Updated Pseudo-seq Protocol for Transcriptome-Wide Detection of Pseudouridines

Pseudouridine (Ψ), the most prevalent modified base in cellular RNAs, has been mapped to numerous sites not only in rRNAs, tRNAs, and snRNAs but also mRNAs. Although there have been multiple techniques to identify Ψs, due to the recent development of sequencing technologies some reagents are not compatible with the current sequencer. Here, we show the updated Pseudo-seq, a technique enabling the genome-wide identification of pseudouridylation sites with single-nucleotide precision. We provide a comprehensive description of Pseudo-seq, covering protocols for RNA isolation from human cells, library preparation, and detailed data analysis procedures. The methodology presented is easily adaptable to any cell or tissue type with high-quality mRNA isolation. It can be used for discovering novel pseudouridylation sites, thus constituting a crucial initial step toward understanding the regulation and function of this modification. Key features • Identification of Ψ sites on mRNAs. • Updated Pseudo-seq provides precise positional and quantitative information of Ψ. • Uses a more efficient library preparation with the latest, currently available materials.

Pseudouridylation-mediated gene expression modulation

RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.

Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes

Nonsense mutations create premature termination codons (PTCs), activating the nonsense-mediated mRNA decay (NMD) pathway to degrade most PTC-containing mRNAs. The undegraded mRNA is translated, but translation terminates at the PTC, leading to no production of the full-length protein. This work presents targeted PTC pseudouridylation, an approach for nonsense suppression in human cells. Specifically, an artificial box H/ACA guide RNA designed to target the mRNA PTC can suppress both NMD and premature translation termination in various sequence contexts. Targeted pseudouridylation exhibits a level of suppression comparable with that of aminoglycoside antibiotic treatments. When targeted pseudouridylation is combined with antibiotic treatment, a much higher level of suppression is observed. Transfection of a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene targeting the PTC also leads to nonsense suppression. Thus, targeted pseudouridylation is an RNA-directed gene-specific approach that suppresses NMD and concurrently promotes PTC readthrough.

In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles

Pseudouridine (Ψ) is the most common chemical modification in RNA. In eukaryotes and archaea, pseudouridine synthases, mainly guided by box H/ACA snoRNAs, convert uridine to Ψ. Ψ stabilizes RNA structure and alters RNA-RNA and RNA-protein interactions, conferring important roles in gene expression. Notably, several Ψ-linked human diseases have been identified over the years. In addition, Ψ has also been extensively used in developing mRNA vaccines. Furthermore, it has been shown that pseudouridylation can be site-specifically directed to modify specific nonsense codons, leading to nonsense suppression. All of these, together with a need to better understand the specific functions of Ψs, have motivated the development of in vitro pseudouridylation assays using purified and reconstituted box H/ACA RNPs. Here, we describe an in vitro system for box H/ACA RNA-guided RNA pseudouridylation using human cell extracts. We show that a half guide RNA (only one hairpin) is just as functionally competent as the full-length guide RNA (two hairpins) in guiding site-specific pseudouridylation in the human cell extracts. This discovery offers the opportunity for direct delivery of a short guide RNA to human cells to promote site-specific nonsense suppression and therefore has potential clinical applications.

Characterizing propagation-dependent spatial entanglement for structured laser beams generated by an astigmatic mode converter

The propagation-dependent spatial entanglement for the structured laser beams generated by an arbitrary incident Hermite-Gaussian (HG) mode passing through an astigmatic mode converter (AMC) is theoretically explored. The structured output beams are analytically decomposed into the expansion of HG modes for any given rotation angle of the AMC. Based on the Schmidt decomposition, the propagation-dependent spatial entanglements of the structured output modes are quantified with the von Neumann entropy. To manifest the propagation-dependent entropy, the probability distribution of the expanded HG modes in the structured output beam is quantitatively analyzed.

