Peculiarities of piRNA-mediated post-transcriptional silencing of Stellate repeats in testes of Drosophila melanogaster

Silencing of Stellate genes in Drosophila melanogaster testes is caused by antisense piRNAs produced as a result of transcription of homologous Suppressor of Stellate (Su(Ste)) repeats. Mechanism of piRNA-dependent Stellate repression remains poorly understood. Here, we show that deletion of Su(Ste) suppressors causes accumulation of spliced, but not nonspliced Stellate transcripts both in the nucleus and cytoplasm, revealing post-transcriptional degradation of Stellate RNA as the predominant mechanism of silencing. We found a significant amount of Su(Ste) piRNAs and piRNA-interacting protein Aubergine (Aub) in the nuclear fraction. Immunostaining of isolated nuclei revealed co-localization of a portion of cellular Aub with the nuclear lamina. We suggest that the piRNA–Aub complex is potentially able to perform Stellate silencing in the cell nucleus. Also, we revealed that the level of the Stellate protein in Su(Ste)-deficient testes is increased much more dramatically than the Stellate mRNA level. Similarly, Su(Ste) repeats deletion exerts an insignificant effect on mRNA abundance of the Ste-lacZ reporter, but causes a drastic increase of β-gal activity. In cell culture, exogenous Su(Ste) dsRNA dramatically decreases β-gal activity of hsp70-Ste-lacZ construct, but not its mRNA level. We suggest that piRNAs, similarly to siRNAs, degrade only unmasked transcripts, which are accessible for translation

Modern temporal network theory: A colloquium

The power of any kind of network approach lies in the ability to simplify a complex system so that one can better understand its function as a whole. Sometimes it is beneficial, however, to include more information than in a simple graph of only nodes and links. Adding information about times of interactions can make predictions and mechanistic understanding more accurate. The drawback, however, is that there are not so many methods available, partly because temporal networks is a relatively young field, partly because it more difficult to develop such methods compared to for static networks. In this colloquium, we review the methods to analyze and model temporal networks and processes taking place on them, focusing mainly on the last three years. This includes the spreading of infectious disease, opinions, rumors, in social networks; information packets in computer networks; various types of signaling in biology, and more. We also discuss future directions.Comment: Final accepted versio

In search for an ideal marker of endometrial receptivity: from histology to comprehensive molecular genetics-based approaches

Background: Despite significant improvements in the efficiency of assisted reproductive technologies (ART) for the past 10 years, proportion of unsuccessful cycles still remains significant and can reach up to 40%. Impairment of embryonic implantation is considered as one of the possible causes for low ART efficiency. Implantation failure may be a consequence of a shift in the “window of implantation”, i.e. the period of a cycle when endometrium is most receptive and ready for embryo implantation. Several methods have been developed to evaluate endometrial receptivity, but their accuracy and efficiency are quite different.Aim: Review and efficiency evaluation of the methods used for endometrial receptivity assessment and the window of implantation determination.Methods: We performed a comprehensive literature search (September 2018) with the key words “endometrial receptivity”, “endometrial receptivity evaluation”, “implantation window”, “window of implantation”, “pinopodes” from PubMed and E-library (Russian) databases. One hundred and thirty four (134) publications were selected for the analysis, including 101 original papers and 33 literature reviews.Results: The methods of conventional histology, scanning electronic microscopy, immunohistochemistry, as well as techniques based on the measurement of prostaglandin levels in endometrial fluid and mRNA profiling in an endometrium biopsy sample to assess endometrial receptivity are reviewed. The issue of a search for an ideal endometrial receptivity marker is discussed.Conclusion: At present, the most efficient and accurate methods to diagnose the window of implantation are those based on the mRNA profile assessment of an endometrial tissue sample. Аnalysis of mRNAs allows not only the accurate diagnosis of endometrial receptivity at the time of biopsy to be determined, but also the window of implantation shift to earlier or later periods to be reliably predicted

Water dynamics and salt-activation of enzymes in organic media: Mechanistic implications revealed by NMR spectroscopy

Deuterium spin relaxation was used to examine the motion of enzyme-bound water on subtilisin Carlsberg colyophilized with inorganic salts for activation in different organic solvents. Spectral editing was used to ensure that the relaxation times were associated with relatively mobile deuterons, which were contributed almost entirely by D(2)O rather than hydrogen–deuteron exchange on the protein. The results indicate that the timescale of motion for residual water molecules on the biocatalyst, (τ(c))(D(2)O), in hexane decreased from 65 ns (salt-free) to 0.58 ns (98% CsF) as (k(cat)/K(M))(app) of the biocatalyst preparation increased from 0.092 s(−1)·M(−1) (salt-free) to 1,140 s(−1)·M(−1) (98% CsF). A similar effect was apparent in acetone; the timescale decreased from 24 ns (salt-free) to 2.87 ns (98% KF), with a corresponding increase in (k(cat)/K(M))(app) of 0.140 s(−1)·M(−1) (salt-free) to 12.8 s(−1)·M(−1) (98% KF). Although a global correlation between water mobility and enzyme activity was not evident, linear correlations between ln[(k(cat)/K(M))(app)] and (τ(c))(D(2)O) were obtained for salt-activated enzyme preparations in both hexane and acetone. Furthermore, a direct correlation was evident between (k(cat)/K(M))(app) and the total amount of mobile water per mass of enzyme. These results suggest that increases in enzyme-bound water mobility mediated by the presence of salt act as a molecular lubricant and enhance enzyme flexibility in a manner functionally similar to temperature. Greater flexibility may permit a larger degree of local transition-state mobility, reflected by a more positive entropy of activation, for the salt-activated enzyme compared with the salt-free enzyme. This increased mobility may contribute to the dramatic increases in biocatalyst activity