RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

<p>Abstract</p> <p>Background</p> <p>In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure.</p> <p>Results</p> <p>We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE) predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of vertices in a graph. The shortest path in this graph is the basis for structural predictions for the molecule. We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. We show that this approach allows us to more deeply explore the suboptimal structure space.</p> <p>Conclusion</p> <p>The algorithm was tested on three datasets which include several ncRNA families taken from the Rfam database. These datasets allowed for comparison of the algorithm with other methods. In these tests, RNAspa performed better than four other programs.</p

A sensitive soil biological indicator to changes in land-use in regions with Mediterranean climate

The demand for reliable indicators to quantify soil health has increased recently. We propose and test the use of soil microbial functional diversity as an indicator of multifunctional performance in agriculturally important areas. Agricultural fields in the Mediterranean and semiarid regions of Israel were selected as test sites and measured in Spring and Autumn seasons. Measurements included microbial parameters, basic soil abiotic properties and biological responses to agricultural management relative to measures of a natural ecosystem. Using a canonical correlation analysis we found that soil moisture was the most important basic soil property with different responses in Spring and Autumn. In Spring, it had a strongly negative relation with microbial biomass (MB), community level physiological profiling (CLPP) and the Shannon-Weaver index H', while in Autumn it had a strong relation with CLPP. We further show a significant interaction between CLPP and climate for land-use type "orchards". CLPP measured in the autumn season was thus identified as a useful and rapid biological soil health indicator, recommended for application in semiarid and Mediterranean agricultural regions. Apart from obtaining a better understanding of CLPP as the soil indicator, the study concludes that CLPP is well suited to differentiate between soils in different climates, seasons and land use types. The study shows a promising direction for further research on characterizing soil health under a larger variety of conditions.</p

Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes

<p>Abstract</p> <p>Background</p> <p>Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms.</p> <p>Results</p> <p>We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally.</p> <p>Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (<it>T. brucei</it>, <it>T. cruzi </it>and <it>L. major</it>) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation.</p> <p>Conclusion</p> <p>The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from <it>T. brucei </it>and <it>L. Major</it>. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function.</p> <p>This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.</p

A long noncoding RNA promotes parasite differentiation in African trypanosomes

Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC)The parasite Trypanosoma brucei causes African sleeping sickness that is fatal to patients if untreated. Parasite differentiation from a replicative slender form into a quiescent stumpy form promotes host survival and parasite transmission. Long noncoding RNAs (lncRNAs) are known to regulate cell differentiation in other eukaryotes. To determine whether lncRNAs are also involved in parasite differentiation, we used RNA sequencing to survey the T. brucei genome, identifying 1428 previously uncharacterized lncRNA genes. We find that grumpy lncRNA is a key regulator that promotes parasite differentiation into the quiescent stumpy form. This function is promoted by a small nucleolar RNA encoded within the grumpy lncRNA. snoGRUMPY binds to messenger RNAs of at least two stumpy regulatory genes, promoting their expression. grumpy overexpression reduces parasitemia in infected mice. Our analyses suggest that T. brucei lncRNAs modulate parasite-host interactions and provide a mechanism by which grumpy regulates cell differentiation in trypanosomes.This work was supported in part by Fundação para a Ciência e Tecnologia (FCT) grant, awarded to F.G. and entitled “Long noncoding RNAs as new diagnostic biomarkers for African Sleeping sickness” (PTDC/DTPEPI/7099/2014, start date: 1 January 2016, end date: 31 December 2018); also by Howard Hughes Medical Institute International Early Career Scientist Program (project title: “How parasites use epigenetics to evade host defenses,” project no. 55007419, start date: 1 February 2012, end date: 31 January 2017); and by the European Research Council (project title: “Exploring the hidden life of African trypanosomes: parasite fat tropism and implications for the disease,” project no. 771714, start date: 1 August 2018, end date: 31 January 2024), both awarded to L.M.F. The project leading to these results have received funding from “la Caixa” Foundation under the agreement LCF/PR/HR20/52400019 [project title: “Mechanism and function of epitranscriptomic poly(A) tail modifications in African trypanosomes,” project no. HR20-00361, start date: 1 March 2021, end date: 29 February 2024]. L.M.F. is supported by FCT (IF/01050/2014, project title: “Molecular basis for the efficient biology of trypanossome parasitism,” start date: 1 January 2015, end date: 31 December 2019) and by CEEC institutional program (CEECINST/00110/2018, start date: 1 January 2020, end date: 14 December 2020). C.N. acknowledges the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya. S. Michaeli acknowledges the support of the Israel Science Foundation (ref. 1959/20) from October 2020 to October 2025, entitled “Functional analysis of rRNA processing and the role of rRNA modification for specialized translation in the two life stages of trypanosomes” and U.S. Binational Science Foundation (ref. 2015/219) from October 2015 to October 2019, entitled “The role and mechanism of RNA pseudo-uridylation and sugar methylation (Nm) during the developmental cycle of trypanosomes.” The work done in A.D.’s laboratory was supported by National Science Center SONATA BIS grant, entitled “Non-canonical RNA tailing and other post-transcriptional regulatory mechanisms in T cell-mediated adaptive immunity” (proposal ID: 492777, agreement no: UMO-2020/38/E/NZ2/00372, start date: 22 March 2021, end date: 21 March 2026); National Science Center OPUS grant, entitled “Analysis of the role of cytoplasmic polyadenylation in the regulation of the innate immune response” (proposal ID: 443521, agreement no.: UMO-2019/33/B/NZ2/01773, start date: 2 March 2020, end date: 1 March 2023); and European Union’s Horizon 2020 (H2020-WIDESPREAD-03-2017)–ERAChair, entitled “MOlecular Signaling in Health and Disease - Interdisciplinary Centre of Excellence” (acronym: MOSaIC, agreement no.: 810425, implementation period: start date: 1 November 2018, end date: 31 October 2023).info:eu-repo/semantics/publishedVersio

RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

The discovery of a plethora of small non-coding RNAs (ncRNAs) has fundamentally changed our understanding of how genes are regulated. In this study, we employed the power of deep sequencing of RNA (RNA-seq) to examine the repertoire of ncRNAs present in small ribonucleoprotein particles (RNPs) of Trypanosoma brucei, an important protozoan parasite. We identified new C/D and H/ACA small nucleolar RNAs (snoRNAs), as well as tens of putative novel non-coding RNAs; several of these are processed from trans-spliced and polyadenylated transcripts. The RNA-seq analysis provided information on the relative abundance of the RNAs, and their 5′- and 3′-termini. The study demonstrated that three highly abundant snoRNAs are involved in rRNA processing and highlight the unique trypanosome-specific repertoire of these RNAs. Novel RNAs were studied using in situ hybridization, association in RNP complexes, and ‘RNA walk’ to detect interaction with their target RNAs. Finally, we showed that the abundance of certain ncRNAs varies between the two stages of the parasite, suggesting that ncRNAs may contribute to gene regulation during the complex parasite’s life cycle. This is the first study to provide a whole-genome analysis of the large repertoire of small RNPs in trypanosomes

SIRT6 Promotes Hepatic Beta-Oxidation via Activation of PPARα

The pro-longevity enzyme SIRT6 regulates various metabolic pathways. Gene expression analyses in SIRT6 heterozygotic mice identify significant decreases in PPARα signaling, known to regulate multiple metabolic pathways. SIRT6 binds PPARα and its response element within promoter regions and activates gene transcription. Sirt6+/− results in significantly reduced PPARα-induced β-oxidation and its metabolites and reduced alanine and lactate levels, while inducing pyruvate oxidation. Reciprocally, starved SIRT6 transgenic mice show increased pyruvate, acetylcarnitine, and glycerol levels and significantly induce β-oxidation genes in a PPARα-dependent manner. Furthermore, SIRT6 mediates PPARα inhibition of SREBP-dependent cholesterol and triglyceride synthesis. Mechanistically, SIRT6 binds PPARα coactivator NCOA2 and decreases liver NCOA2 K780 acetylation, which stimulates its activation of PPARα in a SIRT6-dependent manner. These coordinated SIRT6 activities lead to regulation of whole-body respiratory exchange ratio and liver fat content, revealing the interactions whereby SIRT6 synchronizes various metabolic pathways, and suggest a mechanism by which SIRT6 maintains healthy liver

