Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora

Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.

epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing

Several reduced‐representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user‐friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost‐ and time‐efficient and the computational workflow is designed in a user‐friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with freebayes (epifreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo‐knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).

The Effectiveness of Acupressure Therapy and Aromatherapy of Lemon on the Ability of Coping and Emesis Gravidarum in Trimester I Pregnant Women at Langsa City Community Health Centre, Aceh, Indonesia

BACKGROUND: Acupressure therapy and aromatherapy lemon are now increasingly popular in the treatment of various diseases in Indonesia. One treatment alternative to deal with nausea, vomiting during pregnancy is to use aqua-pressure and aromatherapy techniques. AIM: Analyzing the effects of acupressure therapy and the aroma of lemon therapy on the ability to cope and emesis gravidarum in trimester I pregnant women at the city health center Langsa, Aceh province. METHODS: The design of this study is a quasi-experiment. The design used was a non-randomized pretest-posttest control group design. This research was conducted in the West Langsa health center from January to March 2019. The population was all the first-trimester pregnant women with complaints of nausea and vomiting. The sample was chosen about 60 people using a purposive sampling technique. Respondents were divided into three groups. The first group was acupressure, the second group was acupressure + lemon aromatherapy and the third group was control. Data analysis using univariate analysis, and bivariable analysis using paired t-test, dependent t-test and one-way ANOVA, multi-variable analysis using a multi-covariance test, and ANOVA RESULTS: Research results show that acupressure and acupressure + lemon therapy are effective in reducing nausea experienced by pregnant women. Lemon acupressure + aromatherapy therapy significantly reduced nausea in pregnant women with a p = 0.0001 (p <0.05). The results of paired t-test nausea and vomiting in the acupressure and acupressure + lemon aromatherapy groups decreased the amount of nausea with a decrease of 4.2 and 4.85, respectively. The duration of nausea and vomiting also decreased by 1.55 and 4.3 with a p = 0.0001 (p <0.05). ANOVA test results in the treatment group on coping ability showed that the acupressure + lemon aromatherapy group increased the coping ability of pregnant women by 5.7 compared to the control group. The results of paired t-test coping abilities in pregnant women with acupressure therapy were 3.2 and lemon acupressure + aromatherapy treatments were 6.2. The increase in both treatments was significant with a p = 0.0001, respectively. CONCLUSION: There is an effect of grapefruit aromatherapy on the intensity of nausea and vomiting in pregnant women in the working area of Langsa City Health Center with p < 0.05 (0.0001).

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data

Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.

Multiple isoforms of protein kinase C in lymphocytes and airway smooth muscle of guinea pig

The isoenzyme pattern of protein kinase C (PKC) in lymphocytes and airway smooth muscles (ASM) was examined by Western blot using commercially available monoclonal antibodies. The results showed the presence of PKC alpha, beta, gamma, epsilon, eta, mu and zeta in lymphocytes and PKC alpha, gamma, epsilon, eta and zeta in ASM. The unexpected feature was the presence of PKCgamma in both lymphocytes and ASM of guinea pigs. Expression of this PKC isoform is usually restricted to tissues in the central nervous system or spinal cord. Expression of PKC delta, theta, lambda and tau was not detected in either lymphocytes or ASM.