The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines

The current COVID-19 pandemic is a massive source of global disruption, having led so far to two hundred and fifty million COVID-19 cases and almost five million deaths worldwide. It was recognized in the beginning that only an effective vaccine could lead to a way out of the pandemic, and therefore the race for the COVID-19 vaccine started immediately, boosted by the availability of the viral sequence data. Two novel vaccine platforms, based on mRNA technology, were developed in 2020 by Pfizer-BioNTech and Moderna Therapeutics (comirnaty® and spikevax®, respectively), and were the first ones presenting efficacies higher than 90%. Both consisted of N1-methyl-pseudouridine-modified mRNA encoding the SARS-COVID-19 Spike protein and were delivered with a lipid nanoparticle (LNP) formulation. Because the delivery problem of ribonucleic acids had been known for decades, the success of LNPs was quickly hailed by many as the unsung hero of COVID-19 mRNA vaccines. However, the clinical trial efficacy results of the Curevac mRNA vaccine (CVnCoV) suggested that the delivery system was not the only key to the success. CVnCoV consisted of an unmodified mRNA (encoding the same spike protein as Moderna and Pfizer-BioNTech's mRNA vaccines) and was formulated with the same LNP as Pfizer-BioNTech's vaccine (Acuitas ALC-0315). However, its efficacy was only 48%. This striking difference in efficacy could be attributed to the presence of a critical RNA modification (N1-methyl-pseudouridine) in the Pfizer-BioNTech and Moderna's mRNA vaccines (but not in CVnCoV). Here we highlight the features of N1-methyl-pseudouridine and its contributions to mRNA vaccines.

Quantum entanglement by a beam splitter analogous to laser mode transformation by a cylindrical lens

Quantum entanglement by a beam splitter (BS) is shown to be analogous to laser mode transformation by an astigmatic mode converter (AMC). Schmidt decomposition is used to characterize the entanglement by an AMC for generating orbital angular momentum and by a BS for creating quantum photon interference. The probability distributions of Schmidt decomposition are calculated to manifest the sameness and difference between AMC and BS in generating entanglement. Finally, the theoretical patterns of mode transformations by an AMC are confirmed with experimental results to validate the present analysis.

[Association of hyperuricemia with risk of incident chronic kidney disease in adult in Songjiang district, Shanghai: a follow-up study]

Objective: To evaluate the association of hyperuricemia with the risk for chronic kidney disease (CKD) in community adults. Methods: A community-based follow-up study comprising of 7 276 adults aged 20-74 years who attended the natural population cohort in Eastern China and had no CKD at baseline survey was performed in the Songjiang district, Shanghai. CKD was diagnosed according to the National Kidney Foundation Practice Guidelines for Chronic Kidney Disease criteria. Hyperuricemia was defined as serum uric acid level >420 μmol/L for men and >360 μmol/L for women. Cox proportional hazards model was used to examine the association of hyperuricemia with the risk for CKD. Results: During a median follow-up period of 2.65 year, 301 participants were newly diagnosed with CKD. The cumulative incidence rate and incidence density of CKD were 4.14%, and 16.01/1 000 person-years (95%CI: 14.20-17.82), respectively. A higher prevalence of hyperuricemia was observed in subjects with CKD compared with those without CKD. Multivariate Cox regression model analysis showed that hyperuricemia was associated with the increased risk for CKD, with an adjusted HR of 1.92 (95%CI: 1.46-2.53). Their positive associations remained in almost all the subgroups, including sex, age (<60, ≥60 years), BMI (<25.0, ≥25.0 kg/m²), type 2 diabetes, and hypertension. A significant synergistic effect of the interaction between age and hyperuricemia on CKD was found, and the synergy index was 1.78 (95%CI: 1.18-2.68). Conclusion: The incidence of CKD in adults in Songjiang district was relatively high. Hyperuricemia is an independent risk factor for the development of CKD.

Characterizing the spatial entanglement from laser modes analogous to quantum wave functions

The Schmidt decomposition is exploited to study the spatial entanglement of laser transverse modes analogous to quantum Lissajous states. Based on the inverse Fourier transform, the stationary Lissajous state can be analytically derived as a coherent superposition of degenerate Hermite-Gaussian eigenmodes. With the derived stationary state, the Schmidt modes and the participation number N can be employed to evaluate the spatial localization and the quantum entanglement. The larger the participation number, the more localized is the stationary coherent state on the Lissajous figure. Moreover, the larger the participation number, the higher is the spatial entanglement.

Powerful Q-switched Raman laser at 589 nm with a repetition rate between 200 and 500 kHz

We demonstrate a highly powerful acousto-optically Q-switched Nd:YVO₄ yellow laser at 589 nm by using a N_p-cut KGW crystal and a phase-matching lithium triborate crystal to performance the intracavity stimulated Raman scattering and second-harmonic generation, respectively. We experimentally verify that the design of the separate cavity is superior to the conventional design of the shared cavity. By using the separate cavity, the optical-to-optical efficiency can be generally higher than 32% for the repetition rate within 200-500 kHz. The maximum output power at 589 nm can be up to 15.1 W at an incident pump power of 40 W and a repetition rate of 400 kHz.

