scholarly journals Plugging Small RNAs into the Network

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Lars Barquist
Keyword(s):  
Small Rnas ◽  
Posttranscriptional Regulation ◽  
Network Inference ◽  
Functional Characterization ◽  
The State ◽  
Diverse Range ◽  
Regulatory Interactions ◽  
Link Type ◽  
Wide Range

ABSTRACT Small RNAs (sRNAs) have been discovered in every bacterium examined and have been shown to play important roles in the regulation of a diverse range of behaviors, from metabolism to infection. However, despite a wide range of available techniques for discovering and validating sRNA regulatory interactions, only a minority of these molecules have been well characterized. In part, this is due to the nature of posttranscriptional regulation: the activity of an sRNA depends on the state of the transcriptome as a whole, so characterization is best carried out under the conditions in which it is naturally active. In this issue of mSystems, Arrieta-Ortiz and colleagues (M. L. Arrieta-Ortiz, C. Hafemeister, B. Shuster, N. S. Baliga, et al., mSystems 5:e00057-20, 2020, https://doi.org/10.1128/mSystems.00057-20) present a network inference approach based on estimating sRNA activity across transcriptomic compendia. This shows promise not only for identifying new sRNA regulatory interactions but also for pinpointing the conditions in which these interactions occur, providing a new avenue toward functional characterization of sRNAs.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

scholarly journals Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms

2019 ◽  
Author(s):  
Daniel Morgan ◽  
Matthew Studham ◽  
Andreas Tjärnberg ◽  
Holger Weishaupt ◽  
Fredrik J. Swartling ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Network Inference ◽  
Gene Regulatory Network Inference ◽  
Validation Data ◽  
Regulatory Interactions ◽  
Link Type ◽  
Gene Regulatory ◽  
Novel Interactions

AbstractThe gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. Reliable inference of GRNs is however still a major challenge in systems biology.To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard. The best GRN was significantly more predictive than the null model, both in crossvalidated benchmarks and for an independent dataset of the same genes under a different perturbation design. It agrees with many known links, in addition to predicting a large number of novel interactions from which a subset was experimentally validated. The inferred GRN captures regulatory interactions central to cancer-relevant processes and thus provides mechanistic insights that are useful for future cancer research.Data available at GSE125958Inferred GRNs and inference statistics available at https://dcolin.shinyapps.io/CancerGRN/ Software available at https://bitbucket.org/sonnhammergrni/genespider/src/BFECV/Author SummaryCancer is the second most common cause of death globally, and although cancer treatments have improved in recent years, we need to understand how regulatory mechanisms are altered in cancer to combat the disease efficiently. By applying gene perturbations and inference of gene regulatory networks to 40 genes known or suspected to have a role in cancer due to interactions with the oncogene MYC, we deduce their underlying regulatory interactions. Using a recent computational framework for inference together with a novel method for cross validation, we infer a reliable regulatory model of this system in a completely data driven manner, not reliant on literature or priors. The novel interactions add to the understanding of the progressive oncogenic regulatory process and may provide new targets for therapy.

scholarly journals sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Alisa M. King ◽  
Carin K. Vanderpool ◽  
Patrick H. Degnan
Keyword(s):  
Experimental Data ◽  
Stress Responses ◽  
Small Rnas ◽  
Metabolic Regulation ◽  
Functional Characterization ◽  
Target Prediction ◽  
Structure Stability ◽  
Accurate Identification ◽  
Mrna Targets

Small RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability, or translation. Hundreds of sRNAs have been identified in bacteria, but characterization of their regulatory functions is limited by difficulty with sensitive and accurate identification of mRNA targets. Thus, new robust methods of bacterial sRNA target identification are in demand. Here, we describe our small RNA target prediction organizing tool (SPOT), which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. SPOT allows the user to rapidly produce a prioritized list of predicted sRNA-target mRNA interactions that serves as a basis for further experimental characterization. This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation.

scholarly journals Polarimetry for Photonic Integrated Circuits

2019 ◽  
Vol 9 (15) ◽  
pp. 2987
Author(s):  
Moritz Baier ◽  
Axel Schoenau ◽  
Francisco M. Soares ◽  
Martin Schell
Keyword(s):  
Integrated Circuits ◽  
Photonic Integrated Circuits ◽  
The State ◽  
Polarization Dependence ◽  
Complete Picture ◽  
Wide Range ◽  
State Of Polarization ◽  
Matrix Yielding ◽  
Polarization Of Light

Photonic integrated circuits (PICs) play a key role in a wide range of applications. Very often, the performance of PICs depends strongly on the state of polarization of light. Classically, this is regarded as undesirable, but more and more applications emerge that make explicit use of polarization dependence. In either case, the characterization of the polarization properties of a PIC can be a nontrivial task. We present a way of characterizing PICs in terms of their full Müller matrix, yielding a complete picture of their polarization properties. The approach is demonstrated by carrying out measurements of fabricated PICs.

scholarly journals Proteomics Strategy for Identifying Candidate Bioactive Proteins in Complex Mixtures: Application to the Platelet Releasate

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Roisin O'Connor ◽  
Lorna M. Cryan ◽  
Kieran Wynne ◽  
Andreas de Stefani ◽  
Desmond Fitzgerald ◽  
...  
Keyword(s):  
Ion Exchange ◽  
Functional Characterization ◽  
Biological Tissues ◽  
Biochemical Properties ◽  
Human Platelets ◽  
Intact Proteins ◽  
Large Numbers ◽  
Wide Range ◽  
Platelet Releasate

Proteomic approaches have proven powerful at identifying large numbers of proteins, but there are fewer reports of functional characterization of proteins in biological tissues. Here, we describe an experimental approach that fractionates proteins released from human platelets, linking bioassay activity to identity. We used consecutive orthogonal separation platforms to ensure sensitive detection: (a) ion-exchange of intact proteins, (b) SDS-PAGE separation of ion-exchange fractions and (c) HPLC separation of tryptic digests coupled to electrospray tandem mass spectrometry. Migration of THP-1 monocytes in response to complete or fractionated platelet releasate was assessed and located to just one of the forty-nine ion-exchange fractions. Over 300 proteins were identified in the releasate, with a wide range of annotated biophysical and biochemical properties, in particular platelet activation, adhesion, and wound healing. The presence of PEDF and involucrin, two proteins not previously reported in platelet releasate, was confirmed by western blotting. Proteins identified within the fraction with monocyte promigratory activity and not in other inactive fractions included vimentin, PEDF, and TIMP-1. We conclude that this analytical platform is effective for the characterization of complex bioactive samples.

scholarly journals Scientific approaches to the system of concepts of "national security": international legal aspect

2020 ◽  
Vol 7 (12) ◽  
pp. 70-77
Author(s):  
А. Альван
Keyword(s):  
National Security ◽  
Legal Aspect ◽  
The State ◽  
Constitutional Rights ◽  
External Threats ◽  
Wide Range ◽  
Single Well ◽  
Definition Of ◽  
The Individual

Scientific approaches to the concept of "national security" are systematized in the article. The author substantiates that there are four main approaches to the concept of "national security". The first group - works devoted to the terminological characterization of national security. Another group - the authors define national security because of the state of protection of vital interests, the individual, society and the state against all kinds of threats. The third group is studies that analyze the types of national security, in particular: economic, environmental, financial, personnel, financial, social, etc. These characteristics reflect their socio-political nature, trace the unity of personal, public and state security, developing political and other processes. The fourth group of studies are those that pay attention to problems related to the correct use of the concept of "national security" and the possibility of its replacement. Fifth group - analyzes the interaction and correlation of threats and security.There is no single, well-defined definition of national security today. No matter what approach the authors use, there are different approaches, and in some cases, complications or simplifications of this category.In our opinion, national security should be understood as a state of protection of the individual, society and state against a wide range of internal and external threats, which ensure the realization of citizens' constitutional rights and freedoms, decent quality and standard of living, sovereignty, independence, state and territorial integrity. , sustainable socio-economic development of the state.

scholarly journals Characterization of PPTNs, a Cyanobacterial Phosphopantetheinyl Transferase from Nodularia spumigena NSOR10

2007 ◽  
Vol 189 (8) ◽  
pp. 3133-3139 ◽  
Author(s):  
J. N. Copp ◽  
A. A. Roberts ◽  
M. A. Marahiel ◽  
B. A. Neilan
Keyword(s):  
Acyl Carrier Protein ◽  
Functional Characterization ◽  
Bioactive Metabolites ◽  
Sequence Motifs ◽  
Phosphopantetheinyl Transferase ◽  
Carrier Proteins ◽  
Nodularia Spumigena ◽  
Conserved Sequence ◽  
Wide Range

