Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition.

Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using , documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle.

Registering a proposed business reduces police stops of innocent people? Reconsidering the effects of strip clubs on sex crimes found in Ciacci & Sviatschi's study of New York City.

Ciacci & Sviatschi's (2021) 'The Effect of Adult Entertainment Establishments on Sex Crime: Evidence from New York City,' published in , concluded that opening new adult entertainment businesses reduces sex crimes, with the most compelling finding that '[strip clubs, gentleman's clubs, and escort services] decrease sex crime by 13% per police precinct one week after the opening.' We contend that the study's conclusions speak beyond the data, which cannot support these findings because they do not measure the necessary variables. The study uses the date a business is registered with New York State as a proxy for its opening date, but the actual date of opening comes weeks or months later, after requirements such as inspections, licensure, and community board approval.

Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition.

Rare, full length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envision and test a hypothesis for their formation using , documenting full length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron-lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle.

Implication of nucleotides near the 3' end of 16S rRNA in guarding the translational reading frame.

Loss of the translational reading frame leads to misincorporation and premature termination, which can have lethal consequences. Based on structural evidence that A1503 of 16S rRNA intercalates between specific mRNA bases, we tested the possibility that it plays a role in maintenance of the reading frame by constructing ribosomes with an abasic nucleotide at position 1503. This was done by specific cleavage of 16S rRNA at position 1493 using the colicin E3 endonuclease and replacing the resulting 3'-terminal 49mer fragment with a synthetic oligonucleotide containing the abasic site using a novel splinted RNA ligation method.

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain.

Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity.

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain.

Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity.

The role of GTP hydrolysis by EF-G in ribosomal translocation.

Translocation of transfer RNA (tRNA) and messenger RNA (mRNA) through the ribosome is catalyzed by the GTPase elongation factor G (EF-G) in bacteria. Although guanosine-5'-triphosphate (GTP) hydrolysis accelerates translocation and is required for dissociation of EF-G, its fundamental role remains unclear. Here, we used ensemble Förster resonance energy transfer (FRET) to monitor how inhibition of GTP hydrolysis impacts the structural dynamics of the ribosome.

The universally conserved nucleotides of the small subunit ribosomal RNAs.

The ribosomal RNAs, along with their substrates the transfer RNAs, contain the most highly conserved nucleotides in all of biology. We have assembled a database containing structure-based alignments of sequences of the small-subunit rRNAs from organisms that span the entire phylogenetic spectrum, to identify the nucleotides that are universally conserved. In its simplest (bacterial and archaeal) forms, the small-subunit rRNA has ∼1500 nt, of which we identify 140 that are absolutely invariant among the 1961 species in our alignment.

Remotely projecting states of photonic temporal modes.

Two-photon time-frequency entanglement is a valuable resource in quantum information. Resolving the wavepacket of ultrashort pulsed single-photons, however, is a challenge. Here, we demonstrate remote spectral shaping of single photon states and probe the coherence properties of two-photon quantum correlations in the time-frequency domain, using engineered parametric down-conversion (PDC) and a quantum pulse gate (QPG) in nonlinear waveguides.

Correction: Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome.

[This corrects the article DOI: 10.1371/journal.pgen.

Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome.

Introns are a prevalent feature of eukaryotic genomes, yet their origins and contributions to genome function and evolution remain mysterious. In budding yeast, repression of the highly transcribed intron-containing ribosomal protein genes (RPGs) globally increases splicing of non-RPG transcripts through reduced competition for the spliceosome. We show that under these "hungry spliceosome" conditions, splicing occurs at more than 150 previously unannotated locations we call protointrons that do not overlap known introns.

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.

The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation.

High-performance source of spectrally pure, polarization entangled photon pairs based on hybrid integrated-bulk optics.

Entangled photon pair sources based on bulk optics are approaching optimal design and implementation, with high state fidelities, spectral purities and heralding efficiencies, but generally low brightness. Integrated entanglement sources, while providing higher brightness and low-power operation, often sacrifice performance in output state quality and coupling efficiency. Here we present a polarization-entangled pair source based on a hybrid approach of waveguiding and bulk optics, addressing every metric simultaneously.

Tomography and Purification of the Temporal-Mode Structure of Quantum Light.

High-dimensional quantum information processing promises capabilities beyond the current state of the art, but addressing individual information-carrying modes presents a significant experimental challenge. Here we demonstrate effective high-dimensional operations in the time-frequency domain of nonclassical light. We generate heralded photons with tailored temporal-mode structures through the pulse shaping of a broadband parametric down-conversion pump.

Direct Characterization of Ultrafast Energy-Time Entangled Photon Pairs.

Energy-time entangled photons are critical in many quantum optical phenomena and have emerged as important elements in quantum information protocols. Entanglement in this degree of freedom often manifests itself on ultrafast time scales, making it very difficult to detect, whether one employs direct or interferometric techniques, as photon-counting detectors have insufficient time resolution. Here, we implement ultrafast photon counters based on nonlinear interactions and strong femtosecond laser pulses to probe energy-time entanglement in this important regime.

Autogenous cross-regulation of mRNA processing and translation balances functions in splicing and translation.

Quaking protein isoforms arise from a single gene and bind the same RNA motif to regulate splicing, translation, decay, and localization of a large set of RNAs. However, the mechanisms by which expression is controlled to ensure that appropriate amounts of each isoform are available for such disparate gene expression processes are unknown. Here we explore how levels of two isoforms, nuclear Quaking-5 (Qk5) and cytoplasmic Qk6, are regulated in mouse myoblasts.

Testing the Immunity of the Firearm Industry to Tort Litigation.

In the absence of congressional action to reinstate the federal ban on assault weapons, tort litigation offers an alternative strategy for regulating what have become the weapons of choice in mass shootings. However, opportunities to bring successful claims are limited. To prevail, plaintiffs must show that their suit fits within exceptions to the broad immunity from tort actions that Congress gave the firearm industry in the 2005 Protection of Lawful Commerce in Arms Act.

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation.