The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts.

N6-Methyladenosine (m6A), one of the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression through recruitment of specific m6A readers. In Saccharomyces cerevisiae, the m6A methyltransferase Ime4 is expressed only during meiosis and its deletion impairs this process. To elucidate how m6A control gene expression, we investigated the function of the budding yeast m6A reader Pho92. We show that Pho92 is an early meiotic factor that promotes timely meiotic progression. High-throughput RNA sequencing and mapping of Pho92-binding sites following UV-crosslinking reveal that Pho92 is recruited to specific mRNAs in an m6A-dependent manner during the meiotic prophase, preceding their down-regulation. Strikingly, point mutations altering m6A sites in mRNAs targeted by Pho92 are sufficient to delay their down-regulation and, in one case, to slow down meiotic progression. Altogether, our results indicate that Pho92 facilitate the meiotic progression by accelerating the down-regulation of timely-regulated mRNAs during meiotic recombination.

mRNAs molecules carry information contained in genes to direct the formation of proteins. In specific circumstances, the cellular machinery modifies some mRNAs through the formation of m6A residues. To understand the function of these m6A marks, the authors used the yeast Saccharomyces cerevisiae in which their formation only occurs during meiosis that leads to spore formation. Characterization of the Pho92 protein that specifically recognizes m6A residues revealed its importance for meiosis. m6A sites bound by Pho92 were identified and shown to be biologically functional. Unexpectedly, Pho92 was found to regulate an early step of meiosis by controlling DNA recombination. Overall, this study provides important clues on the role of m6A residues in mRNAs.

Alkene carboamination/oxidative denitrogenation of 3-allyl-3-hydrazinylindolin-2-ones: one-pot entry to spirocyclopropyloxindoles.

A one-pot protocol, consisting of a Pd-catalysed carboamination reaction, followed by N-deprotection and oxidative denitrogenation, has been developed for the synthesis of diversely substituted spirocyclopropyloxindoles, in yields up to 73% and with diastereoselectivity close to 1 : 1. Readily accessible starting materials, mild reaction conditions, an easy to operate one-pot procedure and good functional group tolerance make this transformation a versatile tool for the synthesis of substituted spirocyclopropyloxindoles. This protocol successfully works on the gram-scale and allows access to both diastereoisomers separately. A plausible mechanism was proposed, and a series of post-transformations were performed on the obtained products, showing their remarkable synthetic versatility.

Do Fruit Ripening Volatiles Enable Resource Specialism in Polyphagous Fruit Flies?

Frugivorous tephritid fruit flies have lineages with high levels of host generalism. These insects use olfaction to locate fruits, but how they are able to recognize the odors of so many different host species is poorly understood. We used a series of behavioral experiments to investigate the role of fruit ripening volatiles as host cues in the Queensland fruit fly, Bactrocera tryoni (Froggatt), a polyphagous pest in Australia. Odors of mature guava (Psidium guajava) attracted female and male flies more strongly than three other ripening stages and guava pulp. We analyzed volatiles from guava odor and selected eleven compounds, all of which elicited an electrophysiological response in the antenna of female flies. Three of these, ethyl acetate, ethyl butyrate, and ethyl propionate, were released at the highest rates from the most attractive ripening stage. In behavioral trials, these three esters were not attractive individually, whereas a combination was necessary and sufficient in attracting female flies. The three-component blend was as attractive as the entire 11-component blend, which without these key volatiles was not attractive. Moreover, injecting low ranking hosts (squash and cucumber) with the three volatiles increased attraction in ovipositing female flies. These fruit flies are classed as generalists, but like many polyphagous insects they could be regarded as resource specialists, preferring specific plant reproductive stages with predictable odor cues. Exploring olfaction from this perspective could improve our understanding of host choice in polyphagous insects, and the selection of volatiles to be used as attractants in insect pest management.

Development and Validation of a UAV Based System for Air Pollution Measurements.

Air quality data collection near pollution sources is difficult, particularly when sites are complex, have physical barriers, or are themselves moving. Small Unmanned Aerial Vehicles (UAVs) offer new approaches to air pollution and atmospheric studies. However, there are a number of critical design decisions which need to be made to enable representative data collection, in particular the location of the air sampler or air sensor intake. The aim of this research was to establish the best mounting point for four gas sensors and a Particle Number Concentration (PNC) monitor, onboard a hexacopter, so to develop a UAV system capable of measuring point source emissions. The research included two different tests: (1) evaluate the air flow behavior of a hexacopter, its downwash and upwash effect, by measuring air speed along three axes to determine the location where the sensors should be mounted; (2) evaluate the use of gas sensors for CO2, CO, NO2 and NO, and the PNC monitor (DISCmini) to assess the efficiency and performance of the UAV based system by measuring emissions from a diesel engine. The air speed behavior map produced by test 1 shows the best mounting point for the sensors to be alongside the UAV. This position is less affected by the propeller downwash effect. Test 2 results demonstrated that the UAV propellers cause a dispersion effect shown by the decrease of gas and PN concentration measured in real time. A Linear Regression model was used to estimate how the sensor position, relative to the UAV center, affects pollutant concentration measurements when the propellers are turned on. This research establishes guidelines on how to develop a UAV system to measure point source emissions. Such research should be undertaken before any UAV system is developed for real world data collection.

An Overview of Small Unmanned Aerial Vehicles for Air Quality Measurements: Present Applications and Future Prospectives.

Assessment of air quality has been traditionally conducted by ground based monitoring, and more recently by manned aircrafts and satellites. However, performing fast, comprehensive data collection near pollution sources is not always feasible due to the complexity of sites, moving sources or physical barriers. Small Unmanned Aerial Vehicles (UAVs) equipped with different sensors have been introduced for in-situ air quality monitoring, as they can offer new approaches and research opportunities in air pollution and emission monitoring, as well as for studying atmospheric trends, such as climate change, while ensuring urban and industrial air safety. The aims of this review were to: (1) compile information on the use of UAVs for air quality studies; and (2) assess their benefits and range of applications. An extensive literature review was conducted using three bibliographic databases (Scopus, Web of Knowledge, Google Scholar) and a total of 60 papers was found. This relatively small number of papers implies that the field is still in its early stages of development. We concluded that, while the potential of UAVs for air quality research has been established, several challenges still need to be addressed, including: the flight endurance, payload capacity, sensor dimensions/accuracy, and sensitivity. However, the challenges are not simply technological, in fact, policy and regulations, which differ between countries, represent the greatest challenge to facilitating the wider use of UAVs in atmospheric research.

Pervasive transcription: a controlled risk.

Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.

[68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET/MRI vs. Histopathological Images in Prostate Cancer: A New Workflow for Spatial Co-Registration.

This study proposed a new workflow for co-registering prostate PET images from a dual-tracer PET/MRI study with histopathological images of resected prostate specimens. The method aims to establish an accurate correspondence between PET/MRI findings and histology, facilitating a deeper understanding of PET tracer distribution and enabling advanced analyses like radiomics. To achieve this, images derived by three patients who underwent both [68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET/MRI before radical prostatectomy were selected. After surgery, in the resected fresh specimens, fiducial markers visible on both histology and MR images were inserted. An ex vivo MRI of the prostate served as an intermediate step for co-registration between histological specimens and in vivo MRI examinations. The co-registration workflow involved five steps, ensuring alignment between histopathological images and PET/MRI data. The target registration error (TRE) was calculated to assess the precision of the co-registration. Furthermore, the DICE score was computed between the dominant intraprostatic tumor lesions delineated by the pathologist and the nuclear medicine physician. The TRE for the co-registration of histopathology and in vivo images was 1.59 mm, while the DICE score related to the site of increased intraprostatic uptake on [68Ga]Ga-PSMA and [68Ga]Ga-RM2 PET images was 0.54 and 0.75, respectively. This work shows an accurate co-registration method for histopathological and in vivo PET/MRI prostate examinations that allows the quantitative assessment of dual-tracer PET/MRI diagnostic accuracy at a millimetric scale. This approach may unveil radiotracer uptake mechanisms and identify new PET/MRI biomarkers, thus establishing the basis for precision medicine and future analyses, such as radiomics.

