Regulating the Many to Benefit the Few: Role of Weak Small RNA Targets

AbstractSmall regulatory RNAs are central players in the regulation of many cellular processes across all kingdoms of life. Experiments in mouse and human have shown that a typical small RNA may regulate the expression of many different genes, suggesting that small RNAs act as global regulators. It is noted though that most targets respond only weakly to the presence of the small RNA. At the same time, evidence in bacteria and animals suggest that the phenotypes associated with small RNA mutants are only due to a few of their targets. Here we assume that targets regulated by a small RNA to control function is in fact small, and propose that the role of the many other weak targets is to confer robustness to the regulation of these few principal targets. Through mathematical modeling we show that auxiliary targets may significantly buffer both number and kinetic fluctuations of the principal targets, with only minor slowdown in the kinetics of response. Analysis of genomic data suggests that auxiliary targets experience a nonspecific evolutionary pressure, playing a role at the system level. Our work is of importance for studies on small RNA functions, and impacts on the understanding of small RNA evolution

Strontium isotope compositions of river waters as records of lithology-dependent mass transfers : the Garonne river and its tributaries (SW France)

The relation of lithology in the drainage basin to the dissolved load of the Garonne river and its main tributaries, in southwestern France, was evaluated by determining 87Sr/86Sr ratios, and concentrations of major and trace elements during a 2-year-long survey. In the upper drainage basin, the Garonne river waters were isotopically varied at two observation points: 0.71131+/−0.00030 (2σ) for 84+/−18 ppb (2σ) and 0.71272+/−0.00044 for 86+/−10 ppb, respectively. In the lower drainage basin, the Garonne river waters were isotopically identical at three observation points at 0.71020+/−0.00024 for 125+/−22 ppb. By contrast, the tributaries (Lot, Truyère, Aveyron, Arriège, Gers and Salat) are widely varied in their 87Sr/86Sr ratios and Sr concentrations from 0.70836+/−0.00049 to 0.71058+/−0.00057, and from 18+/−8 to 280+/−116 ppb. The Sr isotope ratios and concentrations suggest a dominant supply of two reservoirs of Sr, one of which is with low 87Sr/86Sr ratios and high Sr contents that is typically characteristic of carbonate rocks, and the other with high 87Sr/86Sr ratios and low Sr concentrations that is characteristic of felsic rocks. Locally as in the Lot waters draining the Massif Central and within the Pyrénées mountains, a third source of Sr from mafic rocks may be involved. Mass-balance calculations based on the mean 87Sr/86Sr ratios and contents of the dissolved Sr, and on the mean discharges integrating the 2-year survey, suggest that contribution of the silicate reservoir amounts 3–8% of the total dissolved Sr flux. Mass-balance calculations also suggest that variation in the supply of Sr from either of the two major reservoirs does not exceed the analytical uncertainty at about +/−5%. The 87Sr/86Sr ratios of HCl and NH4Cl leachates of suspended loads of the Garonne river are different from that of the associated dissolved Sr. This leaching-related supplementary Sr represents less than 10% of the total amount of Sr transported by the Garonne waters. The Sr isotope characteristics of the leachates are probably records of an intermediate pedogenic episode in the weathering-erosion process occurring in the Garonne drainage basin

On the morphology of Anisakis pegreffii: a comparative analysis of three microscopic techniques used to build a new parasite atlas

BACKGROUND: Human anisakidosis is a parasitic anthropozoonosis caused by larval nematodes of the family Anisakidae. Here, we report a detailed description of the morphology of Anisakis pegreffii third-stage larva performed using a conventional light and confocal microscopy, and scanning electron microscopy (SEM) that provide a basis for both phenotypic studies and genetic mutations. METHODS: The collected larvae from fish were morphologically identified as Anisakis larvae Type I, and they were characterized by PCR-RFLP to identify the Anisakis pegreffii specie. Using NC5/NC2 primers, ribosomal genomic regions ITS1, 5.8 SrRNA and ITS2 of DNA were amplified and PCR products were sequenced. Fifteen larvae belonging to Anisakis pegreffii were fixed, sectioned, and examined with a light and confocal microscope and by SEM. RESULTS: In our studies, have been acquired detailed ultrastructural images, which have been integrated with those derived from the dissection of the parasite, obtained with light and confocal microscopy. The structural and ultrastructural images concerning the third stage larvae of Anisakis pegreffii have been studied, analyzed and compared among them. The derived overall view has allowed detecting new interesting details of a well-known parasite and has been schematically showed. CONCLUSIONS: The aim of this study is to furnish an updated atlas of Anisakis pegreffii. Confocal microscopy, as well as the light and electron microscopy have played a pivotal role in the accumulation of new scientific data regarding the anatomical structures of this nematode. This work is the result of one year of engagement by the Authors and the outcome is a comprehensive atlas on Anisakis pegreffii microscopy

Transcriptomic effects of the non-steroidal anti-inflammatory drug Ibuprofen in the marine bivalve Mytilus galloprovincialis Lam

The transcriptomic effects of Ibuprofen (IBU) in the digestive gland tissue of Mytilus galloprovincialis Lam. specimens exposed at low environmental concentrations (250 ng L-1) are presented. Using a 1.7 K feature cDNA microarray along with linear models and empirical Bayes statistical methods 225 differentially expressed genes were identified in mussels treated with IBU across a 15-day period. Transcriptional dynamics were typical of an adaptive response with a peak of gene expression change at day 7 (177 features, representing about 11% of sequences available for analysis) and an almost full recovery at the end of the exposure period. Functional genomics by means of Gene Ontology term analysis unraveled typical mussel stress responses i.e. aminoglycan (chitin) metabolic processes but also more specific effects such as the regulation of NF-kappa B transcription factor activity. (C) 2016 Elsevier Ltd. All rights reserved

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues

PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs

A large number of RNA binding proteins (RBPs) and miRNAs bind to the 3′ untranslated regions of mRNA, but methods to dissect their function and interactions are lacking. Here the authors introduce post-transcriptional regulatory element sequencing (PTRE-seq) to dissect sequence preferences, interactions and consequences of RBP and miRNA binding

Quercetin Induces Mitochondrial Biogenesis through Activation of HO-1 in HepG2 Cells

The regeneration of mitochondria by regulated biogenesis plays an important homeostatic role in cells and tissues and furthermore may provide an adaptive mechanism in certain diseases such as sepsis. The heme oxygenase (HO-1)/carbon monoxide (CO) system is an inducible cytoprotective mechanism in mammalian cells. Natural antioxidants can provide therapeutic benefit, in part, by inducing the HO-1/CO system. This study focused on the mechanism by which the natural antioxidant quercetin can induce mitochondrial biogenesis in HepG2 cells. We found that quercetin treatment induced expression of mitochondrial biogenesis activators (PGC-1α, NRF-1, TFAM), mitochondrial DNA (mtDNA), and proteins (COX IV) in HepG2 cells. The HO inhibitor SnPP and the CO scavenger hemoglobin reversed the effects of quercetin on mitochondrial biogenesis in HepG2 cells. The stimulatory effects of quercetin on mitochondrial biogenesis could be recapitulated in vivo in liver tissue and antagonized by SnPP. Finally, quercetin conferred an anti-inflammatory effect in the liver of mice treated with LPS and prevented impairment of mitochondrial biogenesis by LPS in vivo. These salutary effects of quercetin in vivo were also antagonized by SnPP. Thus, our results suggest that quercetin enhances mitochondrial biogenesis mainly via the HO-1/CO system in vitro and in vivo. The beneficial effects of quercetin may provide a therapeutic basis in inflammatory diseases and sepsis