MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.[Keywords: miRNA; noncoding RNA; computational gene identification; Dicer] Supplemental material is available at http://www.genesdev.org. Noncoding RNAs (ncRNAs) of ∼22 nucleotides (nt) in length are increasingly recognized as playing important roles in regulating gene expression in animals, plants, and fungi. The first such tiny regulatory RNA to be identified was the lin-4 RNA, which controls the timing of Caenorhabditis elegans larval development (Lee et al. 1993;Wightman et al. 1993). This 21-nt RNA pairs to sites within the 3Ј untranslated region (UTR) of target mRNAs, specifying the translational repression of these mRNAs and triggering the transition to the next developmental stage (Lee et al. 1993;Wightman et al. 1993;Ha et al. 1996;Moss et al. 1997;Olsen and Ambros 1999). A second tiny riboregulator, let-7 RNA, is expressed later in development and appears to act in a similar manner to trigger the transition to late-larval and adult stages Slack et al. 2000). The lin-4 and let-7 RNAs are sometimes called small temporal RNAs (stRNAs) because of their important roles in regulating the timing of larval development . The lin-4 and let-7 stRNAs are now recognized as the founding members of a large class of ∼22-nt ncRNAs termed microRNAs (miRNAs), which resemble stRNAs but do not necessarily control developmental timing (Lagos-Quintana et al. 2001;Lau et al. 2001;Lee and Ambros 2001).Understanding the biogenesis and function of miRNAs has been greatly facilitated by analogy and contrast to another class of tiny ncRNAs known as small interfering RNAs (siRNAs), first identified because of their roles in mediating RNA interference (RNAi) in animals and posttranscriptional ge...

RESULTS. From an estimated 340 residency programs around NYC, recruitment yielded 91 responses, representing 24 specialties and 2306 residents. In 45.1% of programs, at least 1 resident with confirmed COVID-19 was reported. One hundred one resident physicians were confirmed COVID-19-positive, with an additional 163 residents presumed positive for COVID-19 based on symptoms but awaiting or unable to obtain testing. Two COVID-19-positive residents were hospitalized, with 1 in intensive care. Among specialties with more than 100 residents represented, negative binomial regression indicated that infection risk differed by specialty (P = 0.039). In 80% of programs, quarantining a resident was reported. Ninety of 91 programs reported reuse or extended mask use, and 43 programs reported that personal protective equipment (PPE) was suboptimal. Sixty-five programs (74.7%) redeployed residents elsewhere to support COVID-19 efforts. CONCLUSION. Many resident physicians around NYC have been affected by COVID-19 through direct infection, quarantine, or redeployment. Lack of access to testing and concern regarding suboptimal PPE are common among residency programs. Infection risk may differ by specialty.

Neuroretinitis can result from a number of infectious and noninfectious causes and it is essential that clinicians recognize the disease and determine the underlying etiology to ensure the best possible treatment and visual prognosis for the patient.

Cell entry by non-enveloped viruses requires translocation into the cytosol of a macromolecular complex—for double-strand RNA viruses, a complete subviral particle. We have used live-cell fluorescence imaging to follow rotavirus entry and penetration into the cytosol of its ∼700 Å inner capsid particle (“double-layered particle”, DLP). We label with distinct fluorescent tags the DLP and each of the two outer-layer proteins and track the fates of each species as the particles bind and enter BSC-1 cells. Virions attach to their glycolipid receptors in the host cell membrane and rapidly become inaccessible to externally added agents; most particles that release their DLP into the cytosol have done so by ∼10 minutes, as detected by rapid diffusional motion of the DLP away from residual outer-layer proteins. Electron microscopy shows images of particles at various stages of engulfment into tightly fitting membrane invaginations, consistent with the interpretation that rotavirus particles drive their own uptake. Electron cryotomography of membrane-bound virions also shows closely wrapped membrane. Combined with high resolution structural information about the viral components, these observations suggest a molecular model for membrane disruption and DLP penetration.

Clp/Hsp100 ATPases remodel and disassemble multiprotein complexes, yet little is known about how they preferentially recognize these complexes rather than their constituent subunits. We explore how substrate multimerization modulates recognition by the ClpX unfoldase using a natural substrate, MuA transposase. MuA is initially monomeric but forms a stable tetramer when bound to transposon DNA. Destabilizing this tetramer by ClpX promotes an essential transition in the phage Mu recombination pathway. We show that ClpX interacts more tightly with tetrameric than with monomeric MuA. Residues exposed only in the MuA tetramer are important for enhanced recognition--which requires the N domain of ClpX--as well as for a high maximal disassembly rate. We conclude that an extended set of potential enzyme contacts are exposed upon assembly of the tetramer and function as internal guides to recruit ClpX, thereby ensuring that the tetrameric complex is a high-priority substrate.

