Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 487 records · Page 27Linked to original sources

bioRxiv2018

CRISPRpic: Fast and precise analysis for CRISPR-induced mutations via prefixed index counting

Analysis of CRISPR-induced mutations at targeted loci can be achieved by PCR amplification followed by massively parallel sequencing. We developed a novel algorithm, called CRISPRpic, to analyze sequencing reads from CRISPR experiments via counting exact-matches and pattern-searching. Compared to other methods that are based on sequence alignment, CRISPRpic provides precise mutation calling and ultrafast analysis of sequencing results. The Python script for CRISPRpic is available at https://github.com/compbio/CRISPRpic.

bioinformatics↗

bioRxiv2018

In silico Drug Repositioning of bortezomib to reverse metastatic effect of GALNT14 in lung cancer

Although many molecular targets for cancer therapy have been discovered, they often show poor druggability, which is a major obstacle to develop targeted drugs. As an alternative route to drug discovery, we adopted an in silico drug repositioning (in silico DR) approach based on large-scale gene expression signatures, with the goal of identifying inhibitors of lung cancer metastasis. Our analysis of clinicogenomic data identified GALNT14, an enzyme involved in O-linked N-acetyl galactosamine glycosylation, as a putative driver of lung cancer metastasis leading to poor survival. To overcome the poor druggability of GALNT14, we leveraged Connectivity Map approach, an in silico screening for drugs that are likely to revert the metastatic expression patterns. It leads to identification of bortezomib (BTZ) as a potent metastatic inhibitor, bypassing direct inhibition of poorly druggable target, GALNT14. The anti-metastatic effect of BTZ was verified in vitro and in vivo. Notably, both BTZ treatment and GALNT14 knockdown attenuated TGF{beta}-mediated gene expression and suppressed TGF{beta}-dependent metastatic genes, suggesting that BTZ acts by modulating TGF{beta} signalingTaken together, these results demonstrate that our in silico DR approach is a viable strategy to identify a candidate drug for undruggable targets, and to uncover its underlying mechanisms.

cancer biology↗

bioRxiv2018

Assembly of Mb-size genome segments from linked read sequencing of CRISPR DNA targets

We developed a targeted sequencing method for intact high molecular weight (HMW) DNA targets as large as 0.2 Mb. This process uses HMW DNA isolated from intact cells, custom designed Cas9-guide RNA complexes to generate 0.1 - 0.2 Mb DNA targets, electrophoretic isolation of the DNA targets and sequencing with barcode linked reads. We used alignment methods as well as local assembly of the target regions to identify haplotypes and structural variants (SVs) across multi-Megabase genomic regions. To demonstrate the performance of this approach, we designed three assays that covered a 0.2 Mb region surrounding the BRCA1 gene, a set of 40 overlapping 0.2 Mb targets covering the entire 4-Mb MHC locus, and 18 well-characterized structural variants. Using the highly characterized NA12878 genome, we achieved on-target coverage of more than 50X, while overall whole genome coverage was approximately 4X. We generated haplotypes that completely covered each targeted locus, with a maximum size of 4 Mb (for the MHC region). This method detected structural variants such as deletions and inversions with determination of the exact breakpoints and genotypes. Even breakpoints inside highly homologous segmental duplications are precisely determined with our high-quality assemblies. Overall, this is a new method to sequence large DNA segments.

