances of the soil factors, especially moisture and organic content, were mainly caused by unequal soil conditions within each biotope rather than changes over time (unpublished data). Nevertheless, the statistical analysis revealed that all four biotopes of region 3 were significantly different from each other regarding the three soil factors. Comparing the means of each soil factor revealed that the AFS contained a higher level of soil moisture, a less acidic pH value and a higher organic content than the other three biotopes of region 3. We could show that significantly more midges (0.4 Culicoides/sample) developed in the AFS compared to the three other biotopes of region 3 with 0.12 (DW), 0.07 (CW) and 0.06 (MA) Culicoides per sample.Previous studies have assumed that the level of moisture be a crucial factor for ceratopogonid development17,20. Also, some studies determined the organic content as pivotal17,27. Our statistical analysis revealed that each soil factor has an impact on the probability of Culicoides to occur. Due to high correlations between the various measured soil factors, it could not be clarified, though, whether they influence the number of specimens, too. But as many culicoid species are known to lay their eggs in batches and previous egg-laying encourages females to oviposit at the same site28, an increase in the probability of biting midge presence should indirectly result in a higher number of specimens, too.The aggregation of larvae in terrestrial habitats29 typically results in a high number of samples completely devoid of midges and an overall low number of specimens sampled by emergence traps30. Thus, the obtained low numbers of collected specimens are not surprising. Nevertheless, emergence traps are still considered to be the best tool for the investigation of breeding site productivity, as it offers a safe assignment of species to their specific developmental sites24,29,31.The Culicoides collected in this study are discussed on species level in regards to existing literature.Culicoides achrayi was found in the AFS. A swamp as a breeding site32 and soil located in stagnant water22 have previously been described for this species. We confirm June as the time of emergence32 and add that C. achrayi co-exists with C. pulicaris.Culicoides albicans was collected in the AFS and DW. Specimens hatched from late April to mid-June, representing one generation per year. We confirm co-habitation with C. pictipennis and C. kibunensis11,33 and the preference for very humid substrates which has been described for the wettest parts of boglands5,34 and for artificially waterlogged soil11. Our results show, that C. albicans larvae can tolerate medium moisture levels, too. The mean organic content of their developmental sites reached from moderate to high, and the pH values lay between strong and ultra-acidic.Culicoides comosioculatus was found on the meadow with cattle dung in mid-June. As only one individual (a gravid female with the presumed intention to oviposit) was collected and no literature regarding breeding sites of this species could be found, our finding only indicates that this species might possibly develop in animal dung although in extremely low numbers.Culicoides grisescens was found within the AFS, the CW and the DW from late May until mid-July. Kremer35 listed soils of swamps and boggy grasslands as developmental sites. We collected C. grisescens in three different biotopes with wide variances of the mean moisture level, mean organic content and mean pH value, which reveals the wide tolerance range of this species towards these three soil factors.Culicoides impunctatus was collected in the AFS and the CW from late May to mid-July, representing one generation per year. This finding differs from earlier observations of two generations per year in Scotland36. Previous studies described breeding sites as acidic, oligotrophic grasslands, swamps, boglands or marshes, often of a peaty consistence5,10,33,34,37 and with soil pH values of 5.0–6.5 (dissolved in distilled water)37. This matches the pH values of the AFS in the present study (lower, but dissolved in CaCl2), but excludes the much lower pH values of the CW. The range considered suitable for C. impunctatus larvae should therefore be extended downwards to as low as pH 2.9–3.9 (CaCl2). We found C. impunctatus in two biotopes comprising a wide variance regarding soil moisture and organic content, which illustrates the wide tolerance range of this species. Individuals of C. impunctatus co-exist with Obsoletus Complex specimens as both were collected within the same sample in the AFS.Culicoides kibunensis was collected in the AFS and MA, which matches earlier observations depicting swamps of eutrophic fresh water bodies17,34, soil of stagnant water bodies22 and acidic grasslands in considerable distances to swamps33 as breeding sites. The AFS and MA revealed pH values between 3.4 and 5.4. Soil moisture and organic content displayed wide variances. All specimens hatched from late May to mid-June. Culicoides kibunensis was found to co-exist with C. albicans as observed by Kettle33. Earlier observations of co-habitations with C. obsoletus s.s. and C. pallidicornis5,34 could not be confirmed.Obsoletus Complex members were present in all study sites except for the ungrazed meadow. In the grazed meadows, Obsoletus Complex midges emerged almost throughout the entire sampling period except for the month of September. Two peaks were observed, one in June/July and a smaller one in October. As in the grazed meadows, the biotopes of region 3 also revealed two generations, but emerging at a slightly earlier time of the year with one peak in May/June and the other one in September/October.Members of the Obsoletus Complex are known to be generalists regarding their choice of breeding sites. Only the identified member species, C. chiopterus