Hyperopia (farsightedness) is a common and significant cause of visual impairment, and extreme hyperopia (nanophthalmos) is a consequence of loss-of-function MFRP mutations. MFRP deficiency causes abnormal eye growth along the visual axis and significant visual comorbidities, such as angle closure glaucoma, cystic macular edema, and exudative retinal detachment. The Mfrp rd6 /Mfrp rd6 mouse is used as a pre-clinical animal model of retinal degeneration, and we found it was also hyperopic. To test the effect of restoring Mfrp expression, we delivered a wild-type Mfrp to the retinal pigmented epithelium (RPE) of Mfrp rd6 /Mfrp rd6 mice via adeno-associated viral (AAV) gene therapy. Phenotypic rescue was evaluated using non-invasive, human clinical testing, including fundus auto-fluorescence, optical coherence tomography, electroretinography, and ultrasound. These analyses showed gene therapy restored retinal function and normalized axial length. Proteomic analysis of RPE tissue revealed rescue of specific proteins associated with eye growth and normal retinal and RPE function. The favorable response to gene therapy in Mfrp rd6 /Mfrp rd6 mice suggests hyperopia and associated refractive errors may be amenable to AAV gene therapy.

Background From March 2-April 12, 2020, New York City (NYC) experienced exponential growth of the COVID-19 pandemic due to novel coronavirus (SARS-CoV-2). Little is known regarding how physicians have been affected. We aimed to characterize COVID-19 impact on NYC resident physicians. Methods IRB-exempt and expedited cross-sectional analysis through survey to NYC residency program directors (PDs) April 3-12, 2020, encompassing events from March 2-April 12, 2020. Findings From an estimated 340 residency programs around NYC, recruitment yielded 91 responses, representing 24 specialties and 2,306 residents. 45.1% of programs reported at least one resident with confirmed COVID-19: 101 resident physicians were confirmed COVID-19-positive, with additional 163 residents presumed positive for COVID-19 based on symptoms but awaiting or unable to obtain testing. 56.5% of programs had a resident waiting for, or unable to obtain, COVID-19 testing. Two COVID-19-positive residents were hospitalized, with one in intensive care. Among specialties with >100 residents represented, negative binomial regression indicated that infection risk differed by specialty (p=0.039). Although most programs (80%) reported quarantining a resident, with 16.8% of residents experiencing quarantine, 14.9% of COVID-19-positive residents were not quarantined. 90 programs, encompassing 99.2% of the resident physicians, reported reuse or extended mask use, and 43 programs, encompassing 60.4% of residents, felt that personal protective equipment (PPE) was suboptimal. 65 programs (74.7%) have redeployed residents elsewhere to support COVID-19 efforts. Interpretation Many resident physicians around NYC have been affected by COVID-19 through direct infection, quarantine, or redeployment. Lack of access to testing and concern regarding suboptimal PPE are common among residency programs. Infection risk may differ by specialty. Funding AHA, MPB, RWSC, CGM, LRDG, and JDH are supported by NEI Core Grant P30EY019007, and unrestricted grant from RPB. ACP and JS are supported by Parker Family Chair. SXX is supported by University of Pennsylvania.

Purpose: To describe the differential response of two distinct inflammatory signs occurring in eyes with punctate inner choroidopathy. Methods: Retrospective, observational case series using multimodal imaging. Results: Four eyes of 4 myopic female patients (mean age of 35 years, range 31–42 years) presenting with retinal manifestations of punctate inner choroidopathy. All study eyes had 2 distinct signs of active disease: 1) acute focal hyperreflective lesions splitting the retinal pigment epithelium/Bruch membrane complex on optical coherence tomography which appeared hypoautofluorescent on fundus autofluorescence and 2) more diffuse areas of outer retinal disruption limited to the ellipsoid zone and interdigitation zone on optical coherence tomography and corresponding to hyperautofluorescence on fundus autofluorescence. All patients were treated with oral prednisone and demonstrated prompt regression of the retinal pigment epithelium/Bruch membrane complex lesions with a concurrent, paradoxical centrifugal expansion of outer retinal disruption. The outer retinal disruption eventually resolved in all eyes (mean time of 6 weeks, range 4–10 weeks). Conclusion: In patients with punctate inner choroidopathy, two distinct inflammatory signs observed with multimodal imaging display a differential response to systemic corticosteroids. Although focal inflammatory lesions splitting the retinal pigment epithelium/Bruch membrane complex seem to respond rapidly, the more diffuse, transient outer retinal disruption shows little response. This difference in treatment response may reflect different immunological phenomena with independent natural history.