Pedagogically fast model to evaluate and optimize passively Q-switched Nd-doped solid-state lasers

The coupled rate equations with the spatial overlap effect for four-level passively Q-switched lasers are fully considered. A transcendental equation is derived for the residual fraction of the inversion density after the finish of the Q-switched pulse. Comprehensive calculations for the transcendental equation were executed to attain an analytical function for precisely fitting the residual fraction of the inversion density. With the fitting function, a pedagogical model with the correction for high output coupling is developed to straightforwardly analyze the output pulse energy and peak power. Detailed experiments are carried out to validate the model.

Spliceosomal snRNA Epitranscriptomics

Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.

Propagation-dependent evolution of interfering multiple beams and kaleidoscopic vortex lattices

In this Letter, we experimentally explore the propagation-dependent evolution of generating the pseudo-nondiffracting quasi-crystalline (crystalline) beams based on the multibeam interference. We originally derived an analytical formula to exactly manifest the propagation evolution of interfering multiple beams. With the analytical formula, the formation of quasi-crystalline structures in the focal plane can be explicitly verified. Furthermore, the distance of the effective propagation-invariant region can be verified in terms of experimental parameters. More importantly, we employed the developed formula to confirm the formation of kaleidoscopic vortex lattices by means of numerically computing the propagation-dependent phase singularities.

Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent

We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events.

Suppression of Nonsense Mutations by New Emerging Technologies

Nonsense mutations often result from single nucleotide substitutions that change a sense codon (coding for an amino acid) to a nonsense or premature termination codon (PTC) within the coding region of a gene. The impact of nonsense mutations is two-fold: (1) the PTC-containing mRNA is degraded by a surveillance pathway called nonsense-mediated mRNA decay (NMD) and (2) protein translation stops prematurely at the PTC codon, and thus no functional full-length protein is produced. As such, nonsense mutations result in a large number of human diseases. Nonsense suppression is a strategy that aims to correct the defects of hundreds of genetic disorders and reverse disease phenotypes and conditions. While most clinical trials have been performed with small molecules, there is an increasing need for sequence-specific repair approaches that are safer and adaptable to personalized medicine. Here, we discuss recent advances in both conventional strategies as well as new technologies. Several of these will soon be tested in clinical trials as nonsense therapies, even if they still have some limitations and challenges to overcome.

Integral-based parallel algorithm for the fast generation of the Zernike polynomials

The integral representation of the Zernike radial functions is well approximated by applying the Riemann sums with a surprisingly rapid convergence. The errors of the Riemann sums are found to averagely be not exceed 3 ×10^-14, 3.3×10^-14, and 1.8×10^-13 for the radial order up to 30, 50, and 100, respectively. Moreover, a parallel algorithm based on the Riemann sums is proposed to directly generate a set of radial functions. With the aid of the graphics processing units (GPUs), the algorithm shows an acceleration ratio up to 200-fold over the traditional CPU computation. The fast generation for a set of Zernike radial polynomials is expected to be valuable in further applications, such as the aberration analysis and the pattern recognition.

Exploring the formation of thermally detuned transverse patterns in a broad-area square VCSEL

The formation of thermally detuned transverse patterns of a broad-area square-aperture vertical-cavity surface-emitting laser (VCSEL) via cryogenic cooling is explored. It is found that the transverse wave vector gradually rotates from the horizontal or vertical direction to the diagonal direction of the square boundary as the transverse mode order increases. A model based on the quantum billiards with a finite potential well is developed to emulate the transition behavior of lasing modes. Combining the effective modal gain analysis with the response wave function of driven finite potential billiards, all experimental lasing patterns under different operation temperatures are well reconstructed.

Detection and Quantification of Pseudouridine in RNA

Pseudouridylation is the most abundant of all RNA modifications. Pseudouridylation is dynamic and widespread among many different types of RNAs in living organisms, thus drawing a lot of recent interest from the RNA and epigenetics communities. To successfully carry out an investigation into RNA pseudouridylation, it is desirable to have a convenient and effective method capable of detection and quantification of pseudouridylation. Here, we present two such methods: one relies on pseudouridine (Ψ)-specific CMCT modification followed by reverse transcription/primer-extension (semiquantitative), and the other is based on site-specific cleavage and radiolabeling followed by nuclease digestion and TLC (quantitative). Although only semiquantitative, the CMCT and reverse transcription-based method is capable of detecting multiple Ψs (present in the same RNA molecule) in one reaction. In contrast, the second method, based on site-specific cleavage/labeling, nuclease digestion, and TLC, is quantitative, but can be used to analyze only one site at a time. These two methods can be used independently or in combination.

