Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.     

八段锦和五行音乐疗法在缓解新型冠状病毒肺炎患者负性情绪中的疗效分析

摘要 目的：观察八段锦和五行音乐疗法对新型冠状病毒肺炎（COVID-19）患者负性情绪的疗效。方法：收集孝感市第一人民医院就诊的COVID-19患者40例，采用随机数字表法将40例患者随机分为对照组（n=20）和观察组（n=20），观察组接受八段锦和子午流注理论指导下的择时五行音乐疗法进行干预，对照组保持日常生活方式。两组在干预前、干预2周采用焦虑自评量表（SAS）和抑郁自评量表(SDS)分别评定两组实验对象在实验前和干预后的负性情绪的改变，用患者生活质量量表(QLQ-C30)分别对两组患者进行生活质量的测评。结果：接受八段锦和子午流注理论指导下的择时五行音乐疗法的患者负性情绪明显减低，SAS、SDS评分明显较前明显改善，观察组患者SAS评分、SDS评分较对照组降低程度明显，差异存在统计学差异（P＜0.05）；干预后观察组、对照组的角色功能、认知功能、情感功能、躯体功能及生活质量评分均明显改善，接受八段锦和子午流注理论指导下的择时五行音乐疗法的患者在角色功能、认知功能、情感功能、躯体功能及生活质量评分方面均优于对照组，差异存在统计学差异（P＜0.05）。结论：COVID-19患者通过八段锦和五行音乐疗法能够明显减低负性情绪，此种疗法可有效起到"精神内守，病安从来"的安慰作用。     

Morphine-element interactions – The influence of selected chemical elements on neural pathways associated with addiction

Addiction is a pressing social problem worldwide and opioid dependence can be considered the strongest and most difficult addiction to treat. Mesolimbic and mesocortical dopaminergic pathways play an important role in modulation of cognitive processes and decision making and, therefore, changes in dopamine metabolism are considered the central basis for the development of dependence. Disturbances caused by excesses or deficiency of certain elements have a significant impact on the functioning of the central nervous system (CNS) both in physiological conditions and in pathology and can affect the cerebral reward system and therefore, may modulate processes associated with the development of addiction. In this paper we review the mechanisms of interactions between morphine and zinc, manganese, chromium, cadmium, lead, fluoride, their impact on neural pathways associated with addiction, and on antinociception and morphine tolerance and dependence.     

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.     

Progress since the first international symposium: ‘Genetic aspects of plant mineral nutrition’, Beograd, 1982, and perspectives of future research

Summary The paper discusses the problems of genetic aspects of plant mineral nutrition in the light of the results presented at the First and Second Symposia on ‘Genetic Aspects of Plant Mineral Nutrition’ organized in Beograd in 1982 and Madison in 1985, respectively. On the basis of the results, future directions of research are discussed. The papers deal with the concentration and content of mineral nutrients in different genotypes, physiological and biochemical aspects of the genetic specificity of plant mineral nutrition, relations between plant genotypes and nitrogen fixing micro-organism strains, as well as with some related problems which have been investigated to a lesser extent. Particular attention is paid to papers and problems referring to genetic and breeding research work linked with genetic aspects of plant mineral nutrition as well as the possibilities of developing new cultivars requiring certain soil and mineral nutrition conditions for their cultivation.     

Comparative genomics of trace element dependence in biology

Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.     

Effects of Acute Swimming Exercise on Some Elements in Rats

The objective of the present study is to explore the effects of acute swimming exercise on plasma levels of some elements in rats, immediately after the exercise, and 24 and 48 h later. The study included 40 adult male rats of Spraque Dawley species, which were equally allocated to four groups. Group 1: General Control Group; Group 2: Swimming Group, the group that was decapitated immediately after 30-min acute swimming exercise; Group 3: Swimming Group, the group that was decapitated 24 h after 30-min acute swimming exercise; Group 4: Swimming Group, the group that was decapitated 48 h after 30-min acute swimming exercise. Plasma copper (Cu), iron (Fe), magnesium (Mg), phosphorus (P), selenium (Se), zinc (Zn) levels were determined according to atomic emission method in the blood samples collected from the animals by decapitation method. Measurements conducted immediately after acute swimming exercise (group 2) showed a significant decrease in Se and Zn levels (p < 0,01) and a significant increase in P levels (p < 0,01), when compared to group 1. Measurements carried out 24 h after the exercise (group 3) demonstrated a significant increase in all parameters except for Mg, in comparison to groups 1 and 2 (p < 0,01). It was seen in the measurements made 48 h after the exercise (group 4) that all parameters were restored to control values. The results of our study show that acute swimming exercise significantly changes plasma Cu, Fe, P, Se, and Zn levels.     

Heavy metals and trace elements in scalp hair samples of children with severe autism spectrum disorder: A case-control study on Jordanian children

BackgroundElemental analysis has been increasingly used for biomonitoring heavy metals and trace elements.MethodsThis study monitored the levels of two heavy metals (Al and Pb), and seven trace elements (Macroelements Mg, K, P and Ca; Microelements Zn, Cu, Fe) in scalp hair of 57 children with severe autism spectrum disorder (ASD) and 50 age-matched controls, using Inductively Coupled Plasma Atomic Emission Spectrophotometry (ICP-AES).ResultsCompared to controls, significantly higher levels of Al (p = 0.001), Pb (p = 0.001) and K (p = 0.021), with lower levels of Mg and Zn (p = 0.038) were observed for the ASD group. ASD boys had higher levels of Al (p = 0.001), Pb (p = 0.001) and K (p = 0.017) than control boys, while ASD girls had higher Pb levels (p = 0.005) than control girls. The ASD subgroup exposed to passive smokers had higher levels of Al (p = 0.033) and Pb (p = 0.001, and the ASD subgroup not exposed to passive smoke had higher levels of Al (p = 0.011), Pb (p = 0.001), K (p = 0.003); and lower levels of Mg (p = 0.011) than their controls. Other confounding factors and the correlation between these elements were also investigated.ConclusionThis data suggests that exposure to Al and Pb, increase intake of K, and decreased intake of magnesium and zinc, may contribute to ASD etiology.     

Ubiquitous Chromatin Opening Elements (UCOEs) effect on transgene position and expression stability in CHO cells following methotrexate (MTX) amplification

The requirement for complex therapeutic proteins has resulted in mammalian cells, especially CHO cells, being the dominant host for recombinant protein manufacturing. In creating recombinant CHO cell lines, the expression vectors integrate into various parts of the genome leading to variable levels of expression and stability of protein production. This makes mammalian cell line development a long and laborious process. Therefore, with the intention to accelerate process development of recombinant protein production in CHO systems, UCOEs are utilized to diminish instability of production by maintaining an open chromatin surrounding in combination with MTX amplification. Chromosome painting and FISH analysis were performed to provide detailed molecular evaluation on the location of amplified genes and its relationship to the productivity and stability of the amplified cell lines. In summary, cell lines generated with vectors containing UCOEs retained stable GFP expression with MTX present (but instability was observed in the absence of MTX). UCOE cell lines displayed a higher frequency of integration into >1 chromosome than non‐UCOE group. Cell populations were more homogenous in terms of transgene location at the end of Long‐term culture (LTC). Overall our findings suggest variation in eGFP fluorescence may be attributed to changes in transgene integration profile over LTC.