Elevated levels of intracellular RNA lariats suppress the antiviral response.

Unlabelled: Recent studies report the genetic loss of the lariat debranching enzyme ( ) activity increases susceptibility to viral infection. Here, we show that more than 25% of human introns contain large hairpin structures created by the folding of two elements inserted in opposite orientation. In wildtype cells, this large reservoir of endogenous dsRNA is efficiently degraded.

The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.

The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover.

Ensemble Detection of DNA Engineering Signatures.

Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy.

Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films.

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline InO-derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques.

The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.

The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover.

BTN3A3 evasion promotes the zoonotic potential of influenza A viruses.

Spillover events of avian influenza A viruses (IAVs) to humans could represent the first step in a future pandemic. Several factors that limit the transmission and replication of avian IAVs in mammals have been identified. There are several gaps in our understanding to predict which virus lineages are more likely to cross the species barrier and cause disease in humans.

The Timing and Magnitude of the Type I Interferon Response Are Correlated with Disease Tolerance in Arbovirus Infection.

Infected hosts possess two alternative strategies to protect themselves against the negative impact of virus infections: resistance, used to abrogate virus replication, and disease tolerance, used to avoid tissue damage without controlling viral burden. The principles governing pathogen resistance are well understood, while less is known about those involved in disease tolerance. Here, we studied bluetongue virus (BTV), the cause of bluetongue disease of ruminants, as a model system to investigate the mechanisms of virus-host interactions correlating with disease tolerance.

Structure-Transport Properties Governing the Interplay in Humidity-Dependent Mixed Ionic and Electronic Conduction of Conjugated Polyelectrolytes.

Polymeric mixed ionic-electronic conductors (MIECs) are of broad interest in the field of energy storage and conversion, optoelectronics, and bioelectronics. A class of polymeric MIECs are conjugated polyelectrolytes (CPEs), which possess a π-conjugated backbone imparting electronic transport characteristics along with side chains composed of a pendant ionic group to allow for ionic transport. Here, our study focuses on the humidity-dependent structure-transport properties of poly[3-(potassium--alkanoate) thiophene-2,5-diyl] (P3KT) CPEs with varied side-chain lengths of = 4-7.

Water splitting with silicon p-i-n superlattices suspended in solution.

Photoelectrochemical (PEC) water splitting to produce hydrogen fuel was first reported 50 years ago, yet artificial photosynthesis has not become a widespread technology. Although planar Si solar cells have become a ubiquitous electrical energy source economically competitive with fossil fuels, analogous PEC devices have not been realized, and standard Si p-type/n-type (p-n) junctions cannot be used for water splitting because the bandgap precludes the generation of the needed photovoltage. An alternative paradigm, the particle suspension reactor (PSR), forgoes the rigid design in favour of individual PEC particles suspended in solution, a potentially low-cost option compared with planar systems.

Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1.

In eukaryotic cells, intron lariats produced by the spliceosome contain a 2'5' phosphodiester linkage. The RNA lariat debranching enzyme, Dbr1, is the only enzyme known to hydrolyze this bond. Dbr1 is a member of the metallophosphoesterase (MPE) family of enzymes, and recent X-ray crystal structures and biochemistry data demonstrate that Dbr1 from uses combinations of Mn, Zn, and Fe as enzymatic cofactors.

Lack of authentic atrial fibrillation in commonly used murine atrial fibrillation models.

The mouse is a useful preclinical species for evaluating disease etiology due to the availability of a wide variety of genetically modified strains and the ability to perform disease-modifying manipulations. In order to establish an atrial filtration (AF) model in our laboratory, we profiled several commonly used murine AF models. We initially evaluated a pharmacological model of acute carbachol (CCh) treatment plus atrial burst pacing in C57BL/6 mice.

Influence of Surface and Structural Variations in Donor-Acceptor-Donor Sensitizers on Photoelectrocatalytic Water Splitting.

Conjugated organic chromophores composed of linked donor (D) and acceptor (A) moieties have attracted considerable attention for photoelectrochemical applications. In this work, we compare the optoelectronic properties and photoelectrochemical performance of two D-A-D structural isomers with thiophene--carboxylic acid ( denotes 3 and 2 positions) derivatives and 2,1,3-benzothiadiazole as the D and A moieties, respectively. 5,5'-(Benzo[][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-3-carboxylic acid), , and 5,5'-(benzo[][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-2-carboxylic acid), , were employed in the study to understand how structural isomers affect surface attachments within chromophore-catalyst assemblies and their influence on charge-transfer dynamics.

ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data.

Background: Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint.

Evaluation of a Quality Improvement Intervention That Eliminated Routine Use of Opioids After Cesarean Delivery.

Objective: To evaluate the effects of eliminating the routine use of oral opioids for postcesarean delivery analgesia on postcesarean opioid consumption.

Methods: At a tertiary care center, we implemented a quality improvement intervention among faculty practice patients undergoing cesarean delivery, which consisted of 1) eliminating routine ordering of oral opioids after cesarean delivery, 2) implementing guidelines for ordering a short course of opioids when deemed necessary, and 3) coupling opioid prescribing at discharge to patterns of opioid use in-hospital combined with shared decision-making. All patients, both before and after the intervention, were administered neuraxial opioids and scheduled acetaminophen and nonsteroidal antiinflammatory medications in the absence of contraindications.

Burkitt Lymphoma Presenting as Menorrhagia and a Vaginal Mass in an Adolescent.

Background: Menorrhagia is a common gynecologic complaint among adolescents, which rarely is secondary to malignancy. Burkitt lymphoma can mimic gynecologic malignancy, however it is rarely seen in adolescents. Burkitt lymphoma of the gynecologic tract requires early diagnosis and intervention for optimal outcomes.

Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection.

Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme.

Widespread intra-dependencies in the removal of introns from human transcripts.

Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing.

Sensitivity to BST-2 restriction correlates with Orthobunyavirus host range.

Orthobunyaviruses include several recently emerging viruses of significant medical and veterinary importance. There is currently very limited understanding on what determines the host species range of these pathogens. In this study we discovered that BST-2/tetherin restricts orthobunyavirus replication in a host-specific manner.

The effects of structure on pre-mRNA processing and stability.

Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research.

Large-scale analysis of branchpoint usage across species and cell lines.

The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states.

Ultraviolet Imaging with Low Cost Smartphone Sensors: Development and Application of a Raspberry Pi-Based UV Camera.

Here, we report, for what we believe to be the first time, on the modification of a low cost sensor, designed for the smartphone camera market, to develop an ultraviolet (UV) camera system. This was achieved via adaptation of Raspberry Pi cameras, which are based on back-illuminated complementary metal-oxide semiconductor (CMOS) sensors, and we demonstrated the utility of these devices for applications at wavelengths as low as 310 nm, by remotely sensing power station smokestack emissions in this spectral region. Given the very low cost of these units, ≈ USD 25, they are suitable for widespread proliferation in a variety of UV imaging applications, e.