A Modified Cross-Linking Analysis of cDNAs (CRAC ) Protocol for Detecting RNA-Protein Interactions and Transcription at Single-Nucleotide Resolution.

Detecting protein-RNA interactions in vivo is essential for deciphering many important cellular pathways. Several methods have been described for this purpose, among which cross-linking analysis of cDNA, CRAC. This method relies on a first step of UV cross-linking of living yeast cells and several subsequent steps of purification of the protein-RNA complexes, some of which under denaturing condition. Without altering the general principle of the method, we have modified and improved the protocol, with the specific aim of sequencing the nascent RNA isolated from transcription complexes and generate high-resolution and directional transcription maps.

Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy.

Pervasive transcription originating from the ubiquitous activity of RNA Polymerase II (RNAPII) generates a vast mass of non-coding RNAs (ncRNAs) that represent a potential harm to gene expression. In the compact genome of the yeast Saccharomyces cerevisiae, the main genomewide safeguard against pervasive ncRNAs is the Nrd1-Nab3-Sen1 (NNS) complex, composed of two RNA-binding proteins (Nrd1 and Nab3) and the helicase Sen1. The NNS complex directs transcription termination of ncRNA genes and promotes the rapid degradation of pervasive transcripts from yeast nuclei through its physical and functional coupling to the nuclear RNA exosome. We have recently shown that inhibition of the exosome in yeast cells leads to the accumulation of ncRNAs complexed with Nab3 and Nrd1, decreasing recycling of these termination factors to sites of transcription and inducing global termination defects at NNS targets. Consistent with the notion that ncRNAs out-titrate Nab3 and Nrd1 termination factors, we have shown that a similar genomewide termination impairment could be achieved by expressing a circular RNA decoy containing a Nab3 binding target [1]. In relation to this previous research article, here we expand our observations on the effect of the circular RNA decoy on NNS termination. We aimed at verifying that the Nab3 binding sequence present on the decoy is indeed efficiently sequestering Nab3 as intended by design, leading to the expected decrease of Nab3 binding on NNS targets. We employed the crosslinking and cDNA analysis protocol (CRAC) on yeast cells expressing the circular ncRNA decoy or a control construct. We present data from high-resolution genomewide RNA binding of Nab3 in three independent biological replicates of these S.cerevisiae cells, normalized by spiked-in S.pombe lysates. These data allow the useful assessment of the extent of co-transcriptional binding decrease of Nab3 by decoy ncRNA titration and will be valuable for further analyses of NNS targeting mechanisms.

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription.

A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. Here, we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, circular RNA containing a natural NNS target in exosome-proficient cells. Our results have important implications for the mechanism of termination, the general impact of ncRNAs abundance, and the importance of nuclear ncRNA degradation.

Nuclear quality control of RNA polymerase II ribonucleoproteins in yeast: tilting the balance to shape the transcriptome.

From the very first time they set foot in the nuclear landscape till the end of their life, RNAs are packaged in ribonucleoproteins (RNPs) and face numerous processing steps to achieve function. To avoid the catastrophic consequences of naturally occurring processing errors, cells employ numerous quality control strategies. Focusing on yeast as a model system, we will review here how nuclear mechanisms ensure the proper assembly and maturation of mRNPs for their release in the cytoplasm, and highlight how these mechanisms are exploited to shape the RNA polymerase II transcriptome.

mRNA journey to the cytoplasm: attire required.

In eukaryotes, copying the genetic information from a DNA template into RNA is not sufficient itself to confer functional competence to the DNA-encoded message. mRNAs have to be processed by enzymes and packaged with proteins within nuclei to generate mRNP (messenger ribonucleoprotein) particles, before these can be exported to the cytoplasm. Processing and packaging factors are believed to interact with the nascent mRNA co-transcriptionally, which protects the highly reactive RNA molecule from a presumably aggressive nuclear environment while providing early commitment to its functional fate. In this review, we will describe the factors that are believed to provide the appropriate 'dress code' to the mRNA and the mechanisms underlying the proofreading events that guarantee its quality, focusing on yeast as a model system.