[Epidemiological features of adult chronic kidney diseases in a community-based population in Songjiang district, Shanghai]

Objective: To investigate the prevalence and associated factors of chronic kidney diseases (CKD) in adult residents living in a community of Songjiang district, Shanghai. Methods: A total of 9 257 residents aged 20-75 years old in Xinqiao township of Songjiang district were selected by random cluster sampling. All the participants were interviewed to complete a set of personal questionnaire and undergo physical examinations. Urine and blood tests including markers of kidney damage and related associated factors with CKD, were carried out. Results: Eligible data from 8 207 subjects were enrolled in the study. After adjustment for age and gender, the prevalence of CKD was 8.4% (95%CI: 7.8%-9.0%), with majority of the patients (76.5%) appeared in the early stage (Ⅰ and Ⅱ) of the disease. The prevalence of CKD increased with age and higher prevalence was seen in females than in males (P<0.001). Results from logistic regression analysis showed that factors as: being elderly or female, having hypertension, hyperuricemia, and hyperlipidemia were all independently associated with CKD. Conclusions: The prevalence of CKD appeared relatively high in adult residents of Xinqiao township, Songjiang district where CKD had become a public health problem. Factors as: being female or elderly, hypertension, hyperuricemia, and hyperlipidemia were found to be associated with CKD. Our findings suggested that early prevention and control on CKD to reduce the incidence of end-stage renal diseases and related complications had called for more urgent attention.

Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs

Pseudouridylation is a post-transcriptional isomerization reaction that converts a uridine to a pseudouridine (Ψ) within an RNA chain. Ψ has chemical properties that are distinct from that of uridine and any other known nucleotides. Experimental data accumulated thus far have indicated that Ψ is present in many different types of RNAs, including coding and noncoding RNAs. Ψ is particularly concentrated in rRNA and spliceosomal snRNAs, and plays an important role in protein translation and pre-mRNA splicing, respectively. Ψ has also been found in mRNA, but its function there remains essentially unknown. In this review, we discuss the mechanisms and functions of RNA pseudouridylation, focusing on rRNA, snRNA and mRNA. We also discuss the methods, which have been developed to detect Ψs in RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.

Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation

Box H/ACA RNAs are a group of small RNAs found in abundance in eukaryotes (as well as in archaea). Although their sequences differ, eukaryotic box H/ACA RNAs all share the same unique hairpin-hinge-hairpin-tail structure. Almost all of them function as guides that primarily direct pseudouridylation of rRNAs and spliceosomal snRNAs at specific sites. Although box H/ACA RNA-guided pseudouridylation has been extensively studied, the detailed rules governing this reaction, especially those concerning the guide RNA-substrate RNA base-pairing interactions that determine the specificity and efficiency of pseudouridylation, are still not exactly clear. This is particularly relevant given that the lengths of the guide sequences involved in base-pairing vary from one box H/ACA RNA to another. Here, we carry out a detailed investigation into guide-substrate base-pairing interactions, and identify the minimum number of base pairs (8), required for RNA-guided pseudouridylation. In addition, we find that the pseudouridylation pocket, present in each hairpin of box H/ACA RNA, exhibits flexibility in fitting slightly different substrate sequences. Our results are consistent across three independent pseudouridylation pockets tested, suggesting that our findings are generally applicable to box H/ACA RNA-guided RNA pseudouridylation.

The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events

Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.

Modeling and Simulation of A Microchannel Cooling System for Vitrification of Cells and Tissues

BACKGROUND

The microchannel heat exchange system has several advantages and can be used to enhance heat transfer for vitrification.

OBJECTIVE

To evaluate the microchannel cooling method and to analyze the effects of key parameters such as channel structure, flow rate and sample size.

MATERIALS AND METHODS

A computational flow dynamics model is applied to study the two-phase flow in microchannels and its related heat transfer process. The fluid-solid coupling problem is solved with a whole field solution method (i.e., flow profile in channels and temperature distribution in the system being simulated simultaneously).

RESULTS AND CONCLUSION

Simulation indicates that a cooling rate >10⁴ C/min is easily achievable using the microchannel method with the high flow rate for a board range of sample sizes. Channel size and material used have significant impact on cooling performance. Computational flow dynamics is useful for optimizing the design and operation of the microchannel system.

Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity

Many ribonucleoproteins (RNPs), which are comprised of noncoding RNA and associated proteins, are involved in essential cellular processes such as translation and pre-mRNA splicing. One class of RNP is the small Cajal body-specific RNP (scaRNP), which contributes to the biogenesis of small nuclear RNPs (snRNPs) that are central components of the spliceosome. Three scaRNAs are internally processed, generating stable nucleolus-enriched RNAs of unknown function. Here, we provide data that show that these RNAs become part of RNPs we term regulatory RNPs (regRNPs). Most modifications within rRNA (predominantly pseudouridylation and ribose 2′-O-methylation) are conducted by small nucleolar RNPs (snoRNPs), and we provide evidence that the activity of at least some of these snoRNPs is under the control of regRNPs. Because modifications within rRNA can vary in different physiological or pathological situations, rRNA modifications are thought to be the major source of ribosome heterogeneity. Our identification of regRNPs thus provides a potential mechanism for how ribosome heterogeneity may be accomplished. This work also provides additional functional connections between the Cajal body and the nucleolus.

Summary: Processed scaRNAs give rise to a novel regulatory RNP, which regulates the modification of ribosomal RNA. These findings provide insight into the mechanisms governing ribosome heterogeneity.

Extracting trajectory equations of classical periodic orbits from the quantum eigenmodes in two-dimensional integrable billiards

The trajectory equations for classical periodic orbits in the equilateral-triangular and circular billiards are systematically extracted from quantum stationary coherent states. The relationship between the phase factors of quantum stationary coherent states and the initial positions of classical periodic orbits is analytically derived. In addition, the stationary coherent states with noncoprime parametric numbers are shown to correspond to the multiple periodic orbits, which cannot be explicable in the one-particle picture. The stationary coherent states are further verified to be linked to the resonant modes that are generally observed in the experimental wave system excited by a localized and unidirectional source. The excellent agreement between the resonant modes and the stationary coherent states not only manifests the importance of classical features in experimental systems but also paves the way to manipulate the mesoscopic wave functions localized on the periodic orbits for applications.

Posttranscriptional RNA Pseudouridylation

Pseudouridine (Ψ) is the most abundant posttranscriptional modification in noncoding RNAs. Pseudouridines are often clustered in important regions of rRNAs (ribosomal RNAs), snRNAs (small nuclear RNAs), and tRNAs (transfer RNAs), contributing to RNA function. Pseudouridylation is governed by two independent mechanisms. The first involves single protein enzymes called pseudouridine synthases (PUSs) that alone recognize the substrate and catalyze the isomerization of uridine to pseudouridine (RNA-independent pseudouridylation). The second is an RNA-guided pseudouridylation by a family of box H/ACA RNPs (ribonucleoproteins), each of which consists of a unique RNA (box H/ACA RNA) and four common core proteins (Cbf5/NAP57/Dyskerin, Nhp2/L7Ae, Nop10, and Gar1). The RNA component serves as a guide that base pairs with the substrate RNA and directs the enzyme (Cbf5) to carry out the pseudouridylation reaction at a specific site. The crystal structures of many PUSs have been solved in numerous organisms including E. coli and human. Several partial and complete crystal structures of archaea and yeast box H/ACA RNPs are available, providing a rich source of information regarding the molecular interactions between protein components and box H/ACA RNA. Over the years, several experimental systems have been developed to study the mechanism and function of pseudouridylation. Apart from noncoding RNA pseudouridylation, recent experiments have provided evidence of mRNA pseudouridylation as well. Despite remarkable progress, there is a need to accelerate efforts in order to understand the detailed mechanisms and functions of RNA pseudouridylation.

Characterizing classical periodic orbits from quantum Green's functions in two-dimensional integrable systems: Harmonic oscillators and quantum billiards

A general method is developed to characterize the family of classical periodic orbits from the quantum Green's function for the two-dimensional (2D) integrable systems. A decomposing formula related to the beta function is derived to link the quantum Green's function with the individual classical periodic orbits. The practicality of the developed formula is demonstrated by numerically analyzing the 2D commensurate harmonic oscillators and integrable quantum billiards. Numerical analyses reveal that the emergence of the classical features in quantum Green's functions principally comes from the superposition of the degenerate states for 2D harmonic oscillators. On the other hand, the damping factor in quantum Green's functions plays a critical role to display the classical features in mesoscopic regime for integrable quantum billiards, where the physical function of the damping factor is to lead to the coherent superposition of the nearly degenerate eigenstates.

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly

Xu et al. show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs. They also determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA.

In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)_4–6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m⁷G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m⁷G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m⁷G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.

The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA

Pseudouridine (Ψ) has been identified in various types of RNAs, including mRNA, rRNA, tRNA, snRNA, and many other noncoding RNAs. We have previously shown that RNA pseudouridylation, like DNA and protein modifications, can be induced by stress. For instance, growing yeast cells to saturation induces the formation of Ψ93 in U2 snRNA. Here, we further investigate this inducible RNA modification. We show that switching yeast cells from nutrient-rich medium to different nutrient-deprived media (including water) results in the formation of Ψ93 in U2 snRNA. Using gene deletion/conditional depletion as well as rapamycin treatment, we further show that the TOR signaling pathway, which controls cell entry into stationary phase, regulates Ψ93 formation. The RAS/cAMP signaling pathway, which parallels the TOR pathway, plays no role in this inducible modification.

Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly

Pseudouridine (Ψ) is the most abundant internal modification identified in RNA, and yet little is understood of its effects on downstream reactions. Yeast U2 snRNA contains three conserved Ψs (Ψ35, Ψ42, and Ψ44) in the branch site recognition region (BSRR), which base pairs with the pre-mRNA branch site during splicing. Here, we show that blocks to pseudouridylation at these positions reduce the efficiency of pre-mRNA splicing, leading to growth-deficient phenotypes. Restoration of pseudouridylation at these positions using designer snoRNAs results in near complete rescue of splicing and cell growth. These Ψs interact genetically with Prp5, an RNA-dependent ATPase involved in monitoring the U2 BSRR-branch site base-pairing interaction. Biochemical analysis indicates that Prp5 has reduced affinity for U2 snRNA that lacks Ψ42 and Ψ44 and that Prp5 ATPase activity is reduced when stimulated by U2 lacking Ψ42 or Ψ44 relative to wild type, resulting in inefficient spliceosome assembly. Furthermore, in vivo DMS probing analysis reveals that pseudouridylated U2, compared to U2 lacking Ψ42 and Ψ44, adopts a slightly different structure in the branch site recognition region. Taken together, our results indicate that the Ψs in U2 snRNA contribute to pre-mRNA splicing by directly altering the binding/ATPase activity of Prp5.

Detection and quantification of RNA 2'-O-methylation and pseudouridylation

RNA-guided RNA modification is a naturally occurring process that introduces 2'-O-methylation and pseudouridylation into rRNA, spliceosomal snRNA and several other types of RNA. The Box C/D ribonucleoproteins (RNP) and Box H/ACA RNP, each containing one unique guide RNA (Box C/D RNA or Box H/ACA RNA) and a set of core proteins, are responsible for 2'-O-methylation and pseudouridylation respectively. Box C/D RNA and Box H/ACA RNA provide the modification specificity through base pairing with their RNA substrate. These post-transcriptional modifications could profoundly alter the properties and functions of substrate RNAs. Thus it is desirable to establish reliable and standardized modification methods to study biological functions of modified nucleotides in RNAs. Here, we present several sensitive and efficient methods and protocols for detecting and quantifying post-transcriptional 2'-O-methylation and pseudouridylation.

Exploiting broad-area surface emitting lasers to manifest the path-length distributions of finite-potential quantum billiards

Broad-area vertical-cavity surface-emitting lasers (VCSELs) with different cavity sizes are experimentally exploited to manifest the influence of the finite confinement strength on the path-length distribution of quantum billiards. The subthreshold emission spectra of VCSELs are measured to obtain the path-length distributions by using the Fourier transform. It is verified that the number of the resonant peaks in the path-length distribution decreases with decreasing the confinement strength. Theoretical analyses for finite-potential quantum billiards are numerically performed to confirm that the mesoscopic phenomena of quantum billiards with finite confinement strength can be analogously revealed by using broad-area VCSELs.

Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles

Pseudouridylation is the most abundant and widespread RNA modification, and it plays an important role in modulating the structure and function of RNA. In eukaryotes and archaea, RNA pseudouridylation is catalyzed largely by box H/ACA ribonucleoproteins (RNPs), a distinct group of RNA-protein complexes each consisting of a unique RNA and four common proteins. The RNA component of the complex serves as a guide that base-pairs with its substrate RNA and specifies the target uridine to be modified. In order to systematically study the function and mechanism of pseudouridylation, it is desirable to have a reconstitution system in which biochemically purified/reconstituted box H/ACA RNPs are capable of introducing pseudouridines into an RNA at any target site. Here, we describe a method for the reconstitution of functional box H/ACA RNPs using designer box H/ACA guide RNAs, which in principle can be adopted to reconstitute other RNA-protein complexes as well.

Requirement for CRIF1 in RNA interference and Dicer-2 stability

RNA interference (RNAi) is a eukaryotic gene-silencing system. Although the biochemistry of RNAi is relatively well defined, how this pathway is regulated remains incompletely understood. To identify genes involved in regulating the RNAi pathway, we screened for genetic mutations in Drosophila that alter the efficiency of RNAi. We identified the Drosophila homolog of the mammalian CR6-interacting factor 1 (CRIF1), also known as growth arrest and DNA-damage-inducible 45-gamma interacting protein (Gadd45GIP1), as a potential new regulator of the RNAi pathway. Loss-of-function mutants of Drosophila CRIF1 (dCRIF) are deficient in RNAi-mediated target gene knock-down, in the biogenesis of small interfering RNA (siRNA) molecules, and in antiviral immunity. Moreover, we show that dCRIF may function by interacting with, and stabilizing, the RNase III enzyme Dicer-2. Our results suggest that dCRIF may play an important role in regulating the RNAi pathway.

