Olivia Yang - Academia.edu (original) (raw)

Papers by Olivia Yang

Frontiers in Neuroscience, Jan 23, 2023

Gene delivery or manipulation with viral vectors is a frequently used tool in basic neuroscience ... more Gene delivery or manipulation with viral vectors is a frequently used tool in basic neuroscience studies. Adeno-associated viruses (AAV) are the most widely used vectors due to their relative safety and long-term efficacy without causing overt immunological complications. Many AAV serotypes have been discovered and engineered that preferentially transduce different populations of neurons. However, efficient targeting of peripheral neurons remains challenging for many researchers, and evaluation of peripheral neuron transduction with AAVs in rats is limited. Here, we aimed to test the efficiency of systemic AAVs to transduce peripheral neurons in rats. We administered AAV9-tdTomato, AAV-PHP.S-tdTomato, or AAV-retro-GFP systemically to neonatal rats via intraperitoneal injection. After 5 weeks, we evaluated expression patterns in peripheral sensory, motor, and autonomic neurons. No significant difference between the serotypes in the transduction of sensory neurons was noted, and all serotypes were more efficient in transducing NF200 + neurons compared to smaller CGRP + neurons. AAV-retro was more efficient at transducing motor neurons compared to other serotypes. Moreover, PHP.S was more efficient at transducing sympathetic neurons, and AAV-retro was more efficient at transducing parasympathetic neurons. These results indicate that specific AAV serotypes target peripheral neuron populations more efficiently than others in the neonatal rat.

bioRxiv (Cold Spring Harbor Laboratory), Oct 18, 2017

CRISPR-Cas9, which imparts adaptive immunity against foreign genomic invaders in certain prokaryo... more CRISPR-Cas9, which imparts adaptive immunity against foreign genomic invaders in certain prokaryotes, has been repurposed for genome-engineering applications. More recently, another RNA-guided CRISPR endonuclease called Cpf1 (also known as Cas12a) was identified and is also being repurposed. Little is known about the kinetics and mechanism of Cpf1 DNA interaction and how sequence mismatches between the DNA target and guide-RNA influence this interaction. We have used single-molecule fluorescence analysis and biochemical assays to characterize DNA interrogation, cleavage, and product release by three Cpf1 orthologues. Our Cpf1 data are consistent with the DNA interrogation mechanism proposed for Cas9, they both bind any DNA in search of PAM (protospacer-adjacent motif) sequences, verifies the target sequence directionally from the PAM-proximal end and rapidly rejects any targets that lack a PAM or that are poorly matched with the guide-RNA. Unlike Cas9, which requires 9 bp for stable binding and ~16 bp for cleavage, Cpf1 requires ~ 17 bp sequence match for both stable binding and cleavage. Unlike Cas9, which does not release the DNA cleavage products, Cpf1 rapidly releases the PAMdistal cleavage product, but not the PAM-proximal product. Solution pH, reducing conditions and 5' guanine in guide-RNA differentially affected different Cpf1 orthologues. Our findings have important implications on Cpf1-based genome engineering and manipulation applications. In bacteria, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) acts as an adaptive defense system against foreign genetic elements(1). The system achieves adaptive immunity by storing short sequences of invader DNA into the host genome, which get transcribed and processed into small CRISPR RNA (crRNA). These crRNAs form a complex with a CRISPR nuclease to guide the nuclease to complementary foreign nucleic acids (protospacers) for cleavage. Binding and cleavage also require that the protospacer be adjacent to the protospacer adjacent motif (PAM)(2, 3). CRISPR-Cas9, chiefly the Cas9 from Streptococcus pyogenes (SpCas9), has been repurposed to create an RNA-programmable endonuclease for gene knockout and editing(4-6). Nuclease deficient Cas9 has also been used for tagging genomic sites in wide-ranging applications(4-6). This repurposing has revolutionized biology and sparked a search for other CRISPR-Cas enzymes(7, 8). One such search led to the discovery of the Cas protein Cpf1, with some of its orthologues reporting