genomics↗

bioRxiv2018

Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation

Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the insects ineffective as vectors. To utilize Wolbachia effectively as a tool against vector-borne viruses a better understanding of the host-Wolbachia relationship is needed. To investigate Wolbachia-insect interactions we used the Wolbachia/Drosophila model that provides a genetically tractable system for studying host-pathogen interactions. We coupled genome-wide RNAi screening with a novel high-throughput fluorescence in situ hybridization (FISH) assay to detect changes in Wolbachia levels in a Wolbachia-infected Drosophila cell line JW18. 1117 genes altered Wolbachia levels when knocked down by RNAi of which 329 genes increased and 788 genes decreased the level of Wolbachia. Validation of hits included in depth secondary screening using in vitro RNAi, Drosophila mutants, and Wolbachia-detection by DNA qPCR. A diverse set of host gene networks was identified to regulate Wolbachia levels and unexpectedly revealed that perturbations of host translation components such as the ribosome and translation initiation factors results in increased Wolbachia levels both in vitro using RNAi and in vivo using mutants and a chemical-based translation inhibition assay. This work provides evidence for Wolbachia-host translation interaction and strengthens our general understanding of the Wolbachia-host intracellular relationship.\n\nAuthor summaryInsects such as mosquitos act as vectors to spread devastating human diseases such as Dengue, West Nile, and Zika. It is critical to develop control strategies to prevent the transmission of these diseases to human populations. A novel strategy takes advantage of an endosymbiotic bacterium Wolbachia pipientis. The presence of this bacterium in insect vectors prevents successful transmission of RNA viruses. The degree to which viruses are blocked by Wolbachia is dependent on the levels of the bacteria present in the host such that higher Wolbachia levels induce a stronger antiviral effect. In order to use Wolbachia as a tool against vector-borne virus transmission a better understanding of host influences on Wolbachia levels is needed. Here we performed a genome-wide RNAi screen in a model host system Drosophila melanogaster infected with Wolbachia to identify host systems that affect Wolbachia levels. We found that host translation can influence Wolbachia levels in the host.

microbiology↗

bioRxiv2018

High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have several technical limitations such as low process throughput from laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire. TrueRepertoire provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire was demonstrated by a phage-displayed single-chain variable fragment (scFv) library targeting human hepatocyte growth factor (hHGF) protein.

bioengineering↗

bioRxiv2018

Programmatic Detection of Diploid-Triploid Mixoploidy via Whole Genome Sequencing

PurposeMixoploidy is a type of mosaicism where an organism is a mixture of cells with different numbers of chromosomes. There are a broad range of phenotypes associated with mixoploidy that vary greatly depending on the fraction of cells that are non-diploid, their chromosome number, their distribution, and presumably the specific variation present in the patient. Clinical detection of mixoploidy is important for diagnosis.\n\nMethodsWe developed a method to detect mixoploidy from clinical whole genome sequencing (WGS) data through the identification of excess of variant calls centered on unusual B-allele frequencies. Our method isolates the signal from these variants using trio calls and then solves a basic linear equation to estimate levels of diploid-triploid mixoploidy within the sample.\n\nResultsWe show that our method reflects the results from a cytogenetic test. We provide examples detailing how our method has been used to identify diploid-triploid mixoploid individuals from within the NIH Undiagnosed Diseases Network. We present confirmatory findings obtained by clinical cytogenetic testing and show that our method can be used to identify the diploid-triploid ratio in these cases.\n\nConclusionWGS data from patients with rare diseases can be used to identify mixoploid individuals. Individuals with certain characteristics as discussed should be tested for mixoploidy as part of standard clinical pipeline procedures. Scripts that perform this calculation are publicly available at https://github.com/HudsonAlpha/mixoviz.

genomics↗

bioRxiv2018

Addition of Degenerate Bases to DNA-based Data Storage for Increased Information Capacity

Introductory paragraphDNA-based data storage has emerged as a promising method to satisfy the exponentially increasing demand for information storage. However, practical implementation of DNA-based data storage remains a challenge because of the high cost of DNA per unit data. Here, we propose the use of eleven degenerate bases as encoding characters in addition to A, C, G, and T, which increases the information capacity (the amount of data that can be stored per length of DNA sequence designed) and reduce the cost of DNA per unit data. Using the proposed method, we experimentally achieved an information capacity of 3.37 bits/character, which is more than twice when compared to the highest information capacity previously achieved. Finally, the platform was projected to reduce the cost of DNA-based data storage by 50%.

synthetic biology↗

bioRxiv2018

Determinants of base-pair substitution patterns revealed by whole-genome sequencing of DNA mismatch repair defective Escherichia coli

Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective E. coli strains yielded {approx}30,000 base-pair substitutions, revealing mutational patterns across the entire chromosome. The base-pair substitution spectrum was dominated by A:T > G:C transitions, which occurred predominantly at the center base of 5'NAC3'+5'GTN3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for base-pair substitutions, and the rate at which these occurred increased with run length. Comparison with {approx}2000 base-pair substitutions accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone or less well corrected by proofreading than was leading strand synthesis.

genetics↗

bioRxiv2018

Inhibitory Effect of Bacillus velezensis on Biofilm Formation by Streptococcus mutans