ABSTRACT The phosphopantetheinyl transferases (PPTs) are a superfamily of essential enzymes required for the synthesis of a wide range of compounds, including fatty acids, polyketides, and nonribosomal peptide metabolites. These enzymes activate carrier proteins in specific biosynthetic pathways by transfer of a phosphopantetheinyl moiety. The diverse PPT superfamily can be divided into two families based on specificity and conserved sequence motifs. The first family is typified by the Escherichia coli acyl carrier protein synthase (AcpS), which is involved in fatty acid synthesis. The prototype of the second family is the broad-substrate-range PPT Sfp, which is required for surfactin biosynthesis in Bacillus subtilis. Most cyanobacteria do not encode an AcpS-like PPT, and furthermore, some of their Sfp-like PPTs belong to a unique phylogenetic subgroup defined by the PPTs involved in heterocyst differentiation. Here, we describe the first functional characterization of a cyanobacterial PPT based on a structural analysis and subsequent functional analysis of the Nodularia spumigena NSOR10 PPT. Southern hybridizations suggested that this enzyme may be the only PPT encoded in the N. spumigena NSOR10 genome. Expression and enzyme characterization showed that this PPT was capable of modifying carrier proteins resulting from both heterocyst glycoplipid synthesis and nodularin toxin synthesis. Cyanobacteria are a unique and vast source of bioactive metabolites; therefore, an understanding of cyanobacterial PPTs is important in order to harness the biotechnological potential of cyanobacterial natural products.

scholarly journals Structural and functional characterization of TesB fromYersinia pestisreveals a unique octameric arrangement of hotdog domains

2015 ◽  
Vol 71 (4) ◽  
pp. 986-995 ◽  
Author(s):  
C. M. D. Swarbrick ◽  
M. A. Perugini ◽  
N. Cowieson ◽  
J. K. Forwood
Keyword(s):  
Analytical Ultracentrifugation ◽  
Quaternary Structure ◽  
Functional Characterization ◽  
Fatty Acyl ◽  
Size Exclusion ◽  
X Ray Scattering ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Enzyme Families

Acyl-CoA thioesterases catalyse the hydrolysis of the thioester bonds present within a wide range of acyl-CoA substrates, releasing free CoASH and the corresponding fatty-acyl conjugate. The TesB-type thioesterases are members of the TE4 thioesterase family, one of 25 thioesterase enzyme families characterized to date, and contain two fused hotdog domains in both prokaryote and eukaryote homologues. Only two structures have been elucidated within this enzyme family, and much of the current understanding of the TesB thioesterases has been based on theEscherichia colistructure.Yersinia pestis, a highly virulent bacterium, encodes only one TesB-type thioesterase in its genome; here, the structural and functional characterization of this enzyme are reported, revealing unique elements both within the protomer and quaternary arrangements of the hotdog domains which have not been reported previously in any thioesterase family. The quaternary structure, confirmed using a range of structural and biophysical techniques including crystallography, small-angle X-ray scattering, analytical ultracentrifugation and size-exclusion chromatography, exhibits a unique octameric arrangement of hotdog domains. Interestingly, the same biological unit appears to be present in both TesB structures solved to date, and is likely to be a conserved and distinguishing feature of TesB-type thioesterases. Analysis of theY. pestisTesB thioesterase activity revealed a strong preference for octanoyl-CoA and this is supported by structural analysis of the active site. Overall, the results provide novel insights into the structure of TesB thioesterases which are likely to be conserved and distinguishing features of the TE4 thioesterase family.

scholarly journals Identification and functional characterization of RNA silencing key-genes in the model pennate diatom species Phaeodactylum tricornutum

2019 ◽  
Author(s):  
Αιμιλία Γρυπιώτη
Keyword(s):  
In Silico ◽  
Small Rnas ◽  
Rna Silencing ◽  
Phaeodactylum Tricornutum ◽  
Functional Characterization ◽  
Diatom Species ◽  
Rna Dependent Rna Polymerase ◽  
Pennate Diatom ◽  
Key Genes