Transcriptome-wide dynamics of RNA pseudouridylation

Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

Exploring the resonant vibration of thin plates: Reconstruction of Chladni patterns and determination of resonant wave numbers

The Chladni nodal line patterns and resonant frequencies for a thin plate excited by an electronically controlled mechanical oscillator are experimentally measured. Experimental results reveal that the resonant frequencies can be fairly obtained by means of probing the variation of the effective impedance of the exciter with and without the thin plate. The influence of the extra mass from the central exciter is confirmed to be insignificant in measuring the resonant frequencies of the present system. In the theoretical aspect, the inhomogeneous Helmholtz equation is exploited to derive the response function as a function of the driving wave number for reconstructing experimental Chladni patterns. The resonant wave numbers are theoretically identified with the maximum coupling efficiency as well as the maximum entropy principle. Substituting the theoretical resonant wave numbers into the derived response function, all experimental Chladni patterns can be excellently reconstructed. More importantly, the dispersion relationship for the flexural wave of the vibrating plate can be determined with the experimental resonant frequencies and the theoretical resonant wave numbers. The determined dispersion relationship is confirmed to agree very well with the formula of the Kirchhoff-Love plate theory.

Pseudouridine in mRNA: Incorporation, Detection, and Recoding

It has long been known that pseudouridine (Ψ) is the most abundant modified nucleotide in stable RNAs, including tRNA, rRNA, and snRNA. Recent studies using massive parallel sequencing have uncovered the presence of hundreds of Ψs in mRNAs as well. In eukaryotes and archaea, RNA pseudouridylation is introduced predominantly by box H/ACA RNPs, RNA-protein complexes each consisting of a single RNA moiety and four core proteins. It has been well established that Ψ plays an essential role in regulating the structure and function of stable RNAs in several model organisms, including yeast, Xenopus laevis, and humans. However, the functional role of Ψ in mRNA remains to be elucidated. One possibility (and true for stop/termination codons) is that Ψ influences decoding during translation. It is imperative, therefore, to establish a system, in which one can site-specifically introduce pseudouridylation into target mRNA and biochemically test the impact of mRNA pseudouridylation on protein translation. Here, we present a method for (1) site-specific conversion of uridine into Ψ in mRNA by designer box H/ACA RNP, (2) detection of Ψ in target mRNA using site-specific labeling followed by nuclease digestion and thin layer chromatography, and (3) analysis of recoding of pseudouridylated premature termination codon in mRNA during translation.

Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation

Pseudouridines (Ψs) are the most abundant and highly conserved modified nucleotides found in various stable RNAs of all organisms. Most Ψs are clustered in regions that are functionally important for pre-mRNA splicing. Ψ has an extra hydrogen bond donor that endows RNA molecules with distinct properties that contribute significantly to RNA-mediated cellular processes. Experimental data indicate that spliceosomal snRNA pseudouridylation can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Recent work has also demonstrated that pseudouridylation can be induced at novel positions under stress conditions, suggesting a regulatory role for Ψ.

Exploring the influence of boundary shapes on emission angular distributions and polarization states of broad-area vertical-cavity surface-emitting lasers

We design the stadium-shaped and rectangular vertical-cavity surface-emitting lasers (VCSELs) to investigate the influence of boundary shapes on the emission angular distributions and polarization states. For the stadium-shaped VCSELs, the emission angular distribution prefers to be almost omnidirectional because the lasing mode with purely scarred structure is seldom to be excited. On the contrary, the rectangular VCSELs usually generate dominant lasing modes with the morphology of quasi-periodic linear ridges, which can make emission angular distribution to be concentrated on the certain direction. From the polarization-resolved light-current curves, the stadium-shaped VCSEL is quite prone to exhibit numerous abrupt changes (kinks) associated with polarization switching with increasing current, whereas for rectangular VCSEL there is no conspicuous kink to be seen during a wide range of current changing from near to far above lasing threshold.