Streptococcus mutans plays a key role in the development of dental caries and promotes the formation of oral biofilm produced by glucosyltransferases (GTFs). Bacillus velezensis K68 was isolated from traditional fermented foods and inhibits biofilm formation mediated by S. mutans. Gene amplification results demonstrated that B. velezensis K68 contained genes for the biosynthesis of 1-deoxynojirimycin (1-DNJ), a known GTF expression inhibitor. The presence of the GabT1, Yktc1, and GutB1 genes required for 1-DNJ synthesis in B. velezensis K68 was confirmed. Supernatant from B. velezensis K68 culture medium inhibited biofilm formation by 84% when S. mutans was cultured for 48 h, and inhibited it maximally when 1% glucose was added to the S. mutans culture medium as a GTF substrate. In addition, supernatant from B. velezensis K68 medium containing 3 ppb 1- DNJ decreased S. mutans cell surface hydrophobicity by 79.0 {+/-} 0.8% compared with that of untreated control. The supernatant containing 1-DNJ decreased S. mutans adherence by 99.97% and 98.83% under sugar-dependent and sugar-independent conditions, respectively. S. mutans treated with the supernatant exhibited significantly reduced expression of the essential GTF genes gtfB, gtfC, and gtfD compared to that in the untreated group. Thus, B. velezensis inhibits the biofilm formation, adhesion, and GTF gene expression of S. mutans through 1- DNJ production.\n\nIMPORTANCEDental caries is among the most common infectious diseases worldwide, and its development is closely associated with physiological factors of bacteria, such as the biofilm formation and glucosyltransferase production of Streptococcus mutans. Biofilms are difficult to remove once they have formed due to the exopolysaccharide matrix produced by the microorganisms residing in them; thus, inhibiting biofilm formation is a current focal point of research into prevention of dental caries. This study describes the inhibitory properties of Bacillus velezensis K68, an organism isolated from traditional Korean fermented foods, against biofilm formation by S. mutans. Herein, we show that B. velezensis inhibits the biofilm formation, adherence to surfaces, and glucosyltransferase production of S. mutans.

microbiology↗

bioRxiv2018

Economic evaluation of a healthy lifestyle intervention for chronic low back pain: a randomised controlled trial

We performed an economic evaluation of a healthy lifestyle intervention targeting weight loss, physical activity and diet for patients with chronic low back pain, who are overweight or obese. Eligible patients with chronic low back pain (n=160) were randomised to an intervention or usual care control group. The intervention included brief advice, a clinical consultation and referral to a 6-month telephone-based healthy lifestyle coaching service. The primary outcome was quality-adjusted life years (QALYs). Secondary outcomes were pain intensity, disability, weight, and body mass index. Costs included intervention costs, healthcare utilisation costs and work absenteeism costs. An economic analysis was performed from the societal perspective. Mean total costs were lower in the intervention group than the control group (-$614; 95%CI: -3133 to 255). The intervention group had significantly lower healthcare costs (-$292; 95%CI: -872 to -33), medication costs (-$30; 95%CI: -65 to -4) and absenteeism costs (-$1000; 95%CI: -3573 to -210). For all outcomes, the intervention was on average less expensive and more effective than usual care, and the probability of the intervention being cost-effective compared to usual care was relatively high (i.e. 0.81) at a willingness-to-pay of $0/unit of effect. However, the probability of cost-effectiveness was not as favourable among sensitivity analyses. The healthy lifestyle intervention seems to be cost-effective from the societal perspective. However, variability in the sensitivity analyses indicates caution is needed when interpreting these findings.

clinical trials↗

bioRxiv2018

Causal mechanisms of a healthy lifestyle intervention for patients with musculoskeletal pain who are overweight or obese

We assessed the causal mechanisms of a healthy lifestyle intervention for patients with chronic low back pain and knee osteoarthritis (OA), who are overweight or obese. We conducted causal mediation analyses of aggregated data from two RCTs; which included 160 patients with chronic low back pain, and 120 patients with knee OA. Participants were randomised via one central randomisation schedule, to the intervention, or usual care. The intervention consisted of brief advice and referral to a 6-month telephone-based healthy lifestyle coaching service. Participants in the back pain trial were also offered a single physiotherapy consultation. The hypothesised primary mediator was self-reported weight, and alternative mediators were diet, physical activity, and pain beliefs. Outcomes were pain intensity, disability, and quality of life (QoL). Data were analysed using causal mediation analyses with sensitivity analyses for sequential ignorability. All mediation models were specified a priori. The intervention had no effect on pain intensity, disability or physical QoL. The intervention significantly improved mental QoL, however, the intervention effect was not channelled via the selected mediators. The intervention did not reduce weight, or the alternative mediators (diet, physical activity, pain beliefs), and these mediators were not associated with the outcomes (with one exception; poor diet was associated with lower mental QoL). The sensitivity analyses showed that our estimates were stable across all possible levels of residual confounding. Our findings show that the intervention did not cause a meaningful change in the hypothesised mediators, and these mediators were not associated with patient outcomes.

clinical trials↗

bioRxiv2018

Humidity as a non-pharmaceutical intervention for influenza A

Influenza is a global problem infecting 5-10 % of adults and 20-30 % of children annually. Non-pharmaceutical interventions (NPIs) are attractive approaches to complement vaccination in the prevention and reduction of influenza. Strong cyclical reduction of absolute humidity has been associated with influenza outbreaks in temperate climates. This study tested the hypothesis that raising absolute humidity above seasonal lows would impact influenza virus survival and transmission in a key source of influenza distribution, a community school. Air samples and objects handled by students (e.g. blocks and markers) were collected from preschool classrooms. All samples were processed and PCR used to determine the presence of influenza and its amount. Additionally samples were tested for their ability to infect cells in cultures. Deliberate classroom humidification (with commercial steam humidifiers) resulted in a significant reduction of the total number of influenza positive samples (air and fomite), viral copy number, and efficiency of viral infectivity. This is the first prospective study suggesting that exogenous humidification could serve as a scalable NPI for influenza or other viral outbreaks.\n\nAuthor summaryHuman influenza infections have a substantial impact on society (including lost productivity and medical costs). Children, 3-4 years of age are the main introducers and spreaders of influenza within a household and community. There is evidence from laboratory and epidemiological studies that suggests that low humidity in winter (in temperate climates) may increase the ability of influenza virus to survive and spread between individuals. We wanted to know if added in humidity (through steam humidifiers) could reduce the amount of influenza present and its spread within preschool classrooms (students aged 3-4 years)? Additionally, we looked at the infectivity of the influenza isolated and if there were differences in the number of students with influenza-like illnesses during our study. We show that humidification can reduce the amount of influenza present within samples from preschool classrooms and that there were fewer infectious samples compared to non-humidified rooms. There were small numbers of students ill with influenza like illnesses during our study so additional studies will need to look further at humidification as a way to reduce influenza infection and transmission.

microbiology↗

bioRxiv2018

Bead Enhancement of EV Analysis

Extracellular vesicles (EVs) are recognized cancer biomarkers, however, clinical analysis has been difficult due to a lack of simple and sensitive assays. Here, we describe a bead-enhanced flow cytometry method, BEAD flow, using biotinylated EVs captured on streptavidin particles. With this method, we show analysis of patient-derived EVs using a panel of pancreatic cancer biomarkers. BEAD flow is easily translatable to any biomarker or cancer type and can be run with conventional flow cytometers, making it highly flexible and adaptable to diverse research and clinical needs.

cancer biology↗

bioRxiv2018

SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution

BackgroundSimulating genome sequence data with features can facilitate the development and benchmarking of structural variant analysis programs. However, there are a limited number of data simulators that provide structural variants in silico. Moreover, there are a paucity of programs that generate structural variants with different allelic fraction and haplotypes.\n\nFindingsWe developed SVEngine, an open source tool to address this need. SVEngine simulates next generation sequencing data with embedded structural variations. As input, SVEngine takes template haploid sequences (FASTA) and an external variant file, a variant distribution file and/or a clonal phylogeny tree file (NEWICK) as input. Subsequently, it simulates and outputs sequence contigs (FASTAs), sequence reads (FASTQs) and/or post-alignment files (BAMs). All of the files contain the desired variants, along with BED files containing the ground truth. SVEngines flexible design process enables one to specify size, position, and allelic fraction for deletion, insertion, duplication, inversion and translocation variants. Finally, SVEngine simulates sequence data that replicates the characteristics of a sequencing library with mixed sizes of DNA insert molecules. To improve the compute speed, SVEngine is highly parallelized to reduce the simulation time.\n\nConclusionsWe demonstrated the versatile features of SVEngine and its improved runtime comparisons with other available simulators. SVEngines features include the simulation of locus-specific variant frequency designed to mimic the phylogeny of cancer clonal evolution. We validated the accuracy of the simulations. Our evaluation included checking various sequencing mapping features such as coverage change, read clipping, insert size shift and neighbouring hanging read pairs for representative variant types. SVEngine is implemented as a standard Python package and is freely available for academic use at: https://bitbucket.org/charade/svengine.