Ο μηχανισμός της RNA Σίγησης, γνωστός και ως μονοπάτι RNA παρεμβολής (RNA interference, RNAi), αποτελεί ένα συντηρημένο μηχανισμό ρύθμισης της γονιδιακής έκφρασης με τη διαμεσολάβηση μικρών RNA μορίων (sRNA), (Fire et al., 1998). Στα διάτομα, και στο διάτομο οργανισμό μοντέλο Phaeodactylum tricornutum, έχει παρατηρηθεί η σίγηση εξωγενών και ενδογενών γονιδίων μετά την εισαγωγή ανάστροφων επαναλήψεων, συμπληρωματικών μεταγράφων και τεχνητών miRNAs (De Riso et al., 2009; Kaur and Spillane, 2015). Στο P. tricornutum έχει προταθεί η παρουσία ενός ενδογενούς RNAi μονοπατιού μετά από μελέτες των sRNAs, της γονιδιακής έκφρασης και της μεθυλίωσης DNA του (Veluchamy et al., 2013; Rogato et al., 2014). Αυτό το RNAi μονοπάτι μπορεί να παίζει σημαντικό ρόλο στη ρύθμιση της έκφρασης γονιδίων που κωδικοποιούν πρωτεΐνες και μεταθετά στοιχεία (Transposable Elements,TEs) και πιθανώς να επηρεάζει την απόκριση προσαρμογής σε συνθήκες περιορισμένων θρεπτικών (Maumus et al., 2009). Ομόλογα των βασικών RNAi γονιδίων DICER (DCR), ARGONAUTE (AGO) και RNA-Dependent RNA polymerase (RDR) έχουν αναγνωριστεί με ανάλυση in silico (De Riso et al., 2009). Ωστόσο, η εξακρίβωση του γονιδιακού μοντέλου τους, ο χαρακτηρισμός της λειτουργίας τους και ο ρόλος τους σε επίπεδο φυσιολογίας παραμένουν άγνωστα. Στην παρούσα διατριβή, επιβεβαιώνεται η ύπαρξη ενός μοναδικού γονιδίου PtDCR, PtAGO και PtRDR στο P. tricornutum μετά από εκτεταμένη ανάλυση in silico των διαθέσιμων γονιδιωματικών και μεταγραφικών δεδομένων του. Η ανεύρεση και φυλογενετική ανάλυση των DCR, AGO και RDR ομόλογων γονιδίων στα διάτομα από όλες τις διαθέσιμες βάσεις δεδομένων παρουσιάζουν μια μη αναμενόμενη διαφοροποίηση του RNAi μονοπατιού σε αυτούς τους οργανισμούς. Το cDNA των PtDCR/AGO/RDR κλωνοποιήθηκε και αναγνωρίστηκαν μετάγραφα εναλλακτικού ματίσματος των PtDCR και PtAGO. Ο υποκυτταρικός εντοπισμός των PtDCR-/AGO-/RDR-YFP διερευνήθηκε με συνεστιακή μικροσκοπία. Για τον χαρακτηρισμό της λειτουργίας των PtDCR και PtAGO γονιδίων δοκιμάστηκε αρχικά η έκφρασή τους στα ετερόλογα συστήματα της ζύμης Saccharomyces cerevisiae και του φυτού Nicotiana bethamiana. Στη συνέχεια, με την εφαρμογή της CRISPR/Cas9-καθοδηγούμενης μεταλλαξιγένεσης, πρόσφατα προσαρμοσμένη στο P. tricornutum, δημιουργήθηκαν επιτυχώς οι μεταλλαγμένες σειρές με εκτοπισμό PtDCR-KO και PtAGO-KO (KnockOut). Η μελέτη του φαινοτύπου στην ανάπτυξη των PtDCR-KO σειρών έγινε σε καλλιέργειες υπό φυσιολογικές συνθήκες, υπό συνθήκες περιορισμένων νιτρικών και μετά από UV-επαγόμενο στρες. Παράλληλα, διεξήχθη αλληλούχιση νέας γενιάς (NGS) και ανάλυση των ολικών μεταγράφων mRNA και small RNAs. Τα πειράματα των καλλιεργειών υποδεικνύουν ότι η PtDCR ίσως παίζει ρόλο στην απόκριση υπό την έλλειψη νιτρικών. Η μεταγραφική ανάλυση αποκάλυψε ότι και τα sRNA και τα mRNA μετάγραφα επηρεάστηκαν στη DCR-KO σειρά. Συνολικά, η κατανομή του μεγέθους των sRNA μετατοπίστηκε προς μεγαλύτερου μεγέθους μόρια στην PtDCR-KO σειρά. Επίσης, ο αριθμός των sRNA που εντοπίζονται σε TEs ήταν δραματικά μειωμένος στη PtDCR-KO σειρά και παρατηρήθηκε μία συνακόλουθη αύξηση του αριθμού των mRNA κάποιων TEs. Ενδιαφέρον παρουσιάζει ότι στα PtDCR-KO sRNA μετάγραφα παρατηρούνται επίσης αλλαγές στους tRNA-παραγόμενους sRNA πληθυσμούς υποδεικνύοντας ένα πιθανό ρόλο της DCR στην επεξεργασία αυτών των μορίων στα διάτομα. Έχει προταθεί ότι η κινητοποίηση των TE παίζει σημαντικό ρόλο στη εξελικτική διαφοροποίηση των διατόμων και στην ικανότητά τους για γρήγορη απόκριση και προσαρμογή σε ποικίλα περιβάλλοντα. Συμπερασματικά, τα αποτελέσματα αυτής της διατριβής δείχνουν ότι το μοναδικό γονίδιο DCR στο P. tricornutum παίζει σημαντικό ρόλο στην παραγωγή των TE-παραγόμενων sRNAs και πιθανά στην κινητοποίηση των TEs, επηρεάζοντας σημαντικά την απόκριση προσαρμογής των διατόμων και την εξέλιξή τους.

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