Therapeutic suppression of premature termination codons: mechanisms and clinical considerations (review)

An estimated one-third of genetic disorders are the result of mutations that generate premature termination codons (PTCs) within protein coding genes. These disorders are phenotypically diverse and consist of diseases that affect both young and old individuals. Various small molecules have been identified that are capable of modulating the efficiency of translation termination, including select antibiotics of the aminoglycoside family and multiple novel synthetic molecules, including PTC124. Several of these agents have proved their effectiveness at promoting nonsense suppression in preclinical animal models, as well as in clinical trials. In addition, it has recently been shown that box H/ACA RNA-guided peudouridylation, when directed to modify PTCs, can also promote nonsense suppression. In this review, we summarize our current understanding of eukaryotic translation termination and discuss various methods for promoting the read-through of disease-causing PTCs, as well as the current obstacles that stand in the way of using the discussed agents broadly in clinical practice.

Identification of a major quantitative trait locus for ear size induced by space flight in sweet corn

The development of molecular markers has contributed to progress in identifying the gene(s) responsible for favorable variations in maize studies. In this study, quantitative trait locus (QTL) mapping was conducted using simple sequence repeat markers in an F2 sweet corn population from a cross between parental line 1132 and space flight-induced mutant line 751 to identify the loci contributing to an increase in some yield traits. A primary mutated genomic region was located on chromosome 9. In total, 26 QTL were detected for eight yield-related traits and assembled into three clusters on chromosome 9. The largest QTL cluster at bin 9.02/03, primarily contributing to >10% of the phenotypic variation in ear and cob diameters, was likely due to a major QTL. Desired alleles of these QTL were provided by the mutant line 751. The primary action of the major mutant allele was an additive effect. Another mutant locus, which was induced in bin 9.01, increased cob and ear diameters by dominant genetic action.

Exploring the distinction between experimental resonant modes and theoretical eigenmodes: from vibrating plates to laser cavities

Experimentally resonant modes are commonly presumed to correspond to eigenmodes in the same bounded domain. However, the one-to-one correspondence between theoretical eigenmodes and experimental observations is never reached. Theoretically, eigenmodes in numerous classical and quantum systems are the solutions of the homogeneous Helmholtz equation, whereas resonant modes should be solved from the inhomogeneous Helmholtz equation. In the present paper we employ the eigenmode expansion method to derive the wave functions for manifesting the distinction between eigenmodes and resonant modes. The derived wave functions are successfully used to reconstruct a variety of experimental results including Chladni figures generated from the vibrating plate, resonant patterns excited from microwave cavities, and lasing modes emitted from the vertical cavity.

Purification of radiolabeled RNA products using denaturing gel electrophoresis

This unit discusses a basic method for purification of radiolabeled RNAs using denaturing polyacrylamide gel electrophoresis. The method consists of a number of experimental procedures, including total RNA preparation from yeast cells, isolation of a specific RNA from total yeast RNA, RNA 3'-terminal labeling using nucleotide (5' [(32) P]pCp) addition (via ligation), denaturing (8 M urea) polyacrylamide gel electrophoresis, and RNA extraction from the gel slice. Key points for achieving good electrophoretic separation of RNA are also discussed.

RNA-guided isomerization of uridine to pseudouridine--pseudouridylation

Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs.

Efficient continuous-wave self-Raman Yb:KGW laser with a shift of 89 cm⁻¹

We demonstrated a continuous-wave (CW) self-Raman laser with high conversion efficiency by using Yb:KGW as the Raman crystal. The first Stokes line of wavelength centered at 1095.2 nm with spectral bandwidth of 8 nm and the cascaded Raman conversion wavelength at 1109.5 nm with spectral bandwidth of 3.4 nm were observed with a Raman shift of 89 cm⁻¹ with respect to the fundamental laser wavelength at 1085.0 nm with spectral bandwidth of 10 nm. The CW Raman output power of 1.7 W was attained under the diode pump power of 7.8 W which corresponds to the slope efficiency and the diode-to-Stokes optical conversion efficiency of 26.6% and 21.8%, respectively.

Unusual base pairing during the decoding of a stop codon by the ribosome

During normal translation, binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires formation of two normally forbidden purine-purine base pairs¹. We have determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA^Ser bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which display an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding center to accommodate non-canonical base pairs.

Synthesis and labeling of RNA in vitro

This unit discusses several methods for generating large amounts of uniformly labeled, end-labeled, and site-specifically labeled RNAs in vitro. The methods involve a number of experimental procedures, including RNA transcription, 5' dephosphorylation and rephosphorylation, 3' terminal nucleotide addition (via ligation), site-specific RNase H cleavage directed by 2'-O-methyl RNA-DNA chimeras, and 2-piece splint ligation. The applications of these RNA radiolabeling approaches are also discussed.