Biology subjects

Steinberg, R.

Publications and source records attributed to Steinberg, R..

5 recordsLinked to original sources

bioRxiv2026

Transcript-Specific Site-Directed RNA Editing Reveals Principles for Splice-aware guide RNA Design

Site-directed RNA editing (SDRE) utilizing the adenosine deaminase acting on RNA (ADAR) enzymes is commonly facilitated by guide RNAs (gRNAs) optimized to enhance on-target editing and minimize bystander effects. However, the impact of gRNA binding and ADAR-mediated SDRE on canonical pre-mRNA splicing remains poorly understood. Here, we developed an in vitro transcript-specific editing strategy that enables selective targeting and direct comparison of SDRE in pre-mRNA and mature mRNA. Using splice-relevant variants associated with inherited retinal diseases, we investigated the effects of SDRE on exonic, near-canonical intronic, and deep intronic splice variants. We identified gRNA-induced splice perturbation at exonic and intronic targets and observed that higher editing levels could be associated with increased splice disruption. Conversely, SDRE of two exonic splice variants and a deep intronic variant resulted in increased production of correctly spliced transcripts, demonstrating the potential of SDRE for splice modulation. Finally, by dissecting the effects of ADAR expression and gRNA design on editing and splicing outcomes, we established a system for identifying design principles that reduce splice interference and enhance the generation of correctly spliced, edited transcripts. These findings highlight the importance of considering transcript context and splicing consequences in the development of SDRE-based therapeutic strategies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/741163v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@55e0cforg.highwire.dtl.DTLVardef@1a5c29org.highwire.dtl.DTLVardef@98aec7org.highwire.dtl.DTLVardef@1fab73b_HPS_FORMAT_FIGEXP M_FIG Created in BioRender. Schneider, N. (2026) https://BioRender.com/59i0tiy C_FIG

molecular biology↗

bioRxiv2023

ENDO-LYSOSOME-TARGETED NANOPARTICLE DELIVERY OF ANTIVIRAL THERAPY FOR CORONAVIRUS INFECTIONS

SARS-CoV-2 can infect cells through endocytic uptake, a process which is targeted by inhibition of lysosomal proteases. However, clinically this approach to treat viral infections has afforded mixed results, with some studies detailing an oral regimen of hydroxychloroquine accompanied by significant off-target toxicities. We rationalized that an organelle-targeted approach will avoid toxicity while increasing the concentration of the drug at the target. Here we describe a lysosome-targeted, mefloquine-loaded poly(glycerol monostearate-co-{varepsilon}-caprolactone) nanoparticle (MFQ-NP) for pulmonary delivery via inhalation. Mefloquine is a more effective inhibitor of viral endocytosis than hydroxychloroquine in cellular models of COVID-19. MFQ-NPs are less toxic than molecular mefloquine, 100-150 nm in diameter, and possess a negative surface charge which facilitates uptake via endocytosis allowing inhibition of lysosomal proteases. MFQ-NPs inhibit coronavirus infection in mouse MHV-A59 and human OC43 coronavirus model systems and inhibit SARS-CoV-2-WA1 and its Omicron variant in a human lung epithelium model. This study demonstrates that organelle-targeted delivery is an effective means to inhibit viral infection.

bioengineering↗

bioRxiv2019

Eye movements predict test scores in online video education

Experienced teachers pay close attention to their students, adjusting their teaching when students seem lost. This dynamic interaction is missing in online education. We propose to measure attention to online videos remotely by tracking eye movements, as we hypothesize that attentive students follow videos similarly with their eyes. Here we show that inter-subject correlation of eye-movements during instructional video presentation is substantially higher for attentive students, and that synchronized eye movement are predictive of individual test scores on the material presented in the video. These findings replicate for videos in a variety of production styles, learning scenarios and for recall and comprehension questions alike. We reproduce the result using standard web cameras to capture eye-movements in a classroom setting, and with over 1,000 participants at-home without the need to transmit user data. Our results suggest that online education could be made adaptive to a students level of attention in real-time.

neuroscience↗

bioRxiv2018

A TauP301L mouse model of dementia; development of pathology, synaptic transmission, microglial response and cognition throughout life

BackgroundLate stage Alzheimers disease and other dementias are associated with neurofibrillary tangles and neurodegeneration. Here we describe a mouse (TauD35) carrying human Tau with the P301L mutation that results in Tau hyperphosphorylation and tangles. Previously we have compared gene expression in TauD35 mice to mice which develop plaques but no tangles. A similar comparison of other pathological features throughout disease progression is made here between amyloid{beta} and Tau mice described in Parts I and II of this study.\n\nMethodsIn vitro CA1 patch clamp and field recordings were used to investigate synaptic transmission and plasticity. Plaque load and microglia were investigated with immunohistochemistry. Cognition, locomotor activity and anxiety-related behaviours were assessed with a forced-alternation T-maze, open field and light/dark box.\n\nResultsTransgene copy number in TauD35 mice fell into two groups (HighTAU and LowTAU), allowing assessment of dose-dependent effects of overexpression and resulting in tangle load increasing 100-fold for a 2-fold change in protein levels. Tangles were first detected at 8 (HighTAU) or 13 months (LowTAU) but the effects on synaptic transmission and plasticity and behaviour were subtle. However severe neurodegeneration occurred in HighTAU mice at around 17 months preceded by considerable proliferation but little additional activation of microglia. Proliferation only started as neurodegeneration began at 13 months. Similarly to HighTau mice at 13 months of age, LowTAU mice at 24 months of age showed a comparable tangle load and microglial proliferation. However, LowTAU mice showed no neurodegeneration at this stage and considerable microglial activation, stressing the dependence of these effects on overexpression and/or age.\n\nConclusionsComparison of the effects of amyloid{beta} and plaques without tangles in a model of preclinical Alzheimers disease to the effects of tangles without amyloid{beta} plaques in the late stage model described here may clarify the progressive stages of Alzheimers disease. While Tau hyperphosphorylation and neurofibrillary tangles are eventually sufficient to cause severe neurodegeneration, initial effects on synaptic transmission and the immune response are subtle. In contrast while even with a heavy plaque load little if any neurodegeneration occurs, considerable effects on synaptic transmission and the immune system result, even before plaques are detectable.

neuroscience↗

bioRxiv2017

Wikipedia as a gateway to biomedical research: The relative distribution and use of citations in the English Wikipedia

Wikipedia is a gateway to knowledge. However, the extent to which this gateway ends at Wikipedia or continues via supporting citations is unknown. Wikipedias gateway functionality has implications for information design and education, notably in medicine. This study aims to establish benchmarks for the relative distribution and referral (click) rate of citations--as indicated by presence of a Digital Object Identifier (DOI)--from Wikipedia, with a focus on medical citations.\n\nDOIs referred from the English Wikipedia in August 2016 were obtained from Crossref.org. Next, based on a DOIs presence on a WikiProject Medicine page, all DOIs in Wikipedia were categorized as medical (WP:MED) or non-medical (non-WP:MED). Using this categorization, referred DOIs were classified as WP:MED, non-WP:MED, or BOTH, meaning the DOI may have been referred from either category. Data were analyzed using descriptive and inferential statistics.\n\nOut of 5.2 million Wikipedia pages, 4.42% (n=229,857) included at least one DOI. 68,870 were identified as WP:MED, with 22.14% (n=15,250) featuring one or more DOIs. WP:MED pages featured on average 8.88 DOI citations per page, whereas non-WP:MED pages had on average 4.28 DOI citations. For DOIs only on WP:MED pages, a DOI was referred every 2,283 pageviews and for non-WP-MED pages every 2,467 pageviews. DOIs from BOTH pages accounted for 12% (n=58,475) of referrals, making determining a referral rate for BOTH impossible.\n\nWhile these results cannot provide evidence of greater citation referral from WP:MED than non-WP:MED, they do provide benchmarks to assess strategies for changing referral patterns. These changes might include editors adopting new methods for designing and presenting citations or the introduction of teaching strategies that address the value of consulting citations as a tool for extending learning.

scientific communication and education↗