Total knee prosthesis polyethylene wear reduction by a new metal part finishing method.

PURPOSE: The purpose of this study was to assess a new metal component finishing designed to improve total knee prosthesis durability. Wear of ultrahigh molecular-weight polyethylene (UHMWPE), with generation of submicrometer- and micrometer-sized particles, has been associated with osteolysis and artificial joint failure. Wear extent is influenced by several factors, some of which are related to manufacturing. METHODS: UHMWPE wear was assessed in metal prosthesis components finished with the Microloy® technology and in traditionally finished components by wear simulation experiments (pin on disk and knee simulator tests) and analysis of wear debris. RESULTS: Microloy®-finished prosthesis showed a 48.5% reduction in UHMWPE total weight loss compared with traditional components (P=0.002). A statistically significant (P<0.05) reduction of UHMWPE debris were detected from the Microloy®-finished compared with the traditionally finished components. CONCLUSIONS: These findings suggest the Microloy® metal finishing may enhance the long-term performance of knee prostheses.

Conformational dynamics of single pre-mRNA molecules during in vitro splicing.

The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5' and 3' splice sites. During splicing in vitro, we observed a multitude of generally reversible time- and ATP-dependent conformational transitions of individual pre-mRNAs. The conformational dynamics of branchpoint and 3'-splice site mutants differ from one another and from wild type. Because all transitions are reversible, spliceosome assembly appears to be occurring close to thermal equilibrium.

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice.

Cryptic unstable transcripts (CUTs) are short, 300-600-nucleotide (nt) RNA polymerase II transcripts that are rapidly degraded by the nuclear RNA exosome in yeast. CUTs are widespread and probably represent the largest share of hidden transcription in the yeast genome. Similarly to small nucleolar and small nuclear RNAs, transcription of CUT-encoding genes is terminated by the Nrd1 complex pathway. We show here that this termination mode and ensuing CUTs degradation crucially depend on the position of RNA polymerase II relative to the transcription start site. Notably, position sensing correlates with the phosphorylation status of the polymerase C-terminal domain (CTD). The Nrd1 complex is recruited to chromatin via interactions with both the nascent RNA and the CTD, but a permissive phosphorylation status of the latter is absolutely required for efficient transcription termination. We discuss the mechanism underlying the regulation of coexisting cryptic and mRNA-productive transcription.

The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing.

Prp16p is a DEAH-box ATPase that transiently associates with the spliceosome to promote the structural transition required for the second chemical step. Yeast strains carrying the cold-sensitive allele prp16-302 stall the release of Prp16p at low temperatures, yet splice precursors with aberrant branchpoints at increased frequency. To identify new factors involved in the regulation of splicing fidelity, we sought suppressors of the prp16-302 growth phenotype. Deletion of the nonessential ISY1 gene (1) improves growth of prp16-302 strains, (2) alleviates stalling, and (3) restores fidelity of branchpoint usage to wild-type levels. Isy1p is a subunit of the NineTeen Complex containing Prp19p, an essential E3 ubiquitin ligase homolog required for splicing. Notably, Deltaisy1 PRP16 strains display reduced fidelity of 3'-splice site selection. Consistent with a recent two-state model of the spliceosome, our genetic and biochemical results suggest that Isy1p acts together with U6 snRNA to promote a spliceosomal conformation favorable for first-step chemistry. We propose that deletion of ISY1 favors the premature release of Prp16p, thus promoting second-step chemistry of precursors with inappropriate 3'-splice sites.

Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core?

Since the discovery of self-splicing RNAs, it has been suspected that the snRNAs are the catalytic components of the spliceosome. Recent evidence supports both the catalytic potential of the spliceosomal snRNAs and their resemblance to elements of group II introns.