International Journal of Science and Mathematics Education, Apr 28, 2006

This study researched the use of writing-to-learn strategies within a highschool (Year 11) chemis... more This study researched the use of writing-to-learn strategies within a highschool (Year 11) chemistry classroom. The writing task itself asked the students to write a business letter to a younger audience of middle-school (Year 7) students. A mixedmethod design was used for the study, incorporating pre/post-testing with semistructured interviews. The evidence supports that the treatment students performed statistically significantly better on a conceptual question compared to the control group. Additionally, the treatment students felt that writing to a younger audience prompted them to use different language than they would have if, for example, writing to their teacher. Further, the treatment students described that the writing task promoted their understanding of and their confidence in their knowledge of the stoichiometry concepts addressed in class.

BACKGROUND LGBTQ+ youth and adults use tobacco at a higher rate than the national average in the ... more BACKGROUND LGBTQ+ youth and adults use tobacco at a higher rate than the national average in the US. There is an urgent need for synthesizing published evidence to inform tobacco control policies to better serve this priority population. OBJECTIVE To develop algorithms to curate peer-reviewed articles that study LGBTQ individuals’ tobacco use and that are published at leading tobacco research journals from 2015 to early 2021, and to extract domain-specific textual entities from these articles. METHODS Our team built a tobacco research domain-specific semantic database to identify and extract data from articles that studied the LGBTQ+ population. We trained and employed a language model to extract named entities after learning patterns and relationships between words and their context in text. RESULTS Among 2,993 paper abstracts, 33 were identified as relevant to LGBTQ individuals’ tobacco use. We extracted the following information: different groups being studied, within the LGBTQ+ ...

Brown Hospital Medicine, Apr 1, 2023

Urothelial cells, which play an essential role in the barrier function, are also thought to play ... more Urothelial cells, which play an essential role in the barrier function, are also thought to play a sensory role in bladder physiology by releasing signaling molecules in response to sensory stimuli that act upon adjacent sensory neurons. However, it is challenging to study this communication due to the overlap in receptor expression and proximity of urothelial cells to sensory neurons. To overcome this challenge, we have developed a mouse model where we can directly stimulate urothelial cells using optogenetics. We have crossed a uroplakin II-cre mouse (UPK2-Cre) with a mouse that expresses the light-activated cation channel, Channelrhodopsin-2 (ChR2), in the presence of cre-expression. Optogenetic stimulation of urothelial cells cultured from UPK2-ChR2 initiates cellular depolarization and release of adenosine triphosphate. Cystometry recordings demonstrate that optical stimulation of urothelial cells increases bladder pressure and pelvic nerve activity. Increases in bladder pressu...

Frontiers in Neuroscience

The Journal of Pain, May 1, 2022

Nucleic Acids Research, 2020

FANCJ, a DNA helicase and interacting partner of the tumor suppressor BRCA1, is crucial for the r... more FANCJ, a DNA helicase and interacting partner of the tumor suppressor BRCA1, is crucial for the repair of DNA interstrand crosslinks (ICL), a highly toxic lesion that leads to chromosomal instability and perturbs normal transcription. In diploid cells, FANCJ is believed to operate in homologous recombination (HR) repair of DNA double-strand breaks (DSB); however, its precise role and molecular mechanism is poorly understood. Moreover, compensatory mechanisms of ICL resistance when FANCJ is deficient have not been explored. In this work, we conducted a siRNA screen to identify genes of the DNA damage response/DNA repair regime that when acutely depleted sensitize FANCJ CRISPR knockout cells to a low concentration of the DNA cross-linking agent mitomycin C (MMC). One of the top hits from the screen was RAP80, a protein that recruits repair machinery to broken DNA ends and regulates DNA end-processing. Concomitant loss of FANCJ and RAP80 not only accentuates DNA damage levels in human ...

