Split or combine? Effects of repeated sampling and data pooling on the estimation of colony numbers obtained from drone genotyping

Repeated sampling of a water (raw, Ssished, recreational) is often used to assess microbial quality. Microbial distributions have often been found to be negative binomial distributed in such repeated samples. Under these conditions, it is shown that it is better to use a large number of small volume samples than vice versa, providing that the negative binomial dispersion parameter remains unaffected by volume. Further research is needed to determine if the latter assumption, which influences the conclusion proposed, is valid for various classes of microorganisms in various types of waters.

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Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

BMC Genomics ◽

10.1186/s12864-020-07329-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Melanie Lindner ◽

Irene Verhagen ◽

Heidi M. Viitaniemi ◽

Veronika N. Laine ◽

Marcel E. Visser ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Environmental Conditions ◽

Brain Regions ◽

Temporal Changes ◽

Egg Laying ◽

Gene Body ◽

Cpg Site ◽

Repeated Sampling ◽

Over Time

Abstract Background DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled. Results We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body. Conclusion Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

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Soil acidity in 1970 and 1989 in a coniferous forest in southwest Finland

Canadian Journal of Soil Science ◽

10.4141/s96-099 ◽

1998 ◽

Vol 78 (3) ◽

pp. 477-479 ◽

Cited By ~ 1

Author(s):

C. J. Westman ◽

S. Jauhiainen

Keyword(s):

Key Words ◽

Soil Ph ◽

Soil Acidity ◽

Mineral Soil ◽

Coniferous Forest ◽

Soil Layers ◽

Water Suspension ◽

Ph Values ◽

Humus Layer ◽

Repeated Sampling

Forest soil pH in southwest Finland was measured with identical sampling and analysing methods in 1970 and 1989. The acidity of the organic humus layer increased significantly as pH values measured on water and on salt suspensions decreased between the two sampling dates. For the mineral soil layers, no unambiguous trend was found. pH values measured on salt suspension tended to be unchanged or lower, while pH on water suspension in some soil layers were even higher in 1989 than in 1970. Key words: pH, repeated sampling

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Pubertal Acceleration of Pulsatile Gonadotropin-Releasing Hormone Release in Male Rats as Revealed by Microdialysis

Endocrinology ◽

10.1210/en.2002-220767 ◽

2003 ◽

Vol 144 (1) ◽

pp. 163-171 ◽

Cited By ~ 54

Author(s):

Glenn C. Harris ◽

Jon E. Levine

Keyword(s):

Vas Deferens ◽

Pulse Generator ◽

Pulse Amplitude ◽

Pulse Frequency ◽

Male Rats ◽

Male Rat ◽

Pubertal Maturation ◽

Repeated Sampling ◽

Generator Activity ◽

Mature Spermatozoa

Abstract A microdialysis technique was used in male rats to directly assess the postulate that pubertal maturation is associated with accelerated GnRH pulsatility. Juvenile male rats, postnatal d 43 or 45 (n = 4) were stereotaxically fitted with guide cannulas directed toward the lateral median eminence, and repeated microdialysis experiments were conducted over 4–6 d. In each session, samples were collected continuously over 12 h (0900–2100 h) at 5-min intervals Results from individual peripubertal animals were pooled into two time bins for postnatal d 45–47 and 48–50, respectively, and GnRH characteristics were compared between the two epochs. The GnRH pulse frequency and mean GnRH concentration were significantly elevated at 48–50 d compared with 45–47 d. The GnRH pulsatility characteristics for 45–47 d vs. 48–50 d were as follows: pulse frequency, 0.74 ± 0.16 vs. 1.79 ± 0.19 pulses/h (P < 0.05); pulse amplitude, 254.1 ± 22.3 vs. 347.2 ± 15.8 Δpg/ml (difference in value from trough to peak); and mean release, 0.55 ± 0.03 vs. 2.04 ± 0.04 pg/5 min (P < 0.05). An additional two rats were dialyzed only once on postnatal d 50 to assess the effects of repeated sampling; the GnRH pulse characteristics in these animals were similar to those in rats sampled for a third or fourth time on postnatal d 48–50. To further assess the possible effects of repeated sampling on GnRH release profiles, a group of adult male rats (postnatal d 95–105; n = 3) was also dialyzed on four consecutive days. In these rats no significant alteration in GnRH pulse generator activity was observed over the four sessions. Moreover, the increase in GnRH pulse frequency observed in the peripubertal rats was found to be sustained in adult animals. To better understand the temporal relationship of GnRH pulse generator activity to reproductive maturation, groups of male rats were killed from postnatal d 45–56 along with an adult group at 95–105 d (n = 5/group) and examined for physiological signs of reproductive development. Gradual increases in serum levels of LH and testosterone and decreases in FSH and inhibin B were seen from postnatal d 45–56 to adulthood. Mature spermatozoa were found in the vas deferens by postnatal d 53. Our results demonstrate that in the late juvenile stage of male rat development, GnRH pulse generator activity is gradually accelerated over the course of consecutive days. This acceleration occurs over a period during which serum LH and testosterone are rising to adult levels, and it precedes the presence of mature spermatozoa in the vas deferens by 3 d. Our observations provide direct support for the hypothesis that an acceleration of GnRH pulsatility is the critical neural stimulus for the initiation of pubertal maturation in males. The peripheral and central cues that prompt the pubertal activation of the GnRH pulse generator remain to be characterized.

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The economic costs of extreme weather events: a hydrometeorological CGE analysis for Malawi

Environment and Development Economics ◽

10.1017/s1355770x10000471 ◽

2011 ◽

Vol 16 (2) ◽

pp. 177-198 ◽

Cited By ~ 56

Author(s):

KARL PAUW ◽

JAMES THURLOW ◽

MURTHY BACHU ◽

DIRK ERNST VAN SEVENTER

Keyword(s):

Computable General Equilibrium ◽

Computable General Equilibrium Model ◽

Extreme Weather ◽

Mitigation Strategies ◽

Extreme Weather Events ◽

Economic Losses ◽

Historical Events ◽

Weather Events ◽

Repeated Sampling ◽

Droughts And Floods

ABSTRACTExtreme weather events such as droughts and floods have potentially damaging implications for developing countries. Previous studies have estimated economic losses during hypothetical or single historical events, and have relied on historical production data rather than explicitly modeling climate. However, effective mitigation strategies require knowledge of the full distribution of weather events and their isolated effects on economic outcomes. We combine stochastic hydrometeorological crop-loss models with a regionalized computable general equilibrium model to estimate losses for the full distribution of possible weather events in Malawi. Results indicate that, based on repeated sampling from historical events, at least 1.7 per cent of Malawi's gross domestic product (GDP) is lost each year due to the combined effects of droughts and floods. Smaller-scale farmers in the southern region of the country are worst affected. However, poverty among urban and nonfarm households also increases due to national food shortages and higher domestic prices.

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