bioinformatics↗

bioRxiv2017

Decomposing parietal memory reactivation to predict consequences of remembering

Memory retrieval can strengthen, but also distort memories. Parietal cortex is a candidate region involved in retrieval-induced memory changes as it reflects retrieval success and represents retrieved content. Here, we conducted an fMRI experiment to test whether different forms of parietal reactivation predict distinct consequences of retrieval. Subjects studied associations between words and pictures of faces, scenes, or objects, and then repeatedly retrieved half of the pictures, reporting the vividness of the retrieved pictures ( retrieval practice). On the following day, subjects completed a recognition memory test for individual pictures. Critically, the test included lures highly similar to studied pictures. Behaviorally, retrieval practice increased both hit and false alarm rates to similar lures, confirming a causal influence of retrieval on subsequent memory. Using pattern similarity analyses, we measured two different levels of reactivation during retrieval practice: generic category-level reactivation and idiosyncratic item-level reactivation. Vivid remembering during retrieval practice was associated with stronger category- and item-level reactivation in parietal cortex. However, these measures differentially predicted subsequent recognition memory performance: whereas higher category-level reactivation tended to predict false alarms to lures, item-level reactivation predicted correct rejections. These findings indicate that parietal reactivation can be decomposed to tease apart distinct consequences of memory retrieval.

neuroscience↗

bioRxiv2017

Patterns and predictors of tic suppressibility in youth with tic disorders

Background: Tic suppression is the primary target of tic disorder treatment, but factors that influence voluntary tic inhibition are not well understood. Several studies using the Tic Suppression Task have demonstrated significant inter-individual variability in tic suppressibility but have individually been underpowered to address correlates of tic suppression. The present study explored patterns and clinical correlates of tic suppression in youth with tic disorders using a large, pooled dataset.\n\nMethods: Individual-level data from 9 studies using the Tic Suppression Task were pooled, yielding a sample of 99 youth with tic disorders. Analyses examined patterns of tic suppressibility and the relationship between tic suppressibility and demographic and clinical characteristics.\n\nResults: A large majority of youth demonstrated a high degree of tic suppression, but heterogeneous patterns of tic suppressibility were also observed. Better tic suppressibility was related to older age and more frequent tics but unrelated to other clinical variables, including presence of psychiatric comorbidity, psychotropic medication status, and tic and premonitory urge severity.\n\nConclusions: The mechanisms underlying the observed heterogeneity in tic suppressibility warrant further investigation. The Tic Suppression Task is a promising method for testing mechanistic hypotheses related to tic suppression.

neuroscience↗

bioRxiv2017

Deep-learning based hologram classification for molecular diagnostics

Lens-free digital in-line holography (LDIH) is a promising microscopic tool that overcomes several drawbacks (e.g., limited field of view) of traditional lens-based microcopy. However, extensive computation is required to reconstruct object images from the complex diffraction patterns produced by LDIH, which limits LDIH utility for point-of-care applications, particularly in resource limited settings. Here, we describe a deep transfer learning (DTL) based approach to process LDIH images in the context of cellular analyses. Specifically, we captured holograms of cells labeled with molecular-specific microbeads and trained neural networks to classify these holograms without reconstruction. Using raw holograms as input, the trained networks were able to classify individual cells according to the number of cell-bound microbeads. The DTL-based approach including a VGG19 pretrained network showed robust performance even with noisy experimental data. Combined with the developed DTL approach, LDIH could be realized as a low-cost, portable tool for point-of-care diagnostics.

bioengineering↗

bioRxiv2017

A whole genome analysis of the red-crowned crane provides insight into avian longevity

The red-crowned crane (Grus japonensis) is an endangered and large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is positively correlated with body size and negatively correlated with metabolic rate; although the genetic mechanisms for the red-crowned cranes long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, we identified candidate genes that are correlated with longevity. Included among these are positively selected genes with known associations with longevity in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12 IL9R, SOD3, NUDT12, PNLIP, CTH, and RPA1). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and we hope this genome will provide a useful genetic resource for future conservation studies of this rare and iconic species.

bioinformatics↗