A comparative genome-wide study of ncRNAs in trypanosomatids

<p>Abstract</p> <p>Background</p> <p>Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen to search for novel small ncRNAs in the genome of <it>Trypanosoma brucei </it>using techniques of comparative genomics.</p> <p>Results</p> <p>In this study, we identified by comparative genomics, and validated by experimental analysis several novel ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our procedure was capable of finding almost half of the known repertoire through homology over six genomes, and about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts, were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental validation. Eighteen of the 50 (36%) were shown to be expressed, and for 11 of them a distinct expression product was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates were shown to be novel H/ACA and C/D snoRNAs; these included three sequences that appear as singletons in the genome, unlike previously identified snoRNA molecules that are found in clusters. The other candidates appear to be novel ncRNA molecules, and their function is, as yet, unknown.</p> <p>Conclusions</p> <p>Using comparative genomic techniques, we predicted 72 sequences as ncRNA candidates in <it>T. brucei</it>. The expression of 50 candidates was tested in laboratory experiments. This resulted in the discovery of 11 novel short ncRNAs in procyclic stage <it>T. brucei</it>, which have homologues in the other trypansomatids. A few of these molecules are snoRNAs, but most of them are novel ncRNA molecules. Based on this study, our analysis suggests that the total number of ncRNAs in trypanosomatids is in the range of several hundred.</p

Demystifying Circalunar and Diel Rhythmicity in Acropora digitifera under Constant Dim Light

Life on earth has evolved under constant environmental changes; in response to these changes, most organisms have developed an endogenous clock that allows them to anticipate daily and seasonal changes and adapt their biology accordingly. Light cycles synchronize biological rhythms and are controlled by an endogenous clock that is entrained by environmental cues. Light is known to play a key role in the biology of symbiotic corals as they exhibit many biological processes entrained by daily light patterns. In this study, we aimed at determining the effect of constant dim light on coral's perception of diel and monthly cycles. Our results show that under constant dim light corals display a loss of rhythmic processes and constant stimuli by light, which initiates signal transduction that results in an abnormal cell cycle, cell proliferation, and protein synthesis. The results emphasize how constant dim light can mask the biological clock of Acropora digitifera

Effect of Soil Aggregate Size on Vineyard Bacterial Communities under Organic and Conventional Agro-Managements

Soil microorganisms are an indispensable component of natural ecosystems and play an important role in agro-management ecosystems. However, the function of soil microbial communities is still a black box. The present study aimed to investigate the effect of organic and conventional agro-management practices in a vineyard on the soil’s bacterial community and its composition in three different soil aggregate sizes using functional profiles derived using 16S rDNA metagenomics analysis for elucidating the metabolic capabilities of soil microbial communities. Soil samples were compared in terms of community composition and functionality. A clear distinction was found between the two managements. The soil samples contained 12 phyla and 45 orders, where Proteobacteria was the most common phylum in all treatments. Twenty-three functional profiles were obtained for both treatments and three aggregate sizes, showing similarity in their function, suggesting that functionality is due to the community’s composition and environmental conditions. The results indicate that organic farming systems have a beneficial effect on microbial diversity and encourage ecosystem multifunctionality

Structure and Function of the Soil Rhizosphere Fungal Communities in Medicinal Plants—A Preliminary Study

Plants regulate their rhizosphere microbiome, which partly comprises the fungal community. We conducted a study in order to determine the effect that five medicinal plant species (Origanum syriacum, Salvia fruticosa, Teucrium capitatum, Myrtus communis and Pistacia lentiscus) have on the fungal community in their rhizosphere. We measured abiotic parameters and used sequencing to determine the structure of the rhizosphere fungal community, both taxonomically, as phyla and genera, and functionally, as trophic modes. Our data shows that the rhizosphere fungal communities were significantly different, both taxonomically and functionally. The rhizosphere of M. communis had a significant relative abundance of saprotrophs and a lower relative abundance of symbiotrophs than the control soil and the rhizosphere of T. capitatum. The relative abundance of the genus Aureobasidium was significantly higher in the rhizosphere of P. lentiscus than in the control and for all other rhizospheres, but that of S. fruiticosa. The relative abundance of genus Alternaria was lower in the rhizospheres of S. fruticosa and M. communis than in the control soil. Our results highlight the potential use of these plants in agroforestry, as a means to influence the soil fungi population