and C. obsoletus s.s., are considered here.Culicoides chiopterus was exclusively found on meadows grazed by cattle, which is in accordance to several earlier studies as this species is described as a dung-breeding species developing in cowpats and horse droppings5,34,35,38.Culicoides obsoletus s.s. was mostly sampled in the AFS. Only one individual was collected on a meadow grazed by cattle. Previous descriptions of breeding sites differed widely. Acidic grasslands in considerable distance to bogs/swamps33 and leaf litter compost5,35 could not be confirmed in the present study, although the MA and AFS were of a comparable character. While Uslu and Dik17 could not find any C. obsoletus s.s. in wet organic matter-rich soil, we collected most specimens of this species in the AFS and can therefore confirm previous findings11,29,32,39. The time of C. obsoletus s.s. activity in Germany (April–October) as described by Havelka32 agrees with our observations.Culicoides pallidicornis was found in the MA in late June. This species revealed the smallest variances of all sampled biting midge species regarding the three soil factors, using soil with pH values of 3.6–5.0 (CaCl2) and a relatively low level of moisture. This contradicts earlier observations where C. pallidicornis developed in the mud of eutrophic fresh-water swamps5. While C. pallidicornis larvae are known to co-exist with C. kibunensis5, we can add C. subfagineus to share the same developmental site.Culicoides pictipennis was collected in the DW and, to a minor part, in the AFS. The preferred physicochemical breeding conditions were ultra to extremely acidic with a medium moisture level and a moderate to slightly increased organic content. This differs from previous studies, which have found this species to develop only at the margin of stillwater bodies like pools and ponds, and the littoral of lakes or in artificially waterlogged soil11,32,34. Havelka32 observed C. pictipennis between May and June, while in our investigation the first specimen emerged as early as mid-April. We can confirm the co-existence of C. pictipennis and C. albicans as previously observed by Harrup11.Culicoides pulicaris was sampled in the AFS from late June until September, which agrees with observations denoting May to September as the activity time of this species32. Culicoides pulicaris seems to prefer breeding substrates with a high moisture level and a high organic content, as previously described17,32,34. We can add that C. pulicaris breeds in soil showing pH values at least between 4.0 and 5.4. We collected C. pulicaris together with C. achrayi and found it to simultaneously emerge from one biotope with C. obsoletus s.s. Additionally, we can confirm the co-existence of C. pulicaris with C. punctatus5,40, since both species have similar breeding habitat preferences11.Culicoides punctatus was sampled in the AFS and, to a minor part, in the CW. Time of emergence was from mid-June to late September, which is in accordance with earlier observations listing April-August and October as times of activity32. In the present study, a strong preference for swampy conditions with soil of high moisture, high organic content and a strong to very strong acidity was found. This is in agreement to previous findings11,32,41. The co-existence of C. punctatus with C. pulicaris is well known5,40 and can be confirmed once more. Additionally, we found C. punctatus to co-occur with C. subfasciipennis.Culicoides subfagineus was caught in the MA in late June. The soil was oligotrophic and contained a relatively low moisture level with pH values between 3.6 and 5.0. The first record of this species in Germany was in 2014, when C. subfagineus was observed to attack cattle42.Culicoides subfasciipennis was sampled in mid-June in the AFS. The time and choice of breeding site are in accordance to previous findings17,32. Breeding conditions for the only individual collected revealed a medium soil moisture factor, a pH value of 5.2 and a medium organic content. The species was found to co-develop with C. punctatus. More

Ethics statementAll procedures were conducted in accordance with the current laws in Thailand on experimental animals and were approved by the safety management committee for experiments of the Laboratory Animal Center, Chiang Mai University (Project Number 2561/FA-0001). The study also followed the recommendations in the ARRIVE guidelines.Species-specific primer designAll the DNA tissue analysed originated from the mucus of the individual giant snakehead. Total DNA was extracted from the mucus sample using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Extracted DNA was used as a template for qPCR assay together with synthetic fragments. DNA samples were quantified using a Qubit fluorometer (Life Technologies) calibrated with the Quant-iT dsDNA HS Assay following the manufacturer’s instructions. For each replicate, 3 µL volumes were measured.Species-specific primers and a minor-groove binding (MGB) probe incorporating a 5′ FAM reporter dye and a 3′ non-fluorescent quencher were designed to amplify an 127 bp targeting within the 16S region for the giant snakehead (C. micropeltes), using Primer Express (V3.0, Life Technologies; Table 3). Probe and primer sequences were matched against the National Centre for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/) nucleotide database with BLASTn (Basic Local Alignment Search Tool) to confirm the species’ specificity for the giant snakehead in silico assays.Table 3 Details of species-specific primers and the probe designed to amplify a 127 bp fragment of the 16S region of Channa micropeltes (Cuvier, 1831).Full size tableTo ensure that the assay only amplified the giant snakehead, it was deployed on a closely related species commonly found in Thai freshwater environments using conventional PCR amplification and visualization on a 1.5% agarose gel stained with SYBR Safe DNA Gel Stain (Life Technologies).qPCR assayThe qPCR assay was deployed using Environmental Master Mix (Applied Biosystems) on mucus samples from the giant snakehead and related species to ensure the species specificity to the qPCR assay. In addition, eDNA qPCR assay for the giant snakehead, a water sample collected from tank at Phayao Freshwater Aquarium (Phayao Inland Fisheries Research and Development Center) was known to have only the giant snakehead was included as a positive control for the presence of amplifiable eDNA in water samples. The tank contains around 4.5 m3 of water with one individual of giant snakehead resides in the tank (the fish is about 60–70 cm in length).All eDNA qPCR amplifications were performed in three replicates in a final volume of 20 µL, using 10.0 µL of 2 × TaqMan Environmental Master Mix 2.0 (Thermo Fisher Scientific), 2.0 µL of DNA template, 900 nM each of the F/R primers, and 125 nM of the probe. Samples were run under the following conditions: an initial 10 min incubation at 95 °C followed by 50 cycles of denaturation at 95 °C for 15 s and annealing/extension at 60 °C for 1 min. Negative controls with all PCR reagents but no template (three replicates) were run in parallel to assess potential contamination. The quantification cycle (Cq) was converted to quantities per unit volume using the linear regression obtained from the synthesized target gene standard curve (Integrated DNA Technologies Pte. Ltd., Singapore). The giant snakehead eDNA concentrations were then reported as copies/mL. The limit of detection (LOD) and the limit of quantification (LOQ) were also measured using the standard dilution series of synthesized target gene fragment with known copy numbers. A dilution series containing 1.5 × 101 to 1.5 × 104 copies per PCR tube were prepared and used as quantification standards. The calculation of LOD and LOQ was done using published R script by Klymus et al.26.DNA extraction from the filtersDNA trapped on the filters obtained from the aquarium experiments and field collections were extracted using Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) using a protocol modified from the manufacturer’s protocol with the following changes: the DNA from all samples were eluted twice with 25 µL AE buffer, in a total volume of 50 µL to obtain a more concentrated eDNA solution. The volume of ATL buffer (360 µL), Proteinase K (40 µL), AL buffer (400 µL) and Ethanol (400 µL) were doubled.Aquarium experimentAn aquarium experiment was used to test the extent to which qPCR of water samples can detect eDNA of giant snakehead at low simulated densities. The juvenile giant snakehead was obtained from the fish store and transported to a laboratory at Chiang Mai University. The giant snakeheads were then held in separate 120 L plastic holding containers in which the water was continuously filtered. The fish were fed frozen shrimp/commercially available flake fish food three times a week, and were held at 23 ± 1 °C.The sensitivity of eDNA detection in the aquaria was evaluated by conducting three aquarium experiments using plastic tanks (30 × 45 × 25 cm) filled with 120 L of aged-tap water. The water in the tanks was continuously aerated through a filter. In each experiment, the giant snakeheads were randomly assigned to the tanks (10 individuals per tank). The average size of the snakeheads was 9.7 cm (body length ranging from 9.1 to 10.6 cm). The average weight was 8.15 g (ranging from 6.7 to 10.6 g). The water in the tanks was maintained at 23 ± 1 °C. A 300 mL water sample from each tank was collected at each time point (0, 3, 6, 12, 24, 48, 72, 96, 120, 144, and 168 after removal of the fishes from the tanks) in triplicate. Collected water was filtered on a GF/F filter (0.7 μm Whatman International Ltd., Maidstone, UK). The eDNA from each sample solution was extracted using a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) in a final volume of 50 µL, detailed in DNA extraction from the filters. To confirm the absence of the giant snakehead eDNA in the water prior to the experiments, three tanks without giant snakehead were prepared and water sample was collected and treated as described above.Real-time PCR was performed with the species-specific primers and probe set using a Rotor-Gene Q system (Qiagen, Hilden, Germany). The reaction conditions were the same as described in qPCR assay. Three replicates were conducted for each sample including the negative PCR control and positive control.eDNA field collectionWater samples were collected at 6 points within Kwan Payao according to the survey locations of the Inland Fisheries Research and Development Center. Additional water samples were collected from 11 and 6 locations in Ing River where water flowed into and out of Kwan Payao, respectively (Fig. 1). To avoid contamination, all field equipment was sterilized using 10% bleach, UV-Crosslinker or autoclaved and sealed prior to transport to the study site, and a separate pair of nitrile disposable gloves were used for each sample. At each site, water samples were collected three replicate in bucket that had been previously decontaminated with a 10% bleach rinse followed by two distilled water rinses.In total, water samples were collected from 6 sites (in Kwan Phayao) and from 17 sites (in the Ing River) from 15th February to 5th March 2019, the middle of the dry season. Each site was sampled in triplicate, 300 mL samples of water were collected and filtered on GF/F filter (0.7 μm Whatman International Ltd., Maidstone, UK). In total, 306 water samples were collected from the surface water of lakes and rivers. For every sampling day, deionised water (300 mL) was filtrated as a negative control. The water samples and real-time PCR was processed as described above in qPCR assay. More

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