A fast and sensitive LC-MS/MS method was developed for the analysis of 22 phthalates utilizing a ... more A fast and sensitive LC-MS/MS method was developed for the analysis of 22 phthalates utilizing a simple extraction, fast LC separation using a Phenomenex KinetexTM C18 column with a run time of 10 minutes, and selective MS/MS detection using an AB SCIEX QTRAP 5500 system operated in Multiple Reaction Monitoring (MRM) mode. Major challenges of method development were the presence of chemical background and matrix interferences. To address these challenges we successfully applied the unique MRM mode to enhance detection selectivity by detecting second generation product ions and Enhanced Product Ion (EPI) scanning to increase confidence in identification using the molecular fingerprint of each target analyte saved into the MS/MS spectrum. In addition, the AB SCIEX SelexIONTM technology was used to separate critical isomers using Differential Mobility Spectrometry (DMS).

Methods in Enzymology, 2018

Single-stranded DNA-binding protein (SSB) is important not only for the protection of single-stra... more Single-stranded DNA-binding protein (SSB) is important not only for the protection of single-stranded DNA (ssDNA) but also for the recruitment of other proteins for DNA replication, recombination, and repair. The interaction of SSB with ssDNA is highly dynamic as it exists as an intermediate during cellular processes that unwind dsDNA. It has been proposed that SSB redistributes itself among multiple ssDNA segments, but transient intermediates are difficult to observe in bulk experiments. We can use single-molecule FRET microscopy to observe intermediates of the transfer of a single Escherichia coli SSB from one ssDNA strand to another or exchange of one SSB for another on a single ssDNA in real time. This single-molecule approach can be further applicable to understand relative binding affinities and competitive dynamics for other SSBs and variants across various systems.

Cell-cell interactions shape cellular function and ultimately organismal phenotype. However, the ... more Cell-cell interactions shape cellular function and ultimately organismal phenotype. However, the code embedded in the molecular interactions driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell, which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans’ body. Leveraging a 3D atlas of C. elegans’ cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, ...

Science Inquiry, Argument and Language, 2008

Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA... more Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA, but the mechanism by which Pif1 unwinds forked dsDNA remains elusive. Here we report the structure of Bacteroides sp Pif1 (BaPif1) in complex with a symmetrical double forked dsDNA. Two interacting BaPif1 molecules are bound to each fork of the partially unwound dsDNA, and interact with the 5′ arm and 3′ ss/dsDNA respectively. Each of the two BaPif1 molecules is an active helicase and their interaction may regulate their helicase activities. The binding of BaPif1 to the 5′ arm causes a sharp bend in the 5′ ss/dsDNA junction, consequently breaking the first base-pair. BaPif1 bound to the 3′ ss/dsDNA junction impacts duplex unwinding by stabilizing the unpaired first base-pair and engaging the second base-pair poised for breaking. Our results provide an unprecedented insight into how two BaPif1 coordinate with each other to unwind the forked dsDNA.

Nature Chemical Biology, 2019

Holliday junction (HJ) resolution by its resolving enzymes is essential for chromosome segregatio... more Holliday junction (HJ) resolution by its resolving enzymes is essential for chromosome segregation and recombination-mediated DNA repair. HJs undergo two types of structural dynamics that determine the outcome of recombination: conformer exchange between two isoforms and branch migration. However, it is unknown how the preferred 1 branch-point and conformer are achieved between enzyme binding and HJ resolution given the extensive binding interactions seen in static crystal structures. Single molecule fluorescence resonance energy transfer analysis of resolving-enzymes from bacteriophages (T7 endonuclease I), bacteria (RuvC), fungi (GEN1) and humans (hMus81-Eme1) showed that both types of HJ dynamics still occur after enzyme binding. These dimeric enzymes use their multivalent interactions to achieve this, going through a partially-dissociated intermediate in which the HJ undergoes nearly unencumbered dynamics. This evolutionarily conserved property of HJ resolving-enzymes provides previously unappreciated insight on how junction resolution, conformer exchange and branch migration may be coordinated.

Proceedings of the National Academy of Sciences of the United States of America, May 22, 2018