Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes.

Poly(UG) or 'pUG' dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3' ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions.

The Time to Negative Conversion among Adult COVID-19 Patients on Chronic Hemodialysis Admitted at the Philippine General Hospital - A Retrospective Cohort Study.

Objectives: In the Philippines, patients on chronic hemodialysis with COVID-19 remain admitted in hospitals despite clinical recovery because most free-standing dialysis units require proof of negative conversion via Reverse Transcriptase - Polymerase Chain Reaction (RT-PCR). This study aims to determine the time to negative conversion of COVID-19 RT-PCR testing among adult patients on chronic hemodialysis with COVID-19 admitted at the Philippine General Hospital (PGH) and bring insight in using the symptom or time-based procedure as recommended by local guideline, and ultimately, to ensure delivery of adequate hemodialysis despite being infected with COVID-19, shorten isolation period, and conserve resources especially in resource-limited settings.

Methods: This is a retrospective cohort study on all adult patients on chronic hemodialysis who were admitted in PGH after the diagnosis of COVID-19 by RT-PCR between March 2020 and February 2021.

Association of Renal Impairment with Interleukin-6 Levels on Clinical Outcomes among COVID-19 Patients in a Tertiary Government COVID-19 Referral Hospital.

Objective: The objective of the study is to determine the association of renal impairment (AKI or CKD) with IL-6 levels on mortality, intubation, and length of hospitalization among COVID-19 positive patients.

Methods: This is a retrospective cohort study involving chart review of COVID-19 patients with IL-6 levels and admitted from May 2020 to April 2021. The KDIGO criteria was used for determining renal impairment.

Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy.

Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA 3'-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release.

An atypical RNA quadruplex marks RNAs as vectors for gene silencing.

The addition of poly(UG) ('pUG') repeats to 3' termini of mRNAs drives gene silencing and transgenerational epigenetic inheritance in the metazoan Caenorhabditis elegans. pUG tails promote silencing by recruiting an RNA-dependent RNA polymerase (RdRP) that synthesizes small interfering RNAs. Here we show that active pUG tails require a minimum of 11.

Flagellar Structures from the Bacterium Caulobacter crescentus and Implications for Phage CbK Predation of Multiflagellin Bacteria.

is a Gram-negative alphaproteobacterium that commonly lives in oligotrophic fresh- and saltwater environments. is a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which require interaction with the bacterial flagellum and pilus complexes during adsorption. It is commonly thought that the six paralogs of the flagellin gene present in are important for bacteriophage evasion.

Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.

Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by only one out of seven subunits.

Teaching Renal Physiology to the Millennial Student: the University of the Philippines Manila Experience.

Objectives: To compare the conventional style from a multi-modal approach in the teaching of renal physiology among University of the Philippines-College of Medicine (UPCM) first-year medical students in terms of their attitudes and rating scale.

Methods: We conducted an exploratory sequential mixed methods design using an online survey employing a likert scale followed by a focus group discussion of medical students taking the excretory module from 2016 to 2019. Abbreviated plenary live lectures, online videos embedded in a learning management system, patient contact experience ward work, role-playing, and quiz shows are used to integrate the lessons being taught.

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group.

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking.

The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U-U mismatch sandwiched between Watson-Crick pairs.

Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.

Post-transcriptional modification of snRNA is central to spliceosome function. Usb1 is an exoribonuclease that shortens the oligo-uridine tail of U6 snRNA, resulting in a terminal 2',3' cyclic phosphate group in most eukaryotes, including humans. Loss of function mutations in human Usb1 cause the rare disorder poikiloderma with neutropenia (PN), and result in U6 snRNAs with elongated 3' ends that are aberrantly adenylated.

Measuring Provider Compliance with an Institution-Based Clinical Pathway for Diverticulitis Using Radiologic Criteria.

Background: Diverticulitis remains a common disease encountered in the acute care setting. Management strategies have been developed to guide treatment decisions based on imaging. By using a multi-faceted clinical pathway approach, a standardized method of diagnosing and categorizing disease severity can be performed in order to guide appropriate management.

Patient with a Subarachnoid Headache.

Subarachnoid hemorrhage (SAH) is a life-threatening cause of headache. The diagnostic approach to this entity continues to evolve with a recent questioning of the classic workup of computed tomography and lumbar puncture. We report a risk management case of a patient with a missed SAH resulting in a fatal outcome.

Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities.

U6 small nuclear ribonucleoprotein (snRNP) biogenesis is essential for spliceosome assembly, but not well understood. Here, we report structures of the U6 RNA processing enzyme Usb1 from yeast and a substrate analog bound complex from humans. Unlike the human ortholog, we show that yeast Usb1 has cyclic phosphodiesterase activity that leaves a terminal 3' phosphate which prevents overprocessing.

Fluorescent Branched RNAs for High-Throughput Analysis of Dbr1 Enzyme Kinetics and Inhibition.

We have developed fluorescent 2',5' branched RNAs (bRNA) that permit real time monitoring of RNA lariat (intron) debranching enzyme (Dbr1) kinetics. These compounds contain fluorescein (FAM) on the 5' arm of the bRNA that is quenched by a dabcyl moiety on the 2' arm. Dbr1-mediated hydrolysis of the 2',5' linkage induces a large increase in fluorescence, providing a convenient assay for Dbr1 hydrolysis.

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.

U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al.

Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.

Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2',5'- and 3',5'-phosphodiester linkages. The 2',5'-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA.

Corrigendum to "Determination of normative reference for the definition of sarcopenia among Filipinos" [Osteoporos. Sarcopenia 2 (2016) 186-190].

[This corrects the article DOI: 10.1016/j.afos.

Determination of normative reference for the definition of sarcopenia among Filipinos.

Background: At present, there is no normative value that can be used in the definition of sarcopenia in the Philippines.

Objective: We identified the reference cut-off values for: 1) muscle mass using bioimpedance analysis; 2) grip strength; 3) usual gait speed; 4) timed get-up-and-go; and 5) short physical performance battery in the Philippines in order to adapt the European Working Group on Sarcopenia in Older People (EWGSOP) criteria for the definition of sarcopenia.

Methods: Two hundred seventy six (135 males and 141 females) healthy Filipino adults, between 20 and 40 years, were included in this cross sectional study.

Workflow efficiency for the treatment planning process in CT-guided high-dose-rate brachytherapy for cervical cancer.

Purpose: To investigate process efficiency, we present a prospective investigation of the treatment planning phase of image-guided brachytherapy (BT) for cervical cancer using a specific checklist.

Methods And Materials: From October 2012 to January 2014, 76 BT procedures were consecutively performed. Prospective data on the CT-based treatment planning process was collected using a specific checklist which details the following steps: (1) dosimetry planning, (2) physician review start, (3) physician review time, (4) dosimetry processing, (5) physics review start, (6) physics review, and (7) procedural pause.

Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

NMR and SAXS (small-angle X-ray scattering)/WAXS (wide-angle X-ray scattering) are highly complementary approaches for the analysis of RNA structure in solution. Here we describe an efficient NMR-SAXS/WAXS approach for structural investigation of multi-helical RNAs. We illustrate this approach by determining the overall fold of a 92-nt 3-helix junction from the U4